SBO:0000000 systems biology representation Systems Biology Ontology Representation of an entity used in a systems biology knowledge reconstruction, such as a model, pathway, network. 1 modified as part of ontology 'refactoring' process [SF bug #3172586] SBO:0000001 rate law Systems Biology Ontology mathematical description that relates quantities of reactants to the reaction velocity. SBO:0000064 SBO:0000002 quantitative systems description parameter Systems Biology Ontology A numerical value that defines certain characteristics of systems or system functions. It may be part of a calculation, but its value is not determined by the form of the equation itself, and may be arbitrarily assigned. Modified as part of ontology 'refactoring' process [SF bug #3172586]. SBO:0000545 SBO:0000003 participant role Systems Biology Ontology The function of a physical entity, that is its role, in the execution of an event. Modified (name) on November 6 2006 by Nicolas Le Novere Name changed from participant functional type to functional parameter on March 17 2007 by Nicolas Le Novere. SBO:0000000 SBO:0000004 modelling framework Systems Biology Ontology Set of assumptions that underlay a mathematical description. SBO:0000000 SBO:0000005 obsolete mathematical expression Systems Biology Ontology The description of a system in mathematical terms. 1 SBO:0000064 SBO:0000006 obsolete parameter Systems Biology Ontology A numerical value that represents the amount of some entity, process or mathematical function of the system. 1 SBO:0000002 SBO:0000007 obsolete participant type Systems Biology Ontology The 'kind' of entity involved in some process, action or reaction in the system. This may be enzyme, simple chemical, etc. 1 SBO:0000235 SBO:0000008 obsolete modelling framework Systems Biology Ontology Basic assumptions that underlie a mathematical model. 1 SBO:0000004 SBO:0000009 kinetic constant Systems Biology Ontology Numerical parameter that quantifies the velocity of a chemical reaction. reaction rate constant SBO:0000002 SBO:0000010 reactant Systems Biology Ontology Substance consumed by a chemical reaction. Reactants react with each other to form the products of a chemical reaction. In a chemical equation the Reactants are the elements or compounds on the left hand side of the reaction equation. A reactant can be consumed and produced by the same reaction, its global quantity remaining unchanged. SBO:0000003 SBO:0000011 product Systems Biology Ontology Substance that is produced in a reaction. In a chemical equation the Products are the elements or compounds on the right hand side of the reaction equation. A product can be produced and consumed by the same reaction, its global quantity remaining unchanged. SBO:0000003 SBO:0000012 mass action rate law Systems Biology Ontology The Law of Mass Action, first expressed by Waage and Guldberg in 1864 (Waage, P.; Guldberg, C. M. Forhandlinger: Videnskabs-Selskabet i Christiana 1864, 35) states that the speed of a chemical reaction is proportional to the quantity of the reacting substances. More formally, the change of a product quantity is proportional to the product of reactant activities. In the case of a reaction occurring in a gas phase, the activities are equal to the partial pressures. In the case of a well-stirred aqueous medium, the activities are equal to the concentrations. In the case of discrete kinetic description, the quantity are expressed in number of molecules and the relevant volume are implicitely embedded in the kinetic constant. SBO:0000001 SBO:0000013 catalyst Systems Biology Ontology Substance that accelerates the velocity of a chemical reaction without itself being consumed or transformed. This effect is achieved by lowering the free energy of the transition state. SBO:0000459 SBO:0000014 enzyme Systems Biology Ontology A protein that catalyzes a chemical reaction. The word comes from en ("at" or "in") and simo ("leaven" or "yeast"). SBO:0000241 SBO:0000015 substrate Systems Biology Ontology Molecule which is acted upon by an enzyme. The substrate binds with the enzyme's active site, and the enzyme catalyzes a chemical reaction involving the substrate. SBO:0000010 SBO:0000016 unimolecular rate constant Systems Biology Ontology Numerical parameter that quantifies the velocity of a chemical reaction involving only one reactant. SBO:0000009 SBO:0000017 bimolecular rate constant Systems Biology Ontology Numerical parameter that quantifies the velocity of a chemical reaction involving two reactants. SBO:0000009 SBO:0000018 trimolecular rate constant Systems Biology Ontology Numerical parameter that quantifies the velocity of a chemical reaction involving three reactants. SBO:0000009 SBO:0000019 modifier Systems Biology Ontology Substance that changes the velocity of a chemical reaction without itself being consumed or transformed by the reaction. SBO:0000003 SBO:0000020 inhibitor Systems Biology Ontology Substance that decreases the probability of a chemical reaction without itself being consumed or transformed by the reaction. SBO:0000019 SBO:0000021 potentiator Systems Biology Ontology Substance that increases the probability of a chemical reaction without itself being consumed or transformed by the reaction. This effect is achieved by increasing the difference of free energy between the reactant(s) and the product(s) activator SBO:0000459 SBO:0000022 forward unimolecular rate constant Systems Biology Ontology Numerical parameter that quantifies the forward velocity of a chemical reaction involving only one reactant. This parameter encompasses all the contributions to the velocity except the quantity of the reactant. SBO:0000016 SBO:0000153 SBO:0000023 forward bimolecular rate constant Systems Biology Ontology Numerical parameter that quantifies the forward velocity of a chemical reaction involving two reactants. This parameter encompasses all the contributions to the velocity except the quantity of the reactants. SBO:0000017 SBO:0000153 SBO:0000024 forward trimolecular rate constant Systems Biology Ontology Numerical parameter that quantifies the forward velocity of a chemical reaction involving three reactants. This parameter encompasses all the contributions to the velocity except the quantity of the reactants. SBO:0000018 SBO:0000153 SBO:0000025 catalytic rate constant Systems Biology Ontology Numerical parameter that quantifies the velocity of an enzymatic reaction. kcat turnover number "irreversible" removed on March 11 2007 by Nicolas Le Novere SBO:0000035 SBO:0000026 new term name Systems Biology Ontology none 1 created in error SBO:0000006 SBO:0000027 Michaelis constant Systems Biology Ontology Substrate concentration at which the velocity of reaction is half its maximum. Michaelis constant is an experimental parameter. According to the underlying molecular mechanism it can be interpreted differently in terms of microscopic constants. Km Michaelis-Menten constant SBO:0000193 SBO:0000028 enzymatic rate law for irreversible non-modulated non-interacting unireactant enzymes Systems Biology Ontology Kinetics of enzymes that react only with one substance, their substrate. The enzymes do not catalyse the reactions in both directions. $\mathrm{kcat}\mathrm{Et}S\mathrm{Ks}\mapsto \frac{\mathrm{kcat}\mathrm{Et}S}{\mathrm{Ks}+S}$ SBO:0000150 SBO:0000326 SBO:0000029 Henri-Michaelis-Menten rate law Systems Biology Ontology First general rate equation for reactions involving enzymes, it was presented in "Victor Henri. Lois Générales de l'Action des Diastases. Paris, Hermann, 1903.". The reaction is assumed to be made of a reversible of the binding of the substrate to the enzyme, followed by the breakdown of the complex generating the product. Ten years after Henri, Michaelis and Menten presented a variant of his equation, based on the hypothesis that the dissociation rate of the substrate was much larger than the rate of the product generation. Leonor Michaelis, Maud Menten (1913). Die Kinetik der Invertinwirkung, Biochem. Z. 49:333-369. $\mathrm{kcat}\mathrm{Et}S\mathrm{Ks}\mapsto \frac{\mathrm{kcat}\mathrm{Et}S}{\mathrm{Ks}+S}$ SBO:0000028 SBO:0000030 Van Slyke-Cullen rate law Systems Biology Ontology Rate-law presented in "Donald D. Van Slyke and Glenn E. Cullen. The mode of action of urease and of enzymes in general. J. Biol. Chem., Oct 1914; 19: 141-180". It assumes that the enzymatic reaction occurs as two irreversible steps.E+S -> ES -> E+P. Although of the same form than the Henri-Michaelis-Menten equation, it is semantically different since K now represents the ratio between the production rate and the association rate of the enzyme and the substrate. $\mathrm{kcat}\mathrm{Et}S\mathrm{Ks}\mapsto \frac{\mathrm{kcat}\mathrm{Et}S}{\mathrm{Ks}+S}$ SBO:0000028 SBO:0000031 Briggs-Haldane rate law Systems Biology Ontology The Briggs-Haldane rate law is a general rate equation that does not require the restriction of equilibrium of Henri-Michaelis-Menten or irreversible reactions of Van Slyke, but instead make the hypothesis that the complex enzyme-substrate is in quasi-steady-state. Although of the same form than the Henri-Michaelis-Menten equation, it is semantically different since Km now represents a pseudo-equilibrium constant, and is equal to the ratio between the rate of consumption of the complex (sum of dissociation of substrate and generation of product) and the association rate of the enzyme and the substrate. Rate-law presented by G.E. Briggs and J.B.S. Haldane (1925): "A note on the kinetics of enzyme action, Biochem. J., 19: 338-339". $\mathrm{kcat}\mathrm{Et}S\mathrm{Km}\mapsto \frac{\mathrm{kcat}\mathrm{Et}S}{\mathrm{Km}+S}$ SBO:0000028 SBO:0000032 reverse unimolecular rate constant Systems Biology Ontology Numerical parameter that quantifies the reverse velocity of a chemical reaction involving only one product. This parameter encompasses all the contributions to the velocity except the quantity of the product. SBO:0000016 SBO:0000156 SBO:0000033 reverse bimolecular rate constant Systems Biology Ontology Numerical parameter that quantifies the reverse velocity of a chemical reaction involving only one product. This parameter encompasses all the contributions to the velocity except the quantity of the product. SBO:0000017 SBO:0000156 SBO:0000034 reverse trimolecular rate constant Systems Biology Ontology Numerical parameter that quantifies the reverse velocity of a chemical reaction involving three products. This parameter encompasses all the contributions to the velocity except the quantity of the products. SBO:0000018 SBO:0000156 SBO:0000035 forward unimolecular rate constant, continuous case Systems Biology Ontology Numerical parameter that quantifies the forward velocity of a chemical reaction involving only one reactant. This parameter encompasses all the contributions to the velocity except the quantity of the reactant. It is to be used in a reaction modelled using a continuous framework. SBO:0000022 SBO:0000154 SBO:0000036 forward bimolecular rate constant, continuous case Systems Biology Ontology Numerical parameter that quantifies the forward velocity of a chemical reaction involving two reactants. This parameter encompasses all the contributions to the velocity except the quantity of the reactants. It is to be used in a reaction modelled using a continuous framework. SBO:0000023 SBO:0000154 SBO:0000037 forward trimolecular rate constant, continuous case Systems Biology Ontology Numerical parameter that quantifies the forward velocity of a chemical reaction involving three reactants. This parameter encompasses all the contributions to the velocity except the quantity of the reactants. It is to be used in a reaction modelled using a continuous framework. SBO:0000024 SBO:0000154 SBO:0000038 reverse unimolecular rate constant, continuous case Systems Biology Ontology Numerical parameter that quantifies the reverse velocity of a chemical reaction involving only one product. This parameter encompasses all the contributions to the velocity except the quantity of the product. It is to be used in a reaction modelled using a continuous framework. SBO:0000032 SBO:0000039 reverse bimolecular rate constant, continuous case Systems Biology Ontology Numerical parameter that quantifies the reverse velocity of a chemical reaction involving only one product. This parameter encompasses all the contributions to the velocity except the quantity of the product. It is to be used in a reaction modelled using a continuous framework. SBO:0000033 SBO:0000040 reverse trimolecular rate constant, continuous case Systems Biology Ontology Numerical parameter that quantifies the reverse velocity of a chemical reaction involving three products. This parameter encompasses all the contributions to the velocity except the quantity of the products. It is to be used in a reaction modelled using a continuous framework. SBO:0000034 SBO:0000041 mass action rate law for irreversible reactions Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. SBO:0000012 SBO:0000042 mass action rate law for reversible reactions Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. SBO:0000012 SBO:0000043 mass action rate law for zeroth order irreversible reactions Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is constant. SBO:0000041 SBO:0000044 mass action rate law for first order irreversible reactions Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to the quantity of one reactant. SBO:0000041 SBO:0000045 mass action rate law for second order irreversible reactions Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to two reactant quantity. SBO:0000041 SBO:0000046 zeroth order rate constant Systems Biology Ontology Numerical parameter that quantifies the velocity of a chemical reaction independant of the reactant quantities. This parameter encompasses all the contributions to the velocity. SBO:0000009 SBO:0000047 mass action rate law for zeroth order irreversible reactions, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is constant. It is to be used in a reaction modelled using a continuous framework. $k\mapsto k()$ SBO:0000043 SBO:0000163 SBO:0000048 forward zeroth order rate constant, continuous case Systems Biology Ontology Numerical parameter that quantifies the forward velocity of a chemical reaction independant of the reactant quantities. This parameter encompasses all the contributions to the velocity. It is to be used in a reaction modelled using a continuous framework. SBO:0000154 SBO:0000162 SBO:0000049 mass action rate law for first order irreversible reactions, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to the quantity of one reactant. It is to be used in a reaction modelled using a continuous framework. $kR\mapsto kR$ SBO:0000044 SBO:0000163 SBO:0000050 mass action rate law for second order irreversible reactions, one reactant Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products, and the change of a product quantity is proportional to the square of one reactant quantity. SBO:0000045 SBO:0000051 new term name Systems Biology Ontology 1 SBO:0000005 SBO:0000052 mass action rate law for second order irreversible reactions, one reactant, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to the square of one reactant quantity. It is to be used in a reaction modelled using a continuous framework. $kR\mapsto kRR$ SBO:0000050 SBO:0000163 SBO:0000053 mass action rate law for second order irreversible reactions, two reactants Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to the quantity of two reactants. SBO:0000045 SBO:0000054 mass action rate law for second order irreversible reactions, two reactants, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to the product of two reactant quantities. It is to be used in a reaction modelled using a continuous framework. $k\mathrm{R1}\mathrm{R2}\mapsto k\mathrm{R1}\mathrm{R2}$ SBO:0000053 SBO:0000163 SBO:0000055 mass action rate law for third order irreversible reactions Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to three reactant quantities. SBO:0000041 SBO:0000056 mass action rate law for third order irreversible reactions, one reactant Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to the cube of one reactant quantity. SBO:0000055 SBO:0000057 mass action rate law for third order irreversible reactions, one reactant, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products, and the change of a product quantity is proportional to the cube of one reactant quantity. It is to be used in a reaction modelled using a continuous framework. $kR\mapsto kRRR$ SBO:0000056 SBO:0000163 SBO:0000058 mass action rate law for third order irreversible reactions, two reactants Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to the quantity of one reactant and the square of the quantity of the other reactant. SBO:0000055 SBO:0000059 mass action rate law for third order irreversible reactions, two reactants, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to the quantity of one reactant and the square of the quantity of the other reactant. It is to be used in a reaction modelled using a continuous framework. $k\mathrm{R1}\mathrm{R2}\mapsto k\mathrm{R1}\mathrm{R1}\mathrm{R2}$ SBO:0000058 SBO:0000163 SBO:0000060 mass action rate law for third order irreversible reactions, three reactants Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to the quantity of three reactants. SBO:0000055 SBO:0000061 mass action rate law for third order irreversible reactions, three reactants, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products, and the change of a product quantity is proportional to the product of three reactant quantities. It is to be used in a reaction modelled using a continuous framework. $k\mathrm{R1}\mathrm{R2}\mathrm{R3}\mapsto k\mathrm{R1}\mathrm{R2}\mathrm{R3}$ SBO:0000060 SBO:0000163 SBO:0000062 continuous framework Systems Biology Ontology Modelling approach where the quantities of participants are considered continuous, and represented by real values. The associated simulation methods make use of differential equations. SBO:0000004 SBO:0000063 discrete framework Systems Biology Ontology Modelling approach where the quantities of participants are considered discrete, and represented by integer values. The associated simulation methods can be deterministic or stochastic. SBO:0000004 SBO:0000064 mathematical expression Systems Biology Ontology Formal representation of a calculus linking parameters and variables of a model. SBO:0000000 SBO:0000065 forward zeroth order rate constant, discrete case Systems Biology Ontology Numerical parameter that quantifies the forward velocity of a chemical reaction independant of the reactant quantities. This parameter encompasses all the contributions to the velocity. It is to be used in a reaction modelled using a discrete framework. SBO:0000155 SBO:0000162 SBO:0000066 forward unimolecular rate constant, discrete case Systems Biology Ontology Numerical parameter that quantifies the forward velocity of a chemical reaction involving only one reactant. This parameter encompasses all the contributions to the velocity except the quantity of the reactant. It is to be used in a reaction modelled using a discrete framework. SBO:0000022 SBO:0000155 SBO:0000067 forward bimolecular rate constant, discrete case Systems Biology Ontology Numerical parameter that quantifies the forward velocity of a chemical reaction involving two reactants. This parameter encompasses all the contributions to the velocity except the quantity of the reactants. It is to be used in a reaction modelled using a discrete framework. SBO:0000023 SBO:0000155 SBO:0000068 forward trimolecular rate constant, discrete case Systems Biology Ontology Numerical parameter that quantifies the forward velocity of a chemical reaction involving three reactants. This parameter encompasses all the contributions to the velocity except the quantity of the reactants. It is to be used in a reaction modelled using a discrete framework. SBO:0000024 SBO:0000155 SBO:0000069 mass action rate law for zeroth order reversible reactions Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is constant. SBO:0000042 SBO:0000070 mass action rate law for zeroth order forward, first order reverse, reversible reactions, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is constant. The rate of the reverse process is proportional to the quantity of one product. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}P\mapsto \mathrm{kf}-\mathrm{kr}P$ SBO:0000069 SBO:0000071 mass action rate law for zeroth order forward, second order reverse, reversible reactions, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is constant. The rate of the reverse process is proportional totwo product quantities. SBO:0000069 SBO:0000072 mass action rate law for zeroth order forward, second order reverse, reversible reactions, one product, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is constant. The rate of the reverse process is proportional to the square of one product quantity. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}P\mapsto \mathrm{kf}-\mathrm{kr}PP$ SBO:0000071 SBO:0000073 mass action rate law for zeroth order forward, second order reverse, reversible reactions, two products, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is constant. The rate of the reverse process is proportional to the product of two product quantities. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}\mathrm{P1}\mathrm{P2}\mapsto \mathrm{kf}-\mathrm{kr}\mathrm{P1}\mathrm{P2}$ SBO:0000071 SBO:0000074 mass action rate law for zeroth order forward, third order reverse, reversible reactions, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is constant. The rate of the reverse process is proportional to three product quantities. SBO:0000069 SBO:0000075 mass action rate law for zeroth order forward, third order reverse, reversible reactions, one product, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is constant. The rate of the reverse process is proportional to the cube of one product quantity. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}P\mapsto \mathrm{kf}-\mathrm{kr}PPP$ SBO:0000074 SBO:0000076 mass action rate law for zeroth order forward, third order reverse, reversible reactions, two products, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is constant. The rate of the reverse process is proportional to the quantity of one product and the square of the quantity of the other product. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}\mathrm{P1}\mathrm{P2}\mapsto \mathrm{kf}-\mathrm{kr}\mathrm{P1}\mathrm{P2}\mathrm{P2}$ SBO:0000074 SBO:0000077 mass action rate law for zeroth order forward, third order reverse, reversible reactions, three products, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is constant. The rate of the reverse process is proportional to the product of three product quantities. