Biomedical Engineering Reference
In-Depth Information
systems that preserve anatomical relationships (e.g. coronary arteries embedded in
a deforming myocardial tissue that is itself part of a heart contained within a torso).
These three standards are recommended both by the US National Institutes of Health
(NIH) and by the European Commission for the VPH project.
CellML has a simple structure based upon connected components. These com-
ponents abstract concepts by providing well-defined interfaces to other components,
and encapsulate concepts by hiding details from other components. Connections pro-
vide the means for sharing information by associating variables visible in the inter-
face of one component with those in the interface of another component. Consis-
tency is enforced by requiring that all variables be assigned appropriate physical
units which must be dimensionally compatible when variables are connected. Pub-
lic and private interfaces enable encapsulation hierarchies, providing further mech-
anisms for information hiding and abstraction. Model reuse is facilitated by the im-
port element, enabling new models to be constructed by combining existing hierar-
chies of components into model hierarchies. The CellML 1.1 standard is available
at www.cellml.org/specifications/cellml 1.1. An overview of CellML structure is
shown in Fig. 8.2. An overview of CellML metadata standards is given in Beard et
al., 2009.
Other markup languages include NeuroML (neuroml.org), used by the neuro-
science modelling community and InSilicoML (physiome.jp/insilicoml), developed
by Physiome Project groups in Japan.
CellML model
(XML)
(RDF Metadata)
im
po
rt
Dublin Core
imported units
imported component
vCard
un
its
BQS
unit
co
mp
onent
variable
math
Other RDF (species, etc)
(OWL format)
co
nne
ction
mapComponent
mapVariable
Annotated against biophysical and
biological
processes
CellMLBio
Ontology
Annotated against biophysical and
biological
entities
gr
oup
relationshipRef
componentRef
Fig. 8.2.
Entities in a CellML model. The CellML model file on the left contains the base model
with its imports, units, components, connections and groups described in XML format, and the
metadata in RDF format. The annotation of CellML variables with biological and biophysical
meaning is handled via cmeta:id links to terms stored in RDF format in a separate OWL file. Fur-
ther metadata are needed to specify the simulation parameters (using the SED-ML standard, see
sed-ml.org) and a graphical output standard. (Reproduced with permission from [30, 31])
