Systems Biology Ontology, OWL export generated by SBO Browser (http://www.ebi.ac.uk/sbo/) Generated: 03:11:2021 07:00 28:08:2021 03:13 part of SBO_0000000 Representation of an entity used in a systems biology knowledge reconstruction, such as a model, pathway, network. systems biology representation SBO_0000001 mathematical description that relates quantities of reactants to the reaction velocity. rate law SBO_0000002 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. quantitative systems description parameter SBO_0000003 The function of a physical or conceptual entity, that is its role, in the execution of an event or process. participant role SBO_0000004 Set of assumptions that underlay a mathematical description. modelling framework SBO_0000005 The description of a system in mathematical terms. obsolete mathematical expression SBO_0000006 A numerical value that represents the amount of some entity, process or mathematical function of the system. obsolete parameter SBO_0000007 The 'kind' of entity involved in some process, action or reaction in the system. This may be enzyme, simple chemical, etc.. obsolete participant type SBO_0000008 Basic assumptions that underlie a mathematical model. obsolete modelling framework SBO_0000009 Synonym: reaction rate constant kinetic constant SBO_0000010 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. reactant SBO_0000011 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. product SBO_0000012 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. mass action rate law SBO_0000013 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. catalyst SBO_0000014 A protein that catalyzes a chemical reaction. The word comes from en ("at" or "in") and simo ("leaven" or "yeast"). enzyme SBO_0000015 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. substrate SBO_0000016 Numerical parameter that quantifies the velocity of a chemical reaction involving only one reactant. unimolecular rate constant SBO_0000017 Numerical parameter that quantifies the velocity of a chemical reaction involving two reactants. bimolecular rate constant SBO_0000018 Numerical parameter that quantifies the velocity of a chemical reaction involving three reactants. trimolecular rate constant SBO_0000019 Substance that changes the velocity of a process without itself being consumed or transformed by the reaction. modifier SBO_0000020 Substance that decreases the probability of a chemical reaction without itself being consumed or transformed by the reaction. inhibitor SBO_0000021 Synonym: activator potentiator SBO_0000022 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. forward unimolecular rate constant SBO_0000023 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. forward bimolecular rate constant SBO_0000024 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. forward trimolecular rate constant SBO_0000025 Synonym: turnover number catalytic rate constant SBO_0000026 none new term name SBO_0000027 Synonym: Michaelis-Menten constant Michaelis constant SBO_0000028 Kinetics of enzymes that react only with one substance, their substrate. The enzymes do not catalyse the reactions in both directions. enzymatic rate law for irreversible non-modulated non-interacting unireactant enzymes kcat Et S Ks kcat Et S Ks S SBO_0000029 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. Henri-Michaelis-Menten rate law kcat Et S Ks kcat Et S Ks S SBO_0000030 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. Van Slyke-Cullen rate law kcat Et S Ks kcat Et S Ks S SBO_0000031 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. Briggs-Haldane rate law kcat Et S Km kcat Et S Km S SBO_0000032 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. reverse unimolecular rate constant SBO_0000033 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. reverse bimolecular rate constant SBO_0000034 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. reverse trimolecular rate constant SBO_0000035 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. forward unimolecular rate constant, continuous case SBO_0000036 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. forward bimolecular rate constant, continuous case SBO_0000037 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. forward trimolecular rate constant, continuous case SBO_0000038 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. reverse unimolecular rate constant, continuous case SBO_0000039 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. reverse bimolecular rate constant, continuous case SBO_0000040 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. reverse trimolecular rate constant, continuous case SBO_0000041 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. mass action rate law for irreversible reactions SBO_0000042 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. mass action rate law for reversible reactions SBO_0000043 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. mass action rate law for zeroth order irreversible reactions SBO_0000044 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. mass action rate law for first order irreversible reactions SBO_0000045 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. mass action rate law for second order irreversible reactions SBO_0000046 Numerical parameter that quantifies the velocity of a chemical reaction independant of the reactant quantities. This parameter encompasses all the contributions to the velocity. zeroth order rate constant SBO_0000047 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. mass action rate law for zeroth order irreversible reactions, continuous scheme k k SBO_0000048 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. forward zeroth order rate constant, continuous case SBO_0000049 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. mass action rate law for first order irreversible reactions, continuous scheme k R k R SBO_0000050 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. mass action rate law for second order irreversible reactions, one reactant SBO_0000051 new term name SBO_0000052 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. mass action rate law for second order irreversible reactions, one reactant, continuous scheme k R k R R SBO_0000053 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. mass action rate law for second order irreversible reactions, two reactants SBO_0000054 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. mass action rate law for second order irreversible reactions, two reactants, continuous scheme k R1 R2 k R1 R2 SBO_0000055 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. mass action rate law for third order irreversible reactions SBO_0000056 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. mass action rate law for third order irreversible reactions, one reactant SBO_0000057 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. mass action rate law for third order irreversible reactions, one reactant, continuous scheme k R k R R R SBO_0000058 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. mass action rate law for third order irreversible reactions, two reactants SBO_0000059 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. mass action rate law for third order irreversible reactions, two reactants, continuous scheme k R1 R2 k R1 R1 R2 SBO_0000060 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. mass action rate law for third order irreversible reactions, three reactants SBO_0000061 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. mass action rate law for third order irreversible reactions, three reactants, continuous scheme k R1 R2 R3 k R1 R2 R3 SBO_0000062 Modelling approach where the quantities of participants are considered continuous, and represented by real values. The associated simulation methods make use of differential equations. continuous framework SBO_0000063 Modelling approach where the quantities of participants are considered discrete, and represented by integer values. The associated simulation methods can be deterministic or stochastic. discrete framework SBO_0000064 Formal representation of a calculus linking parameters and variables of a model. mathematical expression SBO_0000065 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. forward zeroth order rate constant, discrete case SBO_0000066 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. forward unimolecular rate constant, discrete case SBO_0000067 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. forward bimolecular rate constant, discrete case SBO_0000068 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. forward trimolecular rate constant, discrete case SBO_0000069 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. mass action rate law for zeroth order reversible reactions SBO_0000070 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. mass action rate law for zeroth order forward, first order reverse, reversible reactions, continuous scheme kf kr P kf kr P SBO_0000071 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. mass action rate law for zeroth order forward, second order reverse, reversible reactions, continuous scheme SBO_0000072 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. mass action rate law for zeroth order forward, second order reverse, reversible reactions, one product, continuous scheme kf kr P kf kr P P SBO_0000073 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. mass action rate law for zeroth order forward, second order reverse, reversible reactions, two products, continuous scheme kf kr P1 P2 kf kr P1 P2 SBO_0000074 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. mass action rate law for zeroth order forward, third order reverse, reversible reactions, continuous scheme SBO_0000075 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. mass action rate law for zeroth order forward, third order reverse, reversible reactions, one product, continuous scheme kf kr P kf kr P P P SBO_0000076 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. mass action rate law for zeroth order forward, third order reverse, reversible reactions, two products, continuous scheme kf kr P1 P2 kf kr P1 P2 P2 SBO_0000077 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. mass action rate law for zeroth order forward, third order reverse, reversible reactions, three products, continuous scheme kf kr P1 P2 P3 kf kr P1 P2 P3 SBO_0000078 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. mass action rate law for first order reversible reactions SBO_0000079 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. mass action rate law for first order forward, zeroth order reverse, reversible reactions, continuous scheme kf kr R kf R kr SBO_0000080 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. mass action rate law for first order forward, first order reverse, reversible reactions, continuous scheme kf kr R P kf R kr P SBO_0000081 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. mass action rate law for first order forward, second order reverse, reversible reactions SBO_0000082 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. mass action rate law for first order forward, second order reverse, reversible reactions, one product, continuous scheme kf kr R P kf R kr P P SBO_0000083 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. mass action rate law for first order forward, second order reverse, reversible reactions, two products, continuous scheme kf kr R P1 P2 kf R kr P1 P2 SBO_0000084 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. mass action rate law for first order forward, third order reverse, reversible reactions SBO_0000085 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. mass action rate law for first order forward, third order reverse, reversible reactions, one product, continuous scheme kf kr R P kf R kr P P P SBO_0000086 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. mass action rate law for first order forward, third order reverse, reversible reactions, two products, continuous scheme kf kr R P1 P2 kf R kr P1 P1 P2 SBO_0000087 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. mass action rate law for first order forward, third order reverse, reversible reactions, three products, continuous scheme kf kr R P1 P2 P3 kf R kr P1 P2 P3 SBO_0000088 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. mass action rate law for second order reversible reactions SBO_0000089 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. mass action rate law for second order forward, reversible reactions, one reactant SBO_0000090 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. mass action rate law for second order forward, zeroth order reverse, reversible reactions, one reactant, continuous scheme kf kr R kf R R kr SBO_0000091 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. mass action rate law for second order forward, first order reverse, reversible reactions, one reactant, continuous scheme kf kr R P kf R R kr P SBO_0000092 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. mass action rate law for second order forward, second order reverse, reversible reactions, one reactant SBO_0000093 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. mass action rate law for second order forward, second order reverse, reversible reactions, one reactant, one product, continuous scheme kf kr R P kf R R kr P P SBO_0000094 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. mass action rate law for second order forward, second order reverse, reversible reactions, two products, continuous scheme kf kr R P1 P2 kf R