wc_onto/ontologies/KISAO.owl
<?xml version="1.0"?>
<rdf:RDF xmlns="http://www.biomodels.net/kisao/KISAO_FULL#"
xml:base="http://www.biomodels.net/kisao/KISAO_FULL"
xmlns:dc="http://purl.org/dc/terms/"
xmlns:obo="http://purl.obolibrary.org/obo/"
xmlns:ont="http://www.co-ode.org/ontologies/ont.owl#"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:xml="http://www.w3.org/XML/1998/namespace"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:skos="http://www.w3.org/2004/02/skos/core#"
xmlns:kisao="http://www.biomodels.net/kisao/KISAO#"
xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://www.biomodels.net/kisao/KISAO_FULL#">
<owl:imports rdf:resource="http://www.biomodels.net/kisao/KISAO#"/>
<dc:rights>Artistic License 2.0</dc:rights>
<rdfs:comment xml:lang="en">Kinetic Simulation Algorithm Ontology (full version, containing deprecated classes)</rdfs:comment>
<rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://co.mbine.org/standards/kisao</rdfs:seeAlso>
<rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/pubmed/22027554</rdfs:seeAlso>
<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#decimal">2.5</owl:versionInfo>
<skos:definition xml:lang="en">The Kinetic Simulation Algorithm Ontology (KiSAO) classifies algorithms available for the simulation and analysis of models in biology, and their characteristics and the parameters required for their use.</skos:definition>
</owl:Ontology>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Annotation properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://www.geneontology.org/formats/oboInOwl#Comment -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#Comment"/>
<!-- http://www.geneontology.org/formats/oboInOwl#CreatedBy -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#CreatedBy"/>
<!-- http://www.geneontology.org/formats/oboInOwl#CreationDate -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#CreationDate"/>
<!-- http://www.geneontology.org/formats/oboInOwl#Namespace -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#Namespace"/>
<!-- http://www.geneontology.org/formats/oboInOwl#OwlDef -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#OwlDef"/>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Object Properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000247 -->
<owl:ObjectProperty rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000247">
<rdfs:domain rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000000"/>
<rdfs:range rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000097"/>
<oboInOwl:Namespace xml:lang="en">KISAO_DEPRECATED</oboInOwl:Namespace>
<oboInOwl:OwlDef>?X subclassOf not (KISAO_0000245 some ?Y)</oboInOwl:OwlDef>
<rdfs:comment xml:lang="en">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.</rdfs:comment>
<rdfs:label xml:lang="en">lacks property</rdfs:label>
<owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
</owl:ObjectProperty>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Classes
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000001 -->
<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000001">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000025"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000245"/>
<owl:someValuesFrom rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000237"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000025"/>
<kisao:isOrganizational rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</kisao:isOrganizational>
<oboInOwl:Namespace xml:lang="en">KISAO_DEPRECATED</oboInOwl:Namespace>
<rdfs:label xml:lang="en">Gillespie-like approximate stochastic simulation method</rdfs:label>
<owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
</owl:Class>
<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000002 -->
<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000002">
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000262"/>
<rdfs:subClassOf>
<owl:Class>
<owl:complementOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000245"/>
<owl:someValuesFrom rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000102"/>
</owl:Restriction>
</owl:complementOf>
</owl:Class>
</rdfs:subClassOf>
<kisao:isOrganizational rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</kisao:isOrganizational>
<oboInOwl:Namespace xml:lang="en">KISAO_DEPRECATED</oboInOwl:Namespace>
<rdfs:label xml:lang="en">non-spatial tau-leaping method</rdfs:label>
<owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
</owl:Class>
<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000016 -->
<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000016">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000000"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000245"/>
<owl:someValuesFrom rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000105"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000262"/>
<kisao:isOrganizational rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</kisao:isOrganizational>
<oboInOwl:CreatedBy xml:lang="en">NLN</oboInOwl:CreatedBy>
<oboInOwl:CreationDate rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2008-07-08</oboInOwl:CreationDate>
<oboInOwl:Namespace xml:lang="en">KISAO_DEPRECATED</oboInOwl:Namespace>
<rdfs:comment xml:lang="en">Algorithm that allows to change the values of a system's variables by discrete (integral) amounts.</rdfs:comment>
<rdfs:label xml:lang="en">algorithm using discrete variables</rdfs:label>
<owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
</owl:Class>
<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000018 -->
<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000018">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000000"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000245"/>
<owl:someValuesFrom rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000106"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000262"/>
<kisao:isOrganizational rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</kisao:isOrganizational>
<oboInOwl:CreatedBy xml:lang="en">NLN</oboInOwl:CreatedBy>
