mamo
type: Ontology
version info: 2023-02-03

owlDef
type: AnnotationProperty

alternative label
type: AnnotationProperty
comment: The range of skos:altLabel is the class of RDF plain literals.
comment: skos:prefLabel, skos:altLabel and skos:hiddenLabel are pairwise disjoint properties.
definition: An alternative lexical label for a resource.
example: Acronyms, abbreviations, spelling variants, and irregular plural/singular forms may be included among the alternative labels for a concept. Mis-spelled terms are normally included as hidden labels (see skos:hiddenLabel).
sub property of: label

definition
type: AnnotationProperty
definition: A statement or formal explanation of the meaning of a concept.

example
type: AnnotationProperty
definition: An example of the use of a concept.

hidden label
type: AnnotationProperty
comment: skos:prefLabel, skos:altLabel and skos:hiddenLabel are pairwise disjoint properties.
definition: A lexical label for a resource that should be hidden when generating visual displays of the resource, but should still be accessible to free text search operations.
example: The range of skos:hiddenLabel is the class of RDF plain literals.
sub property of: label

preferred label
type: AnnotationProperty
comment: A resource has no more than one value of skos:prefLabel per language tag, and no more than one value of skos:prefLabel without language tag.
comment: The range of skos:prefLabel is the class of RDF plain literals.
comment: skos:prefLabel, skos:altLabel and skos:hiddenLabel are pairwise disjoint properties.
definition: The preferred lexical label for a resource, in a given language.
sub property of: label

hasFeature
type: ObjectProperty
range: modelling entity feature
property disjoint with: lacksFeature

isUsedToModel
type: ObjectProperty
domain: mathematical model
range: domain model

lacksFeature
type: ObjectProperty
range: modelling entity feature
owlDef: ?X subclassOf: not (hasFeature some ?Y)
definition: An object property to be used in the OBO version of MAMO to express negation.

epidemiological compartmental model
type: Class
subclass of: population model
subclass of: domain model
subclass of: Restriction
  on property: hasFeature
  some values from: probabilistic nature
definition: Compartmental models simplify the mathematical modelling of infectious diseases. The population is assigned to compartments with labels - for example, S, I, or R, (Susceptible, Infectious, or Recovered). People may progress between compartments. The order of the labels usually shows the flow patterns between the compartments; for example SEIS means susceptible, exposed, infectious, then susceptible again.

Axiom
annotated source: epidemiological compartmental model
annotated property: seeAlso
annotated target: http://identifiers.org/doi/10.1007/978-3-540-78911-6_2
comment: Brauer F. Compartmental Models in Epidemiology. Mathematical Epidemiology. 2008;1945:19-79.

SIR model
type: Class
subclass of: epidemiological compartmental model
alternative label: SIR
alternative label: susceptible-infectious-removed
alternative label: susceptible-infectious-removed model
definition: A compartmental epidemiological model with three compartments: susceptible S, infectious I, and removed R. The passage of individuals is modelled from S to I to R.

Axiom
annotated source: SIR model
annotated property: seeAlso
annotated target: http://identifiers.org/doi/10.1007/978-3-540-78911-6_2
comment: Brauer F. Compartmental Models in Epidemiology. Mathematical Epidemiology. 2008;1945:19-79.

Axiom
annotated source: SIR model
annotated property: seeAlso
annotated target: http://identifiers.org/doi/10.1098/rspa.1927.0118
comment: Kermack, W. O. and McKendrick, A. G. "A Contribution to the Mathematical Theory of Epidemics." Proc. Roy. Soc. Lond. A 115, 700-721, 1927.

SIS model
type: Class
subclass of: epidemiological compartmental model
alternative label: SIS
alternative label: susceptible-infectious-susceptible
alternative label: susceptible-infectious-susceptible model
definition: A compartmental epidemiological model with two compartments: susceptible S and infectious I. The passage of individuals is modelled from S to I and back.

Axiom
annotated source: SIS model
annotated property: seeAlso
annotated target: http://identifiers.org/doi/10.1007/978-3-540-78911-6_2
comment: Brauer F. Compartmental Models in Epidemiology. Mathematical Epidemiology. 2008;1945:19-79.

SEIR model
type: Class
subclass of: epidemiological compartmental model
alternative label: SEIR
alternative label: susceptible-exposed-infectious-recovered
alternative label: susceptible-exposed-infectious-recovered model
definition: A compartmental epidemiological model with four compartments: susceptible S, exposed E, infectious I, and removed R. The passage of individuals is modelled from S to E to I to R.

Axiom
annotated source: SEIR model
annotated property: seeAlso
annotated target: http://identifiers.org/doi/10.1007/978-3-540-78911-6_2
comment: Brauer F. Compartmental Models in Epidemiology. Mathematical Epidemiology. 2008;1945:19-79.

SEIS model
type: Class
subclass of: epidemiological compartmental model
alternative label: SEIS
alternative label: susceptible-exposed-infectious-susceptible
alternative label: susceptible-exposed-infectious-susceptible model
definition: A compartmental epidemiological model with three compartments: susceptible S, exposed E, and infectious I. The passage of individuals is modelled from S to E to I to S.