R kr P1 P2 SBO_0000095 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. mass action rate law for second order forward, third order reverse, reversible reactions, one reactant SBO_0000096 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. mass action rate law for second order forward, third order reverse, reversible reactions, one reactant, one product, continuous scheme kf kr R P kf R R kr P P P SBO_0000097 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. mass action rate law for second order forward, third order reverse, reversible reactions, one reactant, two products, continuous scheme kf kr R P1 P2 kf R R kr P1 P1 P2 SBO_0000098 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. mass action rate law for second order forward, third order reverse, reversible reactions, one reactant, three products, continuous scheme kf kr R P1 P2 P3 kf R R kr P1 P2 P3 SBO_0000099 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. mass action rate law for second order forward, reversible reactions, two reactants SBO_0000100 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. mass action rate law for second order forward, zeroth order reverse, reversible reactions, two reactants, continuous scheme kf kr R1 R2 kf R1 R2 kr SBO_0000101 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. mass action rate law for second order forward, first order reverse, reversible reactions, two reactants, continuous scheme kf kr R1 R2 P kf R1 R2 kr P SBO_0000102 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. mass action rate law for second order forward, second order reverse, reversible reactions, two reactants SBO_0000103 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. mass action rate law for second order forward, second order reverse, reversible reactions, two reactants, one product, continuous scheme kf kr R1 R2 P kf R1 R2 kr P P SBO_0000104 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. mass action rate law for second order forward, second order reverse, reversible reactions, two reactants, two products, continuous scheme kf kr R1 R2 P1 P2 kf R1 R2 kr P1 P2 SBO_0000105 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. mass action rate law for second order forward, third order reverse, reversible reactions, two reactants SBO_0000106 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. mass action rate law for second order forward, third order reverse, reversible reactions, two reactants, one product, continuous scheme kf kr R1 R2 P kf R1 R2 kr P P P SBO_0000107 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. mass action rate law for second order forward, third order reverse, reversible reactions, two reactants, two products, continuous scheme kf kr R1 R2 P1 P2 kf R1 R2 kr P1 P1 P2 SBO_0000108 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. mass action rate law for second order forward, third order reverse, reversible reactions, two reactants, three products, continuous scheme kf kr R1 R2 P1 P2 P3 kf R1 R2 kr P1 P2 P3 SBO_0000109 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. mass action rate law for third order reversible reactions SBO_0000110 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. mass action rate law for third order forward, reversible reactions, two reactants SBO_0000111 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. mass action rate law for third order forward, zeroth order reverse, reversible reactions, two reactants, continuous scheme kf kr R1 R2 kf R1 R1 R2 kr SBO_0000112 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. mass action rate law for third order forward, first order reverse, reversible reactions, two reactants, continuous scheme kf kr R1 R2 P kf R1 R1 R2 kr P SBO_0000113 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. mass action rate law for third order forward, second order reverse, reversible reactions, two reactants SBO_0000114 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. mass action rate law for third order forward, second order reverse, reversible reactions, two reactants, one product, continuous scheme kf kr R1 R2 P kf R1 R1 R2 kr P P SBO_0000115 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. mass action rate law for third order forward, second order reverse, reversible reactions, two reactants, two products, continuous scheme kf kr R1 R2 P1 P2 kf R1 R1 R2 kr P1 P2 SBO_0000116 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. mass action rate law for third order forward, third order reverse, reversible reactions, two reactants SBO_0000117 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. mass action rate law for third order forward, third order reverse, reversible reactions, two reactants, one product, continuous scheme kf kr R1 R2 P kf R1 R1 R2 kr P P P SBO_0000118 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. mass action rate law for third order forward, third order reverse, reversible reactions, two reactants, two products, continuous scheme kf kr R1 R2 P1 P2 kf R1 R1 R2 kr P1 P1 P2 SBO_0000119 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. mass action rate law for third order forward, third order reverse, reversible reactions, two reactants, three products, continuous scheme kf kr R1 R2 P1 P2 P3 kf R1 R1 R2 kr P1 P2 P3 SBO_0000120 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. mass action rate law for third order forward, reversible reactions, three reactants SBO_0000121 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. mass action rate law for third order forward, zeroth order reverse, reversible reactions, three reactants, continuous scheme kf kr R1 R2 R3 kf R1 R2 R3 kr SBO_0000122 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. mass action rate law for third order forward, first order reverse, reversible reactions, three reactants, continuous scheme kf kr R1 R2 R3 P kf R1 R2 R3 kr P SBO_0000123 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. mass action rate law for third order forward, second order reverse, reversible reactions, three reactants SBO_0000124 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. mass action rate law for third order forward, second order reverse, reversible reactions, three reactants, one product, continuous scheme kf kr R1 R2 R3 P kf R1 R2 R3 kr P P SBO_0000125 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. mass action rate law for third order forward, second order reverse, reversible reactions, three reactants, two products, continuous scheme kf kr R1 R2 R3 P1 P2 kf R1 R2 R3 kr P1 P2 SBO_0000126 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. mass action rate law for third order forward, third order reverse, reversible reactions, three reactants SBO_0000127 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. mass action rate law for third order forward, third order reverse, reversible reactions, three reactants, one product, continuous scheme kf kr R1 R2 R3 P kf R1 R2 R3 kr P P P SBO_0000128 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. mass action rate law for third order forward, third order reverse, reversible reactions, three reactants, two products, continuous scheme kf kr R1 R2 R3 P1 P2 kf R1 R2 R3 kr P1 P1 P2 SBO_0000129 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. mass action rate law for third order forward, third order reverse, reversible reactions, three reactants, three products, continuous scheme kf kr R1 R2 R3 P1 P2 P3 kf R1 R2 R3 kr P1 P2 P3 SBO_0000130 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. mass action rate law for third order forward, reversible reactions, one reactant SBO_0000131 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. mass action rate law for third order forward, zeroth order reverse, reversible reactions, one reactant, continuous scheme kf kr R kf R R R kr SBO_0000132 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. mass action rate law for third order forward, first order reverse, reversible reactions, one reactant, continuous scheme kf kr R P kf R R R kr P SBO_0000133 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. mass action rate law for third order forward, second order reverse, reversible reactions, one reactant SBO_0000134 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. mass action rate law for third order forward, second order reverse, reversible reactions, one reactant, one product, continuous scheme kf kr R P kf R R R kr P P SBO_0000135 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. mass action rate law for third order forward, second order reverse, reversible reactions, one reactant, two products, continuous scheme kf kr R P1 P2 kf R R R kr P1 P2 SBO_0000136 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. mass action rate law for third order forward, third order reverse, reversible reactions, one reactant SBO_0000137 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. mass action rate law for third order forward, third order reverse, reversible reactions, one reactant, one product, continuous scheme kf kr R P kf R R R kr P P P SBO_0000138 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. mass action rate law for third order forward, third order reverse, reversible reactions, one reactant, two products, continuous scheme kf kr R P1 P2 kf R R R kr P1 P1 P2 SBO_0000139 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. mass action rate law for third order forward, third order reverse, reversible reactions, one reactant, three products, continuous scheme kf kr R P1 P2 P3 kf R R R kr P1 P2 P3 SBO_0000140 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. mass action rate law for zeroth order irreversible reactions, discrete scheme c c SBO_0000141 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. mass action rate law for first order irreversible reactions, discrete scheme c R c R SBO_0000142 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. mass action rate law for second order irreversible reactions, one reactant, discrete scheme c R c R R 1 2 SBO_0000143 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. mass action rate law for second order irreversible reactions, two reactants, discrete scheme c R1 R2 c R1 R2 SBO_0000144 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. mass action rate law for third order irreversible reactions, one reactant, discrete scheme c R c R R 1 R 2 6 SBO_0000145 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. mass action rate law for third order irreversible reactions, two reactants, discrete scheme c R1 R2 c R1 R2 R2 1 2 SBO_0000146 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. mass action rate law for third order irreversible reactions, three reactants, discrete scheme c R1 R2 R3 c R1 R2 R3 SBO_0000147 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). thermodynamic temperature SBO_0000148 Quantity resulting from the difference between two thermodynamic temperatures. A difference or interval of temperature may be expressed in Kelvins or in degrees Celsius. temperature difference SBO_0000149 Number of molecules which are acted upon by an enzyme. number of substrates SBO_0000150 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. enzymatic rate law for irreversible non-modulated non-interacting reactant enzymes Et kp n S K Et kp i 1 n S i K i i 1 n 1 S i K i SBO_0000151 Kinetics of enzymes that react with two substances, their substrates, that bind independently. The enzymes do not catalyse the reactions in both directions. enzymatic rate law for irreversible non-modulated non-interacting bireactant enzymes Et kp S1 S2 K1 K2 Et kp S1 K1 S2 K2 1 S1 K1 1 S2 K2 SBO_0000152 Kinetics of enzymes that react with three substances, their substrates, that bind independently. The enzymes do not catalyse the reactions in both directions. enzymatic rate law for irreversible non-modulated non-interacting trireactant enzymes Et kp S1 S2 S3 K1 K2 K3 Et kp S1 K1 S2 K2 S3 K3 1 S1 K1 1 S2 K2 1 S3 K3 SBO_0000153 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. forward rate constant SBO_0000154 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. forward rate constant, continuous case SBO_0000155 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. forward rate constant, discrete case SBO_0000156 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. reverse rate constant SBO_0000157 Number of different substances consumed by a chemical reaction. number of reactants SBO_0000158 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. order of a reaction with respect to a reactant SBO_0000159 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. non-integral order rate constant SBO_0000160 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. forward non-integral order rate constant SBO_0000161 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. reverse non-integral order rate constant SBO_0000162 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. forward zeroth order rate constant SBO_0000163 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. mass action rate law for irreversible reactions, continuous scheme k n mu R k i 0 n R i mu i SBO_0000164 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. second order irreversible mass action kinetics, continuous scheme k R k i 1 2 R i SBO_0000165 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. third order irreversible mass action kinetics, continuous scheme k R k i 1 3 R i SBO_0000166 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. mass action rate law for irreversible reactions, discrete scheme c n mu R c i 0 n R i R i mu i mu i SBO_0000167 An event involving one or more physical