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CellML Scope

This Version:
        http://www.cellml.org/scope/scope
Latest Version:
        http://www.cellml.org/scope/scope
Previous Version:
        http://www.cellml.org/scope/cellml_scope_20000726
        http://www.cellml.org/scope/cellml_scope_20000621
        http://www.cellml.org/scope/cellml_scope_20000620
Authors:
        Melanie Nelson (Physiome Sciences Inc.)
       Warren Hedley (Bioengineering Institute, University of Auckland)
Collaborators:
       David Bullivant (Bioengineering Institute, University of Auckland)
       Kam-Chuen Jim (Physiome Sciences Inc.)
       Scott Lett (Physiome Sciences Inc.)
       Dave Nickerson (Bioengineering Institute, University of Auckland)
       Poul Nielsen (Bioengineering Institute, University of Auckland)


Table of Contents

Introduction
Scope of CellML
Use Of Other Languages

Introduction

It would be very difficult to develop a robust data model to cover all aspects of biology. By limiting the scope of CellML, we increase our chances of developing a robust and flexible data model that will remain valid as biological modeling advances. The scope of CellML is the information that should be contained within the CellML data model and which will therefore be represented by CellML elements (i.e. elements defined in the CellML Document Type Definitions, or DTDs). Note that information can also be included in a CellML document by including an independent DTD (see the section “Use Of Other Languages”).

This document details the scope of CellML, as agreed in a teleconference on June 28, 2000. Physiome Sciences was represented by Melanie Nelson, Kam Jim, and Scott Lett. The University of Auckland was represented by Warren Hedley, Poul Nielsen, David Bullivant, and David Nickerson (standing in for Peter Hunter).

Scope of CellML

The CellML language itself will be limited to the following:

  1. Description of the organizational scheme/structure of the model. This includes the organization of a model into components (parts), and how these parts are connected together to create a complete model. Note that this description is intended primarily for use by computer programs that want to be able to read and run a cell model.

  2. Metadata describing the model and its parts, to be used to help users categorize, organize, and retrieve models and model parts. This metadata is intended for both computer programs accessing the model (so that they can search for models and model components based on user queries) and for human users of the model (who might want to view portions of the metadata to evaluate whether a particular model meets their requirements). [Technical note: The most basic set of metadata can be handled with the Dublin Core RDF specification (RDF is the W3C's method for handling metadata. The Dublin Core is a set of specific metadata elements). Other metadata can be handled in a CellML-specific RDF schema or in elements within CellML itself. A CellML-specific RDF schema would be so tightly coupled with CellML that its development can be considered part of the same project.]

Use Of Other Languages

When a cell model document needs to contain information that is outside of the CellML scope, this will be done using separate languages/storage formats. The CellML data model will only contain the information needed to connect this "outside information" into the biological model. For example, we currently use an <equations> element to indicate where math belongs in the biological model.

The CellML working group will decide which languages can be legally included in CellML as the need to include different types of information arises. In some cases, the CellML specification may limit the subset of valid information from the separate language or format that can be included in CellML.

Here is a list of information that we currently plan to represent using other languages. Inclusion on this list means that this information will not be represented using CellML elements. It does not imply anything about whether or not the information can be included in CellML documents. Some of this information will be included within CellML documents (as we currently do with MathML), while other information may be stored in a separate document (for instance, rendering information may be kept separate).

  1. Math (currently implemented via MathML)

  2. Textual and graphical documentation of the model intended solely for display to human users of the model. (probably implemented via HTML).

  3. Information about the actual computation of a cell model.

  4. Data sets.

  5. Ontologies [Note: An ontology is the set of rules that govern what is allowable in a biologically correct model. We anticipate that different types of modeling will need different ontologies. It should also be possible to define a model without using an ontology at all (in effect, the ontology would be inside the modeller's head). However, using ontologies would allow some "short cuts" in the model definition process. Also note: an ontology can be separate from the model whether we choose to express ontology information in CellML or in some other language.]

  6. Information about rendering of models This list is not meant to be a comprehensive list of information that may be used by CellML documents and represented in another language. Other types of information may be included at the discretion of the CellML working group. However, none of the items on this list will be represented using CellML elements: they are not within the scope of the CellML data model.