       ***   Amount   ***

  URI: http://vcell.org/2008/11/sbpax#Amount
  Is sub class of: Quantity
  Is super class of: SubstanceAmount, SpeciesAmount, Stoichiometry
  Is domain of: quantifies

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


       ***   BinarySetIntersection   ***

  URI: http://vcell.org/2008/11/sbpax#BinarySetIntersection
  Is sub class of: BinarySetOp



       ***   BinarySetOp   ***

  URI: http://vcell.org/2008/11/sbpax#BinarySetOp
  Is sub class of: SetOp
  Is super class of: BinarySetIntersection, BinarySetUnion
  Is domain of: isOpOnSetRight, isOpOnSetLeft



       ***   BinarySetUnion   ***

  URI: http://vcell.org/2008/11/sbpax#BinarySetUnion
  Is sub class of: BinarySetOp



       ***   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.


       ***   consistsOf   ***

  URI: http://vcell.org/2008/11/sbpax#consistsOf
  Has domain: Species
  Has range: Substance

  Comment: Each species consists of exactly one substance.


       ***   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, Model, Unit

  Comment: GenericallyDependentContinuant from BFO.


       ***   hasComponent   ***

  URI: http://vcell.org/2008/11/sbpax#hasComponent



       ***   hasDimensions   ***

  URI: http://vcell.org/2008/11/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.


       ***   hasModel   ***

  URI: http://vcell.org/2008/11/sbpax#hasModel
  Has domain: Model
  Has range: Model



       ***   hasNumber   ***

  URI: http://vcell.org/2008/11/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.


       ***   hasParticipant   ***

  URI: http://vcell.org/2008/11/sbpax#hasParticipant
  Has domain: Process
  Has range: ProcessParticipant

  Comment: A process has a process part for each participating species. 


       ***   hasParticipantCatalyst   ***

  URI: http://vcell.org/2008/11/sbpax#hasParticipantCatalyst
  Has domain: Process
  Has range: ProcessParticipantCatalyst

  Comment: A process part which involves a species which is a catalyst for that process. A catalyst is a substance without which the process does not happen. If the process can happen with and without catalyst, then with and without are considered two different processes.


       ***   hasParticipantLeft   ***

  URI: http://vcell.org/2008/11/sbpax#hasParticipantLeft
  Has domain: Process
  Has range: ProcessParticipantLeft

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


       ***   hasParticipantRight   ***

  URI: http://vcell.org/2008/11/sbpax#hasParticipantRight
  Has domain: Process
  Has range: ProcessParticipantRight

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


       ***   hasProcessModel   ***

  URI: http://vcell.org/2008/11/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.


       ***   hasSequenceFeature   ***

  URI: http://vcell.org/2008/11/sbpax#hasSequenceFeature
  Has domain: Substance
  Has range: SequenceFeature



       ***   hasStoichiometry   ***

  URI: http://vcell.org/2008/11/sbpax#hasStoichiometry
  Has domain: ProcessParticipant
  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.


       ***   hasSystemModel   ***

  URI: http://vcell.org/2008/11/sbpax#hasSystemModel
  Has domain: SystemModel
  Has range: SystemModel



       ***   hasUnit   ***

  URI: http://vcell.org/2008/11/sbpax#hasUnit
  Has domain: Quantity
  Has range: Unit



       ***   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.


       ***   interaction   ***

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



       ***   Interaction   ***

  URI: http://vcell.org/2008/11/sbpax#Interaction
  Is super class of: interaction, Process



       ***   intersectionOf   ***

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

  Comment: intersectionOf from OWL.


       ***   involves   ***

  URI: http://vcell.org/2008/11/sbpax#involves
  Has domain: ProcessParticipant
  Has range: Species

  Comment: Each process part involves exactly one species. While a process part represents a substance and the amount of that substance that is turned over or required by a process, a species represents the same substance and the amount that is located at some location.


       ***   isOpOnSet   ***

  URI: http://vcell.org/2008/11/sbpax#isOpOnSet
  Has domain: SetOp
  Has range: Substance



       ***   isOpOnSetLeft   ***

  URI: http://vcell.org/2008/11/sbpax#isOpOnSetLeft
  Has domain: BinarySetOp



       ***   isOpOnSetRight   ***

  URI: http://vcell.org/2008/11/sbpax#isOpOnSetRight
  Has domain: BinarySetOp



       ***   isSetFromOp   ***

  URI: http://vcell.org/2008/11/sbpax#isSetFromOp
  Has domain: Substance
  Has range: SetOp



       ***   lacksSequenceFeature   ***

  URI: http://vcell.org/2008/11/sbpax#lacksSequenceFeature
  Has domain: Substance
  Has range: SequenceFeature



       ***   LEFT   ***

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

  Comment: LEFT from BioPAX Level 2.


       ***   locatedAt   ***

  URI: http://vcell.org/2008/11/sbpax#locatedAt
  Has domain: Species
  Has range: Location

  Comment: The location of a species.


       ***   Location   ***

  URI: http://vcell.org/2008/11/sbpax#Location
  Is sub class of: openControlledVocabulary, Site
  Is domain of: surroundedBy, hasDimensions
  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.


       ***   Model   ***

  URI: http://vcell.org/2008/11/sbpax#Model
  Is sub class of: GenericallyDependentContinuant
  Is super class of: ProcessModel, SystemModel
  Is domain of: hasModel
  Is range of: hasModel



       ***   modelsProcess   ***

  URI: http://vcell.org/2008/11/sbpax#modelsProcess
  Has domain: ProcessModel
  Has range: Process

  Comment: The process a process model is modeling.


