@prefix bp2: . @prefix xsd: . @prefix bfo-snap: . @prefix bfo-span: . @prefix bfo: . @prefix rdfs: . @prefix rdf: . @prefix : . @prefix owl: . owl:ObjectProperty rdfs:comment "ObjectProperty from OWL."^^xsd:string . xsd:integer rdfs:comment "Integer from XMLSchema."^^xsd:string . :SpeciesAmount a owl:Class ; rdfs:comment "The amount of substance constituting a species."^^xsd:string ; rdfs:subClassOf :Amount . bp2:physicalEntityParticipant rdfs:comment "physicalEntityParticipant from BioPAX Level 2."^^xsd:string ; rdfs:subClassOf :ProcessParticipant . bp2:sequenceFeature rdfs:subClassOf :SequenceFeature . xsd:double rdfs:comment "double from XML Schema."^^xsd:string . :BinarySetIntersection a owl:Class ; rdfs:subClassOf :BinarySetOp . :hasSystemModel a owl:ObjectProperty ; rdfs:domain :SystemModel ; rdfs:range :SystemModel ; rdfs:subPropertyOf :hasModel . :lacksSequenceFeature a owl:ObjectProperty ; rdfs:domain :Substance ; rdfs:range :SequenceFeature . rdfs:subClassOf rdfs:comment "subClassOf from RDF Schema."^^xsd:string . :Stoichiometry a owl:Class ; rdfs:comment "The amount a process adds to or removes from a species."^^xsd:string ; rdfs:subClassOf :Amount , bfo-snap:GenericallyDependentContinuant . owl:imports rdfs:comment "imports from OWL."^^xsd:string . :ProcessParticipantCatalyst a owl:Class ; rdfs:comment "A process part which involves a catalyst. "^^xsd:string ; rdfs:subClassOf :ProcessParticipant ; owl:equivalentClass [ a owl:Class ; owl:intersectionOf (:ProcessParticipantLeft :ProcessParticipantRight) ] . bp2:LEFT rdfs:comment "LEFT from BioPAX Level 2."^^xsd:string ; rdfs:subPropertyOf :hasParticipantLeft . () rdfs:comment "nil from RDF."^^xsd:string . :ProcessModel a owl:Class ; rdfs: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."^^xsd:string ; rdfs:subClassOf :Model ; rdfs:subClassOf [ a owl:Restriction ; owl:cardinality "1"^^xsd:int ; owl:onProperty :modelsProcess ] . :hasParticipantLeft a owl:ObjectProperty ; rdfs: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."^^xsd:string ; rdfs:domain :Process ; rdfs:range :ProcessParticipantLeft ; rdfs:subPropertyOf :hasParticipant . :isOpOnSet a owl:ObjectProperty ; rdfs:domain :SetOp ; rdfs:range :Substance . :hasModel a owl:ObjectProperty ; rdfs:domain :Model ; rdfs:range :Model . rdf:type rdfs:comment "type from RDF."^^xsd:string . :Substance a owl:Class ; rdfs: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."^^xsd:string ; rdfs:subClassOf bfo-snap:ObjectAggregate . owl:intersectionOf rdfs:comment "intersectionOf from OWL."^^xsd:string . owl:cardinality rdfs:comment "cardinality from OWL."^^xsd:string . :hasStoichiometry a owl:ObjectProperty ; rdfs: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."^^xsd:string ; rdfs:domain :ProcessParticipant ; rdfs:range :Stoichiometry . owl:DatatypeProperty rdfs:comment "DatatypeProperty from OWL."^^xsd:string . :BinarySetUnion a owl:Class ; rdfs:subClassOf :BinarySetOp . bp2:RIGHT rdfs:comment "Right from BioPAX Level 2."^^xsd:string ; rdfs:subPropertyOf :hasParticipantRight . :Species a owl:Class ; rdfs:comment "A substance at some location."^^xsd:string ; rdfs:subClassOf bfo-snap:ObjectAggregate ; rdfs:subClassOf [ a owl:Restriction ; owl:cardinality "1"^^xsd:int ; owl:onProperty :consistsOf ] ; rdfs:subClassOf [ a owl:Restriction ; owl:cardinality "1"^^xsd:int ; owl:onProperty :locatedAt ] . :ProcessParticipant a owl:Class ; rdfs: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."