entities that modifies the structure, location or free energy of at least one of the participants. biochemical or transport reaction SBO_0000168 Synonym: regulation control SBO_0000169 Negative modulation of the execution of a process. inhibition SBO_0000170 Positive modulation of the execution of a process. stimulation SBO_0000171 Synonym: trigger necessary stimulation SBO_0000172 Modification of the velocity of a reaction by lowering the energy of the transition state. catalysis SBO_0000173 All the preceding events or participating entities are necessary to perform the control. and SBO_0000174 Any of the preceding events or participating entities are necessary to perform the control. or SBO_0000175 Synonym: exclusive or xor SBO_0000176 An event involving one or more chemical entities that modifies the electrochemical structure of at least one of the participants. biochemical reaction SBO_0000177 Synonym: association non-covalent binding SBO_0000178 Rupture of a covalent bond resulting in the conversion of one physical entity into several physical entities or into a physical entity of a different topological class. cleavage SBO_0000179 Complete disappearance of a physical entity. degradation SBO_0000180 Transformation of a non-covalent complex that results in the formation of several independent biochemical entities dissociation SBO_0000181 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. conformational transition SBO_0000182 Biochemical reaction that results in the modification of some covalent bonds. conversion SBO_0000183 Process through which a DNA sequence is copied to produce a complementary RNA. transcription SBO_0000184 Process in which a polypeptide chain is produced from a messenger RNA. translation SBO_0000185 Movement of a physical entity without modification of the structure of the entity. translocation reaction SBO_0000186 Synonym: Vmax maximal velocity Et kcat Et kcat SBO_0000187 Version of Henri-Michaelis-Menten equation where kp*[E]t is replaced by the maximal velocity, Vmax, reached when all the enzyme is active. Henri-Michaelis-Menten equation, Vmax form Vmax S Ks Vmax S Ks S SBO_0000188 A number of objects of the same type, identical or different, involved in a biochemical event. number of biochemical items SBO_0000189 Number of regions on a reactant to which specific other reactants, in this context collectively called ligands, form a chemical bond. number of binding sites SBO_0000190 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). Hill coefficient SBO_0000191 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. Hill constant SBO_0000192 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). Hill-type rate law, generalised form Vmax R K h n Vmax R h K n R h SBO_0000193 Constant with the dimension of a powered concentration. It is determined at half-saturation, half-activity etc. equilibrium or steady-state constant SBO_0000194 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. pseudo-dissociation constant SBO_0000195 Hill equation rewritten by creating a pseudo-microscopic constant, equal to the Hill constant powered to the opposite of the Hill coefficient. Hill-type rate law, microscopic form Vmax R K h Vmax R h K h R h SBO_0000196 Synonym: [X] concentration of an entity pool SBO_0000197 Concentration of an object divided by the value of another parameter having the dimension of a concentration. specific concentration of an entity SBO_0000198 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. Hill-type rate law, reduced form Vmax R* h Vmax R* h 1 R* h SBO_0000199 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. normalised enzymatic rate law for unireactant enzymes kcat S Ks kcat S Ks S SBO_0000200 Chemical process in which atoms have their oxidation number (oxidation state) changed. redox reaction SBO_0000201 Chemical process during which a molecular entity loses electrons. oxidation SBO_0000202 Chemical process in which a molecular entity gain electrons. reduction SBO_0000203 Reaction in which a reactant gives birth to two products identical to itself. duplication SBO_0000204 Process in which a DNA duplex is transformed into two identical DNA duplexes. DNA replication SBO_0000205 Process that involves the participation of chemical or biological entities and is composed of several elementary steps or reactions. composite biochemical process SBO_0000206 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. competitive inhibitor SBO_0000207 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. non-competitive inhibitor SBO_0000208 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). acid-base reaction SBO_0000209 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. ionisation SBO_0000210 Covalent reaction that results in the addition of a chemical group on a molecule. addition of a chemical group SBO_0000211 Covalent reaction that results in the removal of a chemical group from a molecule. removal of a chemical group SBO_0000212 Addition of a proton (H+) to a chemical entity. protonation SBO_0000213 Removal of a proton (hydrogen ion H+) from a chemical entity. deprotonation SBO_0000214 Addition of a methyl group (-CH3) to a chemical entity. methylation SBO_0000215 Addition of an acetyl group (-COCH3) to a chemical entity. acetylation SBO_0000216 Addition of a phosphate group (-H2PO4) to a chemical entity. phosphorylation SBO_0000217 Addition of a saccharide group to a chemical entity. glycosylation SBO_0000218 Addition of a palmitoyl group (CH3-[CH2]14-CO-) to a chemical entity. palmitoylation SBO_0000219 Addition of a myristoyl (CH3-[CH2]12-CO-) to a chemical entity. myristoylation SBO_0000220 Synonym: sulphation sulfation SBO_0000221 Synonym: isoprenylation prenylation SBO_0000222 Addition of a farnesyl group (CH2-CH=C(CH3)-CH2-CH2-CH=C(CH3)-CH2-CH2-CH=C(CH3)2) to a chemical entity. farnesylation SBO_0000223 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. geranylgeranylation SBO_0000224 Covalent linkage to the protein ubiquitin. ubiquitination SBO_0000225 Time during which some action is awaited. delay SBO_0000226 A quantitative measure of an amount or property of an entity expressed in terms of another dimension, such as unit length, area or volume. density of an entity pool SBO_0000227 The mass of an entity expressed with reference to another dimension, such as unit length, area or volume. mass density of an entity SBO_0000228 Mass of an entity per unit volume. volume density of an entity SBO_0000229 The mass of an entity per unit of surface area. area density of an entity SBO_0000230 Mass of an entity per unit length. linear density of an entity SBO_0000231 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. occurring entity representation SBO_0000232 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. obsolete event SBO_0000233 Addition of an hydroxyl group (-OH) to a chemical entity. hydroxylation SBO_0000234 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. logical framework SBO_0000235 Entity that affects or is affected by an event. participant SBO_0000236 Synonym: new synonym physical entity representation SBO_0000237 Combining the influence of several entities or events in a unique influence. logical combination SBO_0000238 The preceding event or participating entity cannot participate to the control. not SBO_0000239 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. allosteric control SBO_0000240 A real thing that is defined by its physico-chemical structure. material entity SBO_0000241 A real thing, defined by its properties or the actions it performs, rather than it physico-chemical structure. functional entity SBO_0000242 A component that allows another component to pass through itself, possibly connecting different compartments. channel SBO_0000243 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 gene SBO_0000244 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. receptor SBO_0000245 Molecular entity mainly built-up by the repetition of pseudo-identical units. CHEBI:33839 macromolecule SBO_0000246 Macromolecule whose sequence is encoded in the genome of living organisms. information macromolecule SBO_0000247 Simple, non-repetitive chemical entity. simple chemical SBO_0000248 Macromolecule whose sequence is not directly encoded in the genome. chemical macromolecule SBO_0000249 Macromolecule consisting of a large number of monosaccharide residues linked by glycosidic bonds. CHEBI:18154 polysaccharide SBO_0000250 Synonym: RNA ribonucleic acid SBO_0000251 Synonym: DNA deoxyribonucleic acid SBO_0000252 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 polypeptide chain SBO_0000253 Entity composed of several independant components that are not linked by covalent bonds. non-covalent complex SBO_0000254 Measure of the degree to which an object opposes the passage of an electric current. The SI unit of electrical resistance is the ohm. electrical resistance SBO_0000255 Parameter characterising a physical system or the environment, and independent of life's influence. physical characteristic SBO_0000256 Parameter that depends on the biochemical properties of a system. biochemical parameter SBO_0000257 Measure of how easily electricity flows along a certain path through an electrical element. The SI derived unit of conductance is the Siemens. conductance SBO_0000258 Measure of the amount of electric charge stored (or separated) for a given electric potential. The unit of capacitance id the Farad. capacitance SBO_0000259 Synonym: electrical potential difference voltage SBO_0000260 Synonym: simple intersecting linear competitive inhibition of unireactant enzymes enzymatic rate law for simple competitive inhibition of irreversible unireactant enzymes by one inhibitor kcat Et S I Ks Ki kcat Et S Ks 1 I Ki S SBO_0000261 Synonym: Ki inhibitory constant SBO_0000262 Synonym: simple linear uncompetitive inhibition enzymatic rate law for simple uncompetitive inhibition of irreversible unireactant enzymes kcat Et S I Ks Ki kcat Et S S 1 I Ki Ks SBO_0000263 Ratio of an equilibrium constant in a given condition by the same equilibrium constant is not fullfilled. relative equilibrium constant SBO_0000264 Ratio of the dissociation constant of an inhibitor from the complex enzyme-substrate on the dissociation constant of an inhibitor from the free enzyme. relative inhibition constant SBO_0000265 Synonym: simple intersecting linear mixed-type competitive inhibition enzymatic rate law for simple mixed-type inhibition of irreversible unireactant enzymes kcat Et S I Ks Ki a kcat Et S S 1 I a Ki Ks 1 I Ki SBO_0000266 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. enzymatic rate law for simple irreversible non-competitive inhibition of unireactant enzymes kcat Et S I Ks Ki kcat Et S S 1 I Ki Ks 1 I Ki SBO_0000267 Synonym: multiple competitive inhibition by one inhibitor of unireactant enzymes enzymatic rate law for competitive inhibition of irreversible unireactant enzymes by one inhibitor kcat Et S I Ks Ki n kcat Et S S Ks 1 I Ki n SBO_0000268 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. enzymatic rate law SBO_0000269 Kinetics of enzymes that catalyse the transformation of only one substrate. enzymatic rate law for unireactant enzymes SBO_0000270 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. enzymatic rate law for competitive inhibition of irreversible unireactant enzymes by exclusive inhibitors kcat Et S I Ks Ki n kcat Et S Ks 1 i 1 n I i Ki i S SBO_0000271 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. enzymatic rate law for competitive inhibition of irreversible unireactant enzymes by two exclusive inhibitors kcat Et S I1 I2 Ks Ki1 Ki2 kcat Et S Ks 1 I1 Ki1 I2 Ki2 S SBO_0000272 Number of entities that inhibit a reaction. number of inhibitors SBO_0000273 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. enzymatic rate law for competitive inhibition of irreversible unireactant enzymes by non-exclusive non-cooperative inhibitors kcat Et S I Ks Ki n m kcat Et S Ks i 1 n 1 I i Ki i m i S SBO_0000274 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. enzymatic rate law for simple competitive inhibition of irreversible unireactant enzymes by two non-exclusive, non-cooperative inhibitors kcat Et S I1 I2 Ks Ki1 Ki2 kcat Et S Ks 1 I1 Ki1 I2 Ki2 I1 I2 Ki1 Ki2 S SBO_0000275 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. enzymatic rate law for mixed-type inhibition of irreversible enzymes by mutually exclusive inhibitors kcat Et S I Ks Ki a n kcat Et S Ks 1 i 1 n I i Ki i S 1 i 1 n I i a i Ki i SBO_0000276 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. enzymatic rate law for mixed-type inhibition of irreversible unireactant enzymes by two inhibitors kcat Et S I1 I2 Ks Ki1 Ki2 a b kcat Et S S 1 I1 a Ki1 I2 b Ki2 Ks 1 I1 Ki1 I2 Ki2 SBO_0000277 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. enzymatic rate law for non-competitive inhibition of irreversible unireactant enzymes by two exclusively binding inhibitors kcat Et S I1 I2 Ks Ki1 Ki2 kcat Et S S 1 I1 Ki1 I2 Ki2 Ks 1 I1 Ki1 I2 Ki2 SBO_0000278 Synonym: mRNA messenger RNA SBO_0000279 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. pressure SBO_0000280 In biochemistry, a ligand is an effector, a physical entity that binds to a site on a receptor's surface by intermolecular forces. ligand SBO_0000281 Synonym: Keq equilibrium constant SBO_0000282 Synonym: Kd dissociation constant koff Kon koff Kon SBO_0000283 Synonym: Ka acid dissociation constant SBO_0000284 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. transporter SBO_0000285 Material entity whose nature is unknown or