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}\mathrm{P1}\mathrm{P2}\mathrm{P3}\mapsto \mathrm{kf}-\mathrm{kr}\mathrm{P1}\mathrm{P2}\mathrm{P3}$ SBO:0000074 SBO:0000078 mass action rate law for first order reversible reactions Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the quantity of one reactant. SBO:0000042 SBO:0000079 mass action rate law for first order forward, zeroth order reverse, reversible reactions, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the quantity of one reactant. The rate of the reverse process is constant. It is to be used in a reaction modelled using a continuous framework. renamed from "first order forward, zeroth order reverse, reversible mass action kinetics, continuous scheme" $\mathrm{kf}\mathrm{kr}R\mapsto \mathrm{kf}R-\mathrm{kr}$ SBO:0000078 SBO:0000080 mass action rate law for first order forward, first order reverse, reversible reactions, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the quantity of one reactant. The rate of the reverse process is proportional to the quantity of one product. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}RP\mapsto \mathrm{kf}R-\mathrm{kr}P$ SBO:0000078 SBO:0000081 mass action rate law for first order forward, second order reverse, reversible reactions Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the quantity of one reactant. The rate of the reverse process is proportional to two product quantities. SBO:0000078 SBO:0000082 mass action rate law for first order forward, second order reverse, reversible reactions, one product, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the quantity of one reactant. The rate of the reverse process is proportional to the square of one product quantity. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}RP\mapsto \mathrm{kf}R-\mathrm{kr}PP$ SBO:0000081 SBO:0000083 mass action rate law for first order forward, second order reverse, reversible reactions, two products, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the quantity of one reactant. The rate of the reverse process is proportional to the product of two product quantities. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}R\mathrm{P1}\mathrm{P2}\mapsto \mathrm{kf}R-\mathrm{kr}\mathrm{P1}\mathrm{P2}$ SBO:0000081 SBO:0000084 mass action rate law for first order forward, third order reverse, reversible reactions Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the quantity of one reactant. The rate of the reverse process is proportional to three product quantities. SBO:0000078 SBO:0000085 mass action rate law for first order forward, third order reverse, reversible reactions, one product, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the quantity of one reactant. The rate of the reverse process is proportional to the cube of one product quantity. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}RP\mapsto \mathrm{kf}R-\mathrm{kr}PPP$ SBO:0000084 SBO:0000086 mass action rate law for first order forward, third order reverse, reversible reactions, two products, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the quantity of one reactant. The rate of the reverse process is proportional to the quantity of one product and the square of the quantity of the other product. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}R\mathrm{P1}\mathrm{P2}\mapsto \mathrm{kf}R-\mathrm{kr}\mathrm{P1}\mathrm{P1}\mathrm{P2}$ SBO:0000084 SBO:0000087 mass action rate law for first order forward, third order reverse, reversible reactions, three products, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the quantity of one reactant. The rate of the reverse process is proportional to the product of three product quantities. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}R\mathrm{P1}\mathrm{P2}\mathrm{P3}\mapsto \mathrm{kf}R-\mathrm{kr}\mathrm{P1}\mathrm{P2}\mathrm{P3}$ SBO:0000084 SBO:0000088 mass action rate law for second order reversible reactions Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to two reactant quantities. SBO:0000042 SBO:0000089 mass action rate law for second order forward, reversible reactions, one reactant Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the square of one reactant quantity. SBO:0000088 SBO:0000090 mass action rate law for second order forward, zeroth order reverse, reversible reactions, one reactant, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the square of one reactant quantity. The rate of the reverse process is constant. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}R\mapsto \mathrm{kf}RR-\mathrm{kr}$ SBO:0000089 SBO:0000091 mass action rate law for second order forward, first order reverse, reversible reactions, one reactant, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the square of one reactant quantity. The rate of the reverse process is proportional to the quantity of one product. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}RP\mapsto \mathrm{kf}RR-\mathrm{kr}P$ SBO:0000089 SBO:0000092 mass action rate law for second order forward, second order reverse, reversible reactions, one reactant Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the square of one reactant quantity. The rate of the reverse process is proportional to the quantity of two products. SBO:0000089 SBO:0000093 mass action rate law for second order forward, second order reverse, reversible reactions, one reactant, one product, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the square of one reactant quantity. The rate of the reverse process is proportional to the square of one product quantity. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}RP\mapsto \mathrm{kf}RR-\mathrm{kr}PP$ SBO:0000092 SBO:0000094 mass action rate law for second order forward, second order reverse, reversible reactions, two products, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the square of one reactant quantity. The rate of the reverse process is proportional to the product of two product quantities. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}R\mathrm{P1}\mathrm{P2}\mapsto \mathrm{kf}RR-\mathrm{kr}\mathrm{P1}\mathrm{P2}$ SBO:0000092 SBO:0000095 mass action rate law for second order forward, third order reverse, reversible reactions, one reactant Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the square of one reactant quantity. The rate of the reverse process is proportional to the quantity of three products. SBO:0000089 SBO:0000096 mass action rate law for second order forward, third order reverse, reversible reactions, one reactant, one product, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the square of one reactant quantity. The rate of the reverse process is proportional to the cube of one product quantity. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}RP\mapsto \mathrm{kf}RR-\mathrm{kr}PPP$ SBO:0000095 SBO:0000097 mass action rate law for second order forward, third order reverse, reversible reactions, one reactant, two products, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the square of one reactant quantity. The rate of the reverse process is proportional to the quantity of one product and the square of the quantity of the other product. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}R\mathrm{P1}\mathrm{P2}\mapsto \mathrm{kf}RR-\mathrm{kr}\mathrm{P1}\mathrm{P1}\mathrm{P2}$ SBO:0000095 SBO:0000098 mass action rate law for second order forward, third order reverse, reversible reactions, one reactant, three products, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the square of one reactant quantity. The rate of the reverse process is proportional to the product of three product quantities. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}R\mathrm{P1}\mathrm{P2}\mathrm{P3}\mapsto \mathrm{kf}RR-\mathrm{kr}\mathrm{P1}\mathrm{P2}\mathrm{P3}$ SBO:0000095 SBO:0000099 mass action rate law for second order forward, reversible reactions, two reactants Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the product of two reactant quantities. SBO:0000088 SBO:0000100 mass action rate law for second order forward, zeroth order reverse, reversible reactions, two reactants, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the product of two reactant quantities. The rate of the reverse process is constant. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}\mathrm{R1}\mathrm{R2}\mapsto \mathrm{kf}\mathrm{R1}\mathrm{R2}-\mathrm{kr}$ SBO:0000099 SBO:0000101 mass action rate law for second order forward, first order reverse, reversible reactions, two reactants, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the product of two reactant quantities. The rate of the reverse process is proportional to the quantity of one product. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}\mathrm{R1}\mathrm{R2}P\mapsto \mathrm{kf}\mathrm{R1}\mathrm{R2}-\mathrm{kr}P$ SBO:0000099 SBO:0000102 mass action rate law for second order forward, second order reverse, reversible reactions, two reactants Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the product of two reactant quantities. The rate of the reverse process is proportional to the quantity of two products. SBO:0000099 SBO:0000103 mass action rate law for second order forward, second order reverse, reversible reactions, two reactants, one product, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the product of two reactant quantities. The rate of the reverse process is proportional to the square of one product quantity. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}\mathrm{R1}\mathrm{R2}P\mapsto \mathrm{kf}\mathrm{R1}\mathrm{R2}-\mathrm{kr}PP$ SBO:0000102 SBO:0000104 mass action rate law for second order forward, second order reverse, reversible reactions, two reactants, two products, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the product of two reactant quantities. The rate of the reverse process is proportional to the product of two product quantities. It is to be used in a reaction modelled using a continuous framework. renamed from "second order forward with two reactants, second order reverse with two products, reversible mass action kinetics, continuous scheme" $\mathrm{kf}\mathrm{kr}\mathrm{R1}\mathrm{R2}\mathrm{P1}\mathrm{P2}\mapsto \mathrm{kf}\mathrm{R1}\mathrm{R2}-\mathrm{kr}\mathrm{P1}\mathrm{P2}$ SBO:0000102 SBO:0000105 mass action rate law for second order forward, third order reverse, reversible reactions, two reactants Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the product of two reactant quantities. The rate of the reverse process is proportional to the quantity of three products. SBO:0000099 SBO:0000106 mass action rate law for second order forward, third order reverse, reversible reactions, two reactants, one product, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the product of two reactant quantities. The rate of the reverse process is proportional to the cube of one product quantity. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}\mathrm{R1}\mathrm{R2}P\mapsto \mathrm{kf}\mathrm{R1}\mathrm{R2}-\mathrm{kr}PPP$ SBO:0000105 SBO:0000107 mass action rate law for second order forward, third order reverse, reversible reactions, two reactants, two products, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the product of two reactant quantities. The rate of the reverse process is proportional to the quantity of one product and the square of the quantity of the other product. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}\mathrm{R1}\mathrm{R2}\mathrm{P1}\mathrm{P2}\mapsto \mathrm{kf}\mathrm{R1}\mathrm{R2}-\mathrm{kr}\mathrm{P1}\mathrm{P1}\mathrm{P2}$ SBO:0000105 SBO:0000108 mass action rate law for second order forward, third order reverse, reversible reactions, two reactants, three products, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the product of two reactant quantities. The rate of the reverse process is proportional to the product of three product quantities. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}\mathrm{R1}\mathrm{R2}\mathrm{P1}\mathrm{P2}\mathrm{P3}\mapsto \mathrm{kf}\mathrm{R1}\mathrm{R2}-\mathrm{kr}\mathrm{P1}\mathrm{P2}\mathrm{P3}$ SBO:0000105 SBO:0000109 mass action rate law for third order reversible reactions Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the cube of a reactant quantity. SBO:0000042 SBO:0000110 mass action rate law for third order forward, reversible reactions, two reactants Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the quantity of one reactant and the square of quantity of the other reactant. SBO:0000109 SBO:0000111 mass action rate law for third order forward, zeroth order reverse, reversible reactions, two reactants, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the quantity of one reactant and the square of quantity of the other reactant. The rate of the reverse process is constant. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}\mathrm{R1}\mathrm{R2}\mapsto \mathrm{kf}\mathrm{R1}\mathrm{R1}\mathrm{R2}-\mathrm{kr}$ SBO:0000110 SBO:0000112 mass action rate law for third order forward, first order reverse, reversible reactions, two reactants, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the quantity of one reactant and the square of quantity of the other reactant. The rate of the reverse process is proportional to the quantity of one product. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}\mathrm{R1}\mathrm{R2}P\mapsto \mathrm{kf}\mathrm{R1}\mathrm{R1}\mathrm{R2}-\mathrm{kr}P$ SBO:0000110 SBO:0000113 mass action rate law for third order forward, second order reverse, reversible reactions, two reactants Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the quantity of one reactant and the square of quantity of the other reactant. The rate of the reverse process is proportional to the quantity of two products. SBO:0000110 SBO:0000114 mass action rate law for third order forward, second order reverse, reversible reactions, two reactants, one product, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the quantity of one reactant and the square of quantity of the other reactant. The rate of the reverse process is proportional to the square of one product quantity. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}\mathrm{R1}\mathrm{R2}P\mapsto \mathrm{kf}\mathrm{R1}\mathrm{R1}\mathrm{R2}-\mathrm{kr}PP$ SBO:0000113 SBO:0000115 mass action rate law for third order forward, second order reverse, reversible reactions, two reactants, two products, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the quantity of one reactant and the square of quantity of the other reactant. The rate of the reverse process is proportional to the product of two product quantities. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}\mathrm{R1}\mathrm{R2}\mathrm{P1}\mathrm{P2}\mapsto \mathrm{kf}\mathrm{R1}\mathrm{R1}\mathrm{R2}-\mathrm{kr}\mathrm{P1}\mathrm{P2}$ SBO:0000113 SBO:0000116 mass action rate law for third order forward, third order reverse, reversible reactions, two reactants Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the quantity of one reactant and the square of quantity of the other reactant. The rate of the reverse process is proportional to the quantity of three products. SBO:0000110 SBO:0000117 mass action rate law for third order forward, third order reverse, reversible reactions, two reactants, one product, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the quantity of one reactant and the square of quantity of the other reactant. The rate of the reverse process is proportional to the cube of one product quantity. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}\mathrm{R1}\mathrm{R2}P\mapsto \mathrm{kf}\mathrm{R1}\mathrm{R1}\mathrm{R2}-\mathrm{kr}PPP$ SBO:0000116 SBO:0000118 mass action rate law for third order forward, third order reverse, reversible reactions, two reactants, two products, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the quantity of one reactant and the square of quantity of the other reactant. The rate of the reverse process is proportional to the quantity of one product and the square of the quantity of the other product. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}\mathrm{R1}\mathrm{R2}\mathrm{P1}\mathrm{P2}\mapsto \mathrm{kf}\mathrm{R1}\mathrm{R1}\mathrm{R2}-\mathrm{kr}\mathrm{P1}\mathrm{P1}\mathrm{P2}$ SBO:0000116 SBO:0000119 mass action rate law for third order forward, third order reverse, reversible reactions, two reactants, three products, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the quantity of one reactant and the square of quantity of the other reactant. The rate of the reverse process is proportional to the product of three product quantities. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}\mathrm{R1}\mathrm{R2}\mathrm{P1}\mathrm{P2}\mathrm{P3}\mapsto \mathrm{kf}\mathrm{R1}\mathrm{R1}\mathrm{R2}-\mathrm{kr}\mathrm{P1}\mathrm{P2}\mathrm{P3}$ SBO:0000116 SBO:0000120 mass action rate law for third order forward, reversible reactions, three reactants Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the product of three reactant quantities. SBO:0000109 SBO:0000121 mass action rate law for third order forward, zeroth order reverse, reversible reactions, three reactants, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the product of three reactant quantities. The rate of the reverse process is constant. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}\mathrm{R1}\mathrm{R2}\mathrm{R3}\mapsto \mathrm{kf}\mathrm{R1}\mathrm{R2}\mathrm{R3}-\mathrm{kr}$ SBO:0000120 SBO:0000122 mass action rate law for third order forward, first order reverse, reversible reactions, three reactants, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the product of three reactant quantities. The rate of the reverse process is proportional to the quantity of one product. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}\mathrm{R1}\mathrm{R2}\mathrm{R3}P\mapsto \mathrm{kf}\mathrm{R1}\mathrm{R2}\mathrm{R3}-\mathrm{kr}P$ SBO:0000120 SBO:0000123 mass action rate law for third order forward, second order reverse, reversible reactions, three reactants Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the product of three reactant quantities. The rate of the reverse process is proportional to the quantity of two products. SBO:0000120 SBO:0000124 mass action rate law for third order forward, second order reverse, reversible reactions, three reactants, one product, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the product of three reactant quantities. The rate of the reverse process is proportional to the square of one product quantity. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}\mathrm{R1}\mathrm{R2}\mathrm{R3}P\mapsto \mathrm{kf}\mathrm{R1}\mathrm{R2}\mathrm{R3}-\mathrm{kr}PP$ SBO:0000123 SBO:0000125 mass action rate law for third order forward, second order reverse, reversible reactions, three reactants, two products, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the product of three reactant quantities. The rate of the reverse process is proportional to the product of two product quantities. It is to be used in a reaction modelled using a continuous framework. renamed from "third order forward with three reactants, second order reverse with two products, reversible mass action kinetics, continuous scheme" $\mathrm{kf}\mathrm{kr}\mathrm{R1}\mathrm{R2}\mathrm{R3}\mathrm{P1}\mathrm{P2}\mapsto \mathrm{kf}\mathrm{R1}\mathrm{R2}\mathrm{R3}-\mathrm{kr}\mathrm{P1}\mathrm{P2}$ SBO:0000123 SBO:0000126 mass action rate law for third order forward, third order reverse, reversible reactions, three reactants Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the product of three reactant quantities. The rate of the reverse process is proportional to the quantity of three products. SBO:0000120 SBO:0000127 mass action rate law for third order forward, third order reverse, reversible reactions, three reactants, one product, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the product of three reactant quantities. The rate of the reverse process is proportional to the cube of one product quantity. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}\mathrm{R1}\mathrm{R2}\mathrm{R3}P\mapsto \mathrm{kf}\mathrm{R1}\mathrm{R2}\mathrm{R3}-\mathrm{kr}PPP$ SBO:0000126 SBO:0000128 mass action rate law for third order forward, third order reverse, reversible reactions, three reactants, two products, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the product of three reactant quantities. The rate of the reverse process is proportional to the quantity of one product and the square of the quantity of the other product. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}\mathrm{R1}\mathrm{R2}\mathrm{R3}\mathrm{P1}\mathrm{P2}\mapsto \mathrm{kf}\mathrm{R1}\mathrm{R2}\mathrm{R3}-\mathrm{kr}\mathrm{P1}\mathrm{P1}\mathrm{P2}$ SBO:0000126 SBO:0000129 mass action rate law for third order forward, third order reverse, reversible reactions, three reactants, three products, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the product of three reactant quantities. The rate of the reverse process is proportional to the product of three product quantities. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}\mathrm{R1}\mathrm{R2}\mathrm{R3}\mathrm{P1}\mathrm{P2}\mathrm{P3}\mapsto \mathrm{kf}\mathrm{R1}\mathrm{R2}\mathrm{R3}-\mathrm{kr}\mathrm{P1}\mathrm{P2}\mathrm{P3}$ SBO:0000126 SBO:0000130 mass action rate law for third order forward, reversible reactions, one reactant Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the cube of one reactant quantity. SBO:0000109 SBO:0000131 mass action rate law for third order forward, zeroth order reverse, reversible reactions, one reactant, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the cube of one reactant quantity. The rate of the reverse process is constant. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}R\mapsto \mathrm{kf}RRR-\mathrm{kr}$ SBO:0000130 SBO:0000132 mass action rate law for third order forward, first order reverse, reversible reactions, one reactant, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the cube of one reactant quantity. The rate of the reverse process is proportional to the quantity of one product. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}RP\mapsto \mathrm{kf}RRR-\mathrm{kr}P$ SBO:0000130 SBO:0000133 mass action rate law for third order forward, second order reverse, reversible reactions, one reactant Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the cube of one reactant quantity. The rate of the reverse process is proportional to the quantity of two products. SBO:0000130 SBO:0000134 mass action rate law for third order forward, second order reverse, reversible reactions, one reactant, one product, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the cube of one reactant quantity. The rate of the reverse process is proportional to the square of one product quantity. