- Author:
- Dewan Sarwar <dsar941@UoA.auckland.ac.nz>
- Date:
- 2020-02-08 00:01:17+13:00
- Desc:
- updated the protocolSEDML.xml file
- Permanent Source URI:
- https://models.cellml.org/workspace/267/rawfile/00d5f4a8bfad4837a48a60ef3f8519ebf6bf8ebe/GI Model/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="NBC" cmeta:id="NBC">
<units name="millisec">
<unit prefix="milli" units="second" />
</units>
<units name="flux">
<unit exponent="-1.0" units="second" />
<unit prefix="milli" units="mole" />
<unit exponent="-3.0" prefix="centi" units="metre" />
</units>
<units name="mM">
<unit prefix="milli" units="mole" />
<unit exponent="-1.0" units="litre" />
</units>
<units name="per_millisec">
<unit exponent="-1.0" prefix="milli" units="second" />
</units>
<component name="environment">
<variable cmeta:id="environment.time" name="time" public_interface="out" units="second" />
</component>
<component name="NBC">
<variable cmeta:id="NBC.C_tissue_Na" name="C_tissue_Na" public_interface="in" units="mM" />
<variable cmeta:id="NBC.C_int_Na" name="C_int_Na" public_interface="in" units="mM" />
<variable cmeta:id="NBC.C_tissue_HCO3" name="C_tissue_HCO3" public_interface="in" units="mM" />
<variable cmeta:id="NBC.C_int_HCO3" name="C_int_HCO3" public_interface="in" units="mM" />
<variable cmeta:id="NBC.J_Na" name="J_Na" public_interface="in" units="flux" />
<variable cmeta:id="NBC.J_HCO3" name="J_HCO3" public_interface="in" units="flux" />
</component>
<rdf:RDF xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:ro="http://www.obofoundry.org/ro/ro.owl#" xmlns:opb="http://bhi.washington.edu/OPB#">
<rdf:Description rdf:about="">
<dc:title>HH sodium ion channel model</dc:title>
</rdf:Description>
<rdf:Description rdf:about="#NBC">
<ro:modelOf rdf:resource="http://purl.obolibrary.org/obo/PR_Q9JI66" />
<ro:located_in rdf:resource="http://purl.obolibrary.org/obo/FMA_17721" />
<ro:compartmentOf rdf:resource="http://purl.obolibrary.org/obo/FMA_66836" />
</rdf:Description>
<rdf:Description rdf:about="#environment.time" dcterms:description="Time" />
<rdf:Description rdf:about="#NBC.C_tissue_Cl">
<dcterms:description>concentration of chloride in the tissue fluid compartment</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#NBC.C_tissue_Na">
<dcterms:description>concentration of sodium in the tissue fluid compatrment</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#process_0" dcterms:description="" />
<rdf:Description rdf:about="#NBC.C_int_HCO3">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_3">
<semsim:physicalPropertyOf>
<rdf:Description rdf:about="#entity_5">
<ro:part_of>
<rdf:Description rdf:about="#entity_3">
<semsim:hasPhysicalDefinition rdf:resource="http://purl.obolibrary.org/obo/FMA_66836" />
</rdf:Description>
</ro:part_of>
<semsim:hasPhysicalDefinition rdf:resource="http://purl.obolibrary.org/obo/CHEBI_17544" />
</rdf:Description>
</semsim:physicalPropertyOf>
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of bicarbonate in the cytosol compartment</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#NBC.C_int_Na">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_1">
<semsim:physicalPropertyOf>
<rdf:Description rdf:about="#entity_2">
<ro:part_of rdf:resource="#entity_3" />
<semsim:hasPhysicalDefinition rdf:resource="http://purl.obolibrary.org/obo/CHEBI_29101" />
</rdf:Description>
</semsim:physicalPropertyOf>
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of sodium in the cytosol compartment</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#NBC.J_Cl">
<dcterms:description>Flux of chloride from tissue fluid to cytosol compartment through NKCC and basolateral membrane</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#NBC.C_tissue_Na">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_0">
<semsim:physicalPropertyOf>
<rdf:Description rdf:about="#entity_0">
<ro:part_of>
<rdf:Description rdf:about="#entity_1">
<semsim:hasPhysicalDefinition rdf:resource="http://purl.obolibrary.org/obo/FMA_9673" />
</rdf:Description>
</ro:part_of>
<semsim:hasPhysicalDefinition rdf:resource="http://purl.obolibrary.org/obo/CHEBI_29101" />
</rdf:Description>
</semsim:physicalPropertyOf>
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of sodium in the tissue fluid compartment</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#NBC.C_tissue_K">
<dcterms:description>concentration of potassium in the tissue fluid compartment</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#environment.time" dcterms:description="Time">
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_01023" />
</rdf:Description>