irrelevant. material entity of unspecified nature SBO_0000286 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. multimer SBO_0000287 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. EC50 SBO_0000288 Also called half maximal inhibitory concentration, it represents the concentration of an inhibitor substance that is required to suppress 50% of an effect. IC50 SBO_0000289 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. functional compartment SBO_0000290 Specific location of space, that can be bounded or not. A physical compartment can have 1, 2 or 3 dimensions. physical compartment SBO_0000291 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. empty set SBO_0000292 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. spatial continuous framework SBO_0000293 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. non-spatial continuous framework SBO_0000294 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. spatial discrete framework SBO_0000295 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. non-spatial discrete framework SBO_0000296 Non-covalent complex of one or more macromolecules and zero or more simple chemicals. macromolecular complex SBO_0000297 Macromolecular complex containing one or more polypeptide chains possibly associated with simple chemicals. CHEBI:36080 protein complex SBO_0000298 Chemical entity that is engineered by a human-designed process ex-vivo rather than a produced by a living entity. synthetic chemical compound SBO_0000299 Substance produced by metabolism or by a metabolic process. metabolite SBO_0000300 Synonym: Et total concentration of enzyme SBO_0000301 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). total catalytic efficiency Vmax Km Vmax Km SBO_0000302 Constant representing the actual efficiency of an enzyme, taking into account its microscopic catalytic activity and the rates of substrate binding and dissociation. catalytic efficiency kcat Km kcat Km SBO_0000303 Synonym: chemical potential biochemical potential SBO_0000304 Synonym: potential of hydrogen pH SBO_0000305 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-. pOH SBO_0000306 Synonym: dissociation potential pK K K SBO_0000307 Synonym: potential of acid pKa Ka Ka SBO_0000308 Quantitative parameter that characterises a biochemical equilibrium. equilibrium or steady-state characteristic SBO_0000309 Quantitative parameter that characterises a dissociation. dissociation characteristic SBO_0000310 Quantitative parameter that characterises an acid-base reaction. acid dissociation characteristic SBO_0000311 Synonym: Precursor mRNA heterogeneous nuclear RNA SBO_0000312 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. mature messenger RNA SBO_0000313 Synonym: tRNA transfer RNA SBO_0000314 Synonym: rRNA ribosomal RNA SBO_0000315 Synonym: ribonucleic acid enzyme ribozyme SBO_0000316 Synonym: miRNA microRNA SBO_0000317 Synonym: siRNA small interfering RNA SBO_0000318 Synonym: snRNA small nuclear RNA SBO_0000319 Synonym: snoRNA small nucleolar RNA SBO_0000320 Synonym: kcatp product catalytic rate constant SBO_0000321 Synonym: reverse catalytic rate constant substrate catalytic rate constant SBO_0000322 Synonym: Kms Michaelis constant for substrate SBO_0000323 Synonym: Kmp Michaelis constant for product SBO_0000324 Synonym: Vmaxf forward maximal velocity Et kcatp Et kcatp SBO_0000325 Synonym: Vmaxr reverse maximal velocity Et kcats Et kcats SBO_0000326 Kinetics of enzymes that react only with one substance, their substrate, and are not modulated by other compounds. enzymatic rate law for non-modulated unireactant enzymes SBO_0000327 Chemical entity having a net electric charge. non-macromolecular ion SBO_0000328 chemical entity possessing an unpaired electron. non-macromolecular radical SBO_0000329 Synonym: TSS transcription start site SBO_0000330 Removal of a phosphate group (-H2PO4) from a chemical entity. dephosphorylation SBO_0000331 Time interval over which a quantified entity is reduced to half its original value. half-life SBO_0000332 Time taken by a quantity decreasing according to a mono-exponential decay to be divided by two. Sometimes called t1/2. half-life of an exponential decay l 2 l SBO_0000333 Monotonic decrease of a quantity proportionally to its value. monoexponential decay rate law l R R l SBO_0000334 RNA molecule that is not translated into a protein. Sequence Ontology SO:0000655 non-coding RNA SBO_0000335 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). gene coding region SBO_0000336 Entity participating in a physical or functional interaction. interactor SBO_0000337 Synonym: Ka association constant koff Kon kon Koff SBO_0000338 Synonym: kd dissociation rate constant SBO_0000339 Rate with which two components associate into a complex. bimolecular association rate constant SBO_0000340 Rate with which three components associate into a complex. trimolecular association rate constant SBO_0000341 Rate with which components associate into a complex. association rate constant SBO_0000342 Mutual or reciprocal action or influence between molecular entities. molecular or genetic interaction SBO_0000343 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. genetic interaction SBO_0000344 Relationship between molecular entities, based on contacts, direct or indirect. molecular interaction SBO_0000345 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. time SBO_0000346 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. temporal measure SBO_0000347 Amount of time during which an event persists. duration SBO_0000348 Synonym: mean lifetime exponential time constant l 1 l SBO_0000349 Synonym: kinact inactivation rate constant SBO_0000350 The speed of an enzymatic reaction at a defined concentration of substrate(s) and enzyme. forward reaction velocity SBO_0000352 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. reverse zeroth order rate constant SBO_0000353 The speed of an enzymatic reaction at a defined concentration of substrate(s) and enzyme. reverse reaction velocity SBO_0000354 Fragment of a macromolecule that carries genetic information. informational molecule segment SBO_0000355 Mathematical expression stating that a quantity is conserved in a system, whatever happens within the boundaries of that system. conservation law SBO_0000356 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". decay constant t 1 t SBO_0000357 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. biological effect of a perturbation SBO_0000358 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. phenotype SBO_0000359 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. mass conservation law a n S i 0 n a i S i SBO_0000360 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. quantity of an entity pool SBO_0000361 A numerical measure of the quantity, or of some property, of the entities that constitute the entity pool. amount of an entity pool SBO_0000362 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. concentration conservation law a n S i 0 n a i S i SBO_0000363 Synonym: Kx activation constant SBO_0000364 Number of monomers composing a multimeric entity. multimer cardinality SBO_0000365 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. forward non-integral order rate constant, continuous case SBO_0000366 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. forward non-integral order rate constant, discrete case SBO_0000367 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. reverse non-integral order rate constant, discrete case SBO_0000368 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. reverse non-integral order rate constant, continuous case SBO_0000369 Region of a gene that is involved in the modulation of the expression of the gene. gene regulatory region SBO_0000370 Michaelis constant derived or experimentally measured under non-equilibrium conditions. Michaelis constant in non-equilibrium situation SBO_0000371 Michaelis constant derived using a steady-state assumption for enzyme-substrate and enzyme-product intermediates. For example see Briggs-Haldane equation (SBO:0000031). Michaelis constant in quasi-steady state situation SBO_0000372 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). Michaelis constant in irreversible situation SBO_0000373 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). Michaelis constant in fast equilibrium situation SBO_0000374 connectedness between entities and/or interactions representing their relatedness or influence. relationship SBO_0000375 A sequential series of actions, motions, or occurrences, such as chemical reactions, that affect one or more entities in a phenomenologically characteristic manner. process SBO_0000376 Decomposition of a compound by reaction with water, where the hydroxyl and H groups are incorporated into different products hydrolysis SBO_0000377 A reaction in which the principal reactant and principal product are isomers of each other isomerisation SBO_0000378 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. enzymatic rate law for inhibition of irreversible unireactant enzymes by competing substrates kcat Et S Sa Ks Ksa n kcat Et S Ks 1 i 1 n Sa i Ksa i S SBO_0000379 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. enzymatic rate law for simple competitive inhibition of irreversible unireactant enzymes by two non-exclusive inhibitors kcat Et S I1 I2 a Ks Ki1 Ki2 kcat Et S Ks 1 I1 Ki1 I2 Ki2 I1 I2 a Ki1 Ki2 S SBO_0000380 number used as a multiplicative or exponential factor for quantities, expressions or functions biochemical coefficient SBO_0000381 A multiplicative factor for quantities, expressions or functions biochemical proportionality coefficient SBO_0000382 number used as an exponential factor for quantities, expressions or functions biochemical exponential coefficient SBO_0000383 The coefficient used to quantify the effect on inhibition constants of multiple inhibitors binding non-exclusively to the enzyme. biochemical cooperative inhibition coefficient SBO_0000384 Coefficient that quantifies the effect on inhibition constants of either binding of multiple substrates or inhibitors. biochemical inhibitory proportionality coefficient SBO_0000385 The coefficient that describes the proportional change of Ks or Ki when inhibitor or substrate is bound, respectively, to the enzyme. biochemical cooperative inhibitor substrate coefficient SBO_0000386 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. enzymatic rate law for inhibition of irreversible unireactant enzymes by single competing substrate kcat Et S Sa Ks Ksa n kcat Et S Ks 1 Sa Ksa S SBO_0000387 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. enzymatic rate law for competitive inhibition of irreversible unireactant enzyme by product kcat Et S P Ks Kp kcat Et S Ks 1 P Kp S SBO_0000388 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. enzymatic rate law for inhibition of irreversible unireactant enzymes by single competing substrate with product inhibition kcat Et S Sa Ks Ksa Kp Kpa P Pa n kcat Et S Ks 1 Sa Ksa P Kpa Pa Kpa S SBO_0000389 A parameter value taken by a switch, which has a discrete set of values which can be alternated or switched between. switch value SBO_0000390 Synonym: binary switch boolean switch SBO_0000391 A mathematical expression that describes a steady state situation steady state expression SBO_0000392 Term to signify those material or conceptual entities that are identical in some respect within a frame of reference equivalence SBO_0000393 Generation of a material or conceptual entity. production SBO_0000394 Decrease in amount of a material or conceptual entity. consumption SBO_0000395 An aggregation of interactions and entities into a single process. encapsulating process SBO_0000396 An equivocal or conjectural process, whose existence is assumed but not proven. uncertain process SBO_0000397 One or more processes that are not represented in certain representations or interpretations of a model. omitted process SBO_0000398 Relationship between entities (material or conceptual) and logical operators, or between logical operators themselves. logical relationship SBO_0000399 A process in which a carboxyl group (COOH) is removed from a molecule as carbon dioxide. decarboxylation SBO_0000400 Removal of a carbonyl group (-C-O-) from a molecule, usually as carbon monoxide decarbonylation SBO_0000401 Removal of an amine group from a molecule, often under the addition of water deamination SBO_0000402 Covalent reaction that results in the transfer of a chemical group from one molecule to another. transfer of a chemical group SBO_0000403 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. transamination SBO_0000404 Functional entity associated with or derived from a unit of inheritance. unit of genetic information SBO_0000405 A material entity that is responsible for a perturbing effect perturbing agent SBO_0000406 An entity that can be measured quantitatively observable SBO_0000407 Control that precludes the execution of a process. absolute inhibition SBO_0000408 Effect of a biological entity on biological structures or processes. biological activity SBO_0000409 Entity that results from the interaction between other entities. interaction outcome SBO_0000410 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. implicit compartment SBO_0000411 Control that always triggers the controlled process. absolute stimulation SBO_0000412 The potential action that a biological entity has on other entities. Example are enzymatic activity, binding activity etc. biological activity SBO_0000413 The connectedness between entities as related by their position