CellML metadata standards, associated tools and repositories

Abstract

The development of standards for encoding mathematical models is an important component of model building and model sharing among scientists interested in understanding multi-scale physiological processes. CellML provides such a standard, particularly for models based on biophysical mechanisms, and a substantial number of models are now available in the CellML Model Repository. However, there is an urgent need to extend the current CellML metadata standard to provide biological and biophysical annotation of the models in order to facilitate model sharing, automated model reduction and connection to biological databases. This paper gives a broad overview of a number of new developments on CellML metadata and provides links to further methodological details available from the CellML website.

A physiome standards-based model publication paradigm

“…This work is beyond the scope of the present manuscript, but Beard et al (2009) and Christie et al (2009) provide further information on the integration of such ontologies with CellML and FieldML, respectively.…”

“…Further data are, however, required in order to completely define the mathematical models and their application to specific numerical simulations. Here, we highlight some of the annotations we consider to be of high importance, while Beard et al (2009) provide a more complete review.…”

“…In this issue, Beard et al (2009) provide an overview of the current status of such metadata. Of particular relevance to this work are the simulation and graphing metadata specifications currently being developed.…”

“…Furthermore, as much additional information should be associated with each resource as reasonably possible (species, biological entity, graphical representations, literature citations, etc.). Semantic meaning can further enhance the model description and can be achieved via the annotation of resources using various ontologies and constrained vocabularies (further discussion can be found in Beard et al (2009)). …”

“…In this example, the central focus of the model description is a schematic of the system being modelled, a cardiac cell in this example, from which the user can choose which aspects of the biology they wish to investigate by selecting the relevant component from the model diagram. While this example is manually drawn, we envision being able to automate the generation of such a model presentation using biological annotations contained within the model description as described in Beard et al (2009). The PCENV tool (http://www.cellml.org/tools/pcenv/) is capable of displaying a view similar in concept to this type of model view, albeit currently using hand-coded diagrams and scripts (see the Sachse et al (2008) model in the CellML model repository for an example; http://www.cellml.org/models/ sachse_moreno_abildskov_2008_version05).…”