Location: semantic-annotation @ 848b6a8fb585 / test.xml

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/test.xml

<sedML xmlns="http://sed-ml.org/sed-ml/level1/version2" xmlns:cellml="http://www.cellml.org/cellml/1.1#" level="1"
       version="2">
    <listOfSimulations>
        <uniformTimeCourse id="simulation1" initialTime="0" numberOfPoints="1000" outputEndTime="1" outputStartTime="0">
            <algorithm kisaoID="KISAO:0000019">
                <listOfAlgorithmParameters>
                    <algorithmParameter kisaoID="KISAO:0000211" value="1e-7"/>
                    <algorithmParameter kisaoID="KISAO:0000475" value="BDF"/>
                    <algorithmParameter kisaoID="KISAO:0000481" value="true"/>
                    <algorithmParameter kisaoID="KISAO:0000476" value="Newton"/>
                    <algorithmParameter kisaoID="KISAO:0000477" value="Dense"/>
                    <algorithmParameter kisaoID="KISAO:0000480" value="0"/>
                    <algorithmParameter kisaoID="KISAO:0000415" value="500"/>
                    <algorithmParameter kisaoID="KISAO:0000467" value="0"/>
                    <algorithmParameter kisaoID="KISAO:0000478" value="Banded"/>
                    <algorithmParameter kisaoID="KISAO:0000209" value="1e-7"/>
                    <algorithmParameter kisaoID="KISAO:0000479" value="0"/>
                </listOfAlgorithmParameters>
            </algorithm>
        </uniformTimeCourse>
    </listOfSimulations>
    <listOfModels>
        <model id="model" language="urn:sedml:language:cellml.1_1" source="weinstein_1995.cellml"/>
    </listOfModels>
    <listOfTasks>
        <repeatedTask id="repeatedTask" range="once" resetModel="true">
            <listOfRanges>
                <vectorRange id="once">
                    <value>1</value>
                </vectorRange>
            </listOfRanges>
            <listOfSubTasks>
                <subTask order="1" task="task1"/>
            </listOfSubTasks>
        </repeatedTask>
        <task id="task1" modelReference="model" simulationReference="simulation1"/>
    </listOfTasks>
    <listOfDataGenerators>
        <Protocol id="1"
                  name="myAttrib" ploty="undefined"/>
        <Protocol id="2"
                  name="V vs I"
                  opby="http://identifiers.org/opb/OPB_00318"
                  opbx="http://identifiers.org/opb/OPB_00506"
                  chebi="undefined"
                  fma="http://purl.obolibrary.org/obo/FMA_84666"
                  sparqly="protocol2Currrent"
                  sparqlx="protocol2Potential"
                  time="undefined"
                  ploty="undefined"/>
        <Protocol id="3A"
                  name="concentration/flux vs concentration 3A"
                  opby="http://identifiers.org/opb/OPB_00593"
                  opbx="http://identifiers.org/opb/OPB_00340"
                  chebi="http://purl.obolibrary.org/obo/CHEBI_29101"
                  fma="http://purl.obolibrary.org/obo/FMA_74550"
                  sparqly="protocol3Flux"
                  sparqlx="protocol1Concentration"
                  time="undefined"
                  ploty="plot (dimensionless)"/>
        <Protocol id="3B"
                  name="concentration/flux vs concentration 3B"
                  opby="http://identifiers.org/opb/OPB_00593"
                  opbx="http://identifiers.org/opb/OPB_00340"
                  chebi="http://purl.obolibrary.org/obo/CHEBI_29101"
                  fma="http://purl.obolibrary.org/obo/FMA_74550"
                  sparqly="protocol3Flux"
                  sparqlx="protocol1Concentration"
                  time="undefined"
                  ploty="plot (dimensionless)"/>
        <Protocol id="4A"
                  name="1/flux vs concentration 4A"
                  opby="http://identifiers.org/opb/OPB_00593"
                  opbx="http://identifiers.org/opb/OPB_00340"
                  chebi="http://purl.obolibrary.org/obo/CHEBI_28938"
                  fma="http://purl.obolibrary.org/obo/FMA_74550"
                  sparqly="protocol3Flux"
                  sparqlx="protocol4Concentration"
                  time="undefined"
                  ploty="plot (mM)"/>
        <Protocol id="4B"
                  name="1/flux vs concentration 4B"
                  opby="http://identifiers.org/opb/OPB_00593"
                  opbx="http://identifiers.org/opb/OPB_00340"
                  chebi="http://purl.obolibrary.org/obo/CHEBI_28938"
                  fma="http://purl.obolibrary.org/obo/FMA_74550"
                  sparqly="protocol3Flux"
                  sparqlx="protocol4Concentration"
                  time="undefined"
                  ploty="plot (mM)"/>
        <Protocol id="2A"
                  name="flux vs external pH 2A"
                  opby="http://identifiers.org/opb/OPB_00593"
                  opbx="http://identifiers.org/opb/OPB_00340"
                  chebi="http://purl.obolibrary.org/obo/CHEBI_15378"
