Dear friends,

Here are an introduction and some automatically generated
specifications of SBPAX. Sorry if not very polished - work in progress
:)

Attached files are SBPAX in various formats: sbpax.owl (OWL,
abbreviated), sbpax2.owl (OWL, not abbreviated), sbpax.rdf (triple),
sbpax.n3 (N3).

Take care
Oliver

--
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org


Systems Biology Pathway Exchange (SBPAX) Specifications

Systems Biology Pathway Exchange (SBPAX) is a format 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 supports the integration of SBML, BioPAX and other formats by serving as
an intermediary, a glue 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.


*** Amount ***

URI: http://vcell.org/2008/05/sbpax#Amount
Is sub class of: Quantity
Is super class of: PoolAmount, StuffAmount, Stoichiometry
Is domain of: quantifies

Comment: An amount of something, described by a number and a unit.


*** biopax-level2.owl ***

URI: http://www.biopax.org/release/biopax-level2.owl

Comment: The BioPAX Level 2 ontology.


*** cardinality ***

URI: http://www.w3.org/2002/07/owl#cardinality

Comment: cardinality from OWL.


*** Class ***

URI: http://www.w3.org/2002/07/owl#Class

Comment: Class from OWL.


*** comment ***

URI: http://www.w3.org/2000/01/rdf-schema#comment

Comment: comment from RDF Schema.


*** contains ***

URI: http://vcell.org/2008/05/sbpax#contains
Has domain: Pool
Has range: Stuff

Comment: Each pool contains exactly one stuff.


*** conversion ***

URI: http://www.biopax.org/release/biopax-level2.owl#conversion
Is sub class of: Process

Comment: conversion from BioPAX Level 2.


*** DatatypeProperty ***

URI: http://www.w3.org/2002/07/owl#DatatypeProperty

Comment: DatatypeProperty from OWL.


*** domain ***

URI: http://www.w3.org/2000/01/rdf-schema#domain

Comment: domain from RDF.


*** double ***

URI: http://www.w3.org/2001/XMLSchema#double

Comment: double from XML Schema.


*** equivalentClass ***

URI: http://www.w3.org/2002/07/owl#equivalentClass

Comment: equivalentClass from OWL.


*** first ***

URI: http://www.w3.org/1999/02/22-rdf-syntax-ns#first

Comment: first from RDF


*** float ***

URI: http://www.w3.org/2001/XMLSchema#float

Comment: float from XML Schema.


*** GenericallyDependentContinuant ***

URI: http://www.ifomis.org/bfo/1.1/snap#GenericallyDependentContinuant
Is super class of: Quantity, Stoichiometry, ProcessModel, SystemModel

Comment: GenericallyDependentContinuant from BFO.


*** hasDimensions ***

URI: http://vcell.org/2008/05/sbpax#hasDimensions
Has domain: Location
Has range: integer

Comment: The number of spatial dimensions of a location within a
model. For example, volumes have usually three, membranes two. There
really should be a LocationModel for this property, but that is not
implemented yet.


*** hasNumber ***

URI: http://vcell.org/2008/05/sbpax#hasNumber
Has domain: Quantity
Has range:

Comment: An amount has exactly one number. For example, an amount
may be one liter, where one is the number and liter is the unit.


*** hasPartCat ***

URI: http://vcell.org/2008/05/sbpax#hasPartCat
Has domain: Process
Has range: PartCat

Comment: A participant of a process which is catalyst for that
process. A catalyst is stuff without the process does not happen. If
the process can happen with and without catalyst, then with and
without are considered two different processes.


*** hasParticipant ***

URI: http://vcell.org/2008/05/sbpax#hasParticipant
Has domain: Process
Has range: Participant

Comment: A process has a pool as participant means that the process
consumes reactants from the pool, or adds products to the pool, or
relies on catalysts from the pool


*** hasPartLeft ***

URI: http://vcell.org/2008/05/sbpax#hasPartLeft
Has domain: Process
Has range: PartLeft

Comment: A participant of the process on the left side. Whether is
is a reactant or product depends on the direction in which the
proecess proceeds.