Axiom
annotated source: SEIS model
annotated property: seeAlso
annotated target: http://identifiers.org/doi/10.1007/978-3-540-78911-6_2
comment: Brauer F. Compartmental Models in Epidemiology. Mathematical Epidemiology. 2008;1945:19-79.

pharmacokinetic-pharmacodynamic model
type: Class
subclass of: pharmacometrics model
alternative label: PK-PD model
definition: Pharmacokinetic/pharmacodynamic (PK/PD) relationships and modeling builds the bridge between the two classical disciplines of clinical pharmacology: pharmacokinetics and pharmacodynamics. It links the concentration-time profile as assessed by pharmacokinetics to the intensity of observed response as quantified by pharmacodynamics. The resulting so-called integrated PK/PD-models allow the description of the complete time course of the desired and/or undesired effects in response to a drug therapy.

Axiom
annotated source: pharmacokinetic-pharmacodynamic model
annotated property: seeAlso
annotated target: http://identifiers.org/pubmed/11185661
comment: Derendorf H, Lesko LJ, Chaikin P, Colburn WA, Lee P, Miller R, Powell R, Rhodes G, Stanski D, Venitz J. Pharmacokinetic/pharmacodynamic modeling in drug research and development. J Clin Pharmacol. 2000 Dec;40(12 Pt 2):1399-418.

continuous data variable
type: Class
subclass of: statistical variable
definition: statistical data whose individual element can take any real number value.

ordinal data variable
type: Class
subclass of: statistical variable
alternative label: ordinal categorical data variable
definition: statistical variable whose elements take values that exist on an ordinal scale, i.e. an arbitrary numerical scale where the exact numerical quantity of a particular value has no significance beyond its ability to establish a ranking over a set of data points.

mathematical model
type: Class
subclass of: model
definition: Description of a system using mathematical concepts and language. The model is composed of a set of variables and a set of equations that establish relationships between the variables.
example: A set of ordinary differential equation describing a physical process.

statistical model
type: Class
subclass of: mathematical model
subclass of: Restriction
  on property: hasFeature
  some values from: quantitative characteristic
definition: Model that describes how one or more random variables are related to one or more random variables.
example: The relationship between the size and the age.

steady-state model
type: Class
subclass of: mathematical model
subclass of: Restriction
  on property: hasFeature
  some values from: dynamical characteristic
definition: Model which describes a system where the state variable values do not vary.

constraint-based model
type: Class
subclass of: steady-state model
subclass of: Restriction
  on property: hasFeature
  some values from: quantitative characteristic
comment: Can be analysed using flux balance analysis [http://identifiers.org/biomodels.kisao/KISAO_0000437].
definition: The constraint-based modeling procedure does not strive to find a single solution but rather finds a collection of all allowable solutions to the governing equations that can be defined (a solution space). The subsequent application of additional constraints further reduces the solution space and, consequently, reduces the number of allowable solutions that a cell can utilize.

Axiom
annotated source: constraint-based model
annotated property: seeAlso
annotated target: http://identifiers.org/pubmed/12700248
comment: Reed JL, Palsson BO (2003) Thirteen years of building constraint-based in silico models of Escherichia coli. J Bacteriol, 185(9):2692-9.

variable
type: Class
definition: Value that may change within the scope of a given model or set of operations.

independent variable
type: Class
subclass of: variable
disjoint with: dependent variable
comment: Synonyms: input variable
definition: variable which is controlled in an experiment, and that affects other variables during the experiment. An independent variable does not depend on other variables of the model.

dependent variable
type: Class
subclass of: variable
comment: Synonyms: output variable
definition: variable which is measured in an experiment, and that is affected during the experiment. A dependent variable depends on other variables
example: Example: in an experiment one controls x and measure y, with a relationship y = ax+b, y is depending on x.

pharmacokinetic model
type: Class
subclass of: pharmacometrics model
subclass of: Restriction
  on property: hasFeature
  some values from: quantitative characteristic
disjoint with: pharmacodynamic model
alternative label: pharmacokinetics model
definition: Model dedicated to the determination of the fate of substances administered externally to a living organism. Pharmacokinetics models are divided into several areas including the extent and rate of absorption, distribution, metabolism and excretion (ADME) to which Liberation is sometimes added (LADME).

pharmacodynamic model
type: Class
subclass of: pharmacometrics model
subclass of: Restriction
  on property: hasFeature
  some values from: quantitative characteristic
alternative label: pharmacodynamics model
definition: Models dedicated to the study of the biochemical and physiological effects of drugs on the body or on microorganisms or parasites within or on the body and the mechanisms of drug action and the relationship between drug concentration and effect.

multiphysics model
type: Class
subclass of: domain model
subclass of: Restriction
  on property: hasFeature
  some values from: quantitative characteristic
definition: Multiphysics treats simulations that involve multiple physical models or multiple simultaneous physical phenomena. For example, combining chemical kinetics and fluid mechanics or combining finite elements with molecular dynamics. Multiphysics typically involves solving coupled systems of partial differential equations.

rule-based model
type: Class
subclass of: mathematical model
subclass of: Class
  complement of: Restriction
    on property: hasFeature
    some values from: quantitative characteristic
subclass of: Restriction
  on property: hasFeature
  some values from: probabilistic nature
comment: Rule-based modeling is especially effective in cases where the rule-set is significantly simpler than the model it implies, meaning that the model is a repeated manifestation of a limited number of patterns.
definition: Model that uses a set of rules used to describe other model instances. The rule-set can be used to create a model, or suitable tools can use a rule-set in place of a model.