positional relationship SBO_0000414 Positional relationship between entities on the same strand (e.g. in DNA), or on the same side. cis SBO_0000415 Positional relationship between entities on different sides, or strands trans SBO_0000416 One of the two values possible from a boolean switch, which equates to '1', 'on' or 'input'. true SBO_0000417 One of the two values possible from a boolean switch, which equates to '0', 'off' or 'no input'. false SBO_0000418 Non-covalent association between several independant complexes multimer of complexes SBO_0000419 Non-covalent association between portions of macromolecules that carry genetic information multimer of informational molecule segment SBO_0000420 Non-covalent association between several macromolecules multimer of macromolecules SBO_0000421 Non-covalent association between several simple chemicals multimer of simple chemicals SBO_0000422 Inhibitory constant for the binding of a given ligand with an isomeric form of an enzyme. isoinhibition constant SBO_0000423 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. pseudo-dissociation constant for product SBO_0000424 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. pseudo-dissociation constant for substrate SBO_0000425 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. reversible Hill-type enzymatic rate law SBO_0000426 Reversible Hill-type kinetics in the presence of at least one modifier whose binding is affected by the presence of the substrate or product. modulated reversible Hill-type rate law SBO_0000427 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) modulated reversible Hill-type rate law with one modifier substrate product Modifier Keq Vf Ks Kp h Mhalf alpha Vf substrate Ks 1 product substrate Keq substrate Ks product Kp h 1 1 Modifier Mhalf h 1 alpha Modifier Mhalf h substrate Ks product Kp h SBO_0000428 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.). modulated reversible Hill-type rate law with two modifiers substrate product ModifierA ModifierB Keq Vf Shalve Phalve h MAhalf alphaA MBhalf alphaB alphaAB Vf substrate Ks 1 product substrate Keq substrate Ks product Kp h 1 1 ModifierA MAhalf h ModifierB MBhalf h 1 alphaA ModifierA MAhalf h alphaB ModifierB MBhalf h alphaA alphaB alphaAB ModifierA MAhalf h ModifierB MBhalf h substrate Ks product Kp h SBO_0000429 Kinetics of enzyme-catalysed reactions with 2 or more substrates or products enzymatic rate law for multireactant enzymes SBO_0000430 Kinetics of enzymes that react with one substance, and whose activity may be positively or negatively modulated. enzymatic rate law for modulated unireactant enzymes SBO_0000431 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. unmodulated reversible Hill-type rate law substrate product Keq Vf Ks Kp h Vf substrate Ks 1 product substrate Keq substrate Ks product Kp h 1 1 substrate Ks product Kp h SBO_0000432 Enzymatic rate law for an irreversible reaction involving two substrates and one product. irreversible Michaelis Menten rate law for two substrates A B KmA KmB KiA Et kcat Et kcat A B KiA KmB KmB A KmA B A B SBO_0000433 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. Ordered Bi-Bi mechanism rate law Sa Sb Pp Pq Keq Vf Vr Kma Kmb Kmp Kmq Kia Kib Kip Vf Sa Sb Pp Pq Keq Sa Sb 1 Pp Kip Kma Sb Kmb Sa Kia Vf Vr Keq Kmq Pp 1 Sa Kia Pq Kmp 1 Kma Sb Kia Kmb Pp 1 Sb Kib SBO_0000434 Enzymatic rate for a reaction involving two substrates and one product. The substrates A and then B are bound strictly in order. Ordered Bi-Uni mechanism rate law Sa Sb P Kma Kmb Kmp Kia Keq Vf Vr Vf Sa Sb P Keq Sa Sb Kma Sb Kmb Sa Vf Vr Keq Kmp P 1 Sa Kia SBO_0000435 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. Ordered Uni-Bi mechanism rate law substrate productp productq Kms Kmq Kmp Kip Keq Vf Vr Vf substrate productp productq Keq Kms substrate 1 productp Kip Vf Vr Keq Kmq productp Kmp productq productp productq SBO_0000436 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. Ping Pong Bi-Bi mechanism rate law Sa Sb Pp Pq Keq Vf Vr Kma Kmb Kmp Kmq Kia Kiq Vf Sa Sb Pp Pq Keq Sa Sb Kmb Sa Kma Sb 1 Pq Kiq Vf Vr Keq Kmq Pp 1 Sa Kia Pq Kmp Pp SBO_0000437 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. reversible Iso Uni-Uni substrate product Kms Kmp Kii Vf Keq Vf substrate product Keq substrate 1 product Kii Kms 1 product Kmp SBO_0000438 Synonym: Uni-Uni Reversible Simple Michaelis-Menten reversible Uni-Uni substrate product Kms Kmp Et kcatp kcats Et kcatp substrate Kms kcats product Kmp 1 substrate Kms product Kmp SBO_0000439 Synonym: Uni-Uni Uni-Uni Reversible using Haldane relationship substrate product Kms Kmp Vf Keq Vf substrate product Keq substrate Kms 1 product Kmp SBO_0000440 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. enzymatic rate law for irreversible allosteric inhibition substrate Inhibitor V Ks n L Ki V substrate Ks substrate n 1 L Ks 1 Inhibitor Ki n Ks substrate n SBO_0000441 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. enzymatic rate law for mixed-type inhibition of reversible enzymes by mutually exclusive inhibitors substrate product Inhibitor Kms Kmp Vf Vr Kis Kic Vf substrate Kms Vr product Kmp 1 Inhibitor Kis substrate Kms product Kmp 1 Inhibitor Kic SBO_0000442 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. enzymatic rate law for simple reversible non-competitive inhibition of unireactant enzymes substrate product Inhibitor Kms Kmp Vf Vr Ki Vf substrate Kms Vr product Kmp 1 substrate Kms product Kmp 1 Inhibitor Ki SBO_0000443 Synonym: specific activation enzymatic rate law for reversible essential activation SBO_0000444 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. enzymatic rate law for reversible mixed activation substrate product Activator Kms Kmp Vf Vr Kas Kac Vf substrate Kms Vr product Kmp Activator Kas Activator substrate Kms product Kmp Kac Activator SBO_0000445 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. enzymatic rate law for irreversible substrate activation substrate V Ksc Ksa V substrate Ksa 2 1 substrate Ksc substrate Ksa substrate Ksa 2 SBO_0000446 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. enzymatic rate law for irrreversible mixed activation substrate Activator Kms V Kas Kac V substrate Activator Kms Kas Activator substrate Kac Activator SBO_0000447 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). enzymatic rate law for reversible catalytic activation with one activator substrate product Activator Kms Kmp Vf Vr Ka Vf substrate Kms Vr product Kmp Activator 1 substrate Kms product Kmp Ka Activator SBO_0000448 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. enzymatic rate law for reversible specific activation substrate product Activator Kms Kmp Vf Vr Ka Vf substrate Kms Vr product Kmp Activator Ka 1 substrate Kms product Kmp Activator SBO_0000449 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). enzymatic rate law for irreversible catalytic activation with one activator substrate Activator Kms V Ka V substrate Activator Kms substrate Ka Activator SBO_0000450 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. enzymatic rate law for irreversible specific activation substrate Activator Kms V Ka V substrate Activator Kms Ka Kms substrate Activator SBO_0000451 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. enzymatic rate law for reversible reactions with competitive inhibition substrate product Inhibitor Kms Kmp Vf Vr Ki n Vf substrate Kms Vr product Kmp 1 substrate Kms product Kmp i 1 n I i Ki i SBO_0000452 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. enzymatic rate law for reversible competitive inhibition by one inhibitor substrate product Inhibitor Kms Kmp Vf Vr Ki Vf substrate Kms Vr product Kmp 1 substrate Kms product Kmp Inhibitor Ki SBO_0000453 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. enzymatic rate law for reversible empirical allosteric inhibition by one inhibitor substrate product Inhibitor Vf Vr Kms Kmp n Ki Vf substrate Kms Vr product Kmp 1 substrate Kms product Kmp Inhibitor Ki n SBO_0000454 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. enzymatic rate law for reversible substrate inhibition substrate product Kms Kmp Vf Vr Ki Vf substrate Kms Vr product Kmp 1 substrate Kms product Kmp substrate Ki 2 SBO_0000455 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. enzymatic rate law for irreversible substrate inhibition substrate Km V Ki V substrate Km substrate Km substrate Ki 2 SBO_0000456 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. enzymatic rate law for reversible unireactant enzyme with a single hyperbolic modulator substrate product Modifier Kms Kmp Vf Vr Kd a b Vf substrate Kms Vr product Kmp 1 b Modifier a Kd 1 Modifier Kd substrate Kms product Kmp 1 Modifier a Kd SBO_0000457 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. enzymatic rate law for irreversible unireactant enzyme with a single hyperbolic modulator substrate Modifier Km V Kd a b V substrate 1 b Modifier a Kd Km 1 Modifier Kd substrate 1 Modifier a Kd SBO_0000458 Reversible inhibition of a unireactant enzyme by one inhibitor, which binds to the enzyme-substrate complex. The inhibitor is uncompetitive with the substrate. enzymatic rate law for simple uncompetitive inhibition of reversible unireactant enzymes substrate product Inhibitor Kms Kmp Vf Vr Ki Vf substrate Kms Vr product Kmp 1 substrate Kms product Kmp 1 Inhibitor Ki SBO_0000459 Synonym: activator stimulator SBO_0000460 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. enzymatic catalyst SBO_0000461 Synonym: necessary stimulator essential activator SBO_0000462 An activator which is not necessary for an enzymatic reaction, but whose presence will further increase enzymatic activity. non-essential activator SBO_0000463 Synonym: standard chemical potential standard biochemical potential SBO_0000464 Assignment of a state or a value to a state variable, characteristic or property, of a biological entity. state variable assignment SBO_0000465 The measurable dimensions of an object which are minimally required to define the space that an object occupies. spatial measure SBO_0000466 The length of an object is the longest measurable distance between its extremities. length SBO_0000467 The area of an object is a quantity expressing its two-dimensional size, usually part or all of its surface. area SBO_0000468 A quantity representing the three-dimensional space occupied by all or part of an object. volume SBO_0000469 Synonym: inclusion containment SBO_0000470 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. mass fraction SBO_0000471 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. molal concentration of an entity SBO_0000472 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. molar concentration of an entity SBO_0000473 Term to signify where a material or conceptual entity is represented or denoted by a symbol or by some other abbreviated form. denotement SBO_0000474 Mathematical function commonly used in biological modeling, which enable simplification of more complex expressions convenience function SBO_0000475 Synonym: input signal step function periodic forcing function time Theta0 Theta1 Phi Tp Tc Tw Theta0 0.5 Theta1 1 time Phi Tc time Phi Tc Tw 1 time Phi Tc time Phi Tc Tp Tw 1 time Phi Tc time Phi Tc Tc Tw SBO_0000476 The period is the duration of one cycle in a repeating event. [wikipedia] period SBO_0000477 Synonym: temporal offset phase shift SBO_0000478 The product of the Michaelis constants, to the power of their respective stoichiometric coefficients, for either substrates or products. powered product of Michaelis constant Km x n i 1 x Km i n i SBO_0000479 The product of the substrate Michaelis constants, to the power of their respective stoichiometric coefficients. powered product of substrate Michaelis constants Kms x n i 1 x Kms i n i SBO_0000480 The product of the product Michaelis constants, to the power of their respective stoichiometric coefficients. powered product of product Michaelis constants Km x n i 1 x Km i n i SBO_0000481 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. stoichiometric coefficient SBO_0000482 The geometric mean turnover rate of an enzyme in either forward or backward direction for a reaction, measured per second. geometric mean rate constant k n n i 1 n k i SBO_0000483 The geometric mean turnover rate of an enzyme in the forward direction for a reaction, measured per second. forward geometric mean rate constant kf n n i 1 n kf i SBO_0000484 The geometric mean turnover rate of an enzyme in the reverse direction for a reaction, measured per second. reverse geometric mean rate constant kr n n i 1 n kr i SBO_0000485 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. basal rate constant SBO_0000486 The ratio of the basal activity to the maximal velocity of a reaction. The values range between 0 and 1. relative basal rate constant b vmax b vmax SBO_0000487 Function which ranges from 0 to 1, to describe the relative activation or inhibition of a reaction or process, actual or conceptual. relative activity function SBO_0000488 Function which ranges from 0 to 1, to describe the relative activation of a reaction or process, actual or conceptual. relative activation function SBO_0000489 Function which ranges from 0 to 1, to describe the relative inhibition of a reaction or process, actual or conceptual. relative inhibition function SBO_0000490 Number of molecules which are generated by an enzyme. number of products SBO_0000491 Synonym: diffusivity diffusion coefficient SBO_0000492 Amplitude is the magnitude of change in the oscillating variable, with each oscillation, within an