Biomedical Engineering Reference
In-Depth Information
Table 8.1.
The minimum information standards, syntax and semantics being developed for data,
models and simulation experiments
Data
Models
Simulation
MIBBI
a
MIRIAM
b
MIASE
c
Minimal
requirements
PDB
d
,DICOM
e
,
BioSignalML
f
SBML
g
, CellML
h
, FieldML
i
SED-ML
j
Standard
formats
GO
k
, Biopax
l
, FMA
m
,
SBO
n
,OPB
o
GO
KiSAO
p
Ontologies
Biopax, FMA, SBO, OPB
a
www.mibbi.org
b
biomodels.net/miriam
c
biomodels.net/miase
d
www.rcsb.org/pdb
e
medical.nema.org
f
www.embs.org/techcomm/tc-cbap/biosignal.html
g
www.sbml.org
h
www.cellml.org
i
www.fieldml.org
j
www.sed-ml.org
k
www.geneontology.org
l
www.biopax.org
m
sig.biostr.washington.edu/projects/fm/AboutFM.html
n
www.ebi.ac.uk/sbo
o
sig.biostr.washington.edu/projects/biosim/opb-intro.html
p
www.ebi.ac.uk/compneur-srv/kisao
to CellML but is targeted more specifically to representing models of biochemical
reactions.
A useful way of viewing the development of standards is shown in Table 8.1, in-
cluding specification of the minimal requirements for data, models and a simulation
experiment, along with the standards for the syntax of the data, models or simulation
experiments and the ontologies for annotating the semantic meaning of terms in the
data, models or simulation experiments.
8.4 CellML
CellML separates the syntax of a model (e.g. the mathematical equations encoded
in MathML) from the semantics (the biological and biophysical meanings of the
model components and parameters) defined in the model metadata by reference to
suitable ontologies. In addition, models can be broken down into components; this
facilitates building complex models by importing modular components defined in
libraries. SBML is more closely tied to the concepts of biochemical and genetic
networks, and does not maintain such a clear separation between the mathematical
representation and the biological semantics. FieldML deals with the encoding of
anatomy at multiple spatial scales by allowing hierarchies of material coordinate