<rdf:Description rdf:about="#NBC.J_K">
<dcterms:description>Flux of potasium from tissue fluid to cytosol compartment through NKCC and basolateral membrane</dcterms:description>
<dcterms:description>Flux of potassium from tissue fluid to cytosol compartment through NKCC and basolateral membrane</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#NBC.J_Na">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_4">
<semsim:physicalPropertyOf>
<rdf:Description rdf:about="#process_0" dcterms:description="">
<semsim:hasMediatorParticipant>
<rdf:Description rdf:about="#mediator_1">
<semsim:hasPhysicalEntityReference>
<rdf:Description rdf:about="#entity_7">
<semsim:hasPhysicalDefinition rdf:resource="http://purl.obolibrary.org/obo/PR_Q9JI66" />
</rdf:Description>
</semsim:hasPhysicalEntityReference>
</rdf:Description>
</semsim:hasMediatorParticipant>
<semsim:hasMediatorParticipant>
<rdf:Description rdf:about="#mediator_0">
<semsim:hasPhysicalEntityReference>
<rdf:Description rdf:about="#entity_6">
<semsim:hasPhysicalDefinition rdf:resource="http://purl.obolibrary.org/obo/FMA_84669" />
</rdf:Description>
</semsim:hasPhysicalEntityReference>
</rdf:Description>
</semsim:hasMediatorParticipant>
<semsim:hasSinkParticipant>
<rdf:Description rdf:about="#sink_0" semsim:hasMultiplier="1.0">
<semsim:hasPhysicalEntityReference rdf:resource="#entity_2" />
</rdf:Description>
</semsim:hasSinkParticipant>
<semsim:hasSourceParticipant>
<rdf:Description rdf:about="#source_0" semsim:hasMultiplier="1.0">
<semsim:hasPhysicalEntityReference rdf:resource="#entity_0" />
</rdf:Description>
</semsim:hasSourceParticipant>
<semsim:name>Na flow from tissue fluid to cytosol</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 tissue fluid to cytosol compartment through NBC and basolateral membrane</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#NBC.J_HCO3">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_5">
<semsim:physicalPropertyOf>
<rdf:Description rdf:about="#process_1" dcterms:description="">
<semsim:hasMediatorParticipant>
<rdf:Description rdf:about="#mediator_3">
<semsim:hasPhysicalEntityReference rdf:resource="#entity_7" />
</rdf:Description>
</semsim:hasMediatorParticipant>
<semsim:hasMediatorParticipant>
<rdf:Description rdf:about="#mediator_2">
<semsim:hasPhysicalEntityReference rdf:resource="#entity_6" />
</rdf:Description>
</semsim:hasMediatorParticipant>
<semsim:hasSinkParticipant>
<rdf:Description rdf:about="#sink_1" semsim:hasMultiplier="1.0">
<semsim:hasPhysicalEntityReference rdf:resource="#entity_5" />
</rdf:Description>
</semsim:hasSinkParticipant>
<semsim:hasSourceParticipant>
<rdf:Description rdf:about="#source_1" semsim:hasMultiplier="1.0">
<semsim:hasPhysicalEntityReference>
<rdf:Description rdf:about="#entity_4">
<ro:part_of rdf:resource="#entity_1" />
<semsim:hasPhysicalDefinition rdf:resource="http://purl.obolibrary.org/obo/CHEBI_17544" />
</rdf:Description>
</semsim:hasPhysicalEntityReference>
</rdf:Description>
</semsim:hasSourceParticipant>
<semsim:name>HCO3 flow from tissue fluid to cytosol</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 tissue fluid to cytosol compartment through NBC and basolateral membrane</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#process_2" dcterms:description="" />
<rdf:Description rdf:about="#NBC.C_int_K">
<dcterms:description>concentration of potassium in the cytosol compartment</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#model">
<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:Description rdf:about="#NBC" semsim:modelId="NBC" semsim:modelName="NBC" />
<rdf:Description rdf:about="#NBC.J_Na">
<dcterms:description>Flux of sodium from tissue fluid to cytosol compartment through NKCC and basolateral membrane</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#NBC.C_tissue_HCO3">
<semsim:isComputationalComponentFor>
<rdf:Description rdf:about="#property_2">
<semsim:physicalPropertyOf rdf:resource="#entity_4" />
<semsim:hasPhysicalDefinition rdf:resource="http://identifiers.org/opb/OPB_00340" />
</rdf:Description>
</semsim:isComputationalComponentFor>
<dcterms:description>concentration of bicarbonate in the tissue fluid compartment</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#process_1" dcterms:description="" />
<rdf:Description rdf:about="#NBC.C_int_Na">
<dcterms:description>concentration of sodium in the cytosol compartment</dcterms:description>
</rdf:Description>
<rdf:Description rdf:about="#NBC.C_int_Cl">
<dcterms:description>concentration of chloride in the cytosol compartment</dcterms:description>
</rdf:Description>
</rdf:RDF>
</model>