oscillating system. amplitude SBO_0000493 A spatial region of an entity that confers a function functional domain SBO_0000494 A specific domain of a spatio-temporal entity to which another spatio-temporal entity is able to bind, forming chemical bonds. binding site SBO_0000495 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. catalytic site SBO_0000496 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. transmembrane domain SBO_0000497 A parameter that has three discrete values which may be alternated between. ternary switch SBO_0000498 Value which ranges from 0 to 1, to describe the relative activity of a process or reaction. relative activity SBO_0000499 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. genetic interaction SBO_0000500 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. genetic suppression SBO_0000501 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. genetic enhancement SBO_0000502 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. synthetic lethality SBO_0000503 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. number of entity pool constituents SBO_0000504 The mass that comprises an entity pool. mass of an entity pool SBO_0000505 Amount of enzyme present per unit of volume. The participant role 'enzymatic catalyst' is defined in SBO:0000460. concentration of enzyme SBO_0000506 Amount, expressed as a mass, of an enzyme. The participant role 'enzymatic catalyst' is defined in SBO:0000460. mass of enzyme SBO_0000507 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. number of an enzyme SBO_0000508 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. number of a reactant SBO_0000509 The amount of a specific entity pool reactant present per unit of volume. The participant role 'reactant' is defined in SBO:0000010. concentration of reactant SBO_0000510 The amount, expressed as a mass, of a specific reactant entity pool. The participant role 'reactant' is defined in SBO:0000010. mass of reactant SBO_0000511 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. number of a product SBO_0000512 The amount of a specific entity pool product present per unit of volume. The participant role 'product' is defined in SBO:0000011. concentration of product SBO_0000513 The amount, expressed as a mass, of a specific product entity pool. The participant role 'product' is defined in SBO:0000011. mass of product SBO_0000514 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. number of a substrate SBO_0000515 The amount of a specific entity pool substrate present per unit of volume. The participant role 'substrate' is defined in SBO:0000015. concentration of substrate SBO_0000516 The amount, expressed as a mass, of a specific substrate entity pool. The participant role 'substrate' is defined in SBO:0000015. mass of substrate SBO_0000517 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. number of a modifier SBO_0000518 The amount of a specific modifier entity pool present per unit of volume. The participant role 'modifier' is defined in SBO:0000019. concentration of modifier SBO_0000519 The amount, expressed as a mass, of a specific modifier entity pool. The participant role 'modifier' is defined in SBO:0000019. mass of modifier SBO_0000520 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. number of an inhibitor SBO_0000521 The amount of a specific inhibitor entity pool present per unit of volume. The participant role 'inhibitor' is defined in SBO:0000020. concentration of inhibitor SBO_0000522 The amount, expressed as a mass, of a specific inhibitor entity pool. The participant role 'inhibitor' is defined in SBO:0000020. mass of inhibitor SBO_0000523 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. number of an activator SBO_0000524 The amount of a specific activator entity pool present per unit of volume. The participant role 'activator' is defined in SBO:0000459. concentration of activator SBO_0000525 The amount, expressed as a mass, of a specific activator entity pool. The participant role 'activator' is defined in SBO:0000459. mass of activator SBO_0000526 The process by which two or more proteins interact non-covalently to form a protein complex (SBO:0000297). protein complex formation SBO_0000527 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. modular rate law SBO_0000528 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. common modular rate law SBO_0000529 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. direct binding modular rate law SBO_0000530 The simultaneous binding modular rate law makes the assumption that substrates and products can be bound simultaneously, and in any combination. simultaneous binding modular rate law SBO_0000531 For the power-law rate law, the denominator is set to be a constant, and the rate law does not saturate. power-law modular rate law SBO_0000532 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. force-dependent modular rate law SBO_0000533 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. specific activator SBO_0000534 An essential activator that affects the apparent value of the catalytic constant. catalytic activator SBO_0000535 An essential activator that affects the apparent value of the Michaelis constant(s). binding activator SBO_0000536 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. partial inhibitor SBO_0000537 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. complete inhibitor SBO_0000538 Synonym: membrane permeability ionic permeability SBO_0000539 A quantitative parameter that represents a probability value, assigned to a specific event. probabilistic parameter SBO_0000540 A ratio that represents the quantity of a defined constituent entity over the total number of all constituent entities present. fraction of an entity pool SBO_0000541 The number of moles of a constituent entity, divided by the total number of all constituent entities present in a system. mole fraction SBO_0000542 Synonym: R0 basic reproductive ratio SBO_0000543 A nonspecific coalescence of misfolded proteins which may or may not form a precipitate, depending upon particle size. protein aggregate SBO_0000544 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. metadata representation SBO_0000545 A value, numerical or symbolic, that defines certain characteristics of systems or system functions, or is necessary in their derivation. systems description parameter SBO_0000546 A non-numerical value that defines certain characteristics of systems or system functions. qualitative systems description parameter SBO_0000547 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. boolean logical framework SBO_0000548 Extension of the boolean logical framework which associates a defined number of possible integer values (states) with the variables. multi-valued logical framework SBO_0000549 Extension of the Boolean logical framework which allows intermediate or undetermined values for the logical variables. fuzzy logical framework SBO_0000550 Supplementary information that does not modify the semantics of the presented information. annotation SBO_0000551 The use of an abbreviated name, taken from a controlled vocabulary of terms, which is used to represent some information about the entity to which it is attached. controlled short label SBO_0000552 Additional information that supplements existing data, usually in a document, by providing a link to more detailed information, which is held externally, or elsewhere. reference annotation SBO_0000553 An annotation which directs one to information contained within a published body of knowledge, usually a book or scientific journal. bibliographical reference SBO_0000554 Synonym: db xref database cross reference SBO_0000555 Annotation which complies with the full set of defined rules in its construction. controlled annotation SBO_0000556 Annotation which does not comply with, or is not restricted by, any rules in its construction. Examples would include free text annotations. uncontrolled annotation SBO_0000557 Annotation that directly incorporates information into the body of a document. embedded annotation SBO_0000558 A measure of enzyme activity under standard conditions, at a specific substrate concentration (usually saturation), expressed as the amount of product formed per unit time, per amount of enzyme. This is often expressed as micromol per min per mg, rather than the less practical official unit, Katal (1 mol per second). specific activity SBO_0000559 A measure of the amount of active enzyme present, expressed under specified conditions. This is often expressed as micromol per min (also known as enzyme unit, U), rather than the less practical official SI unit, Katal (1 mol per second). Enzyme activity normally refers to the natural substrate for the enzyme, but can also be given for standardised substrates such as gelatin, where it is then referred to as GDU (Gelatin Digesting Units). enzyme activity SBO_0000560 Reaction scheme in which the reaction velocity is direct proportional to the activity or concentration of a single molecular species. 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 the stimulator. It is to be used in a reaction modelled using a continuous framework. mass action rate law for first order irreversible reactions, single essential stimulator, continuous scheme k A k A SBO_0000561 Reaction scheme in which the reaction velocity is direct proportional to the activity or quantity of a single molecular species. 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 the stimulator. It is to be used in a reaction modelled using a discrete framework. mass action rate law for first order irreversible reactions, single essential stimulator, discrete scheme c A c A SBO_0000562 Reaction scheme where the products are created from a reactant and the change of a product quantity is proportional to the product of the reactant and the stimulator activities. The reaction scheme does not include any reverse process that creates the reactant from the products. The change of a product quantity is proportional to the quantity of the reactant and the stimulator. mass action like rate law for second order irreversible reactions, one reactant, one essential stimulator SBO_0000563 Reaction scheme where the products are created from a reactant and the change of a product quantity is proportional to the product of the reactant and the stimulator activities. The reaction scheme does not include any reverse process that creates the reactant from the products. The change of a product quantity is proportional to the quantity of the reactant and the stimulator. It is to be used in a reaction modelled using a continuous framework. mass action like rate law for second order irreversible reactions, one reactant, one essential stimulator, continuous scheme k R A k R A SBO_0000564 Reaction scheme where the products are created from a reactant and the change of a product quantity is proportional to the product of the reactant and the stimulator quantities. The reaction scheme does not include any reverse process that creates the reactant from the products. The change of a product quantity is proportional to the quantity of the reactant and the stimulator. It is to be used in a reaction modelled using a discrete framework. mass action like rate law for second order irreversible reactions, one reactant, one essential stimulator, discrete scheme c R A c R A SBO_0000565 A physical constant that is required in the calculation of a system parameter. systems description constant SBO_0000566 The permeability of an ion through a channel or membrane expressed in relation to the reference ion, which is given the value 1. For example, if a membrane is most permeable to K+, then that is assigned the reference permeability value of 1, and the value for Na+ may be 0.05. relative permeability SBO_0000567 Synonym: molar gas constant universal gas constant SBO_0000568 Named after Michael Faraday, it is the magnitude of electric charge per mole of electrons. It has the value 96,485.3365 C/mol (Coulombs per Mole), and the symbol F. Faraday constant SBO_0000569 Synonym: Goldman-Hodgkin-Katz voltage equation Goldman equation R T F P p C c A a R T F A p c P a p C P SBO_0000570 Synonym: reversal potential Nernst potential R T F z X x R T z F X x SBO_0000571 Parameters used in the study of thermodynamics, a physical science that pertains to the relationship between heat and other forms of energy such as 'work done' in material bodies. thermodynamic parameter SBO_0000572 A thermodynamic potential whose natural variables are entropy (S) and pressure (p). The enthalpy of a system, measured in Joules (J), is defined as H = U + pV (where H is enthalpy, U is the internal energy, p is the pressure at the system boundary, and V is the system volume). symbol: H enthalpy SBO_0000573 Change in enthalpy observed in the constituents of a thermodynamic system when undergoing a transformation or chemical reaction. This is the preferred way of expressing the energy changes to a system at constant pressure, since enthalpy itself cannot be directly measured. The enthalpy change is positive in endothermic reactions, negative in exothermic reactions, and is defined as the difference between the final and initial enthalpy of the system under study: ΔH = Hf - Hi. The standard unit of measure is J. Symbol: ΔH enthalpy change SBO_0000574 The enthalpy change observed in a constituent of a thermodynamic system when one mole of a compound, in its standard state, is formed from its elementary antecedents, in their standard state(s), under standard conditions (1 bar). The standard unit of