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[cellml-discussion] Suggestions regarding search andbrowse utility for CellML Repository


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  • From: david.nickerson at nus.edu.sg (David Nickerson)
  • Subject: [cellml-discussion] Suggestions regarding search andbrowse utility for CellML Repository
  • Date: Tue, 06 May 2008 08:29:33 +0800
> 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"
>> <j.lawson at auckland.ac.nz>
>> To: "CellML Discussion List" <cellml-discussion at 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 at cellml.org
>>>> http://www.cellml.org/mailman/listinfo/cellml-discussion
>>>>
>>>>
>>>
>>
>>
>> --------------------------------------------------------------------------------
>>
>>
>>
>>
>>
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>>
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>
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--
David Nickerson, PhD
Research Fellow
Division of Bioengineering
Faculty of Engineering
National University of Singapore
Email: david.nickerson at nus.edu.sg


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