Virtual Cell at UConn



SBPAX: format for future BioPAX/SBML operations at Virtual Cell


The latest presentation.

 

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 (BioPAX)-type pathways.


  1. 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.

  2. More details about SBPAX (VCell wiki).
  3. Ontology file:
    - sbpax.owl 33K
    - sbpax.n3 17K
  4. 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 EGFR autophoshorylation in Reactome. This figure illustrates the subset substances of EGFR described in the example.
    - The SBPAX version of a reaction, the EGFR autophoshorylation.
    - A variant of above example, with ATP and ADP removed.
    - Another variant, with EGF-EGFR complex treated as an extra species in catalytic role.