computational model
type: Class
subclass of: mathematical model
definition: mathematical model that requires computer simulations to study the behavior of a complex system. The system under study is often a complex nonlinear system for which simple, intuitive analytical solutions are not readily available. Rather than deriving a mathematical analytical solution to the problem, experimentation with the model is done by adjusting the parameters of the system in the computer, and studying the differences in the outcome of the experiments.
example: weather forecasting models, earth simulator models, flight simulator models, molecular protein folding models, neural network models.

agent-based model
type: Class
subclass of: computational model
subclass of: Restriction
  on property: hasFeature
  some values from: discrete characteristic
subclass of: Restriction
  on property: hasFeature
  some values from: probabilistic nature
comment: Synonym: multi-agent model
definition: model simulating the actions and interactions of autonomous agents (both individual or collective entities such as organizations or groups) with a view to assessing their effects on the system as a whole

Petri net
type: Class
subclass of: mathematical model
subclass of: Restriction
  on property: hasFeature
  some values from: static characteristic
definition: directed bipartite graph, in which the nodes represent transitions (i.e. events that may occur, signified by bars) and places (i.e. conditions, signified by circles). The directed arcs describe which places are pre- and/or postconditions for which transitions (signified by arrows) occurs.

computational Neuroscience model
type: Class
subclass of: domain model
subclass of: Restriction
  on property: hasFeature
  some values from: dynamical characteristic
definition: Computational Neuroscience emphasizes descriptions of functional and biologically realistic neurons (and neural systems) and their physiology and dynamics. These models capture the essential features of the biological system at multiple spatial-temporal scales, from membrane currents, protein, and chemical coupling to network oscillations, columnar and topographic architecture, and learning and memory. These computational models are used to frame hypotheses that can be directly tested by current or future biological and/or psychological experiments.

readout
type: Class
definition: information obtained about a system by the application of an analysis procedure to a model of this system
example: timecourse of a concentation; EC50

population model
type: Class
subclass of: mathematical model
subclass of: Restriction
  on property: hasFeature
  some values from: quantitative characteristic
definition: type of mathematical model that is applied to the study of population dynamics.

matrix population model
type: Class
subclass of: population model
definition: specific type of population model that uses matrix algebra. Matrix algebra, in turn, is simply a form of algebraic shorthand for summarizing a larger number of often repetitious and tedious algebraic computations.

logical model
type: Class
subclass of: mathematical model
subclass of: Class
  complement of: Restriction
    on property: hasFeature
    some values from: quantitative characteristic
alternative label: algebraic logic model
alternative label: logic model
definition: model where the discrete values of variables (also called levels) is determined by logical combinations of the values of other variables.

timecourse
type: Class
subclass of: readout
definition: evolution of a variable value over time

spatial characteristic
type: Class
subclass of: modelling entity feature
definition: model which take into account the spatial distribution or geometric characteristics of the entities described by its variables.

chemical reaction diffusion model
type: Class
subclass of: domain model
subclass of: Restriction
  on property: hasFeature
  some values from: dynamical characteristic
definition: mathematical model which explains how the concentration of one or more substances distributed in space changes under the influence of two processes: local chemical reactions in which the substances are transformed into each other, and diffusion which causes the substances to spread out over a domain in space.

finite element spatial model
type: Class
subclass of: chemical reaction diffusion model
definition: model where the space is split into a number of subspaces (sometimes called voxels) that are each considered homegenous and isotropic.

network model
type: Class
subclass of: domain model
definition: model based on a network of nodes or vertices, linked by edges or arcs. nodes can be physical entities, processes, events or logic operators. Edges can represent fluxs, interactions, influences etc.

biochemical network
type: Class
subclass of: network model
definition: Biochemical network studies chemical processes within and relating to, living organisms.

model
type: Class
definition: Purposeful simplification of reality, designed to imitate certain phenomena or characteristics of a system while downplaying non-essential aspects. Its value lies in the ability to generalise insights from the model to a broader class of systems.

signalling network
type: Class
subclass of: biochemical network
definition: Signal transduction is a process for cellular communication where the cell receives (and responds to) external stimuli from other cells and from the environment.

Axiom
annotated source: signalling network
annotated property: seeAlso
annotated target: http://identifiers.org/pubmed/19897097
comment: Albert R, Wang R (2009) Discrete dynamic modeling of cellular signaling networks. Methods Enzymol 467:281–306

gene regulatory network
type: Class
subclass of: biochemical network
definition: Gene regulation controls the expression of genes and, consequently, all cellular functions. Gene expression is a process that involves transcription of the gene into mRNA, followed by translation to a protein, which may be subject to post-translational modification. The transcription process is controlled by transcription factors (TFs) that can work as activators or inhibitors. TFs are themselves encoded by genes and subject to regulation, which altogether forms complex regulatory networks.

Axiom
annotated source: gene regulatory network
annotated property: seeAlso
annotated target: http://identifiers.org/pubmed/17903290
comment: Schlitt T, Brazma A (2007) Current approaches to gene regulatory network modelling. BMC Bioinf 8(Suppl 6):S9

metabolic network
type: Class
subclass of: biochemical network
definition: Metabolism is a mechanism composed by a set of biochemical reactions, by which the cell sustains its growth and energy requirements. It includes several catabolic and anabolic pathways of enzyme-catalyzed reactions that import substrates from the environment and transform them into energy and building blocks required to build the cellular components. Metabolic pathways are interconnected through intermediate metabolites, forming complex networks.