^^xsd:string ; rdfs:subClassOf bfo-span:ProcessualContext ; rdfs:subClassOf [ a owl:Restriction ; owl:cardinality "1"^^xsd:int ; owl:onProperty :hasStoichiometry ] ; rdfs:subClassOf [ a owl:Restriction ; owl:cardinality "1"^^xsd:int ; owl:onProperty :involves ] ; owl:equivalentClass [ a owl:Class ; owl:unionOf (:ProcessParticipantLeft :ProcessParticipantRight) ] . rdfs:comment rdfs:comment "comment from RDF Schema."^^xsd:string . :quantifies a owl:ObjectProperty ; rdfs:comment "The substance quantified by an amount. In other words, the substance the amount is amount of."^^xsd:string ; rdfs:domain :Amount ; rdfs:range :Substance . :Location a owl:Class ; rdfs: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."^^xsd:string ; rdfs:subClassOf bp2:openControlledVocabulary , bfo-snap:Site . :involves a owl:ObjectProperty ; rdfs: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."^^xsd:string ; rdfs:domain :ProcessParticipant ; rdfs:range :Species . rdf:rest rdfs:comment "rest from RDF."^^xsd:string . :particleNumber a :Unit . :subSetOf a owl:TransitiveProperty ; rdfs: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."^^xsd:string ; rdfs:domain :Substance ; rdfs:range :Substance . rdfs:comment "The BFO ontology."^^xsd:string . :modelsProcess a owl:ObjectProperty ; rdfs:comment "The process a process model is modeling."^^xsd:string ; rdfs:domain :ProcessModel ; rdfs:range :Process . rdfs:range rdfs:comment "range from RDF Schema."^^xsd:string . bfo-snap:GenericallyDependentContinuant rdfs:comment "GenericallyDependentContinuant from BFO."^^xsd:string . :hasDimensions a owl:DatatypeProperty ; rdfs: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."^^xsd:string ; rdfs:domain :Location ; rdfs:range xsd:integer . bfo-snap:ObjectAggregate rdfs:comment "ObjectAggregate from BFO."^^xsd:string . :SetOp a owl:Class . :Interaction a owl:Class . :SequenceFeature a owl:Class . :ProcessParticipantLeft a owl:Class ; rdfs:comment "A participant on the left side."^^xsd:string ; rdfs:subClassOf :ProcessParticipant . rdfs:subPropertyOf rdfs:comment "subPropertyOf from RDF Schema."^^xsd:string . :isSetFromOp a owl:ObjectProperty ; rdfs:domain :Substance ; rdfs:range :SetOp . :isOpOnSetRight a owl:ObjectProperty ; rdfs:domain :BinarySetOp ; rdfs:subPropertyOf :isOpOnSet . :isOpOnSetLeft a owl:ObjectProperty ; rdfs:domain :BinarySetOp ; rdfs:subPropertyOf :isOpOnSet . owl:onProperty rdfs:comment "onProperty from OWL."^^xsd:string . :SubstanceAmount a owl:Class ; rdfs:comment "Amount of substance, for example, a liter of water, or three molecules of EGFR"^^xsd:string ; rdfs:subClassOf :Amount . bp2:conversion rdfs:comment "conversion from BioPAX Level 2."^^xsd:string ; rdfs:subClassOf :Process . :Process a owl:Class ; rdfs: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."^^xsd:string ; rdfs:subClassOf :Interaction , bfo-span:ProcessAggregate . a owl:Ontology ; rdfs:comment "The SBPAX ontology"^^xsd:string ; owl:imports , . :hasParticipantRight a owl:ObjectProperty ; rdfs: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."^^xsd:string ; rdfs:domain :Process ; rdfs:range :ProcessParticipantRight ; rdfs:subPropertyOf :hasParticipant . :SystemModel a owl:Class ; rdfs: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."^^xsd:string ; rdfs:subClassOf :Model . :hasParticipant a owl:ObjectProperty ; rdfs:comment "A process has a process part for each participating species. "^^xsd:string ; rdfs:domain :Process ; rdfs:range :ProcessParticipant . owl:Restriction rdfs:comment "Restriction from OWL."^^xsd:string . bfo-span:ProcessAggregate rdfs:comment "ProcessAggregate from BFO."^^xsd:string . bfo-snap:Site rdfs:comment "Site from BFO."