measure is kJ/mol. Symbol: DeltaHf0, DeltafH0 standard enthalpy of formation SBO_0000575 The enthalpy change observed in a constituent of a thermodynamic system when one mole of substance reacts completely, under standard conditions (1 bar). The standard unit of measure is kJ/mol. Symbol: DeltaHr0, DeltarH0 standard enthalpy of reaction SBO_0000576 A thermodynamic property which acts as a measure of the state of disorder of a system. Its natural variables are the internal energy (U) and the volume (V). It is defined by dS = (1/T)dU + (p/T)dV. The second law of thermodynamics states that in an isolated system, natural processes tend to increase in disorder or entropy. The standard unit of measure is Joules per Kelvin (J/K). symbol: S entropy SBO_0000577 The increase or decrease of the entropy of a system. For values greater than zero, there is an implied increase in the disorder of a system, for example during a reaction, and decreased disorder where the values are less than zero. The entropy change of a process is defined as the initial system entropy value minus the final entropy value: DeltaS = Sf - Si. The standard unit of measure is J/K. symbol: DeltaS entropy change SBO_0000578 The entropy change observed in a thermodynamic system when one mole of substance reacts completely, under standard conditions (1 bar). The standard unit of measure is kJ/(mol K). This can be calculated using the entropies for products and reactants: DeltaS(reaction)=sum DeltaS (products) - sum DeltaS reactants. The standard unit of measure is kJ/(mol K). symbol: DeltaSro standard entropy of reaction SBO_0000579 The change in entropy associated with the formation of one mole of a substance from its elements in their standard states under standard conditions (1 bar). The standard unit of measure is kJ/(mol K). symbol: DeltaSfo standard entropy of formation SBO_0000580 Synonym: Gibbs function Gibbs free energy SBO_0000581 The increase or decrease of the Gibbs free energy of a system. During a reaction, this is equal to the change in enthalpy of the system minus the change in the product of the temperature times the entropy of the system: ΔG = ΔH - T ΔS. A negative value indicates that the reaction will be favoured and will release energy. The magnitude of the value indicates how far the reaction is from equilibrium, where there will be no free energy change. The standard unit of measure is kJ/mol. Symbol: ΔG. Gibbs free energy change SBO_0000582 The change in Gibbs free energy associated with the formation of 1 mole of substance from elements in their standard states under standard conditions (1 bar). For aqueous solutions, each solute must be present in 1M concentration. The standard unit of measure is kJ/mol. Symbol: ΔGf°. standard Gibbs free energy of formation SBO_0000583 The Gibbs free energy change observed in a thermodynamic system when one mole of substance reacts completely, under standard conditions (1 bar). For aqueous solutions, each solute must be present in 1M concentration. The standard unit of measure is kJ/mol. Symbol: ΔG°. standard Gibbs free energy of reaction SBO_0000584 A duration of time after which a phase shift occurs. temporal offset SBO_0000585 The total length of time over which a model is simulated, where the time scale is indicated within the model simulation. simulation duration SBO_0000586 A conceptualisation of time which is intrinsic to a mathematical model, and which can be used to describe other variables or parameters of the model. model time SBO_0000587 A transport reaction which results in the entry of the transported entity, into the cell. transcellular membrane influx reaction SBO_0000588 A transport reaction which results in the removal of the transported entity from the cell. transcellular membrane efflux reaction SBO_0000589 A composite biochemical process through which a gene sequence is fully converted into mature gene products. These gene products may include RNA species as well as proteins, and the process encompasses all intermediate steps required to generate the active form of the gene product. genetic production SBO_0000590 A stretch of DNA upstream of a transcription start site, to which a promoter and other transcription factors may bind to initiate or regulate expression. promoter SBO_0000591 A process that can modify the state of petri net 'places'[SBO:0000593]. petri net transition SBO_0000592 A discrete value attributed to an entity pool. discrete amount of an entity pool SBO_0000593 A defined entity pool state which can be modified by a petri net transition [SBO:0000591]. petri net place SBO_0000594 A participant whose presence does not alter the velocity of a process or event. neutral participant SBO_0000595 A modifier that can exhibit either inhibitory or stimulatory effects on a process depending on the context in which it occurs. For example, the observed effect may be dependent upon the concentration of the modifier. dual-activity modifier SBO_0000596 A modifier whose activity is not known or has not been specified. modifier of unknown activity SBO_0000597 A silencer is a modifier which acts in a manner that completely prevents an event or process from occurring. For example, a silencer in gene expression is usually a transcription factor that binds a DNA sequence in such a way as to completely prevent the binding of RNA polymerase, and thus fully suppresses transcription. silencer SBO_0000598 A region of DNA to which various transcription factors and RNA polymerase must bind in order to initiate transcription for a gene. promoter SBO_0000599 A denotement that specifies a point of contact between variables or submodels in a hierarchical model. port SBO_0000600 A connection point to an element in a model that indicates that the element's mathematical interpretation is defined outside the model. input port SBO_0000601 A connection point to an element in a model that indicates that the element's mathematical interpretation is defined within the model. output port SBO_0000602 A parameter that takes only logical values. logical parameter SBO_0000603 A substance that is produced in a chemical reaction but is not itself the primary product or focus of that reaction. Examples include, but are not limited to, currency compounds such as ATP, NADPH and protons. side product SBO_0000604 A substance that is consumed in a chemical reaction but is not itself the primary substrate or focus of that reaction. Examples include, but are not limited to, currency compounds such as ATP, NADPH and protons. side substrate SBO_0000605 A receptor where binding occurs through strong intermolecular forces such as Van der Waals, hydrogen bonds or ionic bonds. high affinity receptor SBO_0000606 A receptor where binding occurs through weak intermolecular forces. low affinity receptor SBO_0000607 A macromolecular complex composed of two monomeric units, which may or may not be identical. Monomers are usually non-covalently bound. dimer SBO_0000608 A macromolecular complex composed of precisely two identical monomeric units, which are usually non-covalently bound. homodimer SBO_0000609 A macromolecular complex composed of precisely two non-identical monomeric units, which are usually non-covalently bound. heterodimer SBO_0000610 A measure of the rate of growth of an organism, usually in culture. This can be expressed as increase in cell number or, more usually as an increase in dry weight of cells (grams), measured over a unit time period. Usually expressed as hour -1. growth rate SBO_0000611 Under nutrient limited conditions, it may be assumed that enzymes are operating below their maximal capacity (Kcat). Keff represents the lumped turnover rate of a reaction, expressed in units per time. effective catalytic rate SBO_0000612 The velocity at which a reaction occurs. This may be calculated through the accumulation of a product or consumption of a reactant, and expressed using entity concentrations or amounts per time interval. The rate of reaction may be influenced by temperature, pressure and other factors. Rate of reaction is often referred to as reaction rate or metabolic flux. rate of reaction SBO_0000613 Parameters that pertain to chemical reactions. reaction parameter SBO_0000614 Rate of reaction expressed as a change in concentration over time. rate of reaction (concentration) SBO_0000615 Rate of reaction expressed as a change in enumerated quantity over time. rate of reaction (amount) SBO_0000616 The extent of a reaction is a measure of how far a reaction has proceeded towards equilibrium. It is denoted by the Greek letter ξ and is expressed in moles. extent of reaction SBO_0000617 The Gibbs free energy change observed in a thermodynamic system when a substance undergoes a reaction under non standard conditions. The unit of measure is kJ/mol. Symbol: ΔG. Gibbs free energy of reaction SBO_0000618 Synonym: thermodynamic driving force reaction affinity SBO_0000619 A Gibbs free energy that is calculated from the standard Gibbs value (at 298K), and extrapolated to a desired pH and ionic strength, and may be determined at a different temperature. Symbol: ΔG´. transformed Gibbs free energy change SBO_0000620 A Gibbs free energy of reaction that is calculated from the standard Gibbs value (at 298K), and extrapolated to a desired pH and ionic strength, and may be determined at a different temperature. Symbol ΔG´. transformed standard Gibbs free energy of reaction SBO_0000621 A Gibbs free energy of formation that is calculated from the standard Gibbs value (at 298K), and extrapolated to a desired pH and ionic strength, and may be determined at a different temperature. Symbol ΔGf´. transformed standard Gibbs free energy of formation SBO_0000622 The Gibbs free energy change observed in a thermodynamic system when a substance undergoes a reaction under non standard conditions, which is extrapolated to a desired pH and ionic strength, and may be determined at a different temperature. Symbol: ΔG´. transformed Gibbs free energy of reaction SBO_0000623 A combined (weighted) measure of the concentration of all electrolytes present in a solution. It is calculated as a half of the sum over all the ions in the solution multiplied by the square of individual ionic valencies. Monovalent electrolytes have a concentration equal to their ionic strength while multivalent electrolytes have greater ionic strength, directly proportional to ionic valency. Symbol: I ionic strength SBO_0000624 Modelling approach, typically used for metabolic models, where the flow of metabolites (flux) through a network can be calculated. This approach will generally produce a set of solutions (solution space), which may be reduced using objective functions and constraints on individual fluxes. flux balance framework SBO_0000625 A parameter that limits the upper or lower value that a flux may assume. This parameter may be determined experimentally, or may be the result of theoretical investigation. flux bound SBO_0000626 A value used for flux bound in cases where a precise value, supported experimentally or theoretically, is not available. default flux bound SBO_0000627 A modeling process to provide matter influx or efflux to a model, for example to replenish a metabolic network with raw materials (eg carbon / energy sources). Such reactions are conceptual, created solely for modeling purposes, and do not have a physical correspondence. Exchange reactions, often represented as 'R_EX_', can operate in the negative (uptake) direction or positive (secretion) direction. By convention, a negative flux through an exchange reaction represents uptake of the corresponding metabolite, and a positive flux represent discharge. exchange reaction SBO_0000628 A modeling process analogous to exchange reaction, but which operates upon "internal" metabolites. Metabolites that are consumed by these reactions are assumed to be used in intra-cellular processes that are not part of the model. Demand reactions, often represented 'R_DM_', can also deliver metabolites (from intra-cellular processes that are not considered in the model). demand reaction SBO_0000629 Biomass production, often represented 'R_BIOMASS_', is usually the optimization target reaction of constraint-based models, and can consume multiple reactants to produce multiple products. It is also assumed that parts of the reactants are also consumed in unrepresented processes and hence products do not have to reflect all the atom composition of the reactants. Formulation of a biomass production process entails definition of the macromolecular content (eg. cellular protein fraction), metabolic constitution of each fraction (eg. amino acids), and subsequently the atomic composition (eg. nitrogen atoms). More complex biomass functions can additionally incorporate details of essential vitamins and cofactors required for growth. biomass production SBO_0000630 Synonym: maintenance energy ATP maintenance SBO_0000631 A conceptual process used for modeling purposes, often created solely to complete model structure, with respect to providing inflow or outflow of matter or material. Unlike other reactions, pseudoreactions are not usually subjected to mass balance considerations. pseudoreaction SBO_0000632 Synonym: source/sink sink reaction SBO_0000633 Term used to indicate the grouping of model components, largely reactions, by some criterion, often processual. This can be used to indicate, for example, the subsystem of a model that is concerned with 'transport'. A designated subsystem includes reactions annotated with the term, as well as reactions participants such as enzymes, modifiers