# CellML.org - CellML Specification - Overview

 CellML 2002/11/06

# Draft — 6 November 2002

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## Abstract

This document specifies CellMLTM 1.1, an XML-based language for describing and exchanging models of cellular and subcellular processes. MathML embedded in CellML documents is used to define the underlying mathematics of models. Models consist of a network of re-usable components, each with variables and equations manipulating those variables. Models may import other models to create systems of increasing complexity. Metadata may be embedded in CellML documents using RDF.

## Status of this document

This document is a draft version of the specification for CellML 1.1. As a Working Draft, this specification may be updated, replaced, or made obsolete at any time. It is distributed for discussion purposes only and should not be used as a reference.

The authors invite feedback from the public. Readers are encouraged to subscribe and send comments to the cellml-discussion mailing list. Alternatively, readers may send comments and questions via e-mail to info@cellml.org.

The latest version of the CellML specification is always available at the following URI:

The list of errata associated with this document is available at the following URI:

The CellML specification can be viewed as one large document in either HTML of PDF formats, or viewed in the following manageable sections:

• Introduction — This section introduces CellML, XML, the terminology used throughout the specification, and the structure of the specification.
• Fundamentals — This section explains concepts used in all other sections of the specification, such as the definition of a valid CellML identifier and the use of XML namespaces in CellML.
• Model Structure — This section describes how models are organised in CellML. It includes an explanation of the use of a network of components to define a model and a discussion of variables in CellML.
• Mathematics — This section describes how mathematical expressions are defined in CellML documents using MathML, and defines the CellML subset of MathML elements.
• Units — This section explains the requirements for units in CellML and describes how a modeller can define arbitrary sets of units.
• Grouping — This section explains how a model can be organised into logical encapsulation and geometric containment hierarchies by grouping components.
• Reactions — This section introduces CellML syntax that allows the modeller to classify the involvement of the participants in the chemical expressions that make up reaction/pathway models.
• Metadata Framework — This section describes how RDF is used in CellML documents to define metadata and associate it with models, model components, and other CellML elements.
• Importing Models — This section explains how a modeller may reuse parts of existing models. This feature also allows a modeller to create an incomplete model, with the expectation that the necessary components and connections may be included in the future when more knowledge is available.
• Appendices — The appendices cover advanced and technical topics including the CellML DTD, recommendations for adding scripts to CellML documents, and units processing algorithms.
                                                                                  E-mail questions, criticism, submissions or info to info@cellml.org.Input document last modified : Tue Jan 14 16:10:24 NZDT 2003