<oboInOwl:CreationDate rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2008-07-08</oboInOwl:CreationDate>
<oboInOwl:Namespace xml:lang="en">KISAO_DEPRECATED</oboInOwl:Namespace>
<rdfs:comment xml:lang="en">Algorithm that allows to change the values of a system's variables by continuous (non-integral) amounts.</rdfs:comment>
<rdfs:label xml:lang="en">algorithm using continuous variables</rdfs:label>
<owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
</owl:Class>
<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000023 -->
<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000023">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000000"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000245"/>
<owl:someValuesFrom rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000102"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000262"/>
<kisao:isOrganizational rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</kisao:isOrganizational>
<oboInOwl:CreatedBy xml:lang="en">NLN</oboInOwl:CreatedBy>
<oboInOwl:CreationDate rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2008-07-08</oboInOwl:CreationDate>
<oboInOwl:Namespace xml:lang="en">KISAO_DEPRECATED</oboInOwl:Namespace>
<rdfs:comment xml:lang="en">Algorithm that takes into account the location of the reacting components.</rdfs:comment>
<rdfs:label xml:lang="en">algorithm using spatial description</rdfs:label>
<owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
</owl:Class>
<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000024 -->
<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000024">
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000262"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000245"/>
<owl:someValuesFrom rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000102"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000245"/>
<owl:someValuesFrom rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000103"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000245"/>
<owl:someValuesFrom rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000106"/>
</owl:Restriction>
</rdfs:subClassOf>
<kisao:isOrganizational rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</kisao:isOrganizational>
<oboInOwl:CreatedBy xml:lang="en">NLN</oboInOwl:CreatedBy>
<oboInOwl:CreationDate rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2008-07-08</oboInOwl:CreationDate>
<oboInOwl:Namespace xml:lang="en">KISAO_DEPRECATED</oboInOwl:Namespace>
<rdfs:comment xml:lang="en">Partial differential equations are used to describe variations in concentrations over both, space and time.</rdfs:comment>
<rdfs:label xml:lang="en">partial differential equation method</rdfs:label>
<owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
</owl:Class>
<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000025 -->
<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000025">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000241"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000245"/>
<owl:someValuesFrom rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000104"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000262"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000245"/>
<owl:someValuesFrom rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000104"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000245"/>
<owl:someValuesFrom rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000105"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000245"/>
<owl:someValuesFrom rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000107"/>
</owl:Restriction>
</rdfs:subClassOf>
<kisao:isOrganizational rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</kisao:isOrganizational>
<oboInOwl:Comment xml:lang="en">This definition is dodgy, as is the name of the term. That will do for the moment, until we redesign the whole stochastic branch, based on algorithm details.</oboInOwl:Comment>
<oboInOwl:CreatedBy xml:lang="en">NLN</oboInOwl:CreatedBy>
<oboInOwl:CreationDate rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2008-07-08</oboInOwl:CreationDate>
<oboInOwl:Namespace xml:lang="en">KISAO_DEPRECATED</oboInOwl:Namespace>
<rdfs:comment xml:lang="en">Stochastic simulation algorithm using the an approach alike the one described in Gillespie's papers of 1976 and 1977.</rdfs:comment>
<rdfs:label xml:lang="en">Gillespie-like stochastic simulation method</rdfs:label>
<owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
</owl:Class>
<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000026 -->
<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000026">
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000262"/>
<kisao:isOrganizational rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</kisao:isOrganizational>
<oboInOwl:CreatedBy xml:lang="en">NLN</oboInOwl:CreatedBy>
<oboInOwl:CreationDate rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2008-07-08</oboInOwl:CreationDate>
<oboInOwl:Namespace xml:lang="en">KISAO_DEPRECATED</oboInOwl:Namespace>
<rdfs:comment xml:lang="en">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.</rdfs:comment>
<rdfs:label xml:lang="en">algorithm using non-spatial description</rdfs:label>
<owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
</owl:Class>
<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000034 -->
<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000034">
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000262"/>
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000333"/>
<rdfs:subClassOf>
<owl:Class>
<owl:complementOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000245"/>
<owl:someValuesFrom rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000102"/>
</owl:Restriction>
</owl:complementOf>
</owl:Class>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000245"/>
<owl:someValuesFrom rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000236"/>
</owl:Restriction>
</rdfs:subClassOf>
<kisao:isOrganizational rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</kisao:isOrganizational>