Axiom
annotated source: metabolic network
annotated property: seeAlso
annotated target: http://identifiers.org/isbn/9780521859035
comment: Palsson B (2006) Systems Biology: Properties of Reconstructed Networks. Cambridge University Press

Bayesian model
type: Class
subclass of: mathematical model
subclass of: Class
  complement of: Restriction
    on property: hasFeature
    some values from: quantitative characteristic
subclass of: Restriction
  on property: hasFeature
  some values from: probabilistic nature
subclass of: Restriction
  on property: isUsedToModel
  some values from: signalling network
subclass of: Restriction
  on property: isUsedToModel
  some values from: gene regulatory network
alternative label: Bayes model
alternative label: Bayes network
alternative label: Bayesian network
alternative label: belief network
alternative label: probabilistic DAG model
alternative label: probabilistic directed acyclic graphical model
definition: Bayesian networks are a special type of probabilistic graphs. Their nodes represent random variables (discrete or continuous) and the edges represent conditional dependencies, forming a directed acyclic graph. Each node contains a probabilistic function that is dependent on the values of its input nodes.

dynamic Bayesian model
type: Class
subclass of: Bayesian model
subclass of: Restriction
  on property: hasFeature
  some values from: dynamical characteristic
alternative label: dynamic Bayes model
alternative label: dynamic Bayes network
alternative label: dynamic Bayesian network
alternative label: dynamic belief network
alternative label: dynamic probabilistic DAG model
alternative label: dynamic probabilistic directed acyclic graphical model
definition: A dynamic Bayesian network is a Bayesian network that overcomes the inability to model feedback loops. In this case, the variables are replicated for each time step and the feedback is modeled by connecting the nodes at adjacent time steps.

Axiom
annotated source: dynamic Bayesian model
annotated property: seeAlso
annotated target: http://identifiers.org/pubmed/15308537
comment: Zou M, Conzen S (2005) A new dynamic Bayesian network (DBN) approach for identifying gene regulatory networks from time course microarray data. Bioinformatics 21(1):71–79

process algebra
type: Class
subclass of: mathematical model
subclass of: Class
  complement of: Restriction
    on property: hasFeature
    some values from: quantitative characteristic
subclass of: Restriction
  on property: hasFeature
  some values from: probabilistic nature
alternative label: process calculus
definition: Process algebras are a family of formal languages for modeling concurrent systems. They generally consist on a set of process primitives, operators for sequential and parallel composition of processes, and communication channels.

differential equation model
type: Class
subclass of: mathematical model
subclass of: Restriction
  on property: hasFeature
  some values from: quantitative characteristic
subclass of: Restriction
  on property: hasFeature
  some values from: continuous characteristic
subclass of: Restriction
  on property: isUsedToModel
  some values from: signalling network
subclass of: Restriction
  on property: isUsedToModel
  some values from: gene regulatory network
subclass of: Restriction
  on property: isUsedToModel
  some values from: metabolic network
alternative label: differential equations model
alternative label: model based on differential equations
alternative label: model using differential equations
definition: Differential equations describe the rate of change of continuous variables. They are typically used for modeling dynamical systems in several areas.

ordinary differential equation model
type: Class
subclass of: differential equation model
subclass of: Restriction
  on property: hasFeature
  some values from: deterministic nature
alternative label: ODE model
alternative label: model based on ordinary differential equations
alternative label: model using ordinary differential equation
alternative label: ordinary differential equations model
definition: model using equations containing a function of one independent variable and its derivatives.

stochastic differential equation model
type: Class
subclass of: differential equation model
subclass of: Restriction
  on property: hasFeature
  some values from: probabilistic nature
alternative label: SDE model
alternative label: model based on stochastic differential equations
alternative label: model using stochastic differential equations
alternative label: stochastic differential equations model
definition: model using differential equations in which one or more of the terms is a stochastic process, resulting in a solution which is itself a stochastic process

partial differential equation model
type: Class
subclass of: differential equation model
subclass of: Restriction
  on property: hasFeature
  some values from: deterministic nature
alternative label: PDE model
alternative label: model based on partial differential equations
alternative label: model using partial differential equations
alternative label: partial differential equations model
definition: model using differential equations that contains unknown multivariable functions and their partial derivatives.

interacting state machine
type: Class
subclass of: mathematical model
subclass of: Restriction
  on property: hasFeature
  some values from: dynamical characteristic
subclass of: Restriction
  on property: hasFeature
  some values from: discrete characteristic
subclass of: Restriction
  on property: hasFeature
  some values from: probabilistic nature
subclass of: Restriction
  on property: isUsedToModel
  some values from: signalling network
definition: Interacting state machines are diagram-based formalisms that describe the temporal behavior of a system based on the changes in the states of its parts. They differ from other approaches as they define a system in terms of its states rather than its components.

cellular automaton
type: Class
subclass of: computational model
subclass of: Restriction
  on property: hasFeature
  some values from: discrete characteristic
subclass of: Restriction
  on property: isUsedToModel
  some values from: signalling network
subclass of: Restriction
  on property: isUsedToModel
  some values from: gene regulatory network
subclass of: Restriction
  on property: isUsedToModel
  some values from: metabolic network
definition: Cellular automata are discrete dynamic models that consist on a grid of cells with a finite number of states. A cellular automaton has an initial configuration that changes at each time step through a predefined rule that calculates the state of each cell as a function of the state of its neighbors at the previous step.

dynamic cellular automaton
type: Class
subclass of: cellular automaton
subclass of: Restriction
  on property: hasFeature
  some values from: dynamical characteristic
alternative label: DSA
definition: Dynamic cellular automata are a variation of cellular automata that allows for movement of the cell contents inside the grid, mimicking brownian motion.

