The SBPAX ontology The BioPAX Level 2 ontology. The BFO ontology. 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. 1 Amount of substance, for example, a liter of water, or three molecules of EGFR The amount of substance constituting a species. A participant on the right side. GenericallyDependentContinuant from BFO. 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 from BFO. A substance at some location. ObjectAggregate from BFO. 1 1 Any physical quantity. For example, a temperature, a voltage, or an amount. 1 1 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. 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. ProcessualContext from BFO. 1 1 The amount a process adds to or removes from a species. 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. A participant on the left side. A process part which involves a catalyst. 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. openControlledVocabulary from BioPAX Level 2. Site from BFO. An amount of something, described by a number and a unit. 1 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. 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. 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. Each species consists of exactly one substance. A system model models a substance if the substance is included in it. In SBML, the substance becomes a speciesType of the model. The location of a species. The process a process model is modeling. 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. 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. 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. A process has a process part for each participating species. The substance quantified by an amount. In other words, the substance the amount is amount of. 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. A species model models a species if the species is included in it. In SBML, the species model becomes a species of the model. 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. Integer from XMLSchema. An amount has exactly one number. For example, an amount may be one liter, where one is the number and liter is the unit. double from XML Schema. float from XML Schema. 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. physicalEntityParticipant from BioPAX Level 2. subClassOf from RDF Schema. imports from OWL. LEFT from BioPAX Level 2. type from RDF. intersectionOf from OWL. cardinality from OWL. Right from BioPAX Level 2. comment from RDF Schema. rest from RDF. range from RDF Schema. subPropertyOf from RDF Schema. onProperty from OWL. conversion from BioPAX Level 2. domain from RDF. physicalEntity from BioPAX Level 2. first from RDF equivalentClass from OWL. unionOf from OWL. ObjectProperty from OWL. nil from RDF. DatatypeProperty from OWL. Restriction from OWL. Class from OWL. TransitiveProperty from OWL. Ontology from OWL.