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}RP\mapsto \mathrm{kf}RRR-\mathrm{kr}PP$ SBO:0000133 SBO:0000135 mass action rate law for third order forward, second order reverse, reversible reactions, one reactant, two products, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the cube of one reactant quantity. The rate of the reverse process is proportional to the product of two product quantities. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}R\mathrm{P1}\mathrm{P2}\mapsto \mathrm{kf}RRR-\mathrm{kr}\mathrm{P1}\mathrm{P2}$ SBO:0000133 SBO:0000136 mass action rate law for third order forward, third order reverse, reversible reactions, one reactant Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the cube of one reactant quantity. The rate of the reverse process is proportional to the quantity of three products. SBO:0000130 SBO:0000137 mass action rate law for third order forward, third order reverse, reversible reactions, one reactant, one product, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the cube of one reactant quantity. The rate of the reverse process is proportional to the cube of one product quantity. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}RP\mapsto \mathrm{kf}RRR-\mathrm{kr}PPP$ SBO:0000136 SBO:0000138 mass action rate law for third order forward, third order reverse, reversible reactions, one reactant, two products, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the cube of one reactant quantity. The rate of the reverse process is proportional to the quantity of one product and the square of the quantity of the other product. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}R\mathrm{P1}\mathrm{P2}\mapsto \mathrm{kf}RRR-\mathrm{kr}\mathrm{P1}\mathrm{P1}\mathrm{P2}$ SBO:0000136 SBO:0000139 mass action rate law for third order forward, third order reverse, reversible reactions, one reactant, three products, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does include a reverse process that creates the reactants from the products. The rate of the forward process is proportional to the cube of one reactant quantity. The rate of the reverse process is proportional to the product of three product quantities. It is to be used in a reaction modelled using a continuous framework. $\mathrm{kf}\mathrm{kr}R\mathrm{P1}\mathrm{P2}\mathrm{P3}\mapsto \mathrm{kf}RRR-\mathrm{kr}\mathrm{P1}\mathrm{P2}\mathrm{P3}$ SBO:0000136 SBO:0000140 mass action rate law for zeroth order irreversible reactions, discrete scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is constant. It is to be used in a reaction modelled using a discrete framework. Gillespie (1976). J Comput Physics 22, 403-434 $c\mapsto c()$ SBO:0000043 SBO:0000166 SBO:0000141 mass action rate law for first order irreversible reactions, discrete scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to the quantity of one reactant. It is to be used in a reaction modelled using a discrete framework. Gillespie (1976). J Comput Physics 22, 403-434 $cR\mapsto cR$ SBO:0000044 SBO:0000166 SBO:0000142 mass action rate law for second order irreversible reactions, one reactant, discrete scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to the square of one reactant quantity. It is to be used in a reaction modelled using a discrete framework. Gillespie (1976). J Comput Physics 22, 403-434 $cR\mapsto c\frac{R(R-1)}{2}$ SBO:0000050 SBO:0000166 SBO:0000143 mass action rate law for second order irreversible reactions, two reactants, discrete scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to the quantity of two reactants. It is to be used in a reaction modelled using a discrete framework. $c\mathrm{R1}\mathrm{R2}\mapsto c\mathrm{R1}\mathrm{R2}$ SBO:0000053 SBO:0000166 SBO:0000144 mass action rate law for third order irreversible reactions, one reactant, discrete scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to the cube of one reactant quantity. It is to be used in a reaction modelled using a discrete framework. Gillespie (1976). J Comput Physics 22, 403-434 $cR\mapsto c\frac{R(R-1)(R-2)}{6}$ SBO:0000056 SBO:0000166 SBO:0000145 mass action rate law for third order irreversible reactions, two reactants, discrete scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to the quantity of one reactant and the square of the quantity of the other reactant. It is to be used in a reaction modelled using a discrete framework. Gillespie (1976). J Comput Physics 22, 403-434 $c\mathrm{R1}\mathrm{R2}\mapsto c\mathrm{R1}\frac{\mathrm{R2}(\mathrm{R2}-1)}{2}$ SBO:0000058 SBO:0000166 SBO:0000146 mass action rate law for third order irreversible reactions, three reactants, discrete scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to the quantity of three reactants. It is to be used in a reaction modelled using a discrete framework. Gillespie (1976). J Comput Physics 22, 403-434 $c\mathrm{R1}\mathrm{R2}\mathrm{R3}\mapsto c\mathrm{R1}\mathrm{R2}\mathrm{R3}$ SBO:0000060 SBO:0000166 SBO:0000147 thermodynamic temperature Systems Biology Ontology Temperature is the physical property of a system which underlies the common notions of "hot" and "cold"; the material with the higher temperature is said to be hotter. Temperature is a quantity related to the average kinetic energy of the particles in a substance. The 10th Conference Generale des Poids et Mesures decided to define the thermodynamic temperature scale by choosing the triple point of water as the fundamental fixed point, and assigning to it the temperature 273,16 degrees Kelvin, exactly (0.01 degree Celsius). Comptes rendus de la 10e CGPM (1954), 1956, 79 SBO:0000002 SBO:0000148 temperature difference Systems Biology Ontology Quantity resulting from the difference between two thermodynamic temperatures. A difference or interval of temperature may be expressed in Kelvins or in degrees Celsius. Comptes rendus de la 13th CGPM, 1967-1968, Resolution 3 SBO:0000002 SBO:0000149 number of substrates Systems Biology Ontology Number of molecules which are acted upon by an enzyme. SBO:0000157 SBO:0000150 enzymatic rate law for irreversible non-modulated non-interacting reactant enzymes Systems Biology Ontology Kinetics of enzymes that react with one or several substances, their substrates, that bind independently. The enzymes do not catalyse the reactions in both directions. $\mathrm{Et}\mathrm{kp}nSK\mapsto \frac{\mathrm{Et}\mathrm{kp}\prod_{i=1}^n \frac{S_i}{K_i}}{\prod_{i=1}^n 1+\frac{S_i}{K_i}}$ SBO:0000268 SBO:0000151 enzymatic rate law for irreversible non-modulated non-interacting bireactant enzymes Systems Biology Ontology Kinetics of enzymes that react with two substances, their substrates, that bind independently. The enzymes do not catalyse the reactions in both directions. $\mathrm{Et}\mathrm{kp}n\mathrm{S1}\mathrm{S2}\mathrm{K1}\mathrm{K2}\mapsto \frac{\mathrm{Et}\mathrm{kp}\frac{\mathrm{S1}}{\mathrm{K1}}\frac{\mathrm{S2}}{\mathrm{K2}}}{(1+\frac{\mathrm{S1}}{\mathrm{K1}})(1+\frac{\mathrm{S2}}{\mathrm{K2}})}$ SBO:0000150 SBO:0000152 enzymatic rate law for irreversible non-modulated non-interacting trireactant enzymes Systems Biology Ontology Kinetics of enzymes that react with three substances, their substrates, that bind independently. The enzymes do not catalyse the reactions in both directions. $\mathrm{Et}\mathrm{kp}n\mathrm{S1}\mathrm{S2}\mathrm{S3}\mathrm{K1}\mathrm{K2}\mathrm{K3}\mapsto \frac{\mathrm{Et}\mathrm{kp}\frac{\mathrm{S1}}{\mathrm{K1}}\frac{\mathrm{S2}}{\mathrm{K2}}\frac{\mathrm{S3}}{\mathrm{K3}}}{(1+\frac{\mathrm{S1}}{\mathrm{K1}})(1+\frac{\mathrm{S2}}{\mathrm{K2}})(1+\frac{\mathrm{S3}}{\mathrm{K3}})}$ SBO:0000150 SBO:0000153 forward rate constant Systems Biology Ontology Numerical parameter that quantifies the forward velocity of a chemical reaction. This parameter encompasses all the contributions to the velocity except the quantity of the reactants. SBO:0000009 SBO:0000154 forward rate constant, continuous case Systems Biology Ontology Numerical parameter that quantifies the forward velocity of a chemical reaction. This parameter encompasses all the contributions to the velocity except the quantity of the reactants. It is to be used in a reaction modelled using a continuous framework. SBO:0000153 SBO:0000155 forward rate constant, discrete case Systems Biology Ontology Numerical parameter that quantifies the forward velocity of a chemical reaction. This parameter encompasses all the contributions to the velocity except the quantity of the reactants. It is to be used in a reaction modelled using a discrete framework. SBO:0000153 SBO:0000156 reverse rate constant Systems Biology Ontology Numerical parameter that quantifies the forward velocity of a chemical reaction. This parameter encompasses all the contributions to the velocity except the quantity of the reactants. SBO:0000009 SBO:0000157 number of reactants Systems Biology Ontology Number of different substances consumed by a chemical reaction. SBO:0000188 SBO:0000158 order of a reaction with respect to a reactant Systems Biology Ontology The order of a reaction with respect to a certain reactant is defined as the power to which its concentration term in the rate equation is raised. SBO:0000382 SBO:0000159 non-integral order rate constant Systems Biology Ontology Numerical parameter that quantifies the velocity of a chemical reaction where reactants have non-integral orders. This parameter encompasses all the contributions to the velocity except the quantity of the reactants. SBO:0000009 SBO:0000160 forward non-integral order rate constant Systems Biology Ontology Numerical parameter that quantifies the forward velocity of a chemical reaction where reactants have non-integral orders. This parameter encompasses all the contributions to the velocity except the quantity of the reactants. SBO:0000153 SBO:0000159 SBO:0000161 reverse non-integral order rate constant Systems Biology Ontology Numerical parameter that quantifies the reverse velocity of a chemical reaction where products have non-integral orders. This parameter encompasses all the contributions to the velocity except the quantity of the products. SBO:0000156 SBO:0000159 SBO:0000162 forward zeroth order rate constant Systems Biology Ontology Numerical parameter that quantifies the forward velocity of a chemical reaction independant of the reactant quantities. This parameter encompasses all the contributions to the velocity. SBO:0000046 SBO:0000153 SBO:0000163 mass action rate law for irreversible reactions, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. It is to be used in a reaction modelled using a continuous framework. $kn\mathrm{mu}R\mapsto k\prod_{i=0}^n R_i^{\mathrm{mu}_i}$ SBO:0000041 SBO:0000164 second order irreversible mass action kinetics, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to two reactant quantity. It is to be used in a reaction modelled using a continuous framework. 1 $kR\mapsto k\prod_{i=1}^2 R_i$ SBO:0000005 SBO:0000165 third order irreversible mass action kinetics, continuous scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to three reactant quantities. It is to be used in a reaction modelled using a continuous framework. 1 $kR\mapsto k\prod_{i=1}^3 R_i$ SBO:0000005 SBO:0000166 mass action rate law for irreversible reactions, discrete scheme Systems Biology Ontology Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. It is to be used in a reaction modelled using a discrete framework. $cn\mathrm{mu}R\mapsto c\prod_{i=0}^n \frac{R_i!}{(R_i-\mathrm{mu}_i)!\mathrm{mu}_i!}$ SBO:0000041 SBO:0000231 occurring entity representation Systems Biology Ontology Representation of an entity that manifests, unfolds or develops through time, such as a discrete event, or a mutual or reciprocal action or influence that happens between participating physical entities, and/or other occurring entities. modified as part of ontology 'refactoring' process [SF bug #3172586] Name changed to "interaction" on November 18 2008 by Nicolas Le Novere. Definition changed to mention interaction with other interactions, in order to cover "process" and "relationship". SBO:0000000 SBO:0000232 obsolete event Systems Biology Ontology A phenomenon that takes place and which may be observable, or may be determined to have occurred as the result of an action or process. 1 SBO:0000231 SBO:0000167 biochemical or transport reaction Systems Biology Ontology An event involving one or more physical entities that modifies the structure, location or free energy of at least one of the participants. Modified on 14 August 2006 by Nicolas Le Novere following the suggestion of Kirill Degtyarenko SBO:0000375 SBO:0000168 control Systems Biology Ontology Modification of the execution of an event or a process. modulation regulation November 10 2006: change "of a reaction" to "of an event" SBO:0000374 SBO:0000169 inhibition Systems Biology Ontology Negative modulation of the execution of a process. Changed "reaction" to "process". NLN SBO:0000168 SBO:0000170 stimulation Systems Biology Ontology Positive modulation of the execution of a process. changed "reaction" to "process" SBO:0000168 SBO:0000171 necessary stimulation Systems Biology Ontology Control that is necessary to the execution of a process. absolute stimulation trigger Changed "reaction" to "process". NLN SBO:0000170 SBO:0000172 catalysis Systems Biology Ontology Modification of the velocity of a reaction by lowering the energy of the transition state. November 10 2006; Nicolas Le Novere: becomes a child of "SBO:0000170 ! stimulation" SBO:0000170 SBO:0000173 and Systems Biology Ontology All the preceding events or participating entities are necessary to perform the control. SBO:0000237 SBO:0000174 or Systems Biology Ontology Any of the preceding events or participating entities are necessary to perform the control. SBO:0000237 SBO:0000175 xor Systems Biology Ontology Only one of the preceding events or participating entities can perform the control at one time. exclusive or SBO:0000237 SBO:0000176 biochemical reaction Systems Biology Ontology An event involving one or more chemical entities that modifies the electrochemical structure of at least one of the participants. Modified on 14 August 2006 by Nicolas Le Novere following the suggestion of Kirill Degtyarenko SBO:0000167 SBO:0000177 non-covalent binding Systems Biology Ontology Interaction between several biochemical entities that results in the formation of a non-covalent complex "non-covalent" added on February 26 2008 by Nicolas Le Novere. SBO:0000176 SBO:0000178 cleavage Systems Biology Ontology Rupture of a covalent bond resulting in the conversion of one physical entity into several physical entities. SBO:0000182 SBO:0000179 degradation Systems Biology Ontology Complete disappearance of a physical entity. SBO:0000176 SBO:0000180 dissociation Systems Biology Ontology Transformation of a non-covalent complex that results in the formation of several independent biochemical entities SBO:0000176 SBO:0000181 conformational transition Systems Biology Ontology Biochemical reaction that does not result in the modification of covalent bonds of reactants, but rather modifies the conformation of some reactants, that is the relative position of their atoms in space. Renamed on September 20 2006, following the suggestion of Hiroaki Kitano. SBO:0000176 SBO:0000182 conversion Systems Biology Ontology Biochemical reaction that results in the modification of some covalent bonds. SBO:0000176 SBO:0000183 transcription Systems Biology Ontology Process through which a DNA sequence is copied to produce a complementary RNA. See GO:0006350 Definition modified on 09 August 2006 by Nicolas Le Novere SBO:0000205 SBO:0000184 translation Systems Biology Ontology Process in which a polypeptide chain is produced from a messenger RNA. see GO:0043037 Definition modified on 09 August 2006 by Nicolas Le Novere SBO:0000205 SBO:0000185 transport reaction Systems Biology Ontology Movement of a physical entity without modification of the structure of the entity. SBO:0000167 SBO:0000186 maximal velocity Systems Biology Ontology Limiting maximal velocity of an enzymatic reaction, reached when the substrate is in large excess and all the enzyme is complexed. Vmax The symbol Vmax and the names maximum rate and maximum velocity are in widespread use although under normal circumstances there is no finite substrate concentration at which v = V and hence no maximum in the mathematical sense (Eur. J. Biochem. 128:281-291). $\mathrm{Et}\mathrm{kcat}\mapsto \mathrm{Et}\mathrm{kcat}$ SBO:0000046 SBO:0000187 Henri-Michaelis-Menten equation, Vmax form Systems Biology Ontology Version of Henri-Michaelis-Menten equation where kp*[E]t is replaced by the maximal velocity, Vmax, reached when all the enzyme is active. 1 $\mathrm{Vmax}S\mathrm{Ks}\mapsto \frac{\mathrm{Vmax}S}{\mathrm{Ks}+S}$ SBO:0000005 SBO:0000188 number of biochemical items Systems Biology Ontology A number of objects of the same type, identical or different, involved in a biochemical event. Added "biochemical" in the name on November 10 2006; Nicolas Le Novere. SBO:0000002 SBO:0000189 number of binding sites Systems Biology Ontology Number of regions on a reactant to which specific other reactants, in this context collectively called ligands, form a chemical bond. SBO:0000188 SBO:0000190 Hill coefficient Systems Biology Ontology Empirical parameter created by Archibald Vivian Hill to describe the cooperative binding of oxygen on hemoglobine (Hill (1910). The possible effects of the aggregation of the molecules of haemoglobin on its dissociation curves. J Physiol 40: iv-vii). Determined from a "Hill plot", it is sometimes assumed to be the number of binding or catalytic sites in a polymer, but it is incorrect. In some mechanistic model, the Hill coefficient gives a lower limit for the number of sites. SBO:0000382 SBO:0000191 Hill constant Systems Biology Ontology Empirical constant created by Archibald Vivian Hill to describe the cooperative binding of oxygen on hemoglobine (Hill (1910). The possible effects of the aggregation of the molecules of haemoglobin on its dissociation curves. J Physiol 40: iv-vii). Different from a microscopic dissociation constant, it has the dimension of concentration to the power of the Hill coefficient. SBO:0000193 SBO:0000192 Hill-type rate law, generalised form Systems Biology Ontology Empirical equation created by Archibald Vivian Hill to describe the cooperative binding of oxygen on hemoglobine (Hill (1910). The possible effects of the aggregation of the molecules of haemoglobin on its dissociation curves. J Physiol 40: iv-vii). The symbol Vmax and the names maximum rate and maximum velocity are in widespread use although under normal circumstances there is no finite substrate concentration at which v = V and hence no maximum in the mathematical sense (Eur. J. Biochem. 128:281-291). $\mathrm{Vmax}RKhn\mapsto \frac{\mathrm{Vmax}R^h}{K^n+R^h}$ SBO:0000001 SBO:0000193 equilibrium or steady-state constant Systems Biology Ontology Constant with the dimension of a powered concentration. It is determined at half-saturation, half-activity etc. SBO:0000308 SBO:0000194 pseudo-dissociation constant Systems Biology Ontology Dissociation constant equivalent to an intrinsic microscopic dissociation constant, but obtained from an averaging process, for instance by extracting the root of a Hill constant. SBO:0000193 SBO:0000195 Hill-type rate law, microscopic form Systems Biology Ontology Hill equation rewritten by creating a pseudo-microscopic constant, equal to the Hill constant powered to the opposite of the Hill coefficient. The symbol Vmax and the names maximum rate and maximum velocity are in widespread use although under normal circumstances there is no finite substrate concentration at which v = V and hence no maximum in the mathematical sense (Eur. J. Biochem. 128:281-291). $\mathrm{Vmax}RKh\mapsto \frac{\mathrm{Vmax}R^h}{K^h+R^h}$ SBO:0000192 SBO:0000196 concentration of an entity pool Systems Biology Ontology The amount of an entity per unit of volume. [X] SBO:0000226 SBO:0000197 specific concentration of an entity Systems Biology Ontology Concentration of an object divided by the value of another parameter having the dimension of a concentration. SBO:0000196 SBO:0000198 Hill-type rate law, reduced form Systems Biology Ontology Hill equation rewritten by replacing the concentration of reactant with its reduced form, that is the concentration divide by a pseudo-microscopic constant, equal to the Hill constant powered to the opposite of the Hill coefficient. The symbol Vmax and the names maximum rate and maximum velocity are in widespread use although under normal circumstances there is no finite substrate concentration at which v = V and hence no maximum in the mathematical sense (Eur. J. Biochem. 128:281-291). $\mathrm{Vmax}\mathrm{R*}h\mapsto \frac{\mathrm{Vmax}\mathrm{R*}^h}{1+\mathrm{R*}^h}$ SBO:0000192 SBO:0000199 normalised enzymatic rate law for unireactant enzymes Systems Biology Ontology Kinetics of enzymes that react only with one substance, their substrate. The total enzyme concentration is considered to be equal to 1, therefore the maximal velocity equals the catalytic constant. $\mathrm{kcat}S\mathrm{Ks}\mapsto \frac{\mathrm{kcat}S}{\mathrm{Ks}+S}$ SBO:0000028 SBO:0000200 redox reaction Systems Biology Ontology Chemical process in which atoms have their oxidation number (oxidation state) changed. Added on 09 August 2006 by Nicolas Le Novere following the suggestion of Emek Demir. SBO:0000176 SBO:0000201 oxidation Systems Biology Ontology Chemical process during which a molecular entity loses electrons. SBO:0000200 SBO:0000202 reduction Systems Biology Ontology Chemical process in which a molecular entity gain electrons. Added on 09 August 2006 by Nicolas Le Novere SBO:0000200 SBO:0000203 duplication Systems Biology Ontology Reaction in which a reactant gives birth to two products identical to itself. 1 Added on 09 August 2006 by Nicolas Le Novere to allow the creation of "replication". SBO:0000232 SBO:0000204 dna replication Systems Biology Ontology Process in which a DNA duplex is transformed into two identical DNA duplexes. See GO:0006260 Added on 09 August 2006 by Nicolas Le Novere on the suggestion of Emek Demir. Modified 04 July 2008 by Nick Juty - changed from replication to dna replication SBO:0000205 SBO:0000205 composite biochemical process Systems Biology Ontology Process that involves the participation of chemical or biological entities and is composed of several elementary steps or reactions. 