*** hasPartRight ***

URI: http://vcell.org/2008/05/sbpax#hasPartRight
Has domain: Process
Has range: PartRight

Comment: A participant of the process on the right side. Whether is
is a reactant or product depends on the direction in which the
proecess proceeds.


*** hasProcessModel ***

URI: http://vcell.org/2008/05/sbpax#hasProcessModel
Has domain: SystemModel
Has range: ProcessModel

Comment: A system model has a process model, if that process model,
and by extension that process, is included in the system model. In
SBML, the process model, with its process, becomes a reaction.


*** hasStoichiometry ***

URI: http://vcell.org/2008/05/sbpax#hasStoichiometry
Has domain: Participant
Has range: Stoichiometry

Comment: The stoichiometry of a participant. Each participant has
exactly one. A different stoichiometry implies a different
participant, and a different set of participants implies a different
process.


*** imports ***

URI: http://www.w3.org/2002/07/owl#imports

Comment: imports from OWL.


*** integer ***

URI: http://www.w3.org/2001/XMLSchema#integer
Is range of: hasDimensions

Comment: Integer from XMLSchema.


*** intersectionOf ***

URI: http://www.w3.org/2002/07/owl#intersectionOf

Comment: intersectionOf from OWL.


*** LEFT ***

URI: http://www.biopax.org/release/biopax-level2.owl#LEFT

Comment: LEFT from BioPAX Level 2.


*** linksPool ***

URI: http://vcell.org/2008/05/sbpax#linksPool
Has domain: Participant
Has range: Pool

Comment: Each participant links to exactly one pool. While a
participant represents stuff and the amount of that stuff that is
turned over or required by a process, a pool represents the same stuff
and the amount that is located at some location.


*** locatedAt ***

URI: http://vcell.org/2008/05/sbpax#locatedAt
Has domain: Pool
Has range: Location

Comment: The location a pool is located.


*** Location ***

URI: http://vcell.org/2008/05/sbpax#Location
Is sub class of: Site, openControlledVocabulary
Is domain of: hasDimensions, surroundedBy
Is range of: surroundedBy, locatedAt

Comment: Anywhere where something can be located. Could be a cell,
an organelle, an organism, a petri dish, a membrane, or any part of
any of the above.


*** modelsPool ***

URI: http://vcell.org/2008/05/sbpax#modelsPool
Has domain: SystemModel
Has range: Pool

Comment: A system model models a pool if the pool is included in it.
In SBML, the pool becomes a species of the model.


*** modelsProcess ***

URI: http://vcell.org/2008/05/sbpax#modelsProcess
Has domain: ProcessModel
Has range: Process

Comment: The process a process model is modeling.


*** modelsStuff ***

URI: http://vcell.org/2008/05/sbpax#modelsStuff
Has domain: SystemModel
Has range: Stuff

Comment: A system model models a stuff if the stuff is included in
it. In SBML, the stuff becomes a speciesType of the model.


*** nil ***

URI: http://www.w3.org/1999/02/22-rdf-syntax-ns#nil

Comment: nil from RDF.


*** ObjectAggregate ***

URI: http://www.ifomis.org/bfo/1.1/snap#ObjectAggregate
Is super class of: Pool, Stuff

Comment: ObjectAggregate from BFO.


*** ObjectProperty ***

URI: http://www.w3.org/2002/07/owl#ObjectProperty

Comment: ObjectProperty from OWL.


*** onProperty ***

URI: http://www.w3.org/2002/07/owl#onProperty

Comment: onProperty from OWL.


*** Ontology ***

URI: http://www.w3.org/2002/07/owl#Ontology

Comment: Ontology from OWL.


*** openControlledVocabulary ***

URI: http://www.biopax.org/release/biopax-level2.owl#openControlledVocabulary
Is super class of: Location

Comment: openControlledVocabulary from BioPAX Level 2.


*** PartCat ***

URI: http://vcell.org/2008/05/sbpax#PartCat
Is sub class of: Participant
Is range of: hasPartCat

Comment: A participant which is catalyst. Participants are divided
into left, right and catalysts. Whether the left or right are
reactants or products respectively depends on the direction, for
example, if the direction is left to right, then the left participants
are reactants and the right participants are products.


