IRI:
http://www.biomodels.net/kisao/KISAO_FULL#
Current version:
2.18
Imported Ontologies:
http://www.biomodels.net/kisao/KISAO# (visualise it with LODE)
Other visualisation:
Ontology source
Artistic License 2.0

Abstract

Kinetic Simulation Algorithm Ontology (full version, containing deprecated classes)

Table of Content

  1. Classes
  2. Object Properties
  3. Annotation Properties
  4. Namespace Declarations

Classes

algorithm using adaptive timestepsc back to ToC or Class ToC

IRI: http://www.biomodels.net/kisao/KISAO#KISAO_0000041

Algorithm that does not use fixed timesteps to update the state of a system during the whole simulation, but on the contrary adapts the length of the timesteps to the local situation.
is equivalent to
k i s a o 0000000 and (k i s a o 0000245 some k i s a o 0000107)
has super-classes
deprecated classc

algorithm using continuous variablesc back to ToC or Class ToC

IRI: http://www.biomodels.net/kisao/KISAO#KISAO_0000018

Algorithm that allows to change the values of a system's variables by continuous (non-integral) amounts.
is equivalent to
k i s a o 0000000 and (k i s a o 0000245 some k i s a o 0000106)
has super-classes
deprecated classc

algorithm using deterministic rulesc back to ToC or Class ToC

IRI: http://www.biomodels.net/kisao/KISAO#KISAO_0000035

Algorithm that simulates the temporal evolution of a system using determined descriptions, that from a precise initial state always provide the same ending state.
is equivalent to
k i s a o 0000000 and (k i s a o 0000245 some k i s a o 0000103)
has super-classes
deprecated classc

algorithm using discrete variablesc back to ToC or Class ToC

IRI: http://www.biomodels.net/kisao/KISAO#KISAO_0000016

Algorithm that allows to change the values of a system's variables by discrete (integral) amounts.
is equivalent to
k i s a o 0000000 and (k i s a o 0000245 some k i s a o 0000105)
has super-classes
deprecated classc

algorithm using fixed timestepsc back to ToC or Class ToC

IRI: http://www.biomodels.net/kisao/KISAO#KISAO_0000037

Algorithm that uses timesteps of constant length to update the state of a system during the whole simulation.
is equivalent to
k i s a o 0000000 and (k i s a o 0000245 some k i s a o 0000108)
has super-classes
deprecated classc

algorithm using non-spatial descriptionc back to ToC or Class ToC

IRI: http://www.biomodels.net/kisao/KISAO#KISAO_0000026

Algorithms that considers the system to be simulated as made of well-stirred components, that is the activity of the components is the same independently of their location.
has super-classes
deprecated classc

algorithm using spatial descriptionc back to ToC or Class ToC

IRI: http://www.biomodels.net/kisao/KISAO#KISAO_0000023

Algorithm that takes into account the location of the reacting components.
is equivalent to
k i s a o 0000000 and (k i s a o 0000245 some k i s a o 0000102)
has super-classes
deprecated classc

algorithm using stochastic rulesc back to ToC or Class ToC

IRI: http://www.biomodels.net/kisao/KISAO#KISAO_0000036

Algorithm that simulates the temporal evolution of a system using probabilistic rules, that from a precise initial state may provide different ending state.
is equivalent to
k i s a o 0000000 and (k i s a o 0000245 some k i s a o 0000104)
has super-classes
deprecated classc

deprecated classc back to ToC or Class ToC

IRI: http://www.biomodels.net/kisao/KISAO#KISAO_0000262

The root of the branch where all the deprecated terms are stored.
has sub-classes
Gillespie based method for stiff systems.c, Gillespie-like exact stochastic simulation methodc, Gillespie-like stochastic simulation methodc, Non-spatial Gillespie-like methodc, algorithm using adaptive timestepsc, algorithm using continuous variablesc, algorithm using deterministic rulesc, algorithm using discrete variablesc, algorithm using fixed timestepsc, algorithm using non-spatial descriptionc, algorithm using spatial descriptionc, algorithm using stochastic rulesc, explicit tau-leaping methodc, implicit tau-leaping methodc, non-spatial tau-leaping methodc, optimized direct methodc, partial differential equation methodc

explicit tau-leaping methodc back to ToC or Class ToC

IRI: http://www.biomodels.net/kisao/KISAO#KISAO_0000079

Explicit tau-leaping method.
is equivalent to
k i s a o 0000039 and (k i s a o 0000245 some k i s a o 0000239)
has super-classes
deprecated classc

Gillespie based method for stiff systems.c back to ToC or Class ToC

IRI: http://www.biomodels.net/kisao/KISAO#KISAO_0000044

has super-classes
deprecated classc

Gillespie-like approximate stochastic simulation methodc back to ToC or Class ToC