30/9/08 - modified term name from 'biochemical process' to 'composite biochemical process' - NJ "event"->"process" in definition on November 18 2008 by Nicolas Le Novere SBO:0000375 SBO:0000206 competitive inhibitor Systems Biology Ontology Substance that decreases the probability of a chemical reaction, without itself being consumed or transformed by the reaction, by stericaly hindering the interaction between reactants. Added on 14 August 2006 by Nicolas Le Novere SBO:0000020 SBO:0000207 non-competitive inhibitor Systems Biology Ontology Substance that decreases the probability of a chemical reaction, without itself being consumed or transformed by the reaction, and without sterically hindering the interaction between reactants. SBO:0000020 SBO:0000208 acid-base reaction Systems Biology Ontology Chemical reaction where a proton is given by a compound, the acid, to another one, the base (Brønsted-Lowry definition). An alternative, more general, definition is a reaction where a compound, the base, gives a pair of electrons to another, the acid (Lewis definition). Created on 24 August 2006 by Nicolas Le Novere SBO:0000176 SBO:0000209 ionisation Systems Biology Ontology Ionization is the physical process of converting an atom or molecule into an ion by changing the difference between the number of protons and electrons. Created on 24 August 2006 by Nicolas Le Novere SBO:0000176 SBO:0000210 addition of a chemical group Systems Biology Ontology Covalent reaction that results in the addition of a chemical group on a molecule. Added on September 13 2006 by Nicolas Le Novere based on Patika ontology. SBO:0000182 SBO:0000211 removal of a chemical group Systems Biology Ontology Covalent reaction that results in the removal of a chemical group from a molecule. Added on September 13 2006 by Nicolas Le Novere based on Patika ontology. SBO:0000182 SBO:0000212 protonation Systems Biology Ontology Addition of a proton (H+) to a chemical entity. Added on September 13 2006 by Nicolas Le Novere. SBO:0000208 SBO:0000210 SBO:0000213 deprotonation Systems Biology Ontology Removal of a proton (hydrogen ion H+) from a chemical entity. Added on September 13 2006 by Nicolas Le Novere. SBO:0000208 SBO:0000211 SBO:0000214 methylation Systems Biology Ontology Addition of a methyl group (-CH3) to a chemical entity. Added on September 13 2006 by Nicolas Le Novere. SBO:0000210 SBO:0000215 acetylation Systems Biology Ontology Addition of an acetyl group (-COCH3) to a chemical entity. Added on September 13 2006 by Nicolas Le Novere. SBO:0000210 SBO:0000216 phosphorylation Systems Biology Ontology Addition of a phosphate group (-H2PO4) to a chemical entity. Added on September 13 2006 by Nicolas Le Novere. SBO:0000210 SBO:0000217 glycosylation Systems Biology Ontology Addition of a saccharide group to a chemical entity. Added on September 13 2006 by Nicolas Le Novere. SBO:0000210 SBO:0000218 palmitoylation Systems Biology Ontology Addition of a palmitoyl group (CH3-[CH2]14-CO-) to a chemical entity. Added on September 13 2006 by Nicolas Le Novere. SBO:0000210 SBO:0000219 myristoylation Systems Biology Ontology Addition of a myristoyl (CH3-[CH2]12-CO-) to a chemical entity. Added on September 13 2006 by Nicolas Le Novere. SBO:0000210 SBO:0000220 sulfation Systems Biology Ontology Addition of a sulfate group (SO4--) to a chemical entity. sulphation Added on September 13 2006 by Nicolas Le Novere. SBO:0000210 SBO:0000221 prenylation Systems Biology Ontology Addition of a prenyl group (generic sense) to a chemical entity. isoprenylation Added on September 13 2006 by Nicolas Le Novere. SBO:0000210 SBO:0000222 farnesylation Systems Biology Ontology Addition of a farnesyl group (CH2-CH=C(CH3)-CH2-CH2-CH=C(CH3)-CH2-CH2-CH=C(CH3)2) to a chemical entity. Added on September 13 2006 by Nicolas Le Novere. SBO:0000221 SBO:0000223 geranylgeranylation Systems Biology Ontology Addition of a geranylgeranyl group (CH2-CH=C(CH3)-CH2-CH2-CH=C(CH3)-CH2-CH2-CH=C(CH3)-CH2-CH2-CH=C(CH3)2) to a chemical entity. Added on September 13 2006 by Nicolas Le Novere. SBO:0000221 SBO:0000224 ubiquitination Systems Biology Ontology Covalent linkage to the protein ubiquitin. Added on September 13 2006 by Nicolas Le Novere. SBO:0000210 SBO:0000225 delay Systems Biology Ontology Time during which some action is awaited. Added on September 13 2006 by Nicolas Le Novere. SBO:0000346 SBO:0000226 density of an entity pool Systems Biology Ontology A quantitative measure of an amount or property of an entity expressed in terms of another dimension, such as unit length, area or volume. SBO:0000360 SBO:0000227 mass density of an entity Systems Biology Ontology The mass of an entity expressed with reference to another dimension, such as unit length, area or volume. SBO:0000226 SBO:0000228 volume density of an entity Systems Biology Ontology Mass of an entity per unit volume. SBO:0000227 SBO:0000229 area density of an entity Systems Biology Ontology The mass of an entity per unit of surface area. Added on September 13 2006 by Nicolas Le Novere. SBO:0000227 SBO:0000230 linear density of an entity Systems Biology Ontology Mass of an entity per unit length. SBO:0000227 SBO:0000233 hydroxylation Systems Biology Ontology Addition of an hydroxyl group (-OH) to a chemical entity. Added on September 20 2006 by Nicolas Le Novere. SBO:0000210 SBO:0000234 logical framework Systems Biology Ontology Modelling approach, pioneered by Rene Thomas and Stuart Kaufman, where the evolution of a system is described by the transitions between discrete activity states of "genes" that control each other. Created on October 17 2006 by Nicolas Le Novere SBO:0000004 SBO:0000235 participant Systems Biology Ontology Entity that affects or is affected by an event. 1 SBO:0000000 SBO:0000236 physical entity representation Systems Biology Ontology Representation of an entity that may participate in an interaction, a process or relationship of significance. new synonym modified as part of ontology 'refactoring' process [SF bug #3172586] 18 November 2008 by Nicolas Le Novere: Name reduced to entity, and definition modified. SBO:0000000 SBO:0000237 logical combination Systems Biology Ontology Combining the influence of several entities or events in a unique influence. Created by Nicolas Le Novere on November 10 2006. "logical" added in the name by Nicolas Le Novere on November 17 2008. SBO:0000374 SBO:0000238 not Systems Biology Ontology The preceding event or participating entity cannot participate to the control. Created on November 10 2006 by Nicolas Le Novere SBO:0000237 SBO:0000239 allosteric control Systems Biology Ontology Regulation of the influence of a reaction participant by binding an effector to a binding site of the participant different of the site of the participant conveying the influence. Create on November 10 2006 by Nicolas Le Novere. SBO:0000168 SBO:0000240 material entity Systems Biology Ontology A real thing that is defined by its physico-chemical structure. Created on November 10 2006 by Nicolas Le Novere. SBO:0000236 SBO:0000241 functional entity Systems Biology Ontology A real thing, defined by its properties or the actions it performs, rather than it physico-chemical structure. Created on November 10 2006 by Nicolas Le Novere. Name changed from "conceptual" to "functional" on November 18 2008 by Nicolas Le Novere. SBO:0000236 SBO:0000242 channel Systems Biology Ontology A component that allows another component to pass through itself, possibly connecting different compartments. SBO:0000241 SBO:0000243 gene Systems Biology Ontology A locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions and/or other functional sequence regions. Sequence Ontology SO:0000704 Created on November 10 2006 by Nicolas Le Novere. SBO:0000404 SBO:0000244 receptor Systems Biology Ontology Participating entity that binds to a specific physical entity and initiates the response to that physical entity.The original concept of the receptor was introduced independently at the end of the 19th century by John Newport Langley (1852-1925) and Paul Ehrlich (1854-1915). Langley JN.On the reaction of cells and of nerve-endings to certain poisons, chiefly as regards the reaction of striated muscle to nicotine and to curari. J Physiol. 1905 Dec 30;33(4-5):374-413. Created on November 10 2006 by Nicolas Le Novere SBO:0000241 SBO:0000245 macromolecule Systems Biology Ontology Molecular entity mainly built-up by the repetition of pseudo-identical units. CHEBI:33839 Created on November 10 2006 by Nicolas Le Novere. SBO:0000240 SBO:0000246 information macromolecule Systems Biology Ontology Macromolecule whose sequence is encoded in the genome of living organisms. Cf. CHEBI:33695 SBO:0000245 SBO:0000247 simple chemical Systems Biology Ontology Simple, non-repetitive chemical entity. Created on November 10 2006 by Nicolas Le Novere. SBO:0000240 SBO:0000248 chemical macromolecule Systems Biology Ontology Macromolecule whose sequence is not directly encoded in the genome. SBO:0000245 SBO:0000249 polysaccharide Systems Biology Ontology Macromolecule consisting of a large number of monosaccharide residues linked by glycosidic bonds. CHEBI:18154 Created on November 10 2006 by Nicolas Le Novere. SBO:0000248 SBO:0000250 ribonucleic acid Systems Biology Ontology Macromolecule formed by a repetition of ribonucleosides linked by phosphodiester bonds. CHEBI:33697 RNA Created on November 10 2006 by Nicolas Le Novere. SBO:0000246 SBO:0000251 deoxyribonucleic acid Systems Biology Ontology Polymer composed of nucleotides containing deoxyribose and linked by phosphodiester bonds. CHEBI:16991 DNA Created on November 10 2006 by Nicolas Le Novere. SBO:0000246 SBO:0000252 polypeptide chain Systems Biology Ontology Naturally occurring macromolecule formed by the repetition of amino-acid residues linked by peptidic bonds. A polypeptide chain is synthesized by the ribosome. CHEBI:16541 Name changed on January 10 2007 by Nicolas Le Novere, to disambiguate from non-ribosomal peptides. Created on November 10 2006 by Nicolas Le Novere. SBO:0000246 SBO:0000253 non-covalent complex Systems Biology Ontology Entity composed of several independant components that are not linked by covalent bonds. Created on November 10 2006 by Nicolas Le Novere. SBO:0000240 SBO:0000254 electrical resistance Systems Biology Ontology Measure of the degree to which an object opposes the passage of an electric current. The SI unit of electrical resistance is the ohm. Created on November 10 2006 by Nicolas Le Novere. SBO:0000002 SBO:0000255 physical characteristic Systems Biology Ontology Parameter characterising a physical system or the environment, and independent of life's influence. 1 Name modified from physical parameter to physical characteristic on March 17 2007 by Nicolas Le Novere. Terms 'biochemical parameter' (SBO:0000256) and 'physical characteristic' (SBO:0000255) obsoleted as described by SourceForge Tracker #3102840. Please use parent term 'quantitative parameter', SBO:0000002, or a more suitable term. SBO:0000002 SBO:0000256 biochemical parameter Systems Biology Ontology Parameter that depends on the biochemical properties of a system. 1 Terms 'biochemical parameter' (SBO:0000256) and 'physical characteristic' (SBO:0000255) obsoleted as described by SourceForge Tracker #3102840. Please use parent term 'quantitative parameter', SBO:0000002, or a more suitable term. SBO:0000002 SBO:0000257 conductance Systems Biology Ontology Measure of how easily electricity flows along a certain path through an electrical element. The SI derived unit of conductance is the Siemens. SBO:0000002 SBO:0000258 capacitance Systems Biology Ontology Measure of the amount of electric charge stored (or separated) for a given electric potential. The unit of capacitance id the Farad. Created on November 10 2006 by Nicolas Le Novere. SBO:0000002 SBO:0000259 voltage Systems Biology Ontology Difference of electrical potential between two points of an electrical network, expressed in volts. electrical potential difference Created on November 10 2006 by Nicolas Le Novere. SBO:0000002 SBO:0000260 enzymatic rate law for simple competitive inhibition of irreversible unireactant enzymes by one inhibitor Systems Biology Ontology Inhibition of a unireactant enzyme by one inhibitor that binds once to the free enzyme and prevents the binding of the substrate. The enzymes do not catalyse the reactions in both directions. simple intersecting linear competitive inhibition of unireactant enzymes $\mathrm{kcat}\mathrm{Et}SI\mathrm{Ks}\mathrm{Ki}\mapsto \frac{\mathrm{kcat}\mathrm{Et}S}{\mathrm{Ks}(1+\frac{I}{\mathrm{Ki}})+S}$ SBO:0000267 SBO:0000270 SBO:0000261 inhibitory constant Systems Biology Ontology Dissociation constant of a compound from a target of which it inhibits the function. inhibition constant Ki Created on November 10 2006 by Nicolas Le Novere. SBO:0000282 SBO:0000262 enzymatic rate law for simple uncompetitive inhibition of irreversible unireactant enzymes Systems Biology Ontology Inhibition of a unireactant enzyme by one inhibitor that binds only to the complex enzyme-substrate and totally prevent the catalysis. The enzymes do not catalyse the reactions in both directions. simple linear uncompetitive inhibition $\mathrm{kcat}\mathrm{Et}SI\mathrm{Ks}\mathrm{Ki}\mapsto \frac{\mathrm{kcat}\mathrm{Et}S}{S(1+\frac{I}{\mathrm{Ki}})+\mathrm{Ks}}$ SBO:0000458 SBO:0000263 relative equilibrium constant Systems Biology Ontology Ratio of an equilibrium constant in a given condition by the same equilibrium constant is not fullfilled. Created on November 10 2006 by Nicolas Le Novere SBO:0000308 SBO:0000264 relative inhibition constant Systems Biology Ontology Ratio of the dissociation constant of an inhibitor from the complex enzyme-substrate on the dissociation constant of an inhibitor from the free enzyme. Created on November 10 2006 by Nicolas Le Novere SBO:0000263 SBO:0000265 enzymatic rate law for simple mixed-type inhibition of irreversible unireactant enzymes Systems Biology Ontology Inhibition of a unireactant enzyme by one inhibitor that can bind to the complex enzyme-substrate and the free enzyme, possibly with different equilibrium constant, and totally prevent the catalysis. The enzymes do not catalyse the reactions in both directions. simple intersecting linear mixed-type competitive inhibition $\mathrm{kcat}\mathrm{Et}SI\mathrm{Ks}\mathrm{Ki}a\mapsto \frac{\mathrm{kcat}\mathrm{Et}S}{S(1+\frac{I}{a\mathrm{Ki}})+\mathrm{Ks}(1+\frac{I}{\mathrm{Ki}})}$ SBO:0000275 SBO:0000266 enzymatic rate law for simple irreversible non-competitive inhibition of unireactant enzymes Systems Biology Ontology Inhibition of a unireactant enzyme by one inhibitor that can bind to the complex enzyme-substrate and the free enzyme with the same equilibrium constant, and totally prevent the catalysis. $\mathrm{kcat}\mathrm{Et}SI\mathrm{Ks}\mathrm{Ki}\mapsto \frac{\mathrm{kcat}\mathrm{Et}S}{S(1+\frac{I}{\mathrm{Ki}})+\mathrm{Ks}(1+\frac{I}{\mathrm{Ki}})}$ SBO:0000442 SBO:0000267 enzymatic rate law for competitive inhibition of irreversible unireactant enzymes by one inhibitor Systems Biology Ontology Inhibition of a unireactant enzyme by one inhibitor that can bind one or several times to the free enzyme, and prevent the binding of the substrate. The enzymes do not catalyse the reactions in both directions. multiple competitive inhibition by one inhibitor of unireactant enzymes n indicates the number of binding sites for the inhibitor I. $\mathrm{kcat}\mathrm{Et}SI\mathrm{Ks}\mathrm{Ki}n\mapsto \frac{\mathrm{kcat}\mathrm{Et}S}{S+\mathrm{Ks}(1+\frac{I}{\mathrm{Ki}})^n}$ SBO:0000273 SBO:0000268 enzymatic rate law Systems Biology Ontology Enzyme kinetics is the study of the rates of chemical reactions that are catalysed by enzymes, how this rate is controlled, and how drugs and poisons can inhibit its activity. SBO:0000001 SBO:0000269 enzymatic rate law for unireactant enzymes Systems Biology Ontology Kinetics of enzymes that catalyse the transformation of only one substrate. SBO:0000268 SBO:0000270 enzymatic rate law for competitive inhibition of irreversible unireactant enzymes by exclusive inhibitors Systems Biology Ontology Inhibition of a unireactant enzyme by inhibitors that bind to the free enzyme on the same binding site than the substrate. The enzymes do not catalyse the reactions in both directions. $\mathrm{kcat}\mathrm{Et}SI\mathrm{Ks}\mathrm{Ki}n\mapsto \frac{\mathrm{kcat}\mathrm{Et}S}{\mathrm{Ks}(1+\sum_{i=1}^n \frac{I_i}{\mathrm{Ki}_i})+S}$ SBO:0000430 SBO:0000271 enzymatic rate law for competitive inhibition of irreversible unireactant enzymes by two exclusive inhibitors Systems Biology Ontology Inhibition of a unireactant enzyme by two inhibitors that bind to the free enzyme on the same binding site than the substrate. The enzymes do not catalyse the reactions in both directions. $\mathrm{kcat}\mathrm{Et}S\mathrm{I1}\mathrm{I2}\mathrm{Ks}\mathrm{Ki1}\mathrm{Ki2}\mapsto \frac{\mathrm{kcat}\mathrm{Et}S}{\mathrm{Ks}(1+\frac{\mathrm{I1}}{\mathrm{Ki1}}+\frac{\mathrm{I2}}{\mathrm{Ki2}})+S}$ SBO:0000270 SBO:0000272 number of inhibitors Systems Biology Ontology Number of entities that inhibit a reaction. Created on November 11 2006 by Nicolas Le Novere. SBO:0000188 SBO:0000273 enzymatic rate law for competitive inhibition of irreversible unireactant enzymes by non-exclusive non-cooperative inhibitors Systems Biology Ontology Inhibition of a unireactant enzyme by inhibitors that bind independently to the free enzyme and preclude the binding of the substrate. The enzymes do not catalyse the reactions in both directions. n indicates the number of inhibitors, and mi the number of binding sites for the inhibitor Ii. $\mathrm{kcat}\mathrm{Et}SI\mathrm{Ks}\mathrm{Ki}nm\mapsto \frac{\mathrm{kcat}\mathrm{Et}S}{\mathrm{Ks}\prod_{i=1}^n (1+\frac{I_i}{\mathrm{Ki}_i})^{m_i}+S}$ SBO:0000430 SBO:0000274 enzymatic rate law for simple competitive inhibition of irreversible unireactant enzymes by two non-exclusive, non-cooperative inhibitors Systems Biology Ontology Inhibition of a unireactant enzyme by two inhibitors that can bind independently once to the free enzyme and preclude the binding of the substrate. The enzymes do not catalyse the reactions in both directions. $\mathrm{kcat}\mathrm{Et}S\mathrm{I1}\mathrm{I2}\mathrm{Ks}\mathrm{Ki1}\mathrm{Ki2}\mapsto \frac{\mathrm{kcat}\mathrm{Et}S}{\mathrm{Ks}(1+\frac{\mathrm{I1}}{\mathrm{Ki1}}+\frac{\mathrm{I2}}{\mathrm{Ki2}}+\frac{\mathrm{I1}\mathrm{I2}}{\mathrm{Ki1}\mathrm{Ki2}})+S}$ SBO:0000273 SBO:0000379 SBO:0000275 enzymatic rate law for mixed-type inhibition of irreversible enzymes by mutually exclusive inhibitors Systems Biology Ontology Inhibition of a unireactant enzyme by inhibitors that can bind to the complex enzyme-substrate and the free enzyme, possibly with different equilibrium constants, and totally prevent the catalysis. The enzymes do not catalyse the reactions in both directions. $\mathrm{kcat}\mathrm{Et}SI\mathrm{Ks}\mathrm{Ki}an\mapsto \frac{\mathrm{kcat}\mathrm{Et}S}{\mathrm{Ks}(1+\sum_{i=1}^n \frac{I_i}{\mathrm{Ki}_i})+S(1+\sum_{i=1}^n \frac{I_i}{a_i\mathrm{Ki}_i})}$ SBO:0000430 SBO:0000276 enzymatic rate law for mixed-type inhibition of irreversible unireactant enzymes by two inhibitors Systems Biology Ontology Inhibition of unireactant enzymes by two inhibitors that can bind to the complex enzyme-substrate and the free enzyme, possibly with different equilibrium constant, and totally prevent the catalysis. The enzymes do not catalyse the reactions in both directions. $\mathrm{kcat}\mathrm{Et}S\mathrm{I1}\mathrm{I2}\mathrm{Ks}\mathrm{Ki1}\mathrm{Ki2}ab\mapsto \frac{\mathrm{kcat}\mathrm{Et}S}{S(1+\frac{\mathrm{I1}}{a\mathrm{Ki1}}+\frac{\mathrm{I2}}{b\mathrm{Ki2}})+\mathrm{Ks}(1+\frac{\mathrm{I1}}{\mathrm{Ki1}}+\frac{\mathrm{I2}}{\mathrm{Ki2}})}$ SBO:0000275 SBO:0000277 enzymatic rate law for non-competitive inhibition of irreversible unireactant enzymes by two exclusively binding inhibitors Systems Biology Ontology Inhibition of unireactant enzymes by two inhibitors that can bind to the complex enzyme-substrate and the free enzyme with the same equilibrium constant and totally prevent the catalysis. $\mathrm{kcat}\mathrm{Et}S\mathrm{I1}\mathrm{I2}\mathrm{Ks}\mathrm{Ki1}\mathrm{Ki2}\mapsto \frac{\mathrm{kcat}\mathrm{Et}S}{S(1+\frac{\mathrm{I1}}{\mathrm{Ki1}}+\frac{\mathrm{I2}}{\mathrm{Ki2}})+\mathrm{Ks}(1+\frac{\mathrm{I1}}{\mathrm{Ki1}}+\frac{\mathrm{I2}}{\mathrm{Ki2}})}$ SBO:0000276 SBO:0000278 messenger RNA Systems Biology Ontology A messenger RNA is a ribonucleic acid synthesized during the transcription of a gene, and that carries the information to encode one or several proteins. mRNA Created on November 16 2006 by Nicolas Le Novere SBO:0000404 SBO:0000279 pressure Systems Biology Ontology Pressure (symbol: p) is the force per unit area applied on a surface in a direction perpendicular to that surface. The unit of pressure is the Pascal (Pa), that is equal to 1 Newton per square meter. Created on November 21 2006 by Nicolas Le Novere SBO:0000002 SBO:0000280 ligand Systems Biology Ontology In biochemistry, a ligand is an effector, a physical entity that binds to a site on a receptor's surface by intermolecular forces. Created on November 27 2006 by Nicolas Le Novere SBO:0000241 SBO:0000281 equilibrium constant Systems Biology Ontology Quantity characterizing a chemical equilibrium in a chemical reaction, which is a useful tool to determine the concentration of various reactants or products in a system where chemical equilibrium occurs. Keq Created on November 27 2006 by Nicolas Le Novere on the suggestion of Martin Golebiewski. SBO:0000193 SBO:0000282 dissociation constant Systems Biology Ontology Equilibrium constant that measures the propensity of a larger object to separate (dissociate) reversibly into smaller components, as when a complex falls apart into its component molecules, or when a salt splits up into its component ions. The dissociation constant is usually denoted Kd and is the inverse of the affinity constant. Kd Created on November 27 2006 by Nicolas Le Novere $\mathrm{koff}\mathrm{Kon}\mapsto \frac{\mathrm{koff}}{\mathrm{Kon}}$ SBO:0000281 SBO:0000309 SBO:0000283 acid dissociation constant Systems Biology Ontology Equilibrium constant that indicates the extent of dissociation of hydrogen ions from an acid. The equilibrium is that of a proton transfer from an acid, HA, to water, H2O. The term for the concentration of water, [H2O], is omitted from the general equilibrium constant expression. Ka=([H3O+]*[A-])/(HA) Ka Created on November 27 2006 by Nicolas Le Novere on a suggestion by Martin Golebviewski SBO:0000282 SBO:0000310 SBO:0000284 transporter Systems Biology Ontology Participating entity that facilitates the movement of another physical entity from a defined subset of the physical environment (for instance a cellular compartment) to another. Created on November 28 2006 by Nicolas Le Novere SBO:0000241 SBO:0000285 material entity of unspecified nature Systems Biology Ontology Material entity whose nature is unknown or irrelevant. SBO:0000240 SBO:0000286 multimer Systems Biology Ontology Non-covalent association of identical, or pseudo-identical, entities. By pseudo-identical entities, we mean biochemical elements that differ chemically, although remaining globally identical in structure and/or function. Examples are homologous subunits in an hetero-oligomeric