SBPAX: format for future BioPAX/SBML operations at Virtual Cell
SBPAX is short for Systems Biology PAthway eXchange.
It is an OWL ontology serving as a bridging format to
integrate SBML/VCML-type models with
- Systems Biology Pathway Exchange (SBPAX) is an ontology
designed to integrate
SBML, BioPAX and a variety of other formats by faithfully representing any
process network (e.g. biological pathway or biochemical reaction network)
expressed in these formats. Networks in the SBPAX sense include
processes (e.g. reactions, transport), their participants (e.g. chemicals)
and the locations and stoichiometric
coefficients of these participants.
SBPAX serves as
bridge and a common repository format. When a direct
conversion from one format to another is not possible due to ambiguities, it is
possible to convert loss-free from the source format to SBPAX as an
intermediary, then add information to resolve ambiguities, and then
export to the target format.
If related data is available in two different formats, SBPAX can serve as the
glue to establish meaningful links across formats. A repository based on SBPAX
allows importing loss free from SBML, BioPAX and other formats, merging the
data and exporting to these formats as far as the necessary data is available.
To achieve the necessary expressive power and flexibility, SBPAX offers a
number of features. Processes and their participants are ensembles in SBPAX
which can be freely extended and restricted to match entries in other formats.
Likewise, locations can also be extended and restricted to match locations in
other formats. SBPAX further distinguishes between actual and effective
stoichiometric coefficients, and the difference between objective reality and
models representing a subjective view of reality.
- More details about SBPAX (VCell wiki).
- Ontology file:
- sbpax.owl 33K
- sbpax.n3 17K
- Simplified sample fragments of SBPAX data in N3 for Illustration
Substances, subset substances and modifications in the
phosphorylated EGF-EGFR complex.
This example relates to the
This figure illustrates the
subset substances of EGFR described in the example.
- The SBPAX version of a reaction, the
A variant of above example, with ATP and ADP removed.
- Another variant,
with EGF-EGFR complex treated as an extra species
in catalytic role.