*** Participant ***

URI: http://vcell.org/2008/05/sbpax#Participant
Is sub class of: ProcessualContext
Is super class of: PartRight, physicalEntityParticipant, PartLeft, PartCat
Is domain of: hasStoichiometry, linksPool
Is range of: hasParticipant

Comment: A participant in a process is some mount of somestuff that
is added to or removed from a pool containing that stuff, or required
to be present for the process to happen.


*** PartLeft ***

URI: http://vcell.org/2008/05/sbpax#PartLeft
Is sub class of: Participant
Is range of: hasPartLeft

Comment: A participant on the left side. Participants are divided
into left, right and catalysts. Whether the left or right are
reactants or products respectively depends on the direction, for
example, if the direction is left to right, then the left participants
are reactants and the right participants are products.


*** PartRight ***

URI: http://vcell.org/2008/05/sbpax#PartRight
Is sub class of: Participant
Is range of: hasPartRight

Comment: A participant on the right side. Participants are divided
into left, right and catalysts. Whether the left or right are
reactants or products respectively depends on the direction, for
example, if the direction is left to right, then the left participants
are reactants and the right participants are products.


*** physicalEntity ***

URI: http://www.biopax.org/release/biopax-level2.owl#physicalEntity
Is sub class of: Stuff

Comment: physicalEntity from BioPAX Level 2.


*** physicalEntityParticipant ***

URI: http://www.biopax.org/release/biopax-level2.owl#physicalEntityParticipant
Is sub class of: Participant

Comment: physicalEntityParticipant from BioPAX Level 2.


*** Pool ***

URI: http://vcell.org/2008/05/sbpax#Pool
Is sub class of: ObjectAggregate
Is domain of: contains, locatedAt
Is range of: modelsPool, linksPool

Comment: The presence of some stuff at some location.


*** PoolAmount ***

URI: http://vcell.org/2008/05/sbpax#PoolAmount
Is sub class of: Amount
Is range of: processesQuantity

Comment: The amount of stuff contained in a pool.


*** Process ***

URI: http://vcell.org/2008/05/sbpax#Process
Is sub class of: ProcessAggregate
Is super class of: conversion
Is domain of: hasPartLeft, hasPartRight, hasParticipant, hasPartCat
Is range of: modelsProcess

Comment: A process that changes the amount of stuff at certain
locations, for example a transport or a chemical (or even nuclear)
reaction. A process may be considered an ensemble of individual
processes such as the individual reactions among molecules. A process
is characterized by how much stuff is consumed or produced at a
certain location or various certain locations, as well as stuff that
is required at certain locations for the process to happen. In the
case of a process being an ensemble of individual processes, the
number of individuals consumed or produced can be given.


*** ProcessAggregate ***

URI: http://www.ifomis.org/bfo/1.1/span#ProcessAggregate
Is super class of: Process

Comment: ProcessAggregate from BFO.


*** processesQuantity ***

URI: http://vcell.org/2008/05/sbpax#processesQuantity
Has domain: ProcessModel
Has range: PoolAmount

Comment: A process model processes a quantity means the quantity is
a pool amount of a pool form the process modeled by this model.


*** ProcessModel ***

URI: http://vcell.org/2008/05/sbpax#ProcessModel
Is sub class of: GenericallyDependentContinuant
Is domain of: modelsProcess, processesQuantity
Is range of: hasProcessModel

Comment: A model of a process. While a process represents objective
reality, a process model includes modelers choices, meaning
information depending on preferences. For example, participant,
locations and stoichiometric coefficients are considered objective
reality, but rate laws are considered subjective, because the choice
between different rate laws may depend on modeler's choices.


*** ProcessualContext ***

URI: http://www.ifomis.org/bfo/1.1/span#ProcessualContext
Is super class of: Participant

Comment: ProcessualContext from BFO.


*** quantifies ***

URI: http://vcell.org/2008/05/sbpax#quantifies
Has domain: Amount
Has range: Stuff

Comment: The stuff quantified by an amount. In other words, the
stuff the amount is amount of.