and genes encoding these subsystem components. subsystem SBO_0000634 Fragment or region of a DNA macromolecule. DNA segment SBO_0000635 Fragment or region of an RNA macromolecule. RNA segment SBO_0000636 Synonym: positive allosteric modulation allosteric activator SBO_0000637 Describes an activator (ligand) which binds to the enzyme, which does not result in a conformational change, but which enhances the enzyme's activity. non-allosteric activator SBO_0000638 An inhibitor which binds irreversibly with the enzyme such that it cannot be removed, and abolishes enzymatic function. irreversible inhibitor SBO_0000639 An inhibitor whose binding to an enzyme results in a conformational change, resulting in a loss of enzymatic activity. This activity can be restored upon removal of the inhibitor. allosteric inhibitor SBO_0000640 Synonym: anti-competitive inhibitor uncompetitive inhibitor SBO_0000641 An enumeration of the concentration of magnesium (Mg) in solution (pMg = -log10[Mg2+]). pMg SBO_0000642 Conceptual or material entity that is the object of an inhibition process, and is acted upon by an inhibitor. inhibited SBO_0000643 Conceptual or material entity that is the object of a stimulation process, and is acted upon by a stimulator. stimulated SBO_0000644 Conceptual or material entity that is the object of a modification process, and is acted upon by a modifier. modified SBO_0000645 An entity that acts as the starting material for genetic production (http://identifiers.org/biomodels.sbo/SBO:0000589). template SBO_0000646 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 includes a reverse process that creates the reactants from the products. It is to be used in a reaction modelled using a continuous framework. mass action rate law for reversible reactions, continuous schema k1 n1 mu1 R k2 n2 mu2 P k1 i 0 n1 R i mu1 i k2 i 0 n2 P i mu2 i SBO_0000647 Synonym: molecular weight molecular mass SBO_0000648 Synonym: protein molecular weight protein molecular mass SBO_0000649 A composite representation of material entities required for organismal growth. It includes macromolecular content (eg. cellular protein fraction), metabolic constitution of each fraction (eg. amino acids), and atomic composition (eg. nitrogen atoms). biomass SBO_0000650 A sequential series of actions, motions, or occurrences, such as chemical reactions, where a reversal of states that bring the system back to its original state in a characteristic manner occurs. reversible process SBO_0000651 A sequential series of actions, motions, or occurrences, such as chemical reactions, where a reversal of states that bring the system back to its original state in a characteristic manner does not occur. irreversible process SBO_0000652 A chemical reaction in which one or more monomer molecules combine to form a larger polymer molecule with repeated structural units. polymerization SBO_0000653 A chemical reaction in which a large polymer breaks into its constituent monomers (or mixture of monomers). depolymerization SBO_0000654 A biochemical process involving the simultaneous transport of two or more substances across a membrane via a protein or protein complex. co-transport reaction SBO_0000655 The movement of an entity/entities across a biological membrane mediated by a transporter protein. transport reaction SBO_0000656 A conformational change in a protein resulting in its activation. activation SBO_0000657 Protein assisted movement of molecules across a membrane from a region of low concentration to high concentration involving the consumption of cellular energy (ATP molecules). active transport SBO_0000658 Movement of molecules without the need for external energy, and usually from a region of high concentration to low concentration. passive transport SBO_0000659 A membrane protein mediated transport of two ore more molecules in the same relative direction across a membrane. symporter-mediated transport SBO_0000660 A membrane protein mediated transport of two or more molecules in opposite directions across a membrane. antiporter-mediated transport SBO_0000661 Total amount that can be contained or produced by a specific entity. This can refer to diverse items, such as the carrying capacity of a membrane with respect to proteins, the capacity of high-energy phosphate bonds, or the maximal count of bacteria in the gut, etc. capacity SBO_0000662 Occopancy is a quantitative systemic property that indicates which number of available places is occupied. This can refer to diverse things, such as the number of occupied high-energy phosphate bonds in ATP, the number of bacteria in the gut, or the number of electrons loaded onto redox carriers, etc. occupancy SBO_0000663 Fractional occupancy is a quantitative dynamic property of a system that can be calculated as the fraction of occupancy over capacity. fractional occupancy SBO_0000664 an entity which physical constituents are partially or totally contained in a defined compartment. contained entity SBO_0000665 a conformation changes to a protein leading to its inactivation inactivation SBO_0000666 describes the number of amino acids,nucleic acid in a protein/DNA/RNA chain chain length SBO_0000667 length of amino acid sequence in a protein protein chain length SBO_0000668 output generated as biomass or product from a/set of chemical reaction/s. yield SBO_0000669 generation of biomass for an substrate through a defined reaction/s. biomass yield on substrate SBO_0000670 generation of product from substrate in a defined chemical reaction. product yield on substrate SBO_0000671 agent driving non-enzymatic reaction. Non-enzymatic reactions resemble catalytic mechanisms as found in all major enzyme classes and occur spontaneously, small molecule (e.g. metal-) catalyzed or light-induced. non-enzymatic catalyst SBO_0000672 Reaction with no catalyst (no enzyme in particular) is needed to proceed. spontaneous reaction SBO_0000673 it represent the catalytic rate driving the reaction in forward direction. forward effective catalytic rate SBO_0000674 it represent the catalytic rate driving the reaction in backward direction. reverse effective catalytic rate SBO_0000675 Modeling approach where the quantities of participants are considered deterministic continuous variables, and represented by real values. The associated simulation methods make use of ordinary differential equations. deterministic non-spatial continuous framework SBO_0000676 Modeling approach where the quantities of participants are considered stochastic continuous variables, and represented by real values. The associated simulation methods make use of stochastic differential equations. The models do take into account the distribution of the entities. stochastic non-spatial continuous framework SBO_0000677 Modeling approach which tracks the sizes of populations of participants in each spatial localization. For biochemical simulations, such populations could represent types of molecular species. population-based discrete spatial simulation SBO_0000678 Modeling approach which tracks the state of individual particles in each spatial localization. For biochemical simulations, such particles could represent individual molecules. particle-based discrete spatial simulation SBO_0000679 Modeling approach which tracks the sizes of populations of participants with minimal or no spatial resolution. For biochemical simulations, such populations could represent types of molecular species. population-based discrete non-spatial simulation SBO_0000680 Modeling approach which tracks the state of individual particles with miimal or no spatial resolution. For biochemical simulations, such particles could represent individual molecules. particle-based discrete non-spatial simulation SBO_0000681 Modeling approach which combines multiple canonical modeling frameworks. For example, a hybrid model could consider both continuous (represented by real values) and discrete (represented by integers) participants. Hybrid models are executed with hybrid simulation algorithms. For example, a hybrid continuous-discrete model may be simulation using a combination of stochastic simulation and ordinary differential equations. hybrid framework SBO_0000682 Modeling approach which combines multiple canonical spatial modeling frameworks. For example, a hybrid model could consider both continuous (represented by real values) and discrete (represented by integers) participants. Hybrid models are executed with hybrid simulation algorithms. For example, a hybrid continuous-discrete model may be simulation using a combination of stochastic simulation and partial differential equations. hybrid spatial framework SBO_0000683 Modeling approach which combines multiple canonical non-spatial modeling frameworks. For example, a hybrid model could consider both continuous (represented by real values) and discrete (represented by integers) participants. Hybrid models are executed with hybrid simulation algorithms. For example, a hybrid continuous-discrete model may be simulation using a combination of stochastic simulation and ordinary differential equations. hybrid non-spatial framework SBO_0000684 Modeling approach which combines flux-balance [SBO:0000624] and deterministic continuous non-spatial [SBO:0000675] simulation. For example, a metabolic network could be simulated using flux balance analysis, while a signaling network could be co-simulated with a method for integrating ordinary differential equations. hybrid flux balance-deterministic continuous non-spatial framework SBO_0000685 Modeling approach which combines flux-balance [SBO:0000624] and discrete non-spatial [SBO:0000295] simulation. For example, a metabolic network could be simulated using flux balance analysis, while the synthesis and turnover of enzymes could be co-simulated with a discrete simulation method such as Gillespie's algorithm. hybrid flux balance-discrete non-spatial framework SBO_0000686 Modeling approach which combines flux-balance [SBO:0000624], non-spatial deterministic continuous [SBO:0000675], and logical [SBO:0000234] simulation. For example, a metabolic network could be simulated using flux balance analysis, while the expression metabolic enzymes could be co-simulated with a logical simulation method and a signaling network could be co-simulated with a method for integrating ordinary differential equations such as CVODE. hybrid flux balance-logical-deterministic continuous non-spatial framework SBO_0000687 Modeling approach which combines flux-balance [SBO:0000624] and logical [SBO:0000234] simulation. For example, a metabolic network could be simulated using flux balance analysis, while the expression metabolic enzymes could be co-simulated with a logical simulation method. hybrid flux balance-logical non-spatial framework SBO_0000688 Modeling approach which combines logical [SBO:0000234] and non-spatial discrete [SBO:0000295] simulation. For example, the MaBoSS simulation method simulates logical regulatory graphs with an algorithm that is similar to Gillespie's algorithm. hybrid flux logical-discrete non-spatial framework SBO_0000689 Modeling approach which combines continuous [SBO:0000293] and discrete [SBO:0000295] simulation, where some participants are represented as continuous variables and others are represented as discrete variables, without a detailed spatial representation of each participant. For example, a model may be simulated using a combination of a discrete simulation method such as Gillespie's algorithm and an ordinary differential equations integration method such as CVODE. hybrid continuous-discrete non-spatial framework SBO_0000690 Modeling approach which combines deterministic continuous [SBO:0000675] and discrete [SBO:0000295] simulation, where some participants are represented as deterministic, continuous variables and others are represented as discrete variables, without a detailed spatial representation of each participant. For example, a model may be simulated using a combination of a discrete simulation method such as Gillespie's algorithm and an ordinary differential equations integration method such as CVODE. hybrid deterministic continuous-discrete non-spatial framework SBO_0000691 Modeling approach which combines stochastic continuous [SBO:0000676] and discrete [SBO:0000295] simulation, where some participants are represented as stochastic, continuous variables and others are represented as discrete variables, without a detailed spatial representation of each participant. For example, a model may be simulated using a combination of a discrete simulation method such as Gillespie's algorithm and an stochastic differential equations integration method. hybrid stochastic continuous-discrete non-spatial framework SBO_0000692 Modeling approach where the flow of resources (flux) through a network can be calculated. This approach will generally produce a set of solutions (solution space), which may be reduced using objective functions and constraints on individual fluxes. resource balance framework SBO_0000693 Modelling approach which captures bounds on the possible behavior of a system, which may be further reduced using an objective function. constraint-based framework SBO_0000694 Modelling approach for finding the optimal state of a system. optimization framework SBO_0000695 Formation of a covalent bond resulting in the creation of a link between the ends of one or more linear polymer molecules. ligation Systems Biology Ontology, OWL export generated by SBO Browser (http://www.ebi.ac.uk/sbo/) Generated: 03:11:2021 07:00 28:08:2021 03:13 28:08:2021 03:13