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Create new 'DAE Solver' category; put IDA-like things in it.
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IDA solvers are ODE solvers plus algebraic rules, not steady state solvers.
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@luciansmith
luciansmith committed Mar 13, 2024
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Showing 1 changed file with 130 additions and 8 deletions.
138 changes: 130 additions & 8 deletions kisao.owl
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Original file line number Diff line number Diff line change
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<dc:creator xml:lang="en">dk</dc:creator>
<isImplementedIn xml:lang="en">SBML-SAT</isImplementedIn>
<isImplementedIn xml:lang="en">SUNDIALS</isImplementedIn>
<isImplementedIn xml:lang="en">libRoadRunner</isImplementedIn>
<isImplementedIn rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/biosimulators/bionetgen</isImplementedIn>
<isImplementedIn rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/biosimulators/jsim</isImplementedIn>
<isImplementedIn rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/biosimulators/opencor</isImplementedIn>
<isImplementedIn rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/biosimulators/pysces</isImplementedIn>
<isImplementedIn rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/biosimulators/tellurium</isImplementedIn>
<isImplementedIn rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/biosimulators/vcell</isImplementedIn>
<isImplementedIn xml:lang="en">libRoadRunner</isImplementedIn>
<rdfs:label xml:lang="en">CVODE</rdfs:label>
<rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">citeulike:1832863</rdfs:seeAlso>
<rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/doi/10.1145/1089014.1089020</rdfs:seeAlso>
Expand Down Expand Up @@ -8720,7 +8720,7 @@ Hierarchical cluster-based partial least squares regression method uses fuzzy C-
<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000432 -->

<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000432">
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000408"/>
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000699"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000259"/>
Expand Down Expand Up @@ -11588,10 +11588,10 @@ Levenberg first suggested an improvement to the Newton method in order to make i
<dc:creator xml:lang="en">JRK</dc:creator>
<isImplementedIn xml:lang="en">SUNDIALS</isImplementedIn>
<isImplementedIn xml:lang="en">SciPy</isImplementedIn>
<isImplementedIn xml:lang="en">libRoadRunner</isImplementedIn>
<isImplementedIn rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/biosimulators/copasi</isImplementedIn>
<isImplementedIn rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/biosimulators/gillespy2</isImplementedIn>
<isImplementedIn rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/biosimulators/tellurium</isImplementedIn>
<isImplementedIn xml:lang="en">libRoadRunner</isImplementedIn>
<rdfs:label xml:lang="en">initial step size</rdfs:label>
<skos:definition xml:lang="en">Initial time step size.</skos:definition>
</owl:Class>
Expand Down Expand Up @@ -13568,8 +13568,8 @@ Example system of equations:
<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000628 -->

<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000628">
<dc:creator rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2012-06-01</dc:creator>
<dc:creator xml:lang="en">JRK</dc:creator>
<dc:creator rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2012-06-01</dc:creator>
<isOrganizational rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</isOrganizational>
<rdfs:label xml:lang="en">modelling and simulation algorithm parameter value</rdfs:label>
<skos:definition xml:lang="en">A value of a parameter of an algorithm</skos:definition>
Expand Down Expand Up @@ -13613,8 +13613,8 @@ Example system of equations:

<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000631">
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000407"/>
<dc:creator rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2021-06-01</dc:creator>
<dc:creator xml:lang="en">JRK</dc:creator>
<dc:creator rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2021-06-01</dc:creator>
<isOrganizational rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</isOrganizational>
<rdfs:label xml:lang="en">iterative root-finding method</rdfs:label>
<skos:definition xml:lang="en">Iterative method for finding the root of a function (f(x) = 0).</skos:definition>
Expand Down Expand Up @@ -13662,8 +13662,8 @@ This method only involves evaluations of f. This method is suitable for non-stif

<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000634">
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000820"/>
<dc:created rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2021-06-04</dc:created>
<dc:created xml:lang="en">JRK</dc:created>
<dc:created rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2021-06-04</dc:created>
<rdfs:label xml:lang="en">scaled property</rdfs:label>
</owl:Class>

Expand Down Expand Up @@ -14965,6 +14965,129 @@ This method only involves evaluations of f. This method is suitable for non-stif



<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000699 -->

<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000699">
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000000"/>
<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_0000373"/>
</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_0000374"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000259"/>
<owl:maxQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:maxQualifiedCardinality>
<owl:onClass rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000209"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000259"/>
<owl:maxQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:maxQualifiedCardinality>
<owl:onClass rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000211"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000259"/>
<owl:maxQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:maxQualifiedCardinality>
<owl:onClass rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000415"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000259"/>
<owl:maxQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:maxQualifiedCardinality>
<owl:onClass rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000475"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000259"/>
<owl:maxQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:maxQualifiedCardinality>
<owl:onClass rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000476"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000259"/>
<owl:maxQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:maxQualifiedCardinality>
<owl:onClass rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000477"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000259"/>
<owl:maxQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:maxQualifiedCardinality>
<owl:onClass rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000478"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000259"/>
<owl:maxQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:maxQualifiedCardinality>
<owl:onClass rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000479"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000259"/>
<owl:maxQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:maxQualifiedCardinality>
<owl:onClass rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000480"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000259"/>
<owl:maxQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:maxQualifiedCardinality>
<owl:onClass rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000481"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000259"/>
<owl:maxQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:maxQualifiedCardinality>
<owl:onClass rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000543"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000259"/>
<owl:maxQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:maxQualifiedCardinality>
<owl:onClass rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000570"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000259"/>
<owl:maxQualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:maxQualifiedCardinality>
<owl:onClass rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000571"/>
</owl:Restriction>
</rdfs:subClassOf>
<dc:created>2024-03-13</dc:created>
<dc:creator xml:lang="en">lps</dc:creator>
<isOrganizational rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">false</isOrganizational>
<rdfs:label>DAE Solver</rdfs:label>
<skos:altLabel xml:lang="en">differential algebraic equation solver</skos:altLabel>
<skos:definition xml:lang="en">A DAE solver is the general category of packages such as IDA-like methods [http://identifiers.org/biomodels.kisao/KISAO_0000432] that solve systems of differential algebraic equations (DAEs). DAEs are a superset of ODEs that may additionally contain algebraic equations or &apos;fast&apos; reactions.</skos:definition>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000699"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2004/02/skos/core#altLabel"/>
<owl:annotatedTarget xml:lang="en">differential algebraic equation solver</owl:annotatedTarget>
<rdfs:comment xml:lang="en">EXACT</rdfs:comment>
</owl:Axiom>



<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000800 -->

<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000800">
Expand Down Expand Up @@ -16457,7 +16580,6 @@ This method only involves evaluations of f. This method is suitable for non-stif
<rdf:Description rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000371"/>
<rdf:Description rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000372"/>
<rdf:Description rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000373"/>
<rdf:Description rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000374"/>
</owl:members>
</rdf:Description>
<rdf:Description>
Expand Down Expand Up @@ -16558,5 +16680,5 @@ This method only involves evaluations of f. This method is suitable for non-stif



<!-- Generated by the OWL API (version 4.5.9.2019-02-01T07:24:44Z) https://github.com/owlcs/owlapi -->
<!-- Generated by the OWL API (version 4.5.26.2023-07-17T20:34:13Z) https://github.com/owlcs/owlapi -->

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