<oboInOwl:CreatedBy xml:lang="en">NLN</oboInOwl:CreatedBy>
<oboInOwl:CreationDate rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2008-07-08</oboInOwl:CreationDate>
<oboInOwl:Namespace xml:lang="en">KISAO_DEPRECATED</oboInOwl:Namespace>
<rdfs:comment xml:lang="en">Algorithm aimed to speed-up Gillespie's direct method.</rdfs:comment>
<rdfs:label xml:lang="en">optimized direct method</rdfs:label>
<owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
</owl:Class>
<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000035 -->
<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000035">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000000"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000245"/>
<owl:someValuesFrom rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000103"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000262"/>
<kisao:isOrganizational rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</kisao:isOrganizational>
<oboInOwl:CreatedBy xml:lang="en">NLN</oboInOwl:CreatedBy>
<oboInOwl:CreationDate rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2008-07-08</oboInOwl:CreationDate>
<oboInOwl:Namespace xml:lang="en">KISAO_DEPRECATED</oboInOwl:Namespace>
<rdfs:comment xml:lang="en">Algorithm that simulates the temporal evolution of a system using determined descriptions, that from a precise initial state always provide the same ending state.</rdfs:comment>
<rdfs:label xml:lang="en">algorithm using deterministic rules</rdfs:label>
<owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
</owl:Class>
<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000036 -->
<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000036">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000000"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000245"/>
<owl:someValuesFrom rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000104"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000262"/>
<kisao:isOrganizational rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</kisao:isOrganizational>
<oboInOwl:CreatedBy xml:lang="en">NLN</oboInOwl:CreatedBy>
<oboInOwl:CreationDate rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2008-07-08</oboInOwl:CreationDate>
<oboInOwl:Namespace xml:lang="en">KISAO_DEPRECATED</oboInOwl:Namespace>
<rdfs:comment xml:lang="en">Algorithm that simulates the temporal evolution of a system using probabilistic rules, that from a precise initial state may provide different ending state.</rdfs:comment>
<rdfs:label xml:lang="en">algorithm using stochastic rules</rdfs:label>
<owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
</owl:Class>
<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000037 -->
<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000037">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000000"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000245"/>
<owl:someValuesFrom rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000108"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000262"/>
<kisao:isOrganizational rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</kisao:isOrganizational>
<oboInOwl:CreatedBy xml:lang="en">NLN</oboInOwl:CreatedBy>
<oboInOwl:CreationDate rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2008-07-08</oboInOwl:CreationDate>
<oboInOwl:Namespace xml:lang="en">KISAO_DEPRECATED</oboInOwl:Namespace>
<rdfs:comment xml:lang="en">Algorithm that uses timesteps of constant length to update the state of a system during the whole simulation.</rdfs:comment>
<rdfs:label xml:lang="en">algorithm using fixed timesteps</rdfs:label>
<owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
</owl:Class>
<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000041 -->
<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000041">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000000"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000245"/>
<owl:someValuesFrom rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000107"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000262"/>
<kisao:isOrganizational rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</kisao:isOrganizational>
<oboInOwl:CreatedBy xml:lang="en">NLN</oboInOwl:CreatedBy>
<oboInOwl:CreationDate rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2008-07-08</oboInOwl:CreationDate>
<oboInOwl:Namespace xml:lang="en">KISAO_DEPRECATED</oboInOwl:Namespace>
<rdfs:comment xml:lang="en">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.</rdfs:comment>
<rdfs:label xml:lang="en">algorithm using adaptive timesteps</rdfs:label>
<owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
</owl:Class>
<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000042 -->
<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000042">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000241"/>
<owl:Class>
<owl:complementOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000245"/>
<owl:someValuesFrom rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000102"/>
</owl:Restriction>
</owl:complementOf>
</owl:Class>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000262"/>
<kisao:isOrganizational rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</kisao:isOrganizational>
<oboInOwl:Namespace xml:lang="en">KISAO_DEPRECATED</oboInOwl:Namespace>
<rdfs:label xml:lang="en">Non-spatial Gillespie-like method</rdfs:label>
<owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
</owl:Class>
<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000044 -->
<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000044">
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000262"/>
<kisao:isOrganizational rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</kisao:isOrganizational>
<oboInOwl:Namespace xml:lang="en">KISAO_DEPRECATED</oboInOwl:Namespace>
<rdfs:label xml:lang="en">Gillespie based method for stiff systems.</rdfs:label>
<owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
</owl:Class>
<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000079 -->
