Biomedical Engineering Reference
In-Depth Information
portant that the tools adhere to these standards to ensure that models from different
groups can be curated, annotated, reused and combined. This chapter discusses the
development and use of the VPH/Physiome standards, tools and databases, and also
discusses the minimum information standards and ontology-based metadata stan-
dards that are complementary to the markup language standards. Data standards
are not as well developed as the model encoding standards (with the DICOM stan-
dard for medical image encoding being the outstanding exception) but one new data
standard being developed as part of the VPH/Physiome suite is BioSignalML and
this is described here also. The PMR2 (Physiome Model Repository 2) database
for CellML and FieldML files is also described, together with the Application Pro-
gramming Interfaces (APIs) that facilitate access to the models from the visualisa-
tion (cmgui and GIMIAS) or computational (OpenCMISS, OpenCell/OpenCOR and
other) software.
8.1 Introduction
Over the last 50 years biomedical science has yielded a wealth of reductive knowl-
edge of the human body, most notably with the Human Genome Project, but has
made relatively little effort to integrate this knowledge back into physiological un-
derstanding and therefore evidence-based medical treatment (Hunter and Viceconti,
2009). In almost every other area of human activity - communication, transport,
entertainment, weather and climate prediction, to name a few - the physical and en-
gineering sciences play a crucial role. Bioengineering has of course had a substantial
impact on medical practice through medical devices and diagnostic imaging equip-
ment, but the impact from 150 years of scientific progress in physics, engineering
and mathematics on the biomedical sciences, and evidence-based medicine, has been
relatively slight (Hunter, 2004; Hunter, 2006).
To help bring the quantitative and predictive power of the mathematical sciences
into the biological sciences, and to take advantage of an engineering approach to
biological materials and a more systematic approach to the knowledge management
of multi-scale physiological data, the International Union of Physiological Sciences
(IUPS) initiated the Physiome Project in 1997
1
. A related US initiative by the Inter-
1
The concept of a “Physiome Project” was presented in a report from the Commission on Bio-
engineering in Physiology to the International Union of Physiological Sciences (IUPS) Council at
the 32nd World Congress in Glasgow in 1993. The term “physiome” comes from “physio” (life) +
“ome” (as a whole), and is intended to provide a “quantitative description of physiological dynam-
ics and functional behaviour of the intact organism” [2,3,4]. A satellite workshop “On designing
the Physiome Project”, organized and chaired by the Chair of the IUPS 'Commission on Bioengi-
neering in Physiology' (Prof Jim Bassingthwaighte), was held in Petrodvoretz, Russia, following
the 33rd World Congress in St Petersburg in 1997. A symposium on the Physiome Project was
held at the 34th World Congress of IUPS in Christchurch, New Zealand, in August 2001 and the
Physiome Project was designated by the IUPS executive as a major focus for IUPS during the next
decade.