Axiom
annotated source: dynamic cellular automaton
annotated property: seeAlso
annotated target: http://identifiers.org/pubmed/15972011
comment: Wishart DS, Yang R, Arndt D, Tang P, Cruz J (2005) Dynamic cellular automata: an alternative approach to cellular simulation. In Silico Biol., 5(2):139-61.

stochastic cellular automaton
type: Class
subclass of: cellular automaton
subclass of: Restriction
  on property: hasFeature
  some values from: probabilistic nature
definition: Cellular automaton whose updating rule is stochastic, which means the new entity's state is not chosen deterministically based on the neighbours' states, but according to some probability distributions depending on the neighbours' states.

boolean model
type: Class
subclass of: logical model
subclass of: Restriction
  on property: isUsedToModel
  some values from: gene regulatory network
definition: Boolean models model networks of genes by boolean variables that represent active and inactive states. At each time step, the state of each gene is determined by a logic rule which is a function of the state of its regulators. The state of all genes forms a global state that changes synchronously.

Axiom
annotated source: boolean model
annotated property: seeAlso
annotated target: http://identifiers.org/pubmed/5803332
comment: Kauffman S (1969) Metabolic stability and epigenesis in randomly constructed genetic nets. J Theor Biol 22(3):437–467

modelling entity feature
type: Class
alternative label: modeling entity feature
definition: Dependent entity which another modelling entity has, i.e., that entity exhibits its property. Other common terms for property in natural language are characteristic, property, quality, etc.

temporal quality
type: Class
subclass of: modelling entity feature
definition: Characterises the evolution of a modelling entity over time.

dynamical characteristic
type: Class
subclass of: temporal quality
disjoint with: static characteristic
definition: Characterises a modelling entity that evolves over time.

static characteristic
type: Class
subclass of: temporal quality
definition: Characterises a modelling entity that does not evolve over time.

quantitative characteristic
type: Class
subclass of: modelling entity feature
definition: Characterises the possibility to be measured numerically.

discrete characteristic
type: Class
subclass of: quantitative characteristic
disjoint with: continuous characteristic
definition: Which values can be enumerated.

continuous characteristic
type: Class
subclass of: quantitative characteristic
definition: Which values cannot be enumerated. Whatever two values, there is always another value in between.

linear quality
type: Class
subclass of: modelling entity feature
definition: Which satisfies the principles of superposition and scaling.

uncertainty level
type: Class
subclass of: modelling entity feature
definition: Characterises the certainty, or lack of, of the modelling entity feature.

deterministic nature
type: Class
subclass of: uncertainty level
disjoint with: probabilistic nature
definition: Which value or behaviour is certain.

probabilistic nature
type: Class
subclass of: uncertainty level
alternative label: stochastic nature
definition: Which can exhibit alternative values or behaviours with differnent probability.

coloured Petri net
type: Class
subclass of: Petri net
alternative label: CP-net
alternative label: CPN
alternative label: colored Petri net
definition: graphical language for modelling and validating concurrent and distributed systems, and other systems in which concurrency plays a major role

Axiom
annotated source: coloured Petri net
annotated property: seeAlso
annotated target: http://identifiers.org/isbn/978-3-642-00284-7
comment: Jensen K, Kristensen LM. Coloured Petri Nets: Modeling and Validation of Concurrent Systems. Berlin: Springer, 2009.

continuous Petri net
type: Class
subclass of: Petri net
subclass of: Restriction
  on property: hasFeature
  some values from: continuous characteristic
alternative label: continuous PN
definition: Petri net model in which the number of marks in the places are real numbers instead of integers

Axiom
annotated source: continuous Petri net
annotated property: seeAlso
annotated target: http://identifiers.org/isbn/978-3-642-10669-9
comment: David R, Alla H. Discrete, continuous, and hybrid Petri Nets. Berlin, London: Springer, 2010.

functional Petri net
type: Class
subclass of: Petri net
alternative label: functional PN
alternative label: functional PNs
alternative label: self-modified PN
alternative label: self-modified PNs
alternative label: self-modified Petri net
definition: A Petri net that allows the flow relations between places and transitions to depend on the marking.

Axiom
annotated source: functional Petri net
annotated property: seeAlso
annotated target: http://identifiers.org/pubmed/17626066
comment: Chaouiya C. Petri net modelling of biological networks. Brief Bioinform. 2007;8(4):210-9.

hybrid functional Petri net
type: Class
subclass of: functional Petri net
subclass of: hybrid Petri net
alternative label: HFPN
alternative label: HFPNs
alternative label: Hybrid functional PNs
alternative label: hybrid functional PN
definition: hybrid Petri nets with additional features: continuous transition firing rates can depend on the values of the input places and the weights of arcs can be defined as a function of the markings of the connected places.

