- Author:
- Dewan Sarwar <sarwarcse@gmail.com>
- Date:
- 2019-01-31 16:34:20+13:00
- Desc:
- Testing with Max's suggested way of annotation for weinstein_1995_max model
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/584/rawfile/848b6a8fb585337adc4f3805c0ed682a6a5fd379/NaHCO3/Ostby_2009_NBC.cellml
<?xml version="1.0" encoding="UTF-8"?>
<model xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqs="http://www.cellml.org/bqs/1.0#" xmlns:semsim="http://www.bhi.washington.edu/SemSim#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" name="Ostby_2009_NBC" cmeta:id="Ostby_2009_NBC">
<import xlink:href="Units/Units.cellml">
<units name="mM" units_ref="mM" />
</import>
<import xlink:href="Units/Units.cellml">
<units name="umol_per_s_per_cm2" units_ref="umol_per_s_per_cm2" />
</import>
<import xlink:href="Units/Units.cellml">
<units name="mJ_per_mol_per_kelvin" units_ref="mJ_per_mol_per_kelvin" />
</import>
<import xlink:href="Units/Units.cellml">
<units name="mS_per_cm2" units_ref="mS_per_cm2" />
</import>
<import xlink:href="Units/Units.cellml">
<units name="C_per_mol" units_ref="C_per_mol" />
</import>
<import xlink:href="Units/Units.cellml">
<units name="mV" units_ref="mV" />
</import>
<component name="NBC">
<variable cmeta:id="NBC.V_m" name="V_m" public_interface="in" units="mV" />
<variable cmeta:id="NBC.Na_int" name="Na_int" public_interface="in" units="mM" />
<variable cmeta:id="NBC.Na_ext" name="Na_ext" public_interface="in" units="mM" />
<variable cmeta:id="NBC.HCO3_int" name="HCO3_int" public_interface="in" units="mM" />
<variable cmeta:id="NBC.HCO3_ext" name="HCO3_ext" public_interface="in" units="mM" />
<variable cmeta:id="NBC.g_NBC" initial_value="0.08" name="g_NBC" public_interface="out" units="mS_per_cm2" />
<variable cmeta:id="NBC.F" initial_value="96485" name="F" units="C_per_mol" />
<variable cmeta:id="NBC.R" initial_value="8314.41" name="R" units="mJ_per_mol_per_kelvin" />
<variable cmeta:id="NBC.T" initial_value="300" name="T" units="kelvin" />
<variable cmeta:id="NBC.n" initial_value="2" name="n" units="dimensionless" />
<variable cmeta:id="NBC.eps" initial_value="1e-15" name="eps" units="mM" />
<variable cmeta:id="NBC.E_NBC" name="E_NBC" public_interface="out" units="mV" />
<variable cmeta:id="NBC.J_NBC_Na" name="J_NBC_Na" public_interface="out" units="umol_per_s_per_cm2" />
<variable cmeta:id="NBC.J_NBC_HCO3" name="J_NBC_HCO3" public_interface="out" units="umol_per_s_per_cm2" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<ci>E_NBC</ci>
<apply>
<times />
<apply>
<divide />
<apply>
<times />
<ci>R</ci>
<ci>T</ci>
</apply>
<apply>
<times />
<apply>
<minus />
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">1</cn>
<ci>n</ci>
</apply>
<ci>F</ci>
</apply>
</apply>
<apply>
<ln />
<apply>
<times />
<apply>
<divide />
<apply>
<plus />
<ci>Na_ext</ci>
<ci>eps</ci>
</apply>
<apply>
<plus />
<ci>Na_int</ci>
<ci>eps</ci>
</apply>
</apply>
<apply>
<power />
<apply>
<divide />
<apply>
<plus />
<ci>HCO3_ext</ci>
<ci>eps</ci>
</apply>
<apply>
<plus />
<ci>HCO3_int</ci>
<ci>eps</ci>
</apply>
</apply>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">2</cn>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq />
<ci>J_NBC_Na</ci>
<apply>
<divide />
<apply>
<times />
<ci>g_NBC</ci>
<apply>
<minus />
<ci>E_NBC</ci>
<ci>V_m</ci>
</apply>
</apply>
<ci>F</ci>
</apply>
</apply>
<apply>
<eq />
<ci>J_NBC_HCO3</ci>
<apply>
<times />
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">3.0</cn>
<ci>J_NBC_Na</ci>
</apply>
</apply>
</math>
</component>
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<rdf:Description rdf:about="">
<dc:title>A kinetically defined Na+/HCO3- cotransporter (NBC) within a mathematical model of the brain.</dc:title>
</rdf:Description>
<rdf:Description rdf:about="#NBC.HCO3_int">
<semsim:isComputationalComponentFor>
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<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of bicarbonate in the Astrocyte compartment (or intracelluar!)</dcterms:description>
</rdf:Description>
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<semsim:isComputationalComponentFor>
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<ro:part_of rdf:resource="#entity_1" />
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<ro:part_of>
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</semsim:hasPhysicalEntityReference>
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</semsim:hasSourceParticipant>
<semsim:name>Na+ flow from extracellular space to astrocyte across NBC and astrocyte membrane</semsim:name>
</rdf:Description>
</semsim:physicalPropertyOf>
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00593" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>flux of sodium from extracellular space to astrocyte compartment across NBC cotransporter and astrocyte membrane (astrocyte membrane not exist in an ontology)</dcterms:description>
</rdf:Description>
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<semsim:isComputationalComponentFor>
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</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of sodium in the extracellular space (ECS) compartment (luminal!)</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#NBC.HCO3_ext">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_3">
<semsim:physicalPropertyOf>
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<ro:part_of rdf:resource="#entity_3" />
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</rdf:Description>
</semsim:physicalPropertyOf>
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of bicarbonate in theextracellular space (ECS) compartment (luminal!)</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#NBC.Na_int">
<semsim:isComputationalComponentFor>
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<semsim:physicalPropertyOf rdf:resource="#entity_0" />
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of sodium in the Astrocyte compartment (or intracellular!)</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Ostby_2009_NBC" semsim:modelId="Ostby_2009_NBC" semsim:modelName="Ostby_2009_NBC" />
<rdf:Description rdf:about="#NBC.J_NBC_HCO3">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_5">
<semsim:physicalPropertyOf>
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<semsim:hasSourceParticipant>
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<semsim:hasPhysicalEntityReference rdf:resource="#entity_5" />
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</semsim:hasSourceParticipant>
<semsim:name>HCO3- flow from extracellular space to astrocyte across NBC and astrocyte membrane</semsim:name>
</rdf:Description>
</semsim:physicalPropertyOf>
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00593" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>flux of bicarbonate from extracellular space to astrocyte compartment across NBC cotransporter and astrocyte membrane (astrocyte membrane not exist in an ontology)</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#Ostby_2009_NBC">
<bqs:reference rdf:parseType="Resource">
<dc:subject rdf:parseType="Resource">
<bqs:subject_type>keyword</bqs:subject_type>
<rdf:value>
<rdf:Bag>
<rdf:li>protein module</rdf:li>
</rdf:Bag>
</rdf:value>
</dc:subject>
</bqs:reference>
</rdf:Description>
</rdf:RDF>
</model>