*** Quantity ***

URI: http://vcell.org/2008/05/sbpax#Quantity
Is sub class of: GenericallyDependentContinuant
Is super class of: Amount
Is domain of: hasNumber

Comment: Any physical quantity. For example, a temperature, a
voltage, or an amount.


*** range ***

URI: http://www.w3.org/2000/01/rdf-schema#range

Comment: range from RDF Schema.


*** rest ***

URI: http://www.w3.org/1999/02/22-rdf-syntax-ns#rest

Comment: rest from RDF.


*** Restriction ***

URI: http://www.w3.org/2002/07/owl#Restriction

Comment: Restriction from OWL.


*** RIGHT ***

URI: http://www.biopax.org/release/biopax-level2.owl#RIGHT

Comment: Right from BioPAX Level 2.


*** sbpax ***

URI: http://vcell.org/2008/05/sbpax

Comment: The SBPAX ontology


*** Site ***

URI: http://www.ifomis.org/bfo/1.1/snap#Site
Is super class of: Location

Comment: Site from BFO.


*** Stoichiometry ***

URI: http://vcell.org/2008/05/sbpax#Stoichiometry
Is sub class of: Amount, GenericallyDependentContinuant
Is range of: hasStoichiometry

Comment: The amount a process adds to or removes from a pool,
optionally with the number of individuals turned over per individual
process event.


*** Stuff ***

URI: http://vcell.org/2008/05/sbpax#Stuff
Is sub class of: ObjectAggregate
Is super class of: physicalEntity
Is domain of: subStuffOf
Is range of: contains, subStuffOf, modelsStuff, quantifies

Comment: Anything that can have an amount at a location. Typically
something that has an amount at each of multiple locations, which
changes by certain amounts by one or more processes. In the context of
molecular reaction networks or pathways, stuff is used to describe
collections of molecules and other compounds, but it could also
describe a variety of other things, such as cells, heat, light,
charge, organisms, stress, strain, pressure, energy. Naturally, it can
also be a group of kinds of proteins, or a certain kind of protein, or
a certain kind of protein in a certain phosphorylation state, which
would then relate to each other through sub stuff relationships.


*** StuffAmount ***

URI: http://vcell.org/2008/05/sbpax#StuffAmount
Is sub class of: Amount

Comment: Amount of stuff, for example, a liter of water, or three
molecules of EGFR


*** subClassOf ***

URI: http://www.w3.org/2000/01/rdf-schema#subClassOf

Comment: subClassOf from RDF Schema.


*** subPropertyOf ***

URI: http://www.w3.org/2000/01/rdf-schema#subPropertyOf

Comment: subPropertyOf from RDF Schema.


*** subStuffOf ***

URI: http://vcell.org/2008/05/sbpax#subStuffOf
Has domain: Stuff
Has range: Stuff

Comment: Some stuff is sub stuff of another stuff, if it is a subset
of it. For example, a certain protein is sub stuff of a set of
proteins including it, and a certain phosphorylation state of a
protein is sub stuff the protein.


*** surroundedBy ***

URI: http://vcell.org/2008/05/sbpax#surroundedBy
Has domain: Location
Has range: Location

Comment: The location surrounding this location. Depending on model,
the nucleoplasm is surrounded by the nuclear membrane, the nuclear
membrane by the cytoplasm,the cytoplasm by the cell membrane and the
cell membrane by the extracellular matrix. This should really be a
property between location models rather than locations, but that has
not been implemented yet.


*** SystemModel ***

URI: http://vcell.org/2008/05/sbpax#SystemModel
Is sub class of: GenericallyDependentContinuant
Is domain of: modelsPool, modelsStuff, hasProcessModel

Comment: A model of a process network, such as a molecular pathway
or reaction network. It can be any collection of ProcessModels, but
typically describes a connected network.


*** TransitiveProperty ***

URI: http://www.w3.org/2002/07/owl#TransitiveProperty

Comment: TransitiveProperty from OWL.


*** type ***

URI: http://www.w3.org/1999/02/22-rdf-syntax-ns#type

Comment: type from RDF.


*** unionOf ***

URI: http://www.w3.org/2002/07/owl#unionOf

Comment: unionOf from OWL.



--
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org