Axiom
annotated source: hybrid functional Petri net
annotated property: seeAlso
annotated target: http://identifiers.org/pubmed/12954096
comment: Matsuno H, Tanaka Y, Aoshima H, Doi A, Matsui M, Miyano S. Biopathways representation and simulation on hybrid functional Petri net. In Silico Biol. 2003;3(3):389-404.

hybrid Petri net
type: Class
subclass of: Petri net
alternative label: HPN
alternative label: HPNs
alternative label: hybrid PN
definition: Petri nets that allow the coexistence of both continuous and discrete processes. They include discrete places (marked with tokens) and continuous places associated with real variables (e.g. concentration levels).

Axiom
annotated source: hybrid Petri net
annotated property: seeAlso
annotated target: http://identifiers.org/pubmed/17626066
comment: Chaouiya C. Petri net modelling of biological networks. Brief Bioinform. 2007;8(4):210-9.

stochastic Petri net
type: Class
subclass of: Petri net
subclass of: Restriction
  on property: hasFeature
  some values from: discrete characteristic
subclass of: Restriction
  on property: hasFeature
  some values from: probabilistic nature
alternative label: SPN
alternative label: stochastic PN
definition: form of Petri net where the transitions fire after a probabilistic delay determined by a random variable.

logistic regression
type: Class
subclass of: statistical model
alternative label: logit regression
definition: type of probabilistic classification model used for predicting the outcome of a categorical dependent variable (i.e., a class label) based on one or more predictor variables (features).

mixed model
type: Class
subclass of: statistical model
subclass of: Restriction
  on property: hasFeature
  some values from: deterministic nature
subclass of: Restriction
  on property: hasFeature
  some values from: probabilistic nature
definition: statistical model containing both fixed effects and random effects, that is mixed effects.

multinomial logistic regression
type: Class
subclass of: statistical model
alternative label: multinomial logit
alternative label: softmax regression
definition: regression model which generalizes logistic regression by allowing more than two discrete outcomes.

Poisson regression
type: Class
subclass of: statistical model
definition: form of regression analysis used to model count data and contingency tables. Poisson regression assumes the response variable Y has a Poisson distribution, and assumes the logarithm of its expected value can be modeled by a linear combination of unknown parameters.

binary data variable
type: Class
subclass of: statistical variable
subclass of: Restriction
  on property: hasFeature
  some values from: discrete characteristic
definition: Data whose individual element can take on only two possible values, traditionally termed 0 and 1 in accordance with the binary numeral system and Boolean algebra.

categorical data variable
type: Class
subclass of: statistical variable
subclass of: Restriction
  on property: hasFeature
  some values from: discrete characteristic
alternative label: nominal categorical data variable
definition: Statistical data type consisting of categorical variables, used for observed data whose value is one of a fixed number of nominal categories, or for data that has been converted into that form, for example as grouped data.

count data variable
type: Class
subclass of: statistical variable
subclass of: Restriction
  on property: hasFeature
  some values from: discrete characteristic
definition: Statistical data type, a type of data in which the observations can take only the non-negative integer values {0, 1, 2, 3, ...}, and where these integers arise from counting rather than ranking.

longitudinal data variable
type: Class
subclass of: statistical variable
definition: repeated observations of the same variables over time.

phase portrait
type: Class
subclass of: readout
definition: representation of the trajectories of a dynamical system in the phase plane. Each set of initial conditions is represented by a different curve, or point.

steady state value
type: Class
subclass of: readout
definition: value that does not change over time

statistical variable
type: Class
subclass of: variable
definition: In statistics, groups of individual data points may be classified as belonging to any of various statistical data types, e.g. categorical ("red", "blue", "green"), real number (1.68, -5, 1.7e+6), etc.

population pharmacokinetics model
type: Class
subclass of: pharmacokinetic model
definition: Model to study the sources and correlates of variability in drug concentrations among individuals who are the target patient population receiving clinically relevant doses of a drug of interest.

Axiom
annotated source: population pharmacokinetics model
annotated property: seeAlso
annotated target: http://www.fda.gov/downloads/Drugs/Guidances/UCM072137.pdf
comment: Guidance for Industry, Population Pharmacokinetics, U.S. Department of Health and Human Services, Food and Drug Administration, Center for Drug Evaluation and Research (CDER), Center for Biologics Evaluation and Research (CBER)February 1999.

single particle spatial model
type: Class
subclass of: domain model
alternative label: mesoscopic model
definition: model where the reactions and diffusion of each particle in a population is described and followed over time. Sometimes called mesoscopic model, because more abstract than an atomic or molecular dynamic model, but more detailed than a concentration based reaction diffusion model.

Axiom
annotated source: single particle spatial model
annotated property: seeAlso
annotated target: http://lenoverelab.org/perso/lenov/PUBLIS/Tolle2006.pdf
comment: Tolle D., Le Novère N. Particle-based Stochastic Simulation in Systems Biology. Current Bioinformatics (2006), 1: 315-320.

delayed differential equation model
type: Class
subclass of: differential equation model
alternative label: DDE model
alternative label: delayed differential equations model
alternative label: model based on delayed differential equations
alternative label: model using delayed differential equations
definition: model using a type of differential equation in which the derivative of the unknown function at a certain time is given in terms of the values of the function at previous times.

differential algebraic equation model
type: Class
subclass of: differential equation model
alternative label: DAE model
alternative label: differential algebraic equations model
alternative label: model based on differential algebraic equations
alternative label: model using differential algebraic equations
definition: general form of (systems of) differential equations for vector–valued functions x in one independent variable,

domain model
type: Class
subclass of: model

pharmacometrics model
type: Class
subclass of: domain model
definition: model used to describe and quantify interactions between xenobiotics and patients.

multi-value logic model
type: Class
subclass of: logical model
definition: logical model in which variables can take more than two levels.