<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000079">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000039"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000245"/>
<owl:someValuesFrom rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000239"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000262"/>
<kisao:isOrganizational rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</kisao:isOrganizational>
<oboInOwl:Namespace xml:lang="en">KISAO_DEPRECATED</oboInOwl:Namespace>
<rdfs:comment xml:lang="en">Explicit tau-leaping method.</rdfs:comment>
<rdfs:label xml:lang="en">explicit tau-leaping method</rdfs:label>
<owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
</owl:Class>
<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000083 -->
<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000083">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000039"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000245"/>
<owl:someValuesFrom rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000240"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000262"/>
<kisao:isOrganizational rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</kisao:isOrganizational>
<oboInOwl:Namespace xml:lang="en">KISAO_DEPRECATED</oboInOwl:Namespace>
<rdfs:comment xml:lang="en">Implicit tau-leaping method.</rdfs:comment>
<rdfs:label xml:lang="en">implicit tau-leaping method</rdfs:label>
<owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
</owl:Class>
<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000096 -->
<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000096">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000241"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000245"/>
<owl:someValuesFrom rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000104"/>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000245"/>
<owl:someValuesFrom rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000236"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000262"/>
<kisao:isOrganizational rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</kisao:isOrganizational>
<oboInOwl:CreatedBy xml:lang="en">NLN</oboInOwl:CreatedBy>
<oboInOwl:CreationDate rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2008-07-14</oboInOwl:CreationDate>
<oboInOwl:Namespace xml:lang="en">KISAO_DEPRECATED</oboInOwl:Namespace>
<rdfs:comment xml:lang="en">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.</rdfs:comment>
<rdfs:label xml:lang="en">Gillespie-like exact stochastic simulation method</rdfs:label>
<owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
</owl:Class>
<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000262 -->
<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000262">
<kisao:isOrganizational rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</kisao:isOrganizational>
<oboInOwl:CreatedBy xml:lang="en">AZ</oboInOwl:CreatedBy>
<oboInOwl:Namespace>KISAO_DEPRECATED</oboInOwl:Namespace>
<rdfs:comment xml:lang="en">The root of the branch where all the deprecated terms are stored.</rdfs:comment>
<rdfs:label xml:lang="en">deprecated class</rdfs:label>
<owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
</owl:Class>
<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000284 -->
<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000284">
<owl:equivalentClass>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000019"/>
<rdf:Description rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000020"/>
<rdf:Description rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000282"/>
<rdf:Description rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000283"/>
<rdf:Description rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000355"/>
<rdf:Description rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000356"/>
</owl:unionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000000"/>
<rdfs:subClassOf>
<owl:Class>
<owl:complementOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000245"/>
<owl:someValuesFrom rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000102"/>
</owl:Restriction>
</owl:complementOf>
</owl:Class>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000245"/>
<owl:someValuesFrom rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000103"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000245"/>
<owl:someValuesFrom rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000106"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000245"/>
<owl:someValuesFrom rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000107"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000245"/>
<owl:someValuesFrom rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000237"/>
</owl:Restriction>
</rdfs:subClassOf>
<dc:created rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2011-05-09</dc:created>
<dc:creator xml:lang="en">AZ</dc:creator>
<kisao:isOrganizational rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</kisao:isOrganizational>
<oboInOwl:Namespace xml:lang="en">KISAO_DEPRECATED</oboInOwl:Namespace>
<rdfs:label xml:lang="en">SUNDIALS method</rdfs:label>
<rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/doi/10.1145/1089014.1089020</rdfs:seeAlso>
<owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
<skos:definition xml:lang="en">One of the methods, implemented in SUNDIALS (a suite of advanced computational codes for solving large-scale problems that can be modeled as a system of nonlinear algebraic equations, or as initial-value problems in ordinary differential or differential-algebraic equations).</skos:definition>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000284"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#seeAlso"/>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/doi/10.1145/1089014.1089020</owl:annotatedTarget>
<rdfs:comment xml:lang="en">Hindmarsh, A. C., et al., SUNDIALS: Suite of Nonlinear and Differential/Algebraic Equation Solvers, ACM Trans. Math. Softw., 31:363-396, 2005.</rdfs:comment>
</owl:Axiom>
</rdf:RDF>
<!-- Generated by the OWL API (version 4.5.7.2018-12-02T02:23:35Z) https://github.com/owlcs/owlapi -->