SBPAX3

SBPAX3 (Systems Biology Pathway Exchange, Version 3) is a BioPAX Level 3 extension and a BioPAX Level 4 proposal to include kinetic data and other systems biology information in BioPAX using systems biology vocabulary such as the Systems Biology Ontology (SBO). The working version of the proposal is for Level 3, but can be trivially adapted for any other level.

SBPAX3 is being developed by the SBPAX Workgroup, which includes interested members of the BioPAX Pathways and Models Workgroup and the Virtual Cell.

SBPAX3 will allow pathway databases such as MetaCyc and Signaling Gateway Molecule Pages that have kinetic data (e.g. Michaelis-Menten constant, Hill coefficient, limiting rate, n-th order rate constants, electric conductance, etc) to include these data in their BioPAX export.

The Systems Biology Ontology (SBO) has terms to identify various types of kinetic rate laws as well as terms to identify various types of kinetic parameters. SBPAX3 provides a way to add structured data that includes numbers with units and controlled vocabulary, such as SBO, to identify what the data means.

To bring in systems biology terms, such as SBO, SBPAX3 adds a new sub class to ControlledVocabulary called SBVocabulary, representing systems biology terms.

A new class sbpax:SBEntity includes any entity that can be described by systems biology terms. This includes BioPAX entities.

SBEntity has two properties: it can have any number of sbTerm objects, which are instances of SBVocabulary describing this entity, and it can have any number of sbSubEntity objects, which are other instances of SBEntity describing parts or attributes of this entity.

One sub-class of SBEntity is SBState, which is used to describe a group of entities occurring together (which would then be sub-entities).

To add a data point, use SBMeasurable, a sub-class of SBEntity which represents something that can be measured. It has a number (of type double) and a unit (of type UnitOfMeasurement from UOME).

To add a set of data points from the same measurement related to some BioPAX entity (physical entity, interaction or pathway), you would add to this BioPAX entity the property sbSubEntity to point to an instance of SBState, which has the property sbSubEntity pointing to other instances of SBEntity, including one instance of SBMeasurable for each data point. You can use entities to group measurables.

Actual SBPAX3 data can be obtained from the Signaling Gateway Molecule Pages. For illustration, we also provide an example with random data for Michaelis-Menten kinetics. The example contains five instances of Catalysis. Each Catalysis instance has one sub-entity of type SBState, which in turn has sub-entities for the measurables temperature, pH and pressure and one entity for the Michaelis-Menten kinetics. The Michaelis-Menten kinetics has sub-entities which are measurables for various Michaelis-Menten parameters. The exact structure of the hierarchy is not that important. Important is that each entity comes with a systems biology term that identifies what it is.

Implementations
Signaling Gateway Molecule Pages has implemented SBPAX3 export, e.g. , , , , ,

SBPAX3 ontology and docs

 * The SBPAX3 ontology can be found here: SBPAX3 in OWL, SBPAX3 in N3
 * Some automatically created summary documentation can be found here: SBPAX3 Doc

Example files
Some examples based on data from Signaling Gateway Molecule Pages. These examples were created before SGMP had implemented SBPAX3. Their BioPAX Level 3 export was taken, some sample fragments extracted, some URIs adjusted, some SBO terms guessed, and their kinetic data added using SBPAX3:


 * Ligand-Receptor binding (C5a receptor) in OWL and in N3 (original data is here)


 * Enzyme kinetics - Michaelis-Menten (Phosphatidylinositol-4-kinase type III beta) in OWL and in N3 (original data is here)


 * Enzyme Kinetics - Positive Cooperativity (Phosphodiesterase 2A, cGMP stimulated) in OWL and in N3 (original data is here)


 * Ion Channel Selectivity (Polycystin 2) in OWL and in N3 (original data is here)


 * Glucose Transport (GLUT4) in OWL and in N3 (original data is here)

Some older completely fictitious sample data can be found here: SBPAX3 Example 1 in OWL, SBPAX3 Example 1 in N3