IRI: http://www.biomodels.net/kisao/KISAO#KISAO_0000001

is equivalent to
Gillespie-like stochastic simulation methodc and (k i s a o 0000245 some k i s a o 0000237)
has super-classes
Gillespie-like stochastic simulation methodc

Gillespie-like exact stochastic simulation methodc back to ToC or Class ToC

IRI: http://www.biomodels.net/kisao/KISAO#KISAO_0000096

Gillespie-like algorithm that produces exact realisation of the vector of entity amounts at each time by choosing rigorously time and reaction at each iteration.
is equivalent to
k i s a o 0000241 and (k i s a o 0000245 some k i s a o 0000104) and (k i s a o 0000245 some k i s a o 0000236)
has super-classes
deprecated classc

Gillespie-like stochastic simulation methodc back to ToC or Class ToC

IRI: http://www.biomodels.net/kisao/KISAO#KISAO_0000025

Stochastic simulation algorithm using the an approach alike the one described in Gillespie's papers of 1976 and 1977.
is equivalent to
k i s a o 0000241 and (k i s a o 0000245 some k i s a o 0000104)
has super-classes
deprecated classc
k i s a o 0000245 some k i s a o 0000105
k i s a o 0000245 some k i s a o 0000107
k i s a o 0000245 some k i s a o 0000104
has sub-classes
Gillespie-like approximate stochastic simulation methodc

implicit tau-leaping methodc back to ToC or Class ToC

IRI: http://www.biomodels.net/kisao/KISAO#KISAO_0000083

Implicit tau-leaping method.
is equivalent to
k i s a o 0000039 and (k i s a o 0000245 some k i s a o 0000240)
has super-classes
deprecated classc

Non-spatial Gillespie-like methodc back to ToC or Class ToC

IRI: http://www.biomodels.net/kisao/KISAO#KISAO_0000042

is equivalent to
k i s a o 0000241 and (not (k i s a o 0000245 some k i s a o 0000102))
has super-classes
deprecated classc

non-spatial tau-leaping methodc back to ToC or Class ToC

IRI: http://www.biomodels.net/kisao/KISAO#KISAO_0000002

has super-classes
deprecated classc
not (k i s a o 0000245 some k i s a o 0000102)

optimized direct methodc back to ToC or Class ToC

IRI: http://www.biomodels.net/kisao/KISAO#KISAO_0000034

Algorithm aimed to speed-up Gillespie's direct method.
has super-classes
deprecated classc
k i s a o 0000333
k i s a o 0000245 some k i s a o 0000236
not (k i s a o 0000245 some k i s a o 0000102)

partial differential equation methodc back to ToC or Class ToC

IRI: http://www.biomodels.net/kisao/KISAO#KISAO_0000024

Partial differential equations are used to describe variations in concentrations over both, space and time.
has super-classes
deprecated classc
k i s a o 0000245 some k i s a o 0000103
k i s a o 0000245 some k i s a o 0000106
k i s a o 0000245 some k i s a o 0000102

SUNDIALS methodc back to ToC or Class ToC

IRI: http://www.biomodels.net/kisao/KISAO#KISAO_0000284

is equivalent to
k i s a o 0000019 or k i s a o 0000020 or k i s a o 0000282 or k i s a o 0000283 or k i s a o 0000355 or k i s a o 0000356
has super-classes
k i s a o 0000000
k i s a o 0000245 some k i s a o 0000237
not (k i s a o 0000245 some k i s a o 0000102)
k i s a o 0000245 some k i s a o 0000103
k i s a o 0000245 some k i s a o 0000107
k i s a o 0000245 some k i s a o 0000106

Object Properties

lacks propertyop back to ToC or Object Property ToC

IRI: http://www.biomodels.net/kisao/KISAO#KISAO_0000247

lacksProperty is an alias for not hasProperty. It should not be used in OWL version of KiSAO. It's used in OBO version of KiSAO, as it is not possible to represent negation in OBO.
has domain
k i s a o 0000000
has range
k i s a o 0000097

Annotation Properties

commentap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#Comment

created byap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#CreatedBy

creation dateap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#CreationDate

namespaceap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#Namespace

owl defap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#OwlDef

Namespace Declarations back to ToC

default namespace
http://www.biomodels.net/kisao/KISAO_FULL#
KISAO
http://www.biomodels.net/kisao/KISAO#
oboInOwl
http://www.geneontology.org/formats/oboInOwl#
owl
http://www.w3.org/2002/07/owl#
rdf
http://www.w3.org/1999/02/22-rdf-syntax-ns#
rdfs
http://www.w3.org/2000/01/rdf-schema#
skos
http://www.w3.org/2004/02/skos/core#
terms
http://purl.org/dc/terms/
xsd
http://www.w3.org/2001/XMLSchema#

This HTML document was obtained by processing the OWL ontology source code through LODE, Live OWL Documentation Environment, developed by Silvio Peroni.