receptor. Created on December 1 2006 by Nicolas Le Novere. SBO:0000253 SBO:0000287 EC50 Systems Biology Ontology Concentration of an active compound at which 50% of its maximal effect is observed. The EC50 is not a pure characteristic of the compound but depends on the conditions or the measurement. Created on December 7th 2006 by Nicolas Le Novere on the suggestion of Martin Golebiewski SBO:0000193 SBO:0000288 IC50 Systems Biology Ontology Also called half maximal inhibitory concentration, it represents the concentration of an inhibitor substance that is required to suppress 50% of an effect. Created on December 7 2006 by Nicolas Le Novere on the request of Martin Golebiewski. SBO:0000193 SBO:0000289 functional compartment Systems Biology Ontology Logical or physical subset of the event space that contains pools, that is sets of participants considered identical when it comes to the event they are involved into. A compartment can have any number of dimensions, including 0, and be of any size including null. Created on December 11 2006 by Nicolas Le Novere SBO:0000003 SBO:0000290 physical compartment Systems Biology Ontology Specific location of space, that can be bounded or not. A physical compartment can have 1, 2 or 3 dimensions. Created on December 14 2006 by Nicolas Le Novere SBO:0000240 SBO:0000291 empty set Systems Biology Ontology Entity defined by the absence of any actual object. An empty set is often used to represent the source of a creation process or the result of a degradation process. moved from conceptual to material entity SBO:0000240 SBO:0000292 spatial continuous framework Systems Biology Ontology Modelling approach where the quantities of participants are considered continuous, and represented by real values. The associated simulation methods make use of differential equations. The models take into account the distribution of the entities and describe the spatial fluxes. Created on December 22 2006 by Nicolas Le Novere SBO:0000062 SBO:0000293 non-spatial continuous framework Systems Biology Ontology Modelling approach where the quantities of participants are considered continuous, and represented by real values. The associated simulation methods make use of differential equations. The models do not take into account the distribution of the entities and describe only the temporal fluxes. Created on December 22 2006 by Nicolas Le Novere SBO:0000062 SBO:0000294 spatial discrete framework Systems Biology Ontology Modelling approach where the quantities of participants are considered discrete, and represented by integer values. The associated simulation methods can be deterministic or stochastic. The models take into account the distribution of the entities and describe the spatial fluxes. Created on December 22 2006 by Nicolas Le Novere SBO:0000063 SBO:0000295 non-spatial discrete framework Systems Biology Ontology Modelling approach where the quantities of participants are considered discrete, and represented by integer values. The associated simulation methods can be deterministic or stochastic.The models do not take into account the distribution of the entities and describe only the temporal fluxes. Created on Decemer 22 2006 by Nicolas Le Novere SBO:0000063 SBO:0000296 macromolecular complex Systems Biology Ontology Non-covalent complex of one or more macromolecules and zero or more simple chemicals. Created on January 10 2007 by Nicolas Le Novere. SBO:0000253 SBO:0000297 protein complex Systems Biology Ontology Macromolecular complex containing one or more polypeptide chains possibly associated with simple chemicals. CHEBI:36080 Created on January 10 2007 by Nicolas Le Novere on the suggestion of Douglas Kell SBO:0000296 SBO:0000298 synthetic chemical compound Systems Biology Ontology Chemical entity that is engineered by a human-designed process ex-vivo rather than a produced by a living entity. Created on January 10 2006 by Nicolas Le Novere SBO:0000241 SBO:0000299 metabolite Systems Biology Ontology Substance produced by metabolism or by a metabolic process. Created on January 10 2007 by Nicolas Le Novere on the suggestion of Douglas Kell SBO:0000241 SBO:0000300 total concentration of enzyme Systems Biology Ontology Total amount of enzyme catalysing a reaction, divided by the volume of reaction. 1 Et Created on January 20 2007 by Nicolas Le Novere SBO:0000006 SBO:0000301 total catalytic efficiency Systems Biology Ontology Constant representing the actual efficiency of an enzyme at a given concentration, taking into account its microscopic catalytic activity and the rates of substrate binding and dissociation. NB. The symbol Vmax and the names maximum rate and maximum velocity are in widespread use although under normal circumstances there is no finite substrate concentration at which v = V and hence no maximum in the mathematical sense (Eur. J. Biochem. 128:281-291). Created on January 20 2007 by Nicolas Le Novere May 15 2008: Added a note of usage of Vmax following comment from Andreas Draeger $\mathrm{Vmax}\mathrm{Km}\mapsto \frac{\mathrm{Vmax}}{\mathrm{Km}}$ SBO:0000035 SBO:0000302 catalytic efficiency Systems Biology Ontology Constant representing the actual efficiency of an enzyme, taking into account its microscopic catalytic activity and the rates of substrate binding and dissociation. Created on January 20 2007 by Nicolas Le Novere $\mathrm{kcat}\mathrm{Km}\mapsto \frac{\mathrm{kcat}}{\mathrm{Km}}$ SBO:0000036 SBO:0000303 biochemical potential Systems Biology Ontology Derivative of a biochemical energy per a substance. chemical potential Created on February 3 2007 by Nicolas Le Novere. SBO:0000308 SBO:0000304 pH Systems Biology Ontology Negative logarithm (base 10) of the activity of hydrogen in a solution. Ina diluted solution, this activity is equal to the concentration of protons (in fact of ions H3O+). The pH is proportional to the chemical potential of hydrogen, by the relation: pH = -µH ÷ 2.3RT. (with µH=-RTln[H+]). potential of hydrogen Created on February 3 2007 by Nicolas Le Novere. SBO:0000303 SBO:0000305 pOH Systems Biology Ontology Negative logarithm (base 10) of the activity of hydroxyde in a solution. In a diluted solution, this activity is equal to the concentration of ions HO-. Created on February 3 2007 by Nicolas Le Novere. SBO:0000303 SBO:0000306 pK Systems Biology Ontology negative logarithm (base 10) of a dissociation constant. dissociation potential Created on February 3 2007 by Nicolas Le Novere on a suggestion of Martin Golebiewski. $K\mapsto -\lg K$ SBO:0000303 SBO:0000309 SBO:0000307 pKa Systems Biology Ontology negative logarithm (base 10) of an acid dissociation constant. potential of acid Created on February 3 2007 by Nicolas Le Novere. $\mathrm{Ka}\mapsto -\lg \mathrm{Ka}$ SBO:0000306 SBO:0000310 SBO:0000308 equilibrium or steady-state characteristic Systems Biology Ontology Quantitative parameter that characterises a biochemical equilibrium. Created on February 3 2007 by Nicolas Le Novere. SBO:0000002 SBO:0000309 dissociation characteristic Systems Biology Ontology Quantitative parameter that characterises a dissociation. Created on February 3 2007 by Nicolas Le Novere SBO:0000308 SBO:0000310 acid dissociation characteristic Systems Biology Ontology Quantitative parameter that characterises an acid-base reaction. Created on February 3 2007 by Nicolas Le Novere. SBO:0000309 SBO:0000311 heterogeneous nuclear RNA Systems Biology Ontology Incompletely processed single strand of messenger ribonucleic acid (mRNA), synthesized from a DNA template in the nucleus of a cell by transcription and containing copies of the introns and exons of a gene. pre-mRNA Precursor mRNA Created on March 12 2007 by Nicolas Le Novere with help from Laure Gambardella SBO:0000278 SBO:0000312 mature messenger RNA Systems Biology Ontology Completely processed single strand of messenger ribonucleic acid (mRNA), synthesized from a DNA template in the nucleus of a cell by transcription and containing copies of only the exons of a gene. Created on March 12 2007 by Nicolas Le Novere with help from Laure Gambardella SBO:0000278 SBO:0000313 transfer RNA Systems Biology Ontology Small RNA chain (73-93 nucleotides) that transfers a specific amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation. It has a site for amino acid attachment and a three-base region called the anticodon that recognizes the corresponding three-base codon region on mRNA via complementary base pairing. Each type of tRNA molecule can be attached to only one type of amino acid, but because the genetic code is degenerate - that is, it contains multiple codons that specify the same amino acid - multiple types of tRNA molecules bearing different anticodons may carry the same amino acid. tRNA Created on March 12 2007 by Nicolas Le Novere with help from Laure Gambardella SBO:0000334 SBO:0000314 ribosomal RNA Systems Biology Ontology Type of RNA that is the central component of the ribosome, the protein manufacturing machinery of all living cells. rRNA Created on March 12 2007 by Nicolas Le Novere with help from Laure Gambardella SBO:0000334 SBO:0000315 ribozyme Systems Biology Ontology RNA molecule that catalyzes a chemical reaction. ribonucleic acid enzyme Created on March 12 2007 by Nicolas Le Novere with help from Laure Gambardella SBO:0000241 SBO:0000316 microRNA Systems Biology Ontology Single-stranded RNA molecules thought to regulate the expression of other genes. miRNAs are encoded by genes that are transcribed from DNA but not translated into protein (non-coding RNA). miRNA Created on March 12 2007 by Nicolas Le Novere with help from Laure Gambardella SBO:0000334 SBO:0000317 small interfering RNA Systems Biology Ontology siRNA are 20-25 nucleotide-long double-stranded RNA molecules involved in the regulation of the expression of specific genes, antiviral mechanisms, shaping the chromatin structure of a genome etc. siRNA Created on March 12 2007 by Nicolas Le Novere with help from Laure Gambardella SBO:0000241 SBO:0000318 small nuclear RNA Systems Biology Ontology Small RNA molecules that are found within the nucleus of eukaryotic cells. They are involved in a variety of important processes such as RNA splicing (removal of introns from heterogeneous nuclear RNA), regulation of transcription factors or RNA polymerase II and maintaining the telomeres. They are always associated with specific proteins, and the complexes are referred to as small nuclear ribonucleoproteins (snRNP). snRNA Created on March 12 2007 by Nicolas Le Novere with help from Laure Gambardella SBO:0000334 SBO:0000319 small nucleolar RNA Systems Biology Ontology Small RNA molecules that guide chemical modifications (methylation or pseudouridylation) of ribosomal RNAs (rRNAs) and other RNA genes. They are frequently encoded in the introns of ribosomal proteins and are synthesized by RNA polymerase II, but can also be transcribed as independent (sometimes polycistronic) transcriptional units. snoRNAs are a component in the small nucleolar ribonucleoprotein (snoRNP), which contains snoRNA and proteins. snoRNA Created on March 12 2007 by Nicolas Le Novere with help from Laure Gambardella SBO:0000334 SBO:0000320 product catalytic rate constant Systems Biology Ontology Numerical parameter that quantifies the velocity of product creation by a reversible enzymatic reaction. kcatp Created on March 11 2007 by Nicolas Le Novere SBO:0000025 SBO:0000321 substrate catalytic rate constant Systems Biology Ontology Numerical parameter that quantifies the velocity of substrate creation by a reversible enzymatic reaction. kcats Created on March 11 2007 by Nicolas Le Novere. SBO:0000025 SBO:0000322 Michaelis constant for substrate Systems Biology Ontology Substrate concentration at which the velocity of product production by the forward activity of a reversible enzyme is half its maximum. Kms Created on March 11 2007 by Nicolas Le Novere SBO:0000027 SBO:0000323 Michaelis constant for product Systems Biology Ontology Product concentration at which the velocity of substrate production by the reverse activity of a reversible enzyme is half its maximum. Kmp Created on March 11 2007 by Nicolas Le Novere SBO:0000027 SBO:0000324 forward maximal velocity Systems Biology Ontology Limiting maximal velocity of the forward reaction of a reversible enzyme, reached when the substrate is in large excess and all the enzyme is complexed. Vmaxf The symbol Vmax and the names maximum rate and maximum velocity are in widespread use although under normal circumstances there is no finite substrate concentration at which v = V and hence no maximum in the mathematical sense (Eur. J. Biochem. 128:281-291). $\mathrm{Et}\mathrm{kcatp}\mapsto \mathrm{Et}\mathrm{kcatp}$ SBO:0000186 SBO:0000350 SBO:0000325 reverse maximal velocity Systems Biology Ontology Limiting maximal velocity of the reverse reaction of a reversible enzyme, reached when the product is in large excess and all the enzyme is complexed. Vmaxr The symbol Vmax and the names maximum rate and maximum velocity are in widespread use although under normal circumstances there is no finite substrate concentration at which v = V and hence no maximum in the mathematical sense (Eur. J. Biochem. 128:281-291). $\mathrm{Et}\mathrm{kcats}\mapsto \mathrm{Et}\mathrm{kcats}$ SBO:0000186 SBO:0000353 SBO:0000326 enzymatic rate law for non-modulated unireactant enzymes Systems Biology Ontology Kinetics of enzymes that react only with one substance, their substrate, and are not modulated by other compounds. SBO:0000269 SBO:0000327 non-macromolecular ion Systems Biology Ontology Chemical entity having a net electric charge. Created on March 18 2007 by Nicolas Le Novere SBO:0000247 SBO:0000328 non-macromolecular radical Systems Biology Ontology chemical entity possessing an unpaired electron. Created on March 18 2007 by Nicolas Le Novere. SBO:0000247 SBO:0000329 transcription start site Systems Biology Ontology First nucleotide of a gene that is copied in the transcribed RNA. Sequence Ontology SO:0000315 TSS Created on September 28 2007 by Nicolas Le Novere. SBO:0000404 SBO:0000330 dephosphorylation Systems Biology Ontology Removal of a phosphate group (-H2PO4) from a chemical entity. SBO:0000211 SBO:0000331 half-life Systems Biology Ontology Time interval over which a quantified entity is reduced to half its original value. SBO:0000009 SBO:0000346 SBO:0000332 half-life of an exponential decay Systems Biology Ontology Time taken by a quantity decreasing according to a mono-exponential decay to be divided by two. Sometimes called t1/2. $l\mapsto \frac{\ln 2}{l}$ SBO:0000331 SBO:0000333 monoexponential decay rate law Systems Biology Ontology Monotonic decrease of a quantity proportionally to its value. $lR\mapsto \frac{R}{l}$ SBO:0000049 SBO:0000334 non-coding RNA Systems Biology Ontology RNA molecule that is not translated into a protein. Sequence Ontology SO:0000655 Created on 03 January 2008 by Nicolas Le Novere SBO:0000404 SBO:0000335 gene coding region Systems Biology Ontology Portion of DNA or RNA that is transcribed into another RNA, such as a messenger RNA or a non-coding RNA (for instance a transfert RNA or a ribosomal RNA). Created on January 03 2008 by Nicolas Le Novere SBO:0000404 SBO:0000336 interactor Systems Biology Ontology Entity participating in a physical or functional interaction. Created on January 31 2008 on the suggestion of Samuel Kerrien. SBO:0000010 SBO:0000337 association constant Systems Biology Ontology Equilibrium constant that measures the propensity of two objects to assemble (associate) reversibly into a larger component. The association constant is usually denoted Ka and is the inverse of the dissociation constant. affinity constant Ka Created on February 26 2008 by Nicolas Le Novere on the request of Samuel Kerrien. $\mathrm{koff}\mathrm{Kon}\mapsto \frac{\mathrm{kon}}{\mathrm{Koff}}$ SBO:0000281 SBO:0000338 dissociation rate constant Systems Biology Ontology Rate with which a complex dissociates into its components. kd Created on February 26 2008 by Nicolas Le Novere on the request of Samuel Kerrien. SBO:0000035 SBO:0000038 SBO:0000339 bimolecular association rate constant Systems Biology Ontology Rate with which two components associate into a complex. Created on February 26 2008 by Nicolas Le Novere on the request of Samuel Kerrien. SBO:0000036 SBO:0000341 SBO:0000340 trimolecular association rate constant Systems Biology Ontology Rate with which three components associate into a complex. created on February 26 2008 by Nicolas Le Novere on the suggestion of Samuel Kerrien. SBO:0000037 SBO:0000341 SBO:0000341 association rate constant Systems Biology Ontology Rate with which components associate into a complex. Created on February 26 2008 by Nicolas Le Novere on the suggestion of Samuel Kerrien. SBO:0000154 SBO:0000342 molecular or genetic interaction Systems Biology Ontology Mutual or reciprocal action or influence between molecular entities. Created on February 16 2008 byt Nicolas Le Novere on the suggestion of Samuel Kerrien. SBO:0000375 SBO:0000343 genetic interaction Systems Biology Ontology A phenomenon whereby an observed phenotype, qualitative or quantative, is not explainable by the simple additive effects of the individual gene pertubations alone. Genetic interaction between perturbed genes is usually expected to generate a 'defective' phenotype. The level of defectiveness is often used to sub-classify this phenomenon. http://en.wikipedia.org/wiki/Genetic_interaction SBO:0000499 'genetic interaction' deprecated. SBO:0000342 SBO:0000344 molecular interaction Systems Biology Ontology Relationship between molecular entities, based on contacts, direct or indirect. Created on February 26 2008 by Nicolas Le Novere on the suggestion of Samuel Kerrien. SBO:0000342 SBO:0000345 time Systems Biology Ontology Fundmental quantity of the measuring system used to sequence events, to compare the durations of events and the intervals between them, and to quantify the motions or the transformation of entities. The SI base unit for time is the SI second. The second is the duration of 9,192,631,770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. 1 Created on February 28 2008 by Nicolas Le Novere on the suggestion of Martin Golebievski SBO:0000255 SBO:0000346 temporal measure Systems Biology Ontology Fundamental quantity of the measuring system used to sequence events, to compare the durations of events and the intervals between them, and to quantify the motions or the transformation of entities. The SI base unit for time is the SI second. The second is the duration of 9,192,631,770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. SBO:0000002 SBO:0000347 duration Systems Biology Ontology Amount of time during which an event persists. SBO:0000346 SBO:0000348 exponential time constant Systems Biology Ontology Time that it takes for an exponential decay to reach 1/e (about 37%) of the original value. This characterises the frequency response of a first-order, linear time-invariant system. This is also the average lifetime of an element in the decaying set. It is the inverse of the exponential decay constant. mean lifetime $l\mapsto \frac{1}{l}$ SBO:0000009 SBO:0000346 SBO:0000349 inactivation rate constant Systems Biology Ontology Kinetic constant describing the rate of an irreversible enzyme inactivation by decay of the active enzyme into its inactive form. kinact Created on February 29 2008 by Nicolas Le Novere on the request of Martin Golebvieski SBO:0000035 SBO:0000350 forward reaction velocity Systems Biology Ontology The speed of an enzymatic reaction at a defined concentration of substrate(s) and enzyme. created by Nick Juty on March 28th 2008 on request of Martin Golebvieski SBO:0000048 SBO:0000352 reverse zeroth order rate constant Systems Biology Ontology Numerical parameter that quantifies the reverse velocity of a chemical reaction independant of the reactant quantities. This parameter encompasses all the contributions to the velocity. It is to be used in a reaction modelled using a continuous framework. Created by Nick Juty 28th March 2008 SBO:0000046 SBO:0000156 SBO:0000353 reverse reaction velocity Systems Biology Ontology The speed of an enzymatic reaction at a defined concentration of substrate(s) and enzyme. Created by Nick Juty 28th March 2008 SBO:0000352 SBO:0000354 informational molecule segment Systems Biology Ontology Fragment of a macromolecule that carries genetic information. Created by Nicolas Le Novere on April 23 2008 on the suggestion of SBGN forum SBO:0000240 SBO:0000355 conservation law Systems Biology Ontology Mathematical expression stating that a quantity is conserved in a system, whatever happens within the boundaries of that system. Created on April 25 by Nicolas Le Novere, on the demand of SBML forum SBO:0000064 SBO:0000356 decay constant Systems Biology Ontology Kinetic constant characterising a mono-exponential decay. It is the inverse of the mean lifetime of the continuant being decayed. Its unit is "per time". Created on April 29 2008 by Nicolas Le Novere $t\mapsto \frac{1}{t}$ SBO:0000035 SBO:0000357 biological effect of a perturbation Systems Biology Ontology Biochemical networks can be affected by external influences. Those influences can be well-defined physical perturbations, such as a light pulse, or a change in temperature but also more complex of not well defined phenomena, for instance a biological process, an experimental setup, or a mutation. Created on May 07 2008 by Nicolas Le Novere for SBGN needs. SBO:0000375 SBO:0000358 phenotype Systems Biology Ontology A biochemical network can generate phenotypes or affects biological processes. Such processes can take place at different levels and are independent of the biochemical network itself. Potentially obsolete....use with caution SBO:0000375 SBO:0000359 mass conservation law Systems Biology Ontology A chemical moiety that exists under different forms but is not created nor destroyed in a biochemical system. In any given system such a conserved moiety is characterized by a finite number of particles that exist in the system and is invariant. Created on May 9th 2008 by Nicolas Le Novere on the suggestion of Pedro Mendes and Stefan Hoops. $anS\mapsto \sum_{i=0}^n a_{i}S_i$ SBO:0000355 SBO:0000360 quantity of an entity pool Systems Biology Ontology The enumeration of co-localised, identical biochemical entities of a specific state, which constitute a pool. The form of enumeration may be purely numerical, or may be given in relation to another dimension such as length or volume. SBO:0000002 SBO:0000361 amount of an entity pool Systems Biology Ontology A numerical measure of the quantity, or of some property, of the entities that constitute the entity pool. SBO:0000360 SBO:0000362 concentration conservation law Systems Biology Ontology If all forms of a moiety exist in a single compartment and the size of that compartment is fixed