<?xml version = "1.0" encoding = "UTF-8"?>
<?xml-stylesheet type="text/xsl" href="gelml-isatab.xsl"?>
<gelml:GelML 
	identifier="ex003:GelML:003"
	name="DIGE example from http://www5.amershambiosciences.com/"
 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
 xmlns:fuge="http://fuge.sourceforge.net/fuge/1.0"
 xmlns:gelml="http://www.psidev.info/gelml/1.0"
 xsi:schemaLocation="http://www.psidev.info/gelml/1.0 GelML-v1.xsd"
 > 

	<fuge:_bibliographicReferences BibliographicReference_ref="ex003:BibliographicReference0"/>

	<gelml:GelMLMaterialCollection>
		<fuge:GenericMaterial name="Brain tissue from rats injected with kainic acid"
			identifier="ex003:GenericMaterial0">
			<fuge:characteristics OntologyTerm_ref="ex003:OntologyIndividual9"/>
		</fuge:GenericMaterial>
		<fuge:GenericMaterial name="Brain tissue from rats - control" identifier="ex003:GenericMaterial1">
			<fuge:characteristics OntologyTerm_ref="ex003:OntologyIndividual10"/>
		</fuge:GenericMaterial>
		<fuge:GenericMaterial name="Pooled Sample" identifier="ex003:GenericMaterial2">
			<fuge:characteristics OntologyTerm_ref="ex003:OntologyIndividual11"/>
		</fuge:GenericMaterial>
	</gelml:GelMLMaterialCollection>

	<gelml:GelMLDataCollection>
		<gelml:Image name="Image for channel Cy2" identifier="ex003:Image0"
			location="http://temp.uri.tocome">
			<!-- Not sure if these are correct for channel, probably should get the actual measurements of wavelengths!! -->
			<gelml:_channel>
				<fuge:ComplexValue> 
					<fuge:_value OntologyTerm_ref="ex003:OntologyIndividual12"/>
				</fuge:ComplexValue>
			</gelml:_channel>
		</gelml:Image>
		<gelml:Image name="Image for Cy3 channel" identifier="ex003:Image1"
			location="http://temp.uri.tocome">
			<gelml:_channel>
				<fuge:ComplexValue>
					<fuge:_value OntologyTerm_ref="ex003:OntologyIndividual13"/>
				</fuge:ComplexValue>				
			</gelml:_channel>
		</gelml:Image>
		<gelml:Image name="Image for Cy5 channel" identifier="ex003:Image2"
			location="http://temp.uri.tocome">
			<gelml:_channel>
				<fuge:ComplexValue>
					<fuge:_value OntologyTerm_ref="ex003:OntologyIndividual14"/>
				</fuge:ComplexValue>
			</gelml:_channel>
		</gelml:Image>
		<gelml:Image name="Image of prep gel" identifier="ex003:Image3" location="http://temp.uri.to.come"/>
	</gelml:GelMLDataCollection>
	<gelml:GelMLProtocolCollection>
		<fuge:GenericEquipment name="Ettan DALTtwelve Large Vertical System"
			identifier="ex003:GenericEquipment0"/>
		<fuge:GenericEquipment name="Typhoon 9400 Variable Imager" identifier="ex003:GenericEquipment1"/>
		<gelml:ElectrophoresisProtocol
			name="1st dimension electrophoresis protocol (enter optional other name here)"
			identifier="ex003:ElectrophoresisProtocol0">
			<gelml:ElectrophoresisStep identifier="ex003:ElectrophoresisStep0" actionOrdinal="1">
				<gelml:ElectricalParameter identifier="ex003:ElectricalParameter0">
					<fuge:AtomicValue value="500">
						<fuge:_unit OntologyTerm_ref="ex003:OntologyIndividual1"/>
					</fuge:AtomicValue>
					<gelml:_electricalSetting OntologyTerm_ref="ex003:OntologyIndividual18"/>			
				</gelml:ElectricalParameter>
				<gelml:Duration