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


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  • From: j.lawson at auckland.ac.nz (James Lawson)
  • Subject: [cellml-discussion] Suggestions regarding search and browse utility for CellML Repository
  • Date: Tue, 06 May 2008 12:02:32 +1200
Hi Ely,

Thanks for your commentary, that sounds very interesting. You should get
in touch with Sarala (sarala.dissanayake at auckland.ac.nz) - she is a PhD
student working on something quite similar. It would be interesting to
see the overlap between your projects. I don't think Sarala has
implemented a database or anything like that.

If you could actually translate some of the fundamental concepts of your
work I think that would be very useful.

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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