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Merge pull request #114 from SED-ML/steadystate-reorg
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Make 407 the root-finding steady state algorithm.
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@luciansmith
luciansmith committed Jun 28, 2023
2 parents c944d8d + 71384fe commit adcaf56
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39 changes: 20 additions & 19 deletions kisao.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -8060,19 +8060,25 @@ DASPK is written in Fortran.</skos:definition>
<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000407 -->

<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000407">
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000000"/>
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000630"/>
<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_0000696"/>
</owl:Restriction>
</rdfs:subClassOf>
<dc:created rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2012-01-17</dc:created>
<dc:creator xml:lang="en">AZ</dc:creator>
<isOrganizational rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</isOrganizational>
<isOrganizational rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">false</isOrganizational>
<rdfs:comment xml:lang="en">Requested by Frank T. Bergmann on Sunday, November 27, 2011 4:45:30 PM.</rdfs:comment>
<rdfs:label xml:lang="en">steady state method</rdfs:label>
<skos:definition xml:lang="en">A method looking for a steady state of a dynamic system.</skos:definition>
<rdfs:label xml:lang="en">steady state root-finding method</rdfs:label>
<skos:definition xml:lang="en">Method for finding the root of a function (f(x) = 0).</skos:definition>
</owl:Class>


Expand Down Expand Up @@ -8950,8 +8956,8 @@ Hierarchical cluster-based partial least squares regression method uses fuzzy C-
<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000437 -->

<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000437">
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000407"/>
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000622"/>
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000630"/>
<dc:created rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2012-11-29</dc:created>
<dc:creator xml:lang="en">AZ</dc:creator>
<rdfs:comment xml:lang="en">Requested by Frank T. Bergmann on Thursday, November 29, 2012 9:51:58 AM.</rdfs:comment>
Expand Down Expand Up @@ -10644,8 +10650,8 @@ Levenberg first suggested an improvement to the Newton method in order to make i
<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000526 -->

<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000526">
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000407"/>
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000622"/>
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000630"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000259"/>
Expand Down Expand Up @@ -12349,8 +12355,8 @@ Min sum(|fluxAi - fluxBi|)</skos:definition>
<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000580 -->

<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000580">
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000407"/>
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000622"/>
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000630"/>
<dc:created rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2020-10-29</dc:created>
<dc:creator xml:lang="en">JRK</dc:creator>
<isImplementedIn rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/biosimulators/cobratoolbox</isImplementedIn>
Expand Down Expand Up @@ -12591,8 +12597,8 @@ Min sum(|fluxAi - fluxBi|)</skos:definition>
<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000588 -->

<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000588">
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000407"/>
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000622"/>
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000630"/>
<dc:created rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2020-10-29</dc:created>
<dc:creator xml:lang="en">JRK</dc:creator>
<isOrganizational rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</isOrganizational>
Expand Down Expand Up @@ -12734,8 +12740,8 @@ Min sum(|fluxAi - fluxBi|)</skos:definition>
<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000593 -->

<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000593">
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000407"/>
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000622"/>
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000630"/>
<dc:created rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2020-10-29</dc:created>
<dc:creator xml:lang="en">JRK</dc:creator>
<isOrganizational rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</isOrganizational>
Expand Down Expand Up @@ -13593,25 +13599,20 @@ Example system of equations:
<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_0000696"/>
</owl:Restriction>
</rdfs:subClassOf>
<dc:created rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2021-06-01</dc:created>
<dc:creator xml:lang="en">JRK</dc:creator>
<isOrganizational rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</isOrganizational>
<rdfs:label xml:lang="en">root-finding method</rdfs:label>
<skos:definition xml:lang="en">Method for finding the root of a function (f(x) = 0).</skos:definition>
<rdfs:label xml:lang="en">general steady state method</rdfs:label>
<skos:altLabel>root-finding method</skos:altLabel>
<skos:definition xml:lang="en">A method looking for a steady state of a dynamic system.</skos:definition>
</owl:Class>



<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000631 -->

<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000631">
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000630"/>
<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>
<isOrganizational rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</isOrganizational>
Expand Down Expand Up @@ -14243,7 +14244,7 @@ This method only involves evaluations of f. This method is suitable for non-stif
<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000669 -->

<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000669">
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000407"/>
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000630"/>
<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000685"/>
<rdfs:subClassOf>
<owl:Restriction>
Expand Down
2 changes: 1 addition & 1 deletion libkisao/python/kisao/_version.py
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Original file line number Diff line number Diff line change
@@ -1 +1 @@
__version__ = '2.32'
__version__ = '2.33'
2 changes: 1 addition & 1 deletion libkisao/python/tests/test_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -149,7 +149,7 @@ def test_steadystate_algorithms(self):
kisao = Kisao()
terms = utils.get_steadystate_algorithms()

self.assertIn(kisao.get_term('KISAO_0000630'), terms) # root-finding algorithm
self.assertIn(kisao.get_term('KISAO_0000407'), terms) # steady state root-finding algorithm
self.assertIn(kisao.get_term('KISAO_0000568'), terms) # NLEQ1
self.assertIn(kisao.get_term('KISAO_0000569'), terms) # NLEQ2
self.assertIn(kisao.get_term('KISAO_0000355'), terms) # DASPK
Expand Down

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