Axiom
annotated source: multi-value logic model
annotated property: seeAlso
annotated target: http://identifiers.org/isbn/978-3-540-09556-9
comment: P Van Ham. How to deal with variables with more than two levels. In Kinetic Logic A Boolean Approach to the Analysis of Complex Regulatory Systems. Lecture Notes in Biomathematics Vol 29, 1979, pp 326-343

cellular Potts model
type: Class
subclass of: cellular automaton
alternative label: Glazier and Graner model
alternative label: extended large-q Potts model
definition: generalized version of a Potts model, where the cell associated with a spin can be composed of several elements, called pixels. Simulations progress by updating the pixels.

Axiom
annotated source: cellular Potts model
annotated property: seeAlso
annotated target: http://dx.doi.org/10.1103/PhysRevLett.69.2013
comment: Graner F and Glazier JA. Simulation of biological cell sorting using a two-dimensional extended Potts model, Phys. Rev. Lett. 69, 2013 - Published 28 September 1992.

standard Potts model
type: Class
subclass of: cellular Potts model
definition: cellular Potts model in which each cell is made up of only one pixel (q-spin). The standard Potts model is a generalisation of the Ising model where the spin can take a discret number of values regularly distributed.

Ising model
type: Class
subclass of: standard Potts model
definition: model that consists of discrete variables, called spins, that can be in one of two states (+1 or −1). The spins are arranged in a graph, usually, a lattice,

Axiom
annotated source: Ising model
annotated property: seeAlso
annotated target: http://identifiers.org/pubmed/10468569
comment: Duke TA, Bray D. Heightened sensitivity of a lattice of membrane receptors. Proc Natl Acad Sci U S A. 1999;96(18):10104-8.

fuzzy logic model
type: Class
subclass of: logical model
definition: logical model which rely on fuzzy logic for deciding the new values of variables, that is the use of truth values instead of truth table to interpret the inputs and the resulting output.

Axiom
annotated source: fuzzy logic model
annotated property: seeAlso
annotated target: http://identifiers.org/pubmed/19343194
comment: Aldridge BB, Saez-Rodriguez J, Muhlich JL, Sorger PK, Lauffenburger DA. Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/insulin-induced signaling. PLoS Comput Biol. 2009;5(4):e1000340.

generalized logical model
type: Class
subclass of: multi-value logic model
definition: multi-valued logical model with multiple thresholds to assign variable values, logical parameters controlling the assignments, and asynchronous update.

Axiom
annotated source: generalized logical model
annotated property: seeAlso
annotated target: http://identifiers.org/doi/10.1080/02681118908806072
comment: Snoussi EH. Qualitative dynamics of piecewise-linear differential equations: a discrete mapping approach. Dyn Stab Syst 1989, 4(3-4): 565-583

S system model
type: Class
subclass of: biochemical network
subclass of: ordinary differential equation model
definition: model in which the creation and destruction of a molecular species are represented using two power-law expansions in the species of the system. Reactions are not represented independently, but are subsumed in the apparent global reaction order (not necessarily integer) for the species affecting its rate.

Axiom
annotated source: S system model
annotated property: seeAlso
annotated target: http://identifier.org/pubmed/5387047
comment: Savageau MA. Biochemical systems analysis. II. The steady-state solutions for an n-pool system using a power-law approximation. J Theor Biol. 1969 Dec;25(3):370-9.

linear pharmacokinetic model
type: Class
subclass of: pharmacokinetic model
disjoint with: nonlinear pharmacokinetic model
definition: pharmacokinetic model expressed as differential equations in which partial derivatives with respect to any of the model parameters are independent of the other parameters

Axiom
annotated source: linear pharmacokinetic model
annotated property: seeAlso
annotated target: http://identifier.org/isbn/978-0387-27197-2
comment: Bonate PL (2006) Pharmacokinetic-Pharmacodynamic; Modeling and simulation. p 57

linear mixed effect pharmacokinetic model
type: Class
subclass of: linear pharmacokinetic model
definition: linear pharmacokinetic model which contain both fixed and random effects (mixed)

Axiom
annotated source: linear mixed effect pharmacokinetic model
annotated property: seeAlso
annotated target: http://identifier.org/isbn/978-0387-27197-2
comment: Bonate PL (2006) Pharmacokinetic-Pharmacodynamic; Modeling and simulation. p 181

nonlinear pharmacokinetic model
type: Class
subclass of: pharmacokinetic model
definition: pharmacokinetic model expressed as differential equations in which any partial derivatives with respect to any of the model parameters are dependent on any other model parameter or for which the derivatives do not exist or are discontinuous

Axiom
annotated source: nonlinear pharmacokinetic model
annotated property: seeAlso
annotated target: http://identifier.org/isbn/978-0387-27197-2
comment: Bonate PL (2006) Pharmacokinetic-Pharmacodynamic; Modeling and simulation. p 93

nonlinear mixed effect pharmacokinetic model
type: Class
subclass of: nonlinear pharmacokinetic model
definition: nonlinear pharmacokinetic model which contain both fixed and random effects (mixed)

Axiom
annotated source: nonlinear mixed effect pharmacokinetic model
annotated property: seeAlso
annotated target: http://identifier.org/isbn/978-0387-27197-2
comment: Bonate PL (2006) Pharmacokinetic-Pharmacodynamic; Modeling and simulation. p 205

Markov model
type: Class
subclass of: mathematical model
subclass of: Restriction
  on property: hasFeature
  some values from: probabilistic nature
definition: a stochastic model, that models a process where the state depends on previous states in a non-deterministic way, and assumes the Markov property: the conditional probability distribution of future states of the process (conditional on both past and present values) depends only upon the present state; that is, given the present, the future does not depend on the past.

hidden Markov model
type: Class
subclass of: Markov model
alternative label: HMM
definition: a Markov model in which the system being modeled is autonomous and its state is only partially observable. In other words, observations are related to the state of the system, but they are typically insufficient to precisely determine the state.