                  fma="http://purl.obolibrary.org/obo/FMA_74550"
                  sparqly="protocol3Flux"
                  sparqlx="protocol2AConcentration"
                  time="undefined"
                  ploty="plot (dimensionless)"/>
        <Protocol id="2B"
                  name="1/flux vs concentration 2B"
                  opby="http://identifiers.org/opb/OPB_00593"
                  opbx="http://identifiers.org/opb/OPB_00340"
                  chebi="http://purl.obolibrary.org/obo/CHEBI_15378"
                  fma="http://purl.obolibrary.org/obo/FMA_74550"
                  sparqly="protocol3Flux"
                  sparqlx="protocol2AConcentration"
                  time="undefined"
                  ploty="plot (dimensionless)"/>
        <Protocol id="experimental"
                  name="experimental"
                  opby="http://identifiers.org/opb/OPB_00340"
                  opbx="http://identifiers.org/opb/OPB_01023"
                  chebi="http://purl.obolibrary.org/obo/CHEBI_29101"
                  fma="http://purl.obolibrary.org/obo/FMA_74550"
                  sparqly="protocol1Concentration"
                  sparqlx="protocol1Time"
                  time="/cellml:model/cellml:component[@name='environment']/cellml:variable[@name='time']"
                  ploty="experimental"/>
        <dataGenerator id="xDataGenerator1_1">
            <listOfVariables>
                <variable id="xVariable1_1"
                          target="xtarget"
                          taskReference="repeatedTask"/>
            </listOfVariables>
            <math xmlns="http://www.w3.org/1998/Math/MathML">
                <ci>xVariable1_1</ci>
            </math>
        </dataGenerator>
        <dataGenerator id="yDataGenerator1_1">
            <listOfVariables>
                <variable id="yVariable1_1"
                          target="ytarget"
                          taskReference="repeatedTask"/>
            </listOfVariables>
            <math xmlns="http://www.w3.org/1998/Math/MathML">
                <ci>yVariable1_1</ci>
            </math>
        </dataGenerator>
    </listOfDataGenerators>
    <listOfOutputs>
        <plot2D id="plot1">
            <annotation>
                <properties xmlns="http://www.opencor.ws/">
                    <backgroundColor>#ffffff</backgroundColor>
                    <fontSize>10</fontSize>
                    <foregroundColor>#000000</foregroundColor>
                    <height>1</height>
                    <gridLines>
                        <style>dot</style>
                        <width>1</width>
                        <color>#a0a0a4</color>
                    </gridLines>
                    <legend>false</legend>
                    <pointCoordinates>
                        <style>dash</style>
                        <width>1</width>
                        <color>#b0008080</color>
                        <fontColor>#ffffff</fontColor>
                    </pointCoordinates>
                    <surroundingArea>
                        <backgroundColor>#f0f0f0</backgroundColor>
                        <foregroundColor>#000000</foregroundColor>
                    </surroundingArea>
                    <title/>
                    <xAxis>
                        <logarithmicScale>false</logarithmicScale>
                        <title/>
                    </xAxis>
                    <yAxis>
                        <logarithmicScale>false</logarithmicScale>
                        <title/>
                    </yAxis>
                    <zoomRegion>
                        <style>solid</style>
                        <width>1</width>
                        <color>#b0800000</color>
                        <fontColor>#ffffff</fontColor>
                        <filled>true</filled>
                        <fillColor>#30ffff00</fillColor>
                    </zoomRegion>
                </properties>
            </annotation>
            <listOfCurves>
                <curve id="curve1_1" logX="false" logY="false" xDataReference="xDataGenerator1_1"
                       yDataReference="yDataGenerator1_1">
                    <annotation>
                        <properties xmlns="http://www.opencor.ws/">
                            <title/>
                            <line>
                                <style>solid</style>
                                <width>1</width>
                                <color>#000080</color>
                            </line>
                            <symbol>
                                <style>none</style>
                                <size>8</size>
                                <color>#000080</color>
                                <filled>true</filled>
                                <fillColor>#ffffff</fillColor>
                            </symbol>
                        </properties>
                    </annotation>
                </curve>
            </listOfCurves>
        </plot2D>
    </listOfOutputs>
</sedML>