then the Mass Conservation is also a Concentration Conservation. Created on May 9th 2008 by Nicolas Le Novere on the suggestion of Stefan Hoops $anS\mapsto \sum_{i=0}^n a_{i}S_i$ SBO:0000359 SBO:0000363 activation constant Systems Biology Ontology Dissociation constant of a potentiator (activator) from a target (e.g. an enzyme) of which it activates the function. Kx Created 20th May 2008 by Nick Juty on the request of Martin Golebiewski. SBO:0000282 SBO:0000364 multimer cardinality Systems Biology Ontology Number of monomers composing a multimeric entity. Created on May 23 by Nicolas Le Novere for SBGN need. SBO:0000188 SBO:0000365 forward non-integral order rate constant, continuous case Systems Biology Ontology Numerical parameter that quantifies the forward velocity of a chemical reaction where reactants have non-integral orders. This parameter encompasses all the contributions to the velocity except the quantity of the reactants.It is to be used in a reaction modelled using a continuous framework. created 4th June 2008 - Nick Juty SBO:0000154 SBO:0000160 SBO:0000366 forward non-integral order rate constant, discrete case Systems Biology Ontology Numerical parameter that quantifies the forward velocity of a chemical reaction where reactants have non-integral orders. This parameter encompasses all the contributions to the velocity except the quantity of the reactants. It is to be used in a reaction modelled using a discrete framework. created 4th June 2008 - Nick Juty SBO:0000155 SBO:0000160 SBO:0000367 reverse non-integral order rate constant, discrete case Systems Biology Ontology Numerical parameter that quantifies the reverse velocity of a chemical reaction where products have non-integral orders. This parameter encompasses all the contributions to the velocity except the quantity of the products. It is to be used in a reaction modelled using a discrete framework. created 4th June 2008 - Nick Juty SBO:0000161 SBO:0000368 reverse non-integral order rate constant, continuous case Systems Biology Ontology Numerical parameter that quantifies the reverse velocity of a chemical reaction where products have non-integral orders. This parameter encompasses all the contributions to the velocity except the quantity of the products. It is to be used in a reaction modelled using a continuous framework. created 4th June 2008 - Nick Juty SBO:0000161 SBO:0000369 gene regulatory region Systems Biology Ontology Region of a gene that is involved in the modulation of the expression of the gene. Created for SBGN purposes. SBO:0000404 SBO:0000370 Michaelis constant in non-equilibrium situation Systems Biology Ontology Michaelis constant derived or experimentally measured under non-equilibrium conditions. Created 11th July 2008 by Nick Juty (with Lukas Endler and Nicolas Le Novere) SBO:0000027 SBO:0000371 Michaelis constant in quasi-steady state situation Systems Biology Ontology Michaelis constant derived using a steady-state assumption for enzyme-substrate and enzyme-product intermediates. For example see Briggs-Haldane equation (SBO:0000031). Created 11th July 2008 by Nick Juty (with Lukas Endler and Nicolas Le Novere) SBO:0000370 SBO:0000372 Michaelis constant in irreversible situation Systems Biology Ontology Michaelis constant derived assuming enzyme-substrate and enzyme-product intermediates are formed in consecutive irreversible reactions. The constant K is the ratio of the forward rate constants. For example see Van Slyke-Cullen equation (SBO:0000030). Created 11th July 2008 by Nick Juty (with Lukas Endler and Nicolas Le Novere) SBO:0000370 SBO:0000373 Michaelis constant in fast equilibrium situation Systems Biology Ontology Michaelis constant as determined in a reaction where the formation of the enzyme-substrate complex occurs at a much faster rate than subsequent steps, and so are assumed to be in a quasi-equilibrium situation. K is equivalent to an equilibrium constant. For example see Henri-Michaelis-Menten equation (SBO:0000029). Modified for clarification [SF req #2969519] SBO:0000027 SBO:0000374 relationship Systems Biology Ontology connectedness between entities and/or interactions representing their relatedness or influence. Name and definition changed on November 18 2008 by Nicolas Le Novere SBO:0000231 SBO:0000375 process Systems Biology Ontology A sequential series of actions, motions, or occurrences, such as chemical reactions, that affect one or more entities in a phenomenologically characteristic manner. definition modified 21/10/08 - NJ name and definition modified 18/Nov/2008 - Nicolas Le Novere SBO:0000231 SBO:0000376 hydrolysis Systems Biology Ontology Decomposition of a compound by reaction with water, where the hydroxyl and H groups are incorporated into different products Created 30/9/08 - NJ SBO:0000176 SBO:0000377 isomerisation Systems Biology Ontology A reaction in which the principal reactant and principal product are isomers of each other Created 30/9/08 - NJ SBO:0000176 SBO:0000378 enzymatic rate law for inhibition of irreversible unireactant enzymes by competing substrates Systems Biology Ontology Inhibition of a unireactant enzyme by competing substrates (Sa) that bind to the free enzyme on the same binding site. The enzyme does not catalyse the reactions in both directions. See Cornish-Bowden Fundementals of Enzyme Kinetics (3rd Edition 2004): Ch5.6, pp127. $\mathrm{kcat}\mathrm{Et}S\mathrm{Sa}\mathrm{Ks}\mathrm{Ksa}n\mapsto \frac{\mathrm{kcat}\mathrm{Et}S}{\mathrm{Ks}(1+\sum_{i=1}^n \frac{\mathrm{Sa}_i}{\mathrm{Ksa}_i})+S}$ SBO:0000270 SBO:0000379 enzymatic rate law for simple competitive inhibition of irreversible unireactant enzymes by two non-exclusive inhibitors Systems Biology Ontology Inhibition of a unireactant enzyme by two inhibitors that can bind once to the free enzyme and preclude the binding of the substrate. Binding of one inhibitor may affect binding of the other, or not. The enzymes do not catalyse the reactions in both directions. See Segel I., Enzyme Kinetics, Wiley-Interscience;1993, ISBN 0-471-30309-7, Chapter 8, System B3, pp481. $\mathrm{kcat}\mathrm{Et}S\mathrm{I1}\mathrm{I2}a\mathrm{Ks}\mathrm{Ki1}\mathrm{Ki2}\mapsto \frac{\mathrm{kcat}\mathrm{Et}S}{\mathrm{Ks}(1+\frac{\mathrm{I1}}{\mathrm{Ki1}}+\frac{\mathrm{I2}}{\mathrm{Ki2}}+\frac{\mathrm{I1}\mathrm{I2}}{a\mathrm{Ki1}\mathrm{Ki2}})+S}$ SBO:0000430 SBO:0000380 biochemical coefficient Systems Biology Ontology number used as a multiplicative or exponential factor for quantities, expressions or functions created by Lukas Endler and Nick Juty 17/9/08 SBO:0000002 SBO:0000381 biochemical proportionality coefficient Systems Biology Ontology A multiplicative factor for quantities, expressions or functions created by Nick Juty and Lukas Endler - 17/9/08 SBO:0000380 SBO:0000382 biochemical exponential coefficient Systems Biology Ontology number used as an exponential factor for quantities, expressions or functions created by Lukas Endler and Nick Juty - 17/9/08 SBO:0000380 SBO:0000383 biochemical cooperative inhibition coefficient Systems Biology Ontology The coefficient used to quantify the effect on inhibition constants of multiple inhibitors binding non-exclusively to the enzyme. Created by Lukas Endler and Nick Juty - 18/9/08 SBO:0000381 SBO:0000384 biochemical inhibitory proportionality coefficient Systems Biology Ontology Coefficient that quantifies the effect on inhibition constants of either binding of multiple substrates or inhibitors. Created by Lukas Endler and Nick Juty - 18/9/08 SBO:0000381 SBO:0000385 biochemical cooperative inhibitor substrate coefficient Systems Biology Ontology The coefficient that describes the proportional change of Ks or Ki when inhibitor or substrate is bound, respectively, to the enzyme. Created by Nick Juty and Lukas Endler - 18/9/08. SBO:0000381 SBO:0000386 enzymatic rate law for inhibition of irreversible unireactant enzymes by single competing substrate Systems Biology Ontology Inhibition of a unireactant enzyme by a competing substrate (Sa) that binds to the free enzyme on the same binding site. The enzyme does not catalyse the reactions in both directions. See Cornish-Bowden Fundementals of Enzyme Kinetics (3rd Edition 2004): Ch5.6, pp127. $\mathrm{kcat}\mathrm{Et}S\mathrm{Sa}\mathrm{Ks}\mathrm{Ksa}n\mapsto \frac{\mathrm{kcat}\mathrm{Et}S}{\mathrm{Ks}(1+\frac{\mathrm{Sa}}{\mathrm{Ksa}})+S}$ SBO:0000378 SBO:0000387 enzymatic rate law for competitive inhibition of irreversible unireactant enzyme by product Systems Biology Ontology Inhibition of a unireactant enzyme by a competing product (P) that binds to the free enzyme on the same binding site. The enzyme does not catalyse the reactions in both directions. See Cornish-Bowden Fundementals of Enzyme Kinetics (3rd Edition 2004): Ch2.8, pp55 $\mathrm{kcat}\mathrm{Et}SP\mathrm{Ks}\mathrm{Kp}\mapsto \frac{\mathrm{kcat}\mathrm{Et}S}{\mathrm{Ks}(1+\frac{P}{\mathrm{Kp}})+S}$ SBO:0000270 SBO:0000388 enzymatic rate law for inhibition of irreversible unireactant enzymes by single competing substrate with product inhibition Systems Biology Ontology Inhibition of a unireactant enzyme by a competing substrate (Sa) that binds to the free enzyme on the same binding site, and competitive inhibition by a product (P) and an alternative product (Pa). The enzyme does not catalyse the reactions in both directions. $\mathrm{kcat}\mathrm{Et}S\mathrm{Sa}\mathrm{Ks}\mathrm{Ksa}\mathrm{Kp}\mathrm{Kpa}P\mathrm{Pa}n\mapsto \frac{\mathrm{kcat}\mathrm{Et}S}{\mathrm{Ks}(1+\frac{\mathrm{Sa}}{\mathrm{Ksa}}+\frac{P}{\mathrm{Kpa}}+\frac{\mathrm{Pa}}{\mathrm{Kpa}})+S}$ SBO:0000378 SBO:0000389 switch value Systems Biology Ontology A parameter value taken by a switch, which has a discrete set of values which can be alternated or switched between. Created by NJ and LE for BioModels Database - 19/9/08 SBO:0000002 SBO:0000390 boolean switch Systems Biology Ontology A parameter that has precisely two discrete values which may be switched between. Usually for the boolean parameter these are indicated as '0 or 1' or 'True or False'. binary switch Created by NJ and LE for Biomodels database - 19/9/08. SBO:0000389 SBO:0000391 steady state expression Systems Biology Ontology A mathematical expression that describes a steady state situation binding or interaction equilibria branch to hold mathematical expressions for equilibrium thermodynamics, electrochemical, binding, solution equilibria, complexes.... SBO:0000064 SBO:0000392 equivalence Systems Biology Ontology Term to signify those material or conceptual entities that are identical in some respect within a frame of reference created 20/10/08 - NJ and LE created for SBGN (equivalence arc - 2.6.9) SBO:0000374 SBO:0000393 production Systems Biology Ontology Generation of a material or conceptual entity. created 20/10/08 - LE and NJ created for SBGN (production - 2.6.2) SBO:0000168 SBO:0000394 consumption Systems Biology Ontology Decrease in amount of a material or conceptual entity. created 20/10/08 - LE and NJ created for SBGN (consumption - 2.6.1) SBO:0000168 SBO:0000395 encapsulating process Systems Biology Ontology An aggregation of interactions and entities into a single process. created 20/10/08 - LE and NJ created for SBGN PD (submap - 2.4.3) Name and definition changed on November 18 2008 by Nicolas Le Novere SBO:0000375 SBO:0000396 uncertain process Systems Biology Ontology An equivocal or conjectural process, whose existence is assumed but not proven. created 20/10/08 - NJ and LE created for SBGN (uncertain process - 2.5.3) SBO:0000375 SBO:0000397 omitted process Systems Biology Ontology One or more processes that are not represented in certain representations or interpretations of a model. created 20/10/08 - LE and NJ created for SBGN (omitted process - 2.5.2) SBO:0000375 SBO:0000398 logical relationship Systems Biology Ontology Relationship between entities (material or conceptual) and logical operators, or between logical operators themselves. created 20/10/08 - LE and NJ. created for SBGN purposes (logical arc - 2.6.8) SBO:0000374 SBO:0000399 decarboxylation Systems Biology Ontology A process in which a carboxyl group (COOH) is removed from a molecule as carbon dioxide. created 21/10/08 - NJ SBO:0000211 SBO:0000400 decarbonylation Systems Biology Ontology Removal of a carbonyl group (-C-O-) from a molecule, usually as carbon monoxide created 21/10/08 - NJ SBO:0000211 SBO:0000401 deamination Systems Biology Ontology Removal of an amine group from a molecule, often under the addition of water SBO:0000211 SBO:0000402 transfer of a chemical group Systems Biology Ontology Covalent reaction that results in the transfer of a chemical group from one molecule to another. created 21/10/08 SBO:0000182 SBO:0000403 transamination Systems Biology Ontology The transfer of an amino group between two molecules. Commonly in biology this is restricted to reactions between an amino acid and an alpha-keto carbonic acid, whereby the reacting amino acid is converted into an alpha-keto acid, and the alpha-keto acid reactant into an amino acid. created 21/10/08 - NJ modified to add more biological detail, to differentiate from alkylamino-de-amination. SBO:0000402 SBO:0000404 unit of genetic information Systems Biology Ontology Functional entity associated with or derived from a unit of inheritance. SBO:0000241 SBO:0000405 perturbing agent Systems Biology Ontology A material entity that is responsible for a perturbing effect SBO:0000240 SBO:0000406 observable Systems Biology Ontology An entity that can be measured quantitatively SBO:0000240 SBO:0000407 absolute inhibition Systems Biology Ontology Control that precludes the execution of a process. Created by Nicolas Le Novere for the needs of SBGN ER. SBO:0000169 SBO:0000408 biological activity Systems Biology Ontology Effect of a biological entity on biological structures or processes. 1 Added for SBGN activity flow. SBO:0000003 SBO:0000409 interaction outcome Systems Biology Ontology Entity that results from the interaction between other entities. Added for SBGN entity relationships SBO:0000236 SBO:0000410 implicit compartment Systems Biology Ontology A compartment whose existence is inferred due to the presence of known material entities which must be bounded, allowing the creation of material entity pools. Created by Nicolas Le Novere on the demand of Frank Bergmann for SBGN purposes. SBO:0000290 SBO:0000411 absolute stimulation Systems Biology Ontology Control that always triggers the controlled process. SBO:0000170 SBO:0000412 biological activity Systems Biology Ontology The potential action that a biological entity has on other entities. Example are enzymatic activity, binding activity etc. Created by Nicolas Le Novere for SBGN purpose SBO:0000231 SBO:0000413 positional relationship Systems Biology Ontology The connectedness between entities as related by their position SBO:0000374 SBO:0000414 cis Systems Biology Ontology Positional relationship between entities on the same strand (e.g. in DNA), or on the same side. cis from the latin for 'same side' SBO:0000413 SBO:0000415 trans Systems Biology Ontology Positional relationship between entities on different sides, or strands From latin 'trans' meaning across, beyond, or through SBO:0000413 SBO:0000416 true Systems Biology Ontology One of the two values possible from a boolean switch, which equates to '1', 'on' or 'input'. SBO:0000390 SBO:0000417 false Systems Biology Ontology One of the two values possible from a boolean switch, which equates to '0', 'off' or 'no input'. SBO:0000390 SBO:0000418 multimer of complexes Systems Biology Ontology Non-covalent association between several independant complexes SBO:0000286 SBO:0000419 multimer of informational molecule segment Systems Biology Ontology Non-covalent association between portions of macromolecules that carry genetic information SBO:0000286 SBO:0000420 multimer of macromolecules Systems Biology Ontology Non-covalent association between several macromolecules SBO:0000286 SBO:0000296 SBO:0000421 multimer of simple chemicals Systems Biology Ontology Non-covalent association between several simple chemicals SBO:0000286 SBO:0000422 isoinhibition constant Systems Biology Ontology Inhibitory constant for the binding of a given ligand with an isomeric form of an enzyme. see Segel Enzyme Kinetics (Wiley Classics Library, 1993), chapter 9 pg. 525 SBO:0000261 SBO:0000423 pseudo-dissociation constant for product Systems Biology Ontology In reversible reactions this is the concentration of product that is required to achieve half activation or inhibition in Hill-type kinetics, in the absence of the substrate. SBO:0000194 SBO:0000424 pseudo-dissociation constant for substrate Systems Biology Ontology In reversible reactions this is the concentration of substrate that is required to achieve half activation or inhibition in Hill-type kinetics, in the absence of the product. SBO:0000194 SBO:0000425 reversible Hill-type enzymatic rate law Systems Biology Ontology Reversible Hill-type kinetics represents the situation where a single substrate and product bind cooperatively and reversibly to the enzyme. Co-operativity is seen if the Hill coefficient (h) is greater than 1, indicating that the binding of one substrate (or product) molecule facilitates the binding of the next. The opposite effect is evident with a coefficient less than 1. SF tracker (2912726) - name change to include 'enzymatic'. SBO:0000268 SBO:0000426 modulated reversible Hill-type rate law Systems Biology Ontology Reversible Hill-type kinetics in the presence of at least one modifier whose binding is affected by the presence of the substrate or product. SBO:0000425 SBO:0000427 modulated reversible Hill-type rate law with one modifier Systems Biology Ontology The modifier can be either an activator or inhibitor depending on the value of alpha (activator for values larger than 1, inhibitor for values smaller than 1; no effect if exactly 1). This reflects the effect of the presence of substrate and product on the binding of the modifier. The equation, derived by Hofmeyr and Cornish-Bowden (Comput. Appl. Biosci. 13, 377 - 385 (1997) Definition modified from WebCell. The equation was originally derived by Hofmeyr and Cornish-Bowden (Comput. Appl. Biosci. 13, 377 - 385 (1997). $\mathrm{substrate}\mathrm{product}\mathrm{Modifier}\mathrm{Keq}\mathrm{Vf}\mathrm{Ks}\mathrm{Kp}h\mathrm{Mhalf}\mathrm{alpha}\mapsto \frac{\frac{\mathrm{Vf}\mathrm{substrate}}{\mathrm{Ks}}(1-\frac{\mathrm{product}}{\mathrm{substrate}\mathrm{Keq}})(\frac{\mathrm{substrate}}{\mathrm{Ks}}+\frac{\mathrm{product}}{\mathrm{Kp}})^{(h-1)}}{\frac{1+\left(\frac{\mathrm{Modifier}}{\mathrm{Mhalf}}\right)^h}{1+\mathrm{alpha}\left(\frac{\mathrm{Modifier}}{\mathrm{Mhalf}}\right)^h}+(\frac{\mathrm{substrate}}{\mathrm{Ks}}+\frac{\mathrm{product}}{\mathrm{Kp}})^h}$ SBO:0000426 SBO:0000428 modulated reversible Hill-type rate law with two modifiers Systems Biology Ontology The modifiers can be either activators or inhibitors depending on the values of and alpha (activators for values larger than 1, inhibitors for values smaller than 1; no effect if exactly 1). The assumption is that the binding of one modifier affects the binding of the second. Modifiers are assumed to bind at different sites. The synergetic effects of the two modifiers depend on the parameter alpha (if unity then they are independent; if zero they compete for the same binding site). and reflect the effect of the presence of substrate and product on the binding of modifier A or modifier B. alphaA and alphaB factors account for the effect of substrate and product binding on the binding of modifier A and modifier B respectively. alphaAB accounts for the interaction of the modifiers on each others binding. (if < 1 Ma is inhibitor, if > 1 activator) alpha_2 : factor accounting for the effect of S and P on the binding of Mb (if < 1 Mb is inhibitor, if > 1 activator) alpha_3 : factor accounting for interaction of Ma to Mb binding to the enzyme (and v. v.). definition modified from WebCell. Equation originally derived by Hofmeyr and Cornish-Bowden (Comput. Appl. Biosci. 