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
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