Markov chain
type: Class
subclass of: Markov model
alternative label: DTMC
alternative label: discrete-time Markov chain
definition: a Markov model that models the state of a system with a random variable that changes through time. In this context, the Markov property suggests that the distribution for this variable depends only on the distribution of the previous state. The system is autonomous and its state is fully observable.

Markov decision process
type: Class
subclass of: Markov model
alternative label: MDP
definition: a mathematical framework for modeling decision making in situations where outcomes are partly random and partly under the control of a decision maker.

Markov random field
type: Class
subclass of: Markov model
alternative label: MRF
alternative label: Markov network
alternative label: undirected graphical model
definition: a set of random variables having a Markov property described by an undirected graph. A Markov random field may be considered to be a generalization of a Markov chain in multiple dimensions. In a Markov chain, state depends only on the previous state in time, whereas in a Markov random field, each state depends on its neighbors in any of multiple directions. A Markov random field may be visualized as a field or graph of random variables, where the distribution of each random variable depends on the neighboring variables with which it is connected.

piecewise linear differential equation model
type: Class
subclass of: differential equation model
alternative label: model based on piecewise linear differential equations
alternative label: model using piecewise linear differential equations
alternative label: piecewise linear differential equations model
definition: model using functions that respond to parameter values via threshold (Heavyside) functions.

Axiom
annotated source: piecewise linear differential equation model
annotated property: seeAlso
annotated target: http://identifiers.org/pubmed/4741704
comment: Glass L, Kauffman SA. The logical analysis of continuous, non-linear biochemical control networks. J Theor Biol. 1973;39(1):103-29.

discrete time piecewise linear differential equation model
type: Class
subclass of: piecewise linear differential equation model
subclass of: Restriction
  on property: hasFeature
  some values from: discrete characteristic
definition: model using piecewise linear differential equations in which variables are updated only at certain times.

Axiom
annotated source: discrete time piecewise linear differential equation model
annotated property: seeAlso
annotated target: http://identifiers.org/pubmed/16521027
comment: Coutinho R, Fernandez B, Lima R, Meyroneinc A. Discrete time piecewise affine models of genetic regulatory networks. J Math Biol. 2006 Apr;52(4):524-70. Epub 2006 Mar 6.

qualitative piecewise linear differential equation model
type: Class
subclass of: piecewise linear differential equation model
definition: piecewise linear differential equation model in which the variables can only take a discrete number of levels.

Axiom
annotated source: qualitative piecewise linear differential equation model
annotated property: seeAlso
annotated target: http://identifiers.org/pubmed/14871568
comment: De Jong H1, Gouze JL, Hernandez C, Page M, Sari T, Geiselmann J. Qualitative simulation of genetic regulatory networks using piecewise-linear models. Bull Math Biol. 2004 Mar;66(2):301-40.

protein-protein interaction network
type: Class
subclass of: biochemical network
alternative label: PIN
alternative label: PPI
alternative label: PPI network
alternative label: PPIN
alternative label: PPIs
definition: A network representing intentional physical contacts established between two or more proteins as a result of biochemical events and/or electrostatic forces.

Axiom
annotated source: protein-protein interaction network
annotated property: seeAlso
annotated target: http://identifiers.org/pubmed/22385417
comment: Koh et al. Analyzing protein-protein interaction networks. J Proteome Res. 2012; 11(4):2014-31.

physiologically based pharmacokinetic model
type: Class
subclass of: pharmacokinetic model
alternative label: PBPK
definition: A model using a series of differential equations that are parametrized with known physiological variables and represent a quantitative mechanistic framework by which the absorption, distribution, metabolism, and excretion (ADME) of new drugs can be described.

Axiom
annotated source: physiologically based pharmacokinetic model
annotated property: seeAlso
annotated target: http://identifiers.org/pubmed/23945604
comment: HM Jones and K Rowland-Yeo Basic Concepts in Physiologically Based Pharmacokinetic Modeling in Drug Discovery and Development (2013) Pharmacometrics Syst Pharmacol. 2(8): e63.

square-lattice Ising model
type: Class
subclass of: Ising model
definition: 2D Ising model [http://identifiers.org/mamo/MAMO_0000185] of interacting magnetic spins on a square lattice.

whole-cell model
type: Class
subclass of: domain model
definition: Computational model that includes all of the molecular components of a biological cell and their interactions.

Axiom
annotated source: whole-cell model
annotated property: seeAlso
annotated target: http://identifiers.org/pubmed/22817898
comment: Karr et al. A whole-cell computational model predicts phenotype from genotype. Cell. 2012; 150(2):389-401.