13, 377 - 385 (1997)). $\mathrm{substrate}\mathrm{product}\mathrm{ModifierA}\mathrm{ModifierB}\mathrm{Keq}\mathrm{Vf}\mathrm{Shalve}\mathrm{Phalve}h\mathrm{MAhalf}\mathrm{alphaA}\mathrm{MBhalf}\mathrm{alphaB}\mathrm{alphaAB}\mapsto \frac{\frac{\mathrm{Vf}\mathrm{substrate}}{\mathrm{Ks}}(1-\frac{\mathrm{product}}{\mathrm{substrate}\mathrm{Keq}})(\frac{\mathrm{substrate}}{\mathrm{Ks}}+\frac{\mathrm{product}}{\mathrm{Kp}})^{(h-1)}}{\frac{1+\left(\frac{\mathrm{ModifierA}}{\mathrm{MAhalf}}\right)^h+\left(\frac{\mathrm{ModifierB}}{\mathrm{MBhalf}}\right)^h}{1+\mathrm{alphaA}\left(\frac{\mathrm{ModifierA}}{\mathrm{MAhalf}}\right)^h+\mathrm{alphaB}\left(\frac{\mathrm{ModifierB}}{\mathrm{MBhalf}}\right)^h+\mathrm{alphaA}\mathrm{alphaB}\mathrm{alphaAB}\left(\frac{\mathrm{ModifierA}}{\mathrm{MAhalf}}\right)^h\left(\frac{\mathrm{ModifierB}}{\mathrm{MBhalf}}\right)^h}+(\frac{\mathrm{substrate}}{\mathrm{Ks}}+\frac{\mathrm{product}}{\mathrm{Kp}})^h}$ SBO:0000426 SBO:0000429 enzymatic rate law for multireactant enzymes Systems Biology Ontology Kinetics of enzyme-catalysed reactions with 2 or more substrates or products SBO:0000268 SBO:0000430 enzymatic rate law for modulated unireactant enzymes Systems Biology Ontology Kinetics of enzymes that react with one substance, and whose activity may be positively or negatively modulated. SBO:0000269 SBO:0000431 unmodulated reversible Hill-type rate law Systems Biology Ontology Reversible equivalent of Hill kinetics, where substrate and product bind co-operatively to the enzyme. A Hill coefficient (h) of greater than 1 indicates positive co-operativity between substrate and product, while h values below 1 indicate negative co-operativity. definition modified from WebCell $\mathrm{substrate}\mathrm{product}\mathrm{Keq}\mathrm{Vf}\mathrm{Ks}\mathrm{Kp}h\mapsto \frac{\frac{\mathrm{Vf}\mathrm{substrate}}{\mathrm{Ks}}(1-\frac{\mathrm{product}}{\mathrm{substrate}\mathrm{Keq}})(\frac{\mathrm{substrate}}{\mathrm{Ks}}+\frac{\mathrm{product}}{\mathrm{Kp}})^{(h-1)}}{1+(\frac{\mathrm{substrate}}{\mathrm{Ks}}+\frac{\mathrm{product}}{\mathrm{Kp}})^h}$ SBO:0000425 SBO:0000432 irreversible Michaelis Menten rate law for two substrates Systems Biology Ontology Enzymatic rate law for an irreversible reaction involving two substrates and one product. $AB\mathrm{KmA}\mathrm{KmB}\mathrm{KiA}\mathrm{Et}\mathrm{kcat}\mapsto \frac{\mathrm{Et}\mathrm{kcat}AB}{\mathrm{KiA}\mathrm{KmB}+\mathrm{KmB}A+\mathrm{KmA}B+AB}$ SBO:0000429 SBO:0000433 Ordered Bi-Bi mechanism rate law Systems Biology Ontology Enzymatic rate law for a reaction involving two substrates and two products. The products P and then Q are released strictly in order, while the substrates are bound strictly in the order A and then B. $\mathrm{Sa}\mathrm{Sb}\mathrm{Pp}\mathrm{Pq}\mathrm{Keq}\mathrm{Vf}\mathrm{Vr}\mathrm{Kma}\mathrm{Kmb}\mathrm{Kmp}\mathrm{Kmq}\mathrm{Kia}\mathrm{Kib}\mathrm{Kip}\mapsto \frac{\mathrm{Vf}(\mathrm{Sa}\mathrm{Sb}-\frac{\mathrm{Pp}\mathrm{Pq}}{\mathrm{Keq}})}{\mathrm{Sa}\mathrm{Sb}(1+\frac{\mathrm{Pp}}{\mathrm{Kip}})+\mathrm{Kma}\mathrm{Sb}+\mathrm{Kmb}(\mathrm{Sa}+\mathrm{Kia})+\frac{\mathrm{Vf}}{\mathrm{Vr}\mathrm{Keq}}(\mathrm{Kmq}\mathrm{Pp}(1+\frac{\mathrm{Sa}}{\mathrm{Kia}})+\mathrm{Pq}(\mathrm{Kmp}(1+\frac{\mathrm{Kma}\mathrm{Sb}}{\mathrm{Kia}\mathrm{Kmb}})+\mathrm{Pp}(1+\frac{\mathrm{Sb}}{\mathrm{Kib}})))}$ SBO:0000429 SBO:0000434 Ordered Bi-Uni mechanism rate law Systems Biology Ontology Enzymatic rate for a reaction involving two substrates and one product. The substrates A and then B are bound strictly in order. $\mathrm{Sa}\mathrm{Sb}P\mathrm{Kma}\mathrm{Kmb}\mathrm{Kmp}\mathrm{Kia}\mathrm{Keq}\mathrm{Vf}\mathrm{Vr}\mapsto \frac{\mathrm{Vf}(\mathrm{Sa}\mathrm{Sb}-\frac{P}{\mathrm{Keq}})}{\mathrm{Sa}\mathrm{Sb}+\mathrm{Kma}\mathrm{Sb}+\mathrm{Kmb}\mathrm{Sa}+\frac{\mathrm{Vf}}{\mathrm{Vr}\mathrm{Keq}}(\mathrm{Kmp}+P(1+\frac{\mathrm{Sa}}{\mathrm{Kia}}))}$ SBO:0000429 SBO:0000435 Ordered Uni-Bi mechanism rate law Systems Biology Ontology Enzymatic rate law for a reaction with one substrate and two products. The products P and then Q are released in the strict order P and then Q. $\mathrm{substrate}\mathrm{productp}\mathrm{productq}\mathrm{Kms}\mathrm{Kmq}\mathrm{Kmp}\mathrm{Kip}\mathrm{Keq}\mathrm{Vf}\mathrm{Vr}\mapsto \frac{\mathrm{Vf}(\mathrm{substrate}-\frac{\mathrm{productp}\mathrm{productq}}{\mathrm{Keq}})}{\mathrm{Kms}+\mathrm{substrate}(1+\frac{\mathrm{productp}}{\mathrm{Kip}})+\frac{\mathrm{Vf}}{\mathrm{Vr}\mathrm{Keq}}(\mathrm{Kmq}\mathrm{productp}+\mathrm{Kmp}\mathrm{productq}+\mathrm{productp}\mathrm{productq})}$ SBO:0000429 SBO:0000436 Ping Pong Bi-Bi mechanism rate law Systems Biology Ontology Enzymatic rate law for a reaction involving two substrates and two products. The first product (P) is released after the first substrate (A) has been bound. The second product (Q) is released after the second substrate (B) has been bound. $\mathrm{Sa}\mathrm{Sb}\mathrm{Pp}\mathrm{Pq}\mathrm{Keq}\mathrm{Vf}\mathrm{Vr}\mathrm{Kma}\mathrm{Kmb}\mathrm{Kmp}\mathrm{Kmq}\mathrm{Kia}\mathrm{Kiq}\mapsto \frac{\mathrm{Vf}(\mathrm{Sa}\mathrm{Sb}-\frac{\mathrm{Pp}\mathrm{Pq}}{\mathrm{Keq}})}{\mathrm{Sa}\mathrm{Sb}+\mathrm{Kmb}\mathrm{Sa}+\mathrm{Kma}\mathrm{Sb}(1+\frac{\mathrm{Pq}}{\mathrm{Kiq}})+\frac{\mathrm{Vf}}{\mathrm{Vr}\mathrm{Keq}}(\mathrm{Kmq}\mathrm{Pp}(1+\frac{\mathrm{Sa}}{\mathrm{Kia}})+\mathrm{Pq}(\mathrm{Kmp}+\mathrm{Pp}))}$ SBO:0000429 SBO:0000437 reversible Iso Uni-Uni Systems Biology Ontology Enzyme catalysed reaction involving one substrate and one product. Unlike the reversible uni-uni mechanism (SBO:0000326), the mechanism assumes an enzyme intermediate. Therefore, the free enzyme generated after the release of product from enzyme-product complex is not the same form as that which bind the substrate to form enzyme-substrate complex. Some permeases are thought to follow this mechanism, such that isomerization in the membrane may be accomplished through re-orientation in the membrane. modified from Webcell $\mathrm{substrate}\mathrm{product}\mathrm{Kms}\mathrm{Kmp}\mathrm{Kii}\mathrm{Vf}\mathrm{Keq}\mapsto \frac{\mathrm{Vf}(\mathrm{substrate}-\frac{\mathrm{product}}{\mathrm{Keq}})}{\mathrm{substrate}(1+\frac{\mathrm{product}}{\mathrm{Kii}})+\mathrm{Kms}(1+\frac{\mathrm{product}}{\mathrm{Kmp}})}$ SBO:0000326 SBO:0000438 reversible Uni-Uni Systems Biology Ontology The reversible equivalent of the Henri-Michaelis-Menten rate law (SBO:0000029). Reversible Michaelis Menten Uni-Uni Reversible Simple Michaelis-Menten $\mathrm{substrate}\mathrm{product}\mathrm{Kms}\mathrm{Kmp}\mathrm{Et}\mathrm{kcatp}\mathrm{kcats}\mapsto \frac{\mathrm{Et}(\frac{\mathrm{kcatp}\mathrm{substrate}}{\mathrm{Kms}}-\frac{\mathrm{kcats}\mathrm{product}}{\mathrm{Kmp}})}{1+\frac{\mathrm{substrate}}{\mathrm{Kms}}+\frac{\mathrm{product}}{\mathrm{Kmp}}}$ SBO:0000326 SBO:0000439 Uni-Uni Reversible using Haldane relationship Systems Biology Ontology Enzyme catalysed reaction involving one substrate and one product. It is a modification of SBO:0000326 that directly incorporates the equilibrium constant in the rate law. Uni-Uni $\mathrm{substrate}\mathrm{product}\mathrm{Kms}\mathrm{Kmp}\mathrm{Vf}\mathrm{Keq}\mapsto \frac{\mathrm{Vf}(\mathrm{substrate}-\frac{\mathrm{product}}{\mathrm{Keq}})}{\mathrm{substrate}+\mathrm{Kms}(1+\frac{\mathrm{product}}{\mathrm{Kmp}})}$ SBO:0000326 SBO:0000440 enzymatic rate law for irreversible allosteric inhibition Systems Biology Ontology Enzymatic rate law which follows from the allosteric concerted model (symmetry model or MWC model).This states that enzyme subunits can assume one of two conformational states (relaxed or tense), and that the state of one subunit is shared or enforced on the others. The binding of a ligand to a site other than that bound by the substrate (active site) can shift the conformation from one state to the other. L represents the equilibrium constant between active and inactive states of the enzyme, and n represents the number of binding sites for the substrate and inhibitor. Monod-Wyman-Changeaux model - see Monod et. al., J. Mol. Biol. 12: 88-118, 1965. $\mathrm{substrate}\mathrm{Inhibitor}V\mathrm{Ks}nL\mathrm{Ki}\mapsto \frac{V\mathrm{substrate}(\mathrm{Ks}+\mathrm{substrate})^{(n-1)}}{L(\mathrm{Ks}(1+\frac{\mathrm{Inhibitor}}{\mathrm{Ki}}))^n+(\mathrm{Ks}+\mathrm{substrate})^n}$ SBO:0000430 SBO:0000441 enzymatic rate law for mixed-type inhibition of reversible enzymes by mutually exclusive inhibitors Systems Biology Ontology Reversible inhibition of a unireactant enzyme by inhibitors that can bind to the enzyme-substrate complex and to the free enzyme with the same equilibrium constant. The inhibitor is noncompetitive with the substrate. $\mathrm{substrate}\mathrm{product}\mathrm{Inhibitor}\mathrm{Kms}\mathrm{Kmp}\mathrm{Vf}\mathrm{Vr}\mathrm{Kis}\mathrm{Kic}\mapsto \frac{\frac{\mathrm{Vf}\mathrm{substrate}}{\mathrm{Kms}}-\frac{\mathrm{Vr}\mathrm{product}}{\mathrm{Kmp}}}{1+\frac{\mathrm{Inhibitor}}{\mathrm{Kis}}+(\frac{\mathrm{substrate}}{\mathrm{Kms}}+\frac{\mathrm{product}}{\mathrm{Kmp}})(1+\frac{\mathrm{Inhibitor}}{\mathrm{Kic}})}$ SBO:0000275 SBO:0000442 enzymatic rate law for simple reversible non-competitive inhibition of unireactant enzymes Systems Biology Ontology Reversible inhibition of a unireactant enzyme by one inhibitor that can bind to the enzyme-substrate complex and to the free enzyme with the same equilibrium constant. The inhibitor is noncompetitive with the substrate. $\mathrm{substrate}\mathrm{product}\mathrm{Inhibitor}\mathrm{Kms}\mathrm{Kmp}\mathrm{Vf}\mathrm{Vr}\mathrm{Ki}\mapsto \frac{\frac{\mathrm{Vf}\mathrm{substrate}}{\mathrm{Kms}}-\frac{\mathrm{Vr}\mathrm{product}}{\mathrm{Kmp}}}{(1+\frac{\mathrm{substrate}}{\mathrm{Kms}}+\frac{\mathrm{product}}{\mathrm{Kmp}})(1+\frac{\mathrm{Inhibitor}}{\mathrm{Ki}})}$ SBO:0000265 SBO:0000443 enzymatic rate law for reversible essential activation Systems Biology Ontology Enzymatic rate law where the free enzyme, in the absence of the activator, is unable to bind substrate and has no activity. compulsory activation specific activation SBO:0000430 SBO:0000444 enzymatic rate law for reversible mixed activation Systems Biology Ontology Enzymatic rate law where the activator enhances the rate of reaction through specific and catalytic effects, which increase the apparent limiting rate and decrease apparent Michaelis constant. The activator can bind reversibly both the free enzyme and enzyme-substrate complex, while the substrate can bind only to enzyme-activator complex. Catalytic activity is seen only when enzyme, substrate and activator are complexed. Definition modified from WebCell TODO : potentiator -> activator? $\mathrm{substrate}\mathrm{product}\mathrm{Activator}\mathrm{Kms}\mathrm{Kmp}\mathrm{Vf}\mathrm{Vr}\mathrm{Kas}\mathrm{Kac}\mapsto \frac{(\frac{\mathrm{Vf}\mathrm{substrate}}{\mathrm{Kms}}-\frac{\mathrm{Vr}\mathrm{product}}{\mathrm{Kmp}})\mathrm{Activator}}{\mathrm{Kas}+\mathrm{Activator}+(\frac{\mathrm{substrate}}{\mathrm{Kms}}+\frac{\mathrm{product}}{\mathrm{Kmp}})(\mathrm{Kac}+\mathrm{Activator})}$ SBO:0000443 SBO:0000445 enzymatic rate law for irreversible substrate activation Systems Biology Ontology This enzymatic rate law is available only for irreversible reactions, with one substrate and one product. There is a second binding site for the enzyme which, when occupied, activates the enzyme. Substrate binding at either site can occur at random. Definition modified from WebCell. $\mathrm{substrate}V\mathrm{Ksc}\mathrm{Ksa}\mapsto \frac{V\left(\frac{\mathrm{substrate}}{\mathrm{Ksa}}\right)^2}{1+\frac{\mathrm{substrate}}{\mathrm{Ksc}}+\frac{\mathrm{substrate}}{\mathrm{Ksa}}+\left(\frac{\mathrm{substrate}}{\mathrm{Ksa}}\right)^2}$ SBO:0000444 SBO:0000446 enzymatic rate law for irrreversible mixed activation Systems Biology Ontology Enzymatic rate law where the activator enhances the rate of reaction through specific and catalytic effects, which increase the apparent limiting rate and decrease apparent Michaelis constant. The activator can bind irreversibly both free enzyme and enzyme-substrate complex, while the substrate can bind only to enzyme-activator complex. Catalytic activity is seen only when enzyme, substrate and activator are complexed. Definition modified from WebCell TODO : potentiator -> activator? $\mathrm{substrate}\mathrm{Activator}\mathrm{Kms}V\mathrm{Kas}\mathrm{Kac}\mapsto \frac{V\mathrm{substrate}\mathrm{Activator}}{\mathrm{Kms}(\mathrm{Kas}+\mathrm{Activator})+\mathrm{substrate}(\mathrm{Kac}+\mathrm{Activator})}$ SBO:0000444 SBO:0000447 enzymatic rate law for reversible catalytic activation with one activator Systems Biology Ontology Enzymatic rate law where an activator enhances the rate of reaction by increasing the apparent limiting rate; The reversible binding of the activator to the enzyme-substrate complex is required for enzyme catalytic activity (to generate the product). Definition adapted from WebCell TODO : potentiator -> activator $\mathrm{substrate}\mathrm{product}\mathrm{Activator}\mathrm{Kms}\mathrm{Kmp}\mathrm{Vf}\mathrm{Vr}\mathrm{Ka}\mapsto \frac{(\frac{\mathrm{Vf}\mathrm{substrate}}{\mathrm{Kms}}-\frac{\mathrm{Vr}\mathrm{product}}{\mathrm{Kmp}})\mathrm{Activator}}{(1+\frac{\mathrm{substrate}}{\mathrm{Kms}}+\frac{\mathrm{product}}{\mathrm{Kmp}})(\mathrm{Ka}+\mathrm{Activator})}$ SBO:0000444 SBO:0000448 enzymatic rate law for reversible specific activation Systems Biology Ontology Enzymatic rate law for one substrate, one product and one modifier which acts as an activator. The activator enhances the rate of reaction by decreasing the apparent Michaelis constant. The activator reversibly binds to the enzyme before the enzyme can bind the substrate. Definition modified from WebCell TODO : potentiator -> activator? $\mathrm{substrate}\mathrm{product}\mathrm{Activator}\mathrm{Kms}\mathrm{Kmp}\mathrm{Vf}\mathrm{Vr}\mathrm{Ka}\mapsto \frac{(\frac{\mathrm{Vf}\mathrm{substrate}}{\mathrm{Kms}}-\frac{\mathrm{Vr}\mathrm{product}}{\mathrm{Kmp}})\mathrm{Activator}}{\mathrm{Ka}+(1+\frac{\mathrm{substrate}}{\mathrm{Kms}}+\frac{\mathrm{product}}{\mathrm{Kmp}})\mathrm{Activator}}$ SBO:0000444 SBO:0000449 enzymatic rate law for irreversible catalytic activation with one activator Systems Biology Ontology Enzymatic rate law where an activator enhances the rate of reaction by increasing the apparent limiting rate; The activator binding to the enzyme-substrate complex (irreversibly) is required for enzyme catalytic activity (to generate the product). Definition modified from WebCell TODO : potentiator -> activator? $\mathrm{substrate}\mathrm{Activator}\mathrm{Kms}V\mathrm{Ka}\mapsto \frac{V\mathrm{substrate}\mathrm{Activator}}{(\mathrm{Kms}+\mathrm{substrate})(\mathrm{Ka}+\mathrm{Activator})}$ SBO:0000447 SBO:0000450 enzymatic rate law for irreversible specific activation Systems Biology Ontology Enzymatic rate law for one substrate, one product and one modifier which acts as an activator. The activator enhances the rate of reaction by decreasing the apparent Michaelis constant. The activator must bind to the enzyme before the enzyme can bind the substrate. Definition modified from WebCell. TODO : Possibly replace potentiator term for something more specific (activator?) $\mathrm{substrate}\mathrm{Activator}\mathrm{Kms}V\mathrm{Ka}\mapsto \frac{V\mathrm{substrate}\mathrm{Activator}}{\mathrm{Kms}\mathrm{Ka}+(\mathrm{Kms}+\mathrm{substrate})\mathrm{Activator}}$ SBO:0000448 SBO:0000451 enzymatic rate law for reversible reactions with competitive inhibition Systems Biology Ontology This enzymatic rate law involves one substrate, one product and one or more modifiers. The modifiers act as competitive inhibitors of the substrate at the enzyme binding site; The modifiers (inhibitors) reversibly bound to the enzyme block access to the substrate. The inhibitors have the effect of increasing the apparent Km, and bind exclusively to the enzymes. $\mathrm{substrate}\mathrm{product}\mathrm{Inhibitor}\mathrm{Kms}\mathrm{Kmp}\mathrm{Vf}\mathrm{Vr}\mathrm{Ki}n\mapsto \frac{\frac{\mathrm{Vf}\mathrm{substrate}}{\mathrm{Kms}}-\frac{\mathrm{Vr}\mathrm{product}}{\mathrm{Kmp}}}{1+\frac{\mathrm{substrate}}{\mathrm{Kms}}+\frac{\mathrm{product}}{\mathrm{Kmp}}+\sum_{i=1}^n \frac{I_i}{\mathrm{Ki}_i}}$ SBO:0000430 SBO:0000452 enzymatic rate law for reversible competitive inhibition by one inhibitor Systems Biology Ontology This enzymatic rate law involves one substrate, one product and one modifier. The modifier acts as a competitive inhibitor with the substrate at the enzyme binding site; The modifier (inhibitor) reversibly bound to the enzyme blocks access to the substrate. The inhibitor has the effect of increasing the apparent Km. Definition modified from WebCell $\mathrm{substrate}\mathrm{product}\mathrm{Inhibitor}\mathrm{Kms}\mathrm{Kmp}\mathrm{Vf}\mathrm{Vr}\mathrm{Ki}\mapsto \frac{\frac{\mathrm{Vf}\mathrm{substrate}}{\mathrm{Kms}}-\frac{\mathrm{Vr}\mathrm{product}}{\mathrm{Kmp}}}{1+\frac{\mathrm{substrate}}{\mathrm{Kms}}+\frac{\mathrm{product}}{\mathrm{Kmp}}+\frac{\mathrm{Inhibitor}}{\mathrm{Ki}}}$ SBO:0000451 SBO:0000453 enzymatic rate law for reversible empirical allosteric inhibition by one inhibitor Systems Biology Ontology Enzymatic rate law where the reversible binding of one ligand decreases the affinity for substrate at other active sites. The ligand does not bind the same site as the substrate on the enzyme. This is an empirical equation, where n represents the Hill coefficient. $\mathrm{substrate}\mathrm{product}\mathrm{Inhibitor}\mathrm{Vf}\mathrm{Vr}\mathrm{Kms}\mathrm{Kmp}n\mathrm{Ki}\mapsto \frac{\frac{\mathrm{Vf}\mathrm{substrate}}{\mathrm{Kms}}-\frac{\mathrm{Vr}\mathrm{product}}{\mathrm{Kmp}}}{1+\frac{\mathrm{substrate}}{\mathrm{Kms}}+\frac{\mathrm{product}}{\mathrm{Kmp}}+\left(\frac{\mathrm{Inhibitor}}{\mathrm{Ki}}\right)^n}$ SBO:0000451 SBO:0000454 enzymatic rate law for reversible substrate inhibition Systems Biology Ontology Enzymatic rate law where the substrate for an enzyme also acts as a reversible inhibitor. This may entail a second (non-active) binding site for the enzyme. The inhibition constant is then the dissociation constant for the substrate from this second site. Definition adapted from WebCell. $\mathrm{substrate}\mathrm{product}\mathrm{Kms}\mathrm{Kmp}\mathrm{Vf}\mathrm{Vr}\mathrm{Ki}\mapsto \frac{\frac{\mathrm{Vf}\mathrm{substrate}}{\mathrm{Kms}}-\frac{\mathrm{Vr}\mathrm{product}}{\mathrm{Kmp}}}{1+\frac{\mathrm{substrate}}{\mathrm{Kms}}+\frac{\mathrm{product}}{\mathrm{Kmp}}+\left(\frac{\mathrm{substrate}}{\mathrm{Ki}}\right)^2}$ SBO:0000430 SBO:0000455 enzymatic rate law for irreversible substrate inhibition Systems Biology Ontology Enzymatic rate law where the substrate for an enzyme also acts as an irreversible inhibitor. This may entail a second (non-active) binding site for the enzyme. The inhibition constant is then the dissociation constant for the substrate from this second site. Definition adapted from WebCell. $\mathrm{substrate}\mathrm{Km}V\mathrm{Ki}\mapsto \frac{V\mathrm{substrate}}{\mathrm{Km}+\mathrm{substrate}+\mathrm{Km}\left(\frac{\mathrm{substrate}}{\mathrm{Ki}}\right)^2}$ SBO:0000454 SBO:0000456 enzymatic rate law for reversible unireactant enzyme with a single hyperbolic modulator Systems Biology Ontology Enzymatic rate law where the modifier can act as an activator or inhibitor, depending upon the values of the kinetic constants. The modifier can bind reversibly to all forms of the enzyme and all enzyme-substrate complexes are reactive. 'a' represents the ratio of dissociation constant of the elementary step Enzyme-Substrate complex + Modifier = Enzyme-Substrate-Modifier complex over that of Enzyme + Modifier = Enzyme-Modifier complex. 'b' represents ratio of the rate constant of elementary step Enzyme-Substrate-Modifier complex -> Enzyme-Modifier complex + Product over that of Enzyme-Substrate complex -> Enzyme + Product. Definition modified from WebCell $\mathrm{substrate}\mathrm{product}\mathrm{Modifier}\mathrm{Kms}\mathrm{Kmp}\mathrm{Vf}\mathrm{Vr}\mathrm{Kd}ab\mapsto \frac{(\frac{\mathrm{Vf}\mathrm{substrate}}{\mathrm{Kms}}-\frac{\mathrm{Vr}\mathrm{product}}{\mathrm{Kmp}})(1+\frac{b\mathrm{Modifier}}{a\mathrm{Kd}})}{1+\frac{\mathrm{Modifier}}{\mathrm{Kd}}+(\frac{\mathrm{substrate}}{\mathrm{Kms}}+\frac{\mathrm{product}}{\mathrm{Kmp}})(1+\frac{\mathrm{Modifier}}{a\mathrm{Kd}})}$ SBO:0000430 SBO:0000457 enzymatic rate law for irreversible unireactant enzyme with a single hyperbolic modulator Systems Biology Ontology Enzymatic rate law where the modifier can act as an activator or inhibitor, depending upon the values of the kinetic constants. The modifier can bind irreversibly to all forms of the enzyme and all enzyme-substrate complexes are reactive. 'a' represents the ratio of dissociation constant of the elementary step Enzyme-Substrate complex + Modifier = Enzyme-Substrate-Modifier complex) over that of Enzyme + Modifier = Enzyme-Modifier complex. 'b' represents ratio of the rate constant of elementary step Enzyme-Substrate-Modifier complex -> Enzyme-Modifier complex + Product over that of Enzyme-Substrate complex -> Enzyme + Product. Definition modified from WebCell $\mathrm{substrate}\mathrm{Modifier}\mathrm{Km}V\mathrm{Kd}ab\mapsto \frac{V\mathrm{substrate}(1+\frac{b\mathrm{Modifier}}{a\mathrm{Kd}})}{\mathrm{Km}(1+\frac{\mathrm{Modifier}}{\mathrm{Kd}})+\mathrm{substrate}(1+\frac{\mathrm{Modifier}}{a\mathrm{Kd}})}$ SBO:0000456 SBO:0000458 enzymatic rate law for simple uncompetitive inhibition of reversible unireactant enzymes Systems Biology Ontology Reversible inhibition of a unireactant enzyme by one inhibitor, which binds to the enzyme-substrate complex. The inhibitor is uncompetitive with the substrate. $\mathrm{substrate}\mathrm{product}\mathrm{Inhibitor}\mathrm{Kms}\mathrm{Kmp}\mathrm{Vf}\mathrm{Vr}\mathrm{Ki}\mapsto \frac{\frac{\mathrm{Vf}\mathrm{substrate}}{\mathrm{Kms}}-\frac{\mathrm{Vr}\mathrm{product}}{\mathrm{Kmp}}}{1+(\frac{\mathrm{substrate}}{\mathrm{Kms}}+\frac{\mathrm{product}}{\mathrm{Kmp}})(1+\frac{\mathrm{Inhibitor}}{\mathrm{Ki}})}$ SBO:0000430 SBO:0000459 stimulator Systems Biology Ontology Substance that accelerates the velocity of a chemical reaction without itself being consumed or transformed. activator SBO:0000019 SBO:0000460 enzymatic catalyst Systems Biology Ontology A substance that accelerates the velocity of a chemical reaction without itself being consumed or transformed, by lowering the free energy of the transition state. The substance acting as a catalyst is an enzyme. SBO:0000013 SBO:0000461 essential activator Systems Biology Ontology A substance that is absolutely required for occurrence and stimulation of a reaction. necessary stimulator SBO:0000459 SBO:0000462 non-essential activator Systems Biology Ontology An activator which is not necessary for an enzymatic reaction, but whose presence will further increase enzymatic activity. SBO:0000459 SBO:0000463 standard biochemical potential Systems Biology Ontology The biochemical potential of a substance measured at standard concentrations and under standard conditions. standard chemical potential SBO:0000303 SBO:0000464 state variable assignment Systems Biology Ontology Assignment of a state or a value to a state variable, characteristic or property, of a biological entity. For instance assignment of the state "phosphorylated" to a phosphorylation site, or the state "open" to a channel pore. SBO:0000375 SBO:0000465 spatial measure Systems Biology Ontology The measurable dimensions of an object which are minimally required to define the space that an object occupies. should correspond to spatial dimension in OPB (child of physical dimension) SBO:0000002 SBO:0000466 length Systems Biology Ontology The length of an object is the longest measurable distance between its extremities. SBO:0000465 SBO:0000467 area Systems Biology Ontology The area of an object is a quantity expressing its two-dimensional size, usually part or all of its surface. SBO:0000465 SBO:0000468 volume Systems Biology Ontology A quantity representing the three-dimensional space occupied by all or part of an object. SBO:0000465 SBO:0000469 containment Systems Biology Ontology An entity that is a subset of another entity or object. inclusion SBO:0000413 SBO:0000470 mass fraction Systems Biology Ontology For a given substance, A, its mass fraction (x A) is defined as the ratio of its mass (m A) to the total mass (m total) in which it is present, where the sum of all mass fractions is equal to 1. This provides a means to express concentration in a dimensionless size. http://en.wikipedia.org/wiki/Mass_fraction_(chemistry) SBO:0000540 SBO:0000471 molal concentration of an entity Systems Biology Ontology Molality denotes the number of moles of solute per kilogram of solvent (not solution). The term molal solution is used as a shorthand for a "one molal solution", i.e. a solution which contains one mole of the solute per kilogram of the solvent. The SI unit for molality is mol/kg. http://en.wikipedia.org/wiki/Molality#Molality SBO:0000196 SBO:0000472 molar concentration of an entity Systems Biology Ontology Molarity, or molar concentration, denotes the number of moles of a given substance per litre of solution. The unit of measure of molarity is mol/L, molar, or the capital letter M as an abbreviated form. http://en.wikipedia.org/wiki/Molarity SBO:0000196 SBO:0000473 denotement Systems Biology Ontology Term to signify where a material or conceptual entity is represented or denoted by a symbol or by some other abbreviated form. created for SBGN purposes, at the suggestion of NLN, to represent the SBGN glyph 'tag' ( see SBGN specification 2.3.9 Glyph: Tag) SBO:0000552 