^^xsd:string . rdfs:domain rdfs:comment "domain from RDF."^^xsd:string . :hasUnit a owl:ObjectProperty ; rdfs:domain :Quantity ; rdfs:range :Unit . :modelsSubstance a owl:ObjectProperty ; rdfs:comment "A system model models a substance if the substance is included in it. In SBML, the substance becomes a speciesType of the model."^^xsd:string ; rdfs:domain :SystemModel ; rdfs:range :Substance . :ProcessParticipantRight a owl:Class ; rdfs:comment "A participant on the right side."^^xsd:string ; rdfs:subClassOf :ProcessParticipant . :Model a owl:Class ; rdfs:subClassOf bfo-snap:GenericallyDependentContinuant . :locatedAt a owl:ObjectProperty ; rdfs:comment "The location of a species."^^xsd:string ; rdfs:domain :Species ; rdfs:range :Location . bp2:openControlledVocabulary rdfs:comment "openControlledVocabulary from BioPAX Level 2."^^xsd:string . :Quantity a owl:Class ; rdfs:comment "Any physical quantity. For example, a temperature, a voltage, or an amount."^^xsd:string ; rdfs:subClassOf bfo-snap:GenericallyDependentContinuant ; rdfs:subClassOf [ a owl:Restriction ; owl:cardinality "1"^^xsd:int ; owl:onProperty :hasNumber ] ; rdfs:subClassOf [ a owl:Restriction ; owl:cardinality "1"^^xsd:int ; owl:onProperty :hasUnit ] . :hasComponent a owl:ObjectProperty . bfo-span:ProcessualContext rdfs:comment "ProcessualContext from BFO."^^xsd:string . :consistsOf a owl:ObjectProperty ; rdfs:comment "Each species consists of exactly one substance."^^xsd:string ; rdfs:domain :Species ; rdfs:range :Substance . bp2:physicalEntity rdfs:comment "physicalEntity from BioPAX Level 2."^^xsd:string ; rdfs:subClassOf :Substance . owl:Class rdfs:comment "Class from OWL."^^xsd:string . :hasSequenceFeature a owl:ObjectProperty ; rdfs:domain :Substance ; rdfs:range :SequenceFeature . rdfs:comment "The BioPAX Level 2 ontology."^^xsd:string . :BinarySetOp a owl:Class ; rdfs:subClassOf :SetOp . rdf:first rdfs:comment "first from RDF"^^xsd:string . bp2:interaction rdfs:subClassOf :Interaction . :Unit a owl:Class ; rdfs:subClassOf bfo-snap:GenericallyDependentContinuant . owl:equivalentClass rdfs:comment "equivalentClass from OWL."^^xsd:string . :hasProcessModel a owl:ObjectProperty ; rdfs: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."^^xsd:string ; rdfs:domain :SystemModel ; rdfs:range :ProcessModel ; rdfs:subPropertyOf :hasModel . owl:TransitiveProperty rdfs:comment "TransitiveProperty from OWL."^^xsd:string . :hasNumber a owl:DatatypeProperty ; rdfs: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."^^xsd:string ; rdfs:domain :Quantity ; rdfs:range [ a owl:Class ; owl:unionOf (xsd:double xsd:float) ] . owl:Ontology rdfs:comment "Ontology from OWL."^^xsd:string . :hasParticipantCatalyst a owl:ObjectProperty ; rdfs: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."^^xsd:string ; rdfs:domain :Process ; rdfs:range :ProcessParticipantCatalyst ; rdfs:subPropertyOf :hasParticipant . :surroundedBy a owl:ObjectProperty ; rdfs: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."^^xsd:string ; rdfs:domain :Location ; rdfs:range :Location . owl:unionOf rdfs:comment "unionOf from OWL."^^xsd:string . xsd:float rdfs:comment "float from XML Schema."^^xsd:string . :Amount a owl:Class ; rdfs:comment "An amount of something, described by a number and a unit."^^xsd:string ; rdfs:subClassOf :Quantity ; rdfs:subClassOf [ a owl:Restriction ; owl:cardinality "1"^^xsd:int ; owl:onProperty :quantifies ] . :modelsSpecies a owl:ObjectProperty ; rdfs: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."^^xsd:string ; rdfs:domain :SystemModel ; rdfs:range :Species .