       ***   modelsSpecies   ***

  URI: http://vcell.org/2008/11/sbpax#modelsSpecies
  Has domain: SystemModel
  Has range: Species

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


       ***   modelsSubstance   ***

  URI: http://vcell.org/2008/11/sbpax#modelsSubstance
  Has domain: SystemModel
  Has range: Substance

  Comment: A system model models a substance if the substance is included in it. In SBML, the substance 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: Species, Substance

  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.


       ***   particleNumber   ***

  URI: http://vcell.org/2008/11/sbpax#particleNumber



       ***   physicalEntity   ***

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

  Comment: physicalEntity from BioPAX Level 2.


       ***   physicalEntityParticipant   ***

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

  Comment: physicalEntityParticipant from BioPAX Level 2.


       ***   Process   ***

  URI: http://vcell.org/2008/11/sbpax#Process
  Is sub class of: Interaction, ProcessAggregate
  Is super class of: conversion
  Is domain of: hasParticipantRight, hasParticipantLeft, hasParticipant, hasParticipantCatalyst
  Is range of: modelsProcess

  Comment: A process that changes the amounts of substances 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 of a substance is consumed or produced at a certain location or various certain locations, as well as a substance 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.


       ***   ProcessModel   ***

  URI: http://vcell.org/2008/11/sbpax#ProcessModel
  Is sub class of: Model
  Is domain of: modelsProcess
  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.


       ***   ProcessParticipant   ***

  URI: http://vcell.org/2008/11/sbpax#ProcessParticipant
  Is sub class of: ProcessualContext
  Is super class of: ProcessParticipantLeft, physicalEntityParticipant, ProcessParticipantRight, ProcessParticipantCatalyst
  Is domain of: hasStoichiometry, involves
  Is range of: hasParticipant

  Comment: A process is divided into process parts, one for each reactant, product or catalyst.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.


       ***   ProcessParticipantCatalyst   ***

  URI: http://vcell.org/2008/11/sbpax#ProcessParticipantCatalyst
  Is sub class of: ProcessParticipant
  Is range of: hasParticipantCatalyst

  Comment: A process part which involves a catalyst. 


       ***   ProcessParticipantLeft   ***

  URI: http://vcell.org/2008/11/sbpax#ProcessParticipantLeft
  Is sub class of: ProcessParticipant
  Is range of: hasParticipantLeft

  Comment: A participant on the left side.


       ***   ProcessParticipantRight   ***

  URI: http://vcell.org/2008/11/sbpax#ProcessParticipantRight
  Is sub class of: ProcessParticipant
  Is range of: hasParticipantRight

  Comment: A participant on the right side.


       ***   ProcessualContext   ***

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

  Comment: ProcessualContext from BFO.


       ***   quantifies   ***

  URI: http://vcell.org/2008/11/sbpax#quantifies
  Has domain: Amount
  Has range: Substance

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


       ***   Quantity   ***

  URI: http://vcell.org/2008/11/sbpax#Quantity
  Is sub class of: GenericallyDependentContinuant
  Is super class of: Amount
  Is domain of: hasUnit, 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/2008/11/sbpax

  Comment: The SBPAX ontology


       ***   SequenceFeature   ***

  URI: http://vcell.org/2008/11/sbpax#SequenceFeature
  Is super class of: sequenceFeature
  Is range of: lacksSequenceFeature, hasSequenceFeature



       ***   sequenceFeature   ***

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



       ***   SetOp   ***

  URI: http://vcell.org/2008/11/sbpax#SetOp
  Is super class of: BinarySetOp
  Is domain of: isOpOnSet
  Is range of: isSetFromOp



       ***   Site   ***

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

  Comment: Site from BFO.


       ***   Species   ***

  URI: http://vcell.org/2008/11/sbpax#Species
  Is sub class of: ObjectAggregate
  Is domain of: consistsOf, locatedAt
  Is range of: involves, modelsSpecies

  Comment: A substance at some location.


       ***   SpeciesAmount   ***

  URI: http://vcell.org/2008/11/sbpax#SpeciesAmount
  Is sub class of: Amount

  Comment: The amount of substance constituting a species.


       ***   Stoichiometry   ***

  URI: http://vcell.org/2008/11/sbpax#Stoichiometry
  Is sub class of: Amount, GenericallyDependentContinuant
  Is range of: hasStoichiometry

  Comment: The amount a process adds to or removes from a species.


       ***   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.


       ***   subSetOf   ***

  URI: http://vcell.org/2008/11/sbpax#subSetOf
  Has domain: Substance
  Has range: Substance

  Comment: Some substance is sub set of another substance, if anything included in the first is included in the second For example, a certain protein is sub set of a set of proteins including it,  and a certain phosphorylation state of a protein is sub set the protein.


       ***   Substance   ***

  URI: http://vcell.org/2008/11/sbpax#Substance
  Is sub class of: ObjectAggregate
  Is super class of: physicalEntity
  Is domain of: subSetOf, lacksSequenceFeature, isSetFromOp, hasSequenceFeature
  Is range of: subSetOf, modelsSubstance, consistsOf, isOpOnSet, 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, substance 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 set relationships.


       ***   SubstanceAmount   ***

  URI: http://vcell.org/2008/11/sbpax#SubstanceAmount
  Is sub class of: Amount

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


       ***   surroundedBy   ***

  URI: http://vcell.org/2008/11/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/2008/11/sbpax#SystemModel
  Is sub class of: Model
  Is domain of: hasProcessModel, hasSystemModel, modelsSubstance, modelsSpecies
  Is range of: hasSystemModel

  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.


       ***   Unit   ***

  URI: http://vcell.org/2008/11/sbpax#Unit
  Is sub class of: GenericallyDependentContinuant
  Is range of: hasUnit