SBO:0000474 convenience function Systems Biology Ontology Mathematical function commonly used in biological modeling, which enable simplification of more complex expressions SBO:0000064 SBO:0000475 periodic forcing function Systems Biology Ontology Function that enables the modeling of cyclic inputs with on and off phases, such as the light and dark phases in circadian rhythm. It includes parameters for the 'on' period (Tp), the cycle period (Tc), and the time taken to move or 'ramp' between 'on' and 'off' stages (Tw). Theta0 and Theta1 represent the minimal offset and maximal values of 'on' stage, respectively. Small values of Tw result in step-like changes. Phi is the time of the phase shift offset. In the case of light forcing, Tp represents 'light' period, Tc the cycle period, and Tw the 'twilight' timescale. Theta0 is the light value at the off state, and Theta1 the additional value at the on phase. input signal step function Modified bvars to refer to more specific terms as requested [SF bug #3477686]. Request submitted by Akman et al., "Working Title: SBML functions for periodic light forcing in models of circadian clocks" - function recoded by LE $\mathrm{time}\mathrm{Theta0}\mathrm{Theta1}\mathrm{Phi}\mathrm{Tp}\mathrm{Tc}\mathrm{Tw}\mapsto \mathrm{Theta0}+0.5\mathrm{Theta1}(1+\tanh \left(\frac{\mathrm{time}+\mathrm{Phi}-\mathrm{Tc}\lfloor \frac{\mathrm{time}+\mathrm{Phi}}{\mathrm{Tc}}\rfloor }{\mathrm{Tw}}\right)-1+\tanh \left(\frac{\mathrm{time}+\mathrm{Phi}-\mathrm{Tc}\lfloor \frac{\mathrm{time}+\mathrm{Phi}}{\mathrm{Tc}}\rfloor -\mathrm{Tp}}{\mathrm{Tw}}\right)+1+\tanh \left(\frac{\mathrm{time}+\mathrm{Phi}-\mathrm{Tc}\lfloor \frac{\mathrm{time}+\mathrm{Phi}}{\mathrm{Tc}}\rfloor -\mathrm{Tc}}{\mathrm{Tw}}\right))$ SBO:0000474 SBO:0000476 period Systems Biology Ontology The period is the duration of one cycle in a repeating event. [wikipedia] SBO:0000347 SBO:0000477 phase shift Systems Biology Ontology The measurable amount of time by which a periodic or cyclic is shifted or offset from defined reference point. temporal offset SBO:0000346 SBO:0000478 powered product of Michaelis constant Systems Biology Ontology The product of the Michaelis constants, to the power of their respective stoichiometric coefficients, for either substrates or products. $\mathrm{Km}xn\mapsto \prod_{i=1}^x \mathrm{Km}_i^{n_i}$ SBO:0000193 SBO:0000479 powered product of substrate Michaelis constants Systems Biology Ontology The product of the substrate Michaelis constants, to the power of their respective stoichiometric coefficients. $\mathrm{Kms}xn\mapsto \prod_{i=1}^x \mathrm{Kms}_i^{n_i}$ SBO:0000478 SBO:0000480 powered product of product Michaelis constants Systems Biology Ontology The product of the product Michaelis constants, to the power of their respective stoichiometric coefficients. $\mathrm{Km}xn\mapsto \prod_{i=1}^x \mathrm{Km}_i^{n_i}$ SBO:0000478 SBO:0000481 stoichiometric coefficient Systems Biology Ontology The stoichiometric coefficient represents the degree to which a chemical species participates in a reaction. It corresponds to the number of molecules of a reactant that are consumed or produced with each occurrence of a reaction event. adapted from wikipedia [http://en.wikipedia.org/wiki/Stoichiometry] SBO:0000380 SBO:0000482 geometric mean rate constant Systems Biology Ontology The geometric mean turnover rate of an enzyme in either forward or backward direction for a reaction, measured per second. Liebermeister W. and Klipp E. (2006), Bringing metabolic networks to life: convenience rate law and thermodynamic constraints, Theoretical Biology and Medical Modelling 3:41. $kn\mapsto \sqrt[n]{\prod_{i=1}^n k_i}$ SBO:0000009 SBO:0000483 forward geometric mean rate constant Systems Biology Ontology The geometric mean turnover rate of an enzyme in the forward direction for a reaction, measured per second. 1 Liebermeister W. and Klipp E. (2006), Bringing metabolic networks to life: convenience rate law and thermodynamic constraints, Theoretical Biology and Medical Modelling 3:41. $\mathrm{kf}n\mapsto \sqrt[n]{\prod_{i=1}^n \mathrm{kf}_i}$ SBO:0000482 SBO:0000484 reverse geometric mean rate constant Systems Biology Ontology The geometric mean turnover rate of an enzyme in the reverse direction for a reaction, measured per second. 1 Liebermeister W. and Klipp E. (2006), Bringing metabolic networks to life: convenience rate law and thermodynamic constraints, Theoretical Biology and Medical Modelling 3:41. $\mathrm{kr}n\mapsto \sqrt[n]{\prod_{i=1}^n \mathrm{kr}_i}$ SBO:0000482 SBO:0000485 basal rate constant Systems Biology Ontology The minimal velocity observed under defined conditions, which may or may not include the presence of an effector. For example in an inhibitory system, this would be the residual velocity observed under full inhibition. In non-essential activation, this would be the velocity in the absence of any activator. SBO:0000046 SBO:0000486 relative basal rate constant Systems Biology Ontology The ratio of the basal activity to the maximal velocity of a reaction. The values range between 0 and 1. $b\mathrm{vmax}\mapsto \frac{b}{\mathrm{vmax}}$ SBO:0000381 SBO:0000487 relative activity function Systems Biology Ontology Function which ranges from 0 to 1, to describe the relative activation or inhibition of a reaction or process, actual or conceptual. SBO:0000474 SBO:0000488 relative activation function Systems Biology Ontology Function which ranges from 0 to 1, to describe the relative activation of a reaction or process, actual or conceptual. SBO:0000487 SBO:0000489 relative inhibition function Systems Biology Ontology Function which ranges from 0 to 1, to describe the relative inhibition of a reaction or process, actual or conceptual. SBO:0000487 SBO:0000490 number of products Systems Biology Ontology Number of molecules which are generated by an enzyme. SBO:0000188 SBO:0000491 diffusion coefficient Systems Biology Ontology A proportionality constant representing the amount of substance diffusing across a unit area through a unit concentration gradient in unit time. The higher the diffusion coefficient (of one substance with respect to another), the faster they diffuse into each other. This coefficient has an SI unit of m²/s (length²/time). diffusivity see also: http://goldbook.iupac.org/D01719.html http://en.wikipedia.org/wiki/Mass_diffusivity SBO:0000009 SBO:0000492 amplitude Systems Biology Ontology Amplitude is the magnitude of change in the oscillating variable, with each oscillation, within an oscillating system. http://en.wikipedia.org/wiki/Amplitude SBO:0000002 SBO:0000493 functional domain Systems Biology Ontology A spatial region of an entity that confers a function SBO:0000241 SBO:0000494 binding site Systems Biology Ontology A specific domain of a spatio-temporal entity to which another spatio-temporal entity is able to bind, forming chemical bonds. http://en.wikipedia.org/wiki/Binding_site SBO:0000493 SBO:0000495 catalytic site Systems Biology Ontology A catalytic site is the region which confers specificity of a substrate for the binding entity, and where specific reactions take place in the conversion of the substrate to the product. SBO:0000493 SBO:0000496 transmembrane domain Systems Biology Ontology A transmembrane domain is any three-dimensional protein structure which is thermodynamically stable in a membrane. This may be a single alpha helix, a stable complex of several transmembrane alpha helices, a transmembrane beta barrel, a beta-helix of gramicidin A, or any other structure. http://en.wikipedia.org/wiki/Transmembrane_domain SBO:0000493 SBO:0000497 ternary switch Systems Biology Ontology A parameter that has three discrete values which may be alternated between. SBO:0000389 SBO:0000498 relative activity Systems Biology Ontology Value which ranges from 0 to 1, to describe the relative activity of a process or reaction. SBO:0000381 SBO:0000499 genetic interaction Systems Biology Ontology A phenomenon whereby an observed phenotype, qualitative or quantative, is not explainable by the simple additive effects of the individual gene pertubations alone. Genetic interaction between perturbed genes is usually expected to generate a 'defective' phenotype. The level of defectiveness is often used to sub-classify this phenomenon. 1 http://en.wikipedia.org/wiki/Genetic_interaction SBO:0000231 SBO:0000500 genetic suppression Systems Biology Ontology Genetic suppression is said to have occurred when the phenotypic effect of an initial mutation in a gene is less severe, or entirely negated, by a subsequent mutation. SBO:0000343 SBO:0000501 genetic enhancement Systems Biology Ontology Genetic enhancement is said to have occurred when the phenotypic effect of an initial mutation in a gene is made increasingly severe by a subsequent mutation. SBO:0000343 SBO:0000502 synthetic lethality Systems Biology Ontology Synthetic lethality is said to have occurred where gene mutations, each of which map to a separate locus, fail to complement in an offspring to correct a phenotype, as would be expected. SBO:0000343 SBO:0000503 number of entity pool constituents Systems Biology Ontology The numerical quantification of an entity pool. This may be expressed as, for example, the number of molecules or the number of moles of identical entities of which an specific entity pool is comprised. SBO:0000361 SBO:0000504 mass of an entity pool Systems Biology Ontology The mass that comprises an entity pool. SBO:0000361 SBO:0000505 concentration of enzyme Systems Biology Ontology Amount of enzyme present per unit of volume. The participant role 'enzymatic catalyst' is defined in SBO:0000460. SBO:0000518 SBO:0000506 mass of enzyme Systems Biology Ontology Amount, expressed as a mass, of an enzyme. The participant role 'enzymatic catalyst' is defined in SBO:0000460. SBO:0000504 SBO:0000507 number of an enzyme Systems Biology Ontology Amount, expressed as a number, of a specific enzyme comprising an entity pool. This may be expressed, for example, as the number of molecules, or the number of moles. The participant role 'enzymatic catalyst' is defined in SBO:0000460. SBO:0000517 SBO:0000508 number of a reactant Systems Biology Ontology The amount, expressed as a number, of a specific reactant comprising an entity pool. This may be expressed, for example, as the number of molecules, or the number of moles. The participant role 'reactant' is defined in SBO:0000010. SBO:0000503 SBO:0000509 concentration of reactant Systems Biology Ontology The amount of a specific entity pool reactant present per unit of volume. The participant role 'reactant' is defined in SBO:0000010. SBO:0000196 SBO:0000510 mass of reactant Systems Biology Ontology The amount, expressed as a mass, of a specific reactant entity pool. The participant role 'reactant' is defined in SBO:0000010. SBO:0000504 SBO:0000511 number of a product Systems Biology Ontology The amount, expressed as a number, of a specific product comprising an entity pool. This may be expressed, for example, as the number of molecules, or the number of moles. The participant role 'product' is defined in SBO:0000011. SBO:0000503 SBO:0000512 concentration of product Systems Biology Ontology The amount of a specific entity pool product present per unit of volume. The participant role 'product' is defined in SBO:0000011. SBO:0000196 SBO:0000513 mass of product Systems Biology Ontology The amount, expressed as a mass, of a specific product entity pool. The participant role 'product' is defined in SBO:0000011. SBO:0000504 SBO:0000514 number of a substrate Systems Biology Ontology The amount, expressed as a number, of a specific substrate comprising an entity pool. This may be expressed, for example, as the number of molecules, or the number of moles. The participant role 'substrate' is defined in SBO:0000015. SBO:0000508 SBO:0000515 concentration of substrate Systems Biology Ontology The amount of a specific entity pool substrate present per unit of volume. The participant role 'substrate' is defined in SBO:0000015. SBO:0000509 SBO:0000516 mass of substrate Systems Biology Ontology The amount, expressed as a mass, of a specific substrate entity pool. The participant role 'substrate' is defined in SBO:0000015. SBO:0000510 SBO:0000517 number of a modifier Systems Biology Ontology The amount, expressed as a number, of a specific modifier comprising an entity pool. This may be expressed, for example, as the number of molecules, or the number of moles. The participant role 'modifier' is defined in SBO:0000019. SBO:0000503 SBO:0000518 concentration of modifier Systems Biology Ontology The amount of a specific modifier entity pool present per unit of volume. The participant role 'modifier' is defined in SBO:0000019. SBO:0000196 SBO:0000519 mass of modifier Systems Biology Ontology The amount, expressed as a mass, of a specific modifier entity pool. The participant role 'modifier' is defined in SBO:0000019. SBO:0000504 SBO:0000520 number of an inhibitor Systems Biology Ontology The amount, expressed as a number, of a specific inhibitor comprising an entity pool. This may be expressed, for example, as the number of molecules, or the number of moles. The participant role 'inhibitor' is defined in SBO:0000020. SBO:0000517 SBO:0000521 concentration of inhibitor Systems Biology Ontology The amount of a specific inhibitor entity pool present per unit of volume. The participant role 'inhibitor' is defined in SBO:0000020. SBO:0000518 SBO:0000522 mass of inhibitor Systems Biology Ontology The amount, expressed as a mass, of a specific inhibitor entity pool. The participant role 'inhibitor' is defined in SBO:0000020. SBO:0000519 SBO:0000523 number of an activator Systems Biology Ontology The amount, expressed as a number, of a specific activator comprising an entity pool. This may be expressed, for example, as the number of molecules, or the number of moles. The participant role 'activator' is defined in SBO:0000459. SBO:0000517 SBO:0000524 concentration of activator Systems Biology Ontology The amount of a specific activator entity pool present per unit of volume. The participant role 'activator' is defined in SBO:0000459. SBO:0000518 SBO:0000525 mass of activator Systems Biology Ontology The amount, expressed as a mass, of a specific activator entity pool. The participant role 'activator' is defined in SBO:0000459. SBO:0000519 SBO:0000526 protein complex formation Systems Biology Ontology The process by which two or more proteins interact non-covalently to form a protein complex (SBO:0000297). see also GO:0006461 (protein complex assembly) SBO:0000344 SBO:0000527 modular rate law Systems Biology Ontology Modular rate laws are a set of rate laws that provide a means to parameterise a system in a manner that is a compromise between mathematical abstraction and biochemical detail. They share the same common form: v = u f (T/(D + Dreg)) The individual numerator and denominator terms can substituted with alternative forms, depending on reaction details and model formulation, to generate specific modular rate laws. The terms represented are; v, reaction rate; u, enzyme amount; T, modular term derived from stoichiometries, metabolite concentrations and reactant constants; D, modular term for polynomial of scaled concentrations; Dreg, competitive regulation binding states term; f, modular term for regulation factor. under review: Liebermeister, Uhlendorf and Klipp (2010), "Modular rate laws for enzymatic reactions: thermodynamics, elasticities, and implementation." journal, xyz:abc-def). SBO:0000001 SBO:0000528 common modular rate law Systems Biology Ontology The common modular rate law is a generalised form of reversible Michaelis Menten kinetics, using a denominator where each binding state of the enzyme is represented. It is assumed that substrates and products bind independently and randomly, and that substrates and products cannot be bound at the same time. under review: Liebermeister, Uhlendorf and Klipp (2010), "Modular rate laws for enzymatic reactions: thermodynamics, elasticities, and implementation." journal, xyz:abc-def). SBO:0000527 SBO:0000529 direct binding modular rate law Systems Biology Ontology The direct binding modular rate law makes the assumption that both substrates and products bind simultaneously and in a single step, hence the total binding states possible enumerate to 3; nothing bound, substrates bound, and products bound. Substrates and products cannot be bound at the same time. under review: Liebermeister, Uhlendorf and Klipp (2010), "Modular rate laws for enzymatic reactions: thermodynamics, elasticities, and implementation." journal, xyz:abc-def). SBO:0000527 SBO:0000530 simultaneous binding modular rate law Systems Biology Ontology The simultaneous binding modular rate law makes the assumption that substrates and products can be bound simultaneously, and in any combination. under review: Liebermeister, Uhlendorf and Klipp (2010), "Modular rate laws for enzymatic reactions: thermodynamics, elasticities, and implementation." journal, xyz:abc-def). SBO:0000527 SBO:0000531 power-law modular rate law Systems Biology Ontology For the power-law rate law, the denominator is set to be a constant, and the rate law does not saturate. under review: Liebermeister, Uhlendorf and Klipp (2010), "Modular rate laws for enzymatic reactions: thermodynamics, elasticities, and implementation." journal, xyz:abc-def). SBO:0000527 SBO:0000532 force-dependent modular rate law Systems Biology Ontology Modular rate law where the D term is given by the square root of the product of terms (c/KM)^m where c, KM, and m denote the concentrations, Michaelis constants, and molecularities, respectively, and the product is taken over all reactants and products involved in the reaction. under review: Liebermeister, Uhlendorf and Klipp (2010), "Modular rate laws for enzymatic reactions: thermodynamics, elasticities, and implementation." journal, xyz:abc-def). SBO:0000527 SBO:0000533 specific activator Systems Biology Ontology An essential activator that affects the apparent value of the specificity constant. Mechanistically, the activator would need to be bound before reactant and product binding can take place. see also: http://www.chem.qmul.ac.uk/iubmb/kinetics/ek7.html#p7 SBO:0000461 SBO:0000534 catalytic activator Systems Biology Ontology An essential activator that affects the apparent value of the catalytic constant. see also: http://www.chem.qmul.ac.uk/iubmb/kinetics/ek7.html#p7 SBO:0000461 SBO:0000535 binding activator Systems Biology Ontology An essential activator that affects the apparent value of the Michaelis constant(s). see also: http://www.chem.qmul.ac.uk/iubmb/kinetics/ek7.html#p7 SBO:0000461 SBO:0000536 partial inhibitor Systems Biology Ontology Substance that, when bound, decreases enzymatic activity to a lower, nonzero value, without itself being consumed or transformed by the reaction, and without sterically hindering the interaction between reactants. The enzyme-inhibitor complex does retain some basal level of activity. see also: http://www.chem.qmul.ac.uk/iubmb/kinetics/ek7.html#p7 SBO:0000207 SBO:0000537 complete inhibitor Systems Biology Ontology Substance that, when bound, completely negates enzymatic activity, without itself being consumed or transformed by the reaction, and without sterically hindering the interaction between reactants. The inhibitor binds to all enzyme species independently and with the same affinity, completely inhibiting any enzymatic activity. see also: http://www.chem.qmul.ac.uk/iubmb/kinetics/ek7.html#p7 SBO:0000207 SBO:0000538 ionic permeability Systems Biology Ontology A parameter that represents the permeability of an ion channel with respect to a particular ion. membrane permeability SBO:0000002 SBO:0000539 probabilistic parameter Systems Biology Ontology A quantitative parameter that represents a probability value, assigned to a specific event. term request by Benedetta Baldi, see SF#3132390 SBO:0000002 SBO:0000540 fraction of an entity pool Systems Biology Ontology A ratio that represents the quantity of a defined constituent entity over the total number of all constituent entities present. see also http://goldbook.iupac.org/A00296.html created in response to SourceForge term request [SF req #3154729] SBO:0000360 SBO:0000541 mole fraction Systems Biology Ontology The number of moles of a constituent entity, divided by the total number of all constituent entities present in a system. see also http://en.wikipedia.org/wiki/Mole_fraction; created in response to SourceForge term request [SF req #3154729] SBO:0000540 SBO:0000542 basic reproductive ratio Systems Biology Ontology An epidemiological term representing the mean number of secondary cases which result from a single infection, where the population under consideration has no immunity, and no intervention is performed. basic reproduction number basic reproductive rate R0 see also http://en.wikipedia.org/wiki/Basic_reproduction_number; created in response to SourceForge term request [SF req #3154757] SBO:0000002 SBO:0000543 protein aggregate Systems Biology Ontology A nonspecific coalescence of misfolded proteins which may or may not form a precipitate, depending upon particle size. in response to SourceForge term request [SF req #3160919] SBO:0000296 SBO:0000544 metadata representation Systems Biology Ontology Supplementary information relating to a primary item of data, traditionally termed 'data about data'. It can describe, for example, the location or type of the data, or its relationship to other data. SBO:0000000 SBO:0000545 systems description parameter Systems Biology Ontology A value, numerical or symbolic, that defines certain characteristics of systems or system functions, or is necessary in their derivation. Modified as part of the ontology refactoring' process [SF bug #3172586]. SBO:0000000 SBO:0000546 qualitative systems description parameter Systems Biology Ontology A non-numerical value that defines certain characteristics of systems or system functions. Modified as part of ontology 'refactoring' process [SF bug #3172586]. SBO:0000545 SBO:0000547 boolean logical framework Systems Biology Ontology Equationally defined algebraic framework usually interpreted as a two-valued logic using the basic Boolean operations (conjunction, disjunction and negation), together with the constants '0' and '1' denoting false and true values, respectively. Definition contributed by Denis Thieffry; refer to [SF req #3125359]; see also [PMID:4588055] SBO:0000234 SBO:0000548 multi-valued logical framework Systems Biology Ontology Extension of the boolean logical framework which associates a defined number of possible integer values (states) with the variables. Definition contributed by Denis Thieffry; refer to [SF req #3125359]; see also [PMID:20824124] SBO:0000547 SBO:0000549 fuzzy logical framework Systems Biology Ontology