Biomedical Engineering Reference
In-Depth Information
The only requirement is that the model needs to be referenced by using an unam-
biguous identifier which allows for finding it, for example by using an MIRIAM
URI. A set of predefined language Uniform Resource Names (URNs) is provided to
specify the language in which the model is encoded
The SED-ML Change class facilitates applying changes to the referenced models,
including changes on the XML attributes, e.g. changing the value of an observable,
computing the change of a value using mathematics, or general changes on any XML
element of the model representation that is addressable by XPath expressions, e.g.
substituting a piece of XML with an updated one.
The
Simulation class
defines the simulation settings and the steps taken during
simulation. These include the particular type of simulation and the algorithm used
for the execution of the simulation; preferably an unambiguous reference to such an
algorithm should be given, using controlled vocabulary, or ontologies. One example
for an ontology of simulation algorithms is the Kinetic Simulation Algorithm On-
tology (KiSAO). Further information encodable in the Simulation class includes the
step size, simulation duration, and other simulation-type dependent information.
SED-ML makes use of the notion of a
Task class
to combine a defined model
(from the Model class) and a defined simulation setting (from the Simulation class).
A task always holds one reference each.
The raw simulation result sometimes does not correspond to the desired output of
the simulation (e.g. one might want to normalize a plot before output, or apply post-
processing such as a mean-value calculation). The
DataGenerator class
allows for
the encoding of post-processing to be applied to the simulation results before out-
put. To define data generators, any addressable variable or parameter of any defined
model (from instances of the Model class) may be referenced, and new entities might
be specified using MathML definitions.
The
Output class
defines the output of the simulation, in the sense that it specifies
what shall be plotted in the output. To do so, an output type is defined (e.g. 2D-plot,
3D-plot or data table), and each corresponding axis or column is assigned to one of
the previously specified instances of the DataGenerator class.
8.10 BioSignalML
More than 100 different file formats exist to store and exchange biosignal data
(Schlogl, 2008). Several are likely to be used in a given project, not by design, but
because manufacturers, software vendors and in-house developers are unlikely to be
using a common format, with archived recordings in yet more formats; the numbers
compound when collaborating with other research teams. Although a number of con-
version tools and standard libraries exist, e.g. libRASCH (Schneider, 2007) and the
BioSig Project (Schl ogl, 2009), they do not provide any standard view of metadata
contained in a biosignal file. The lack of a standard, domain-neutral framework for
working with biosignals has hampered their easy interchange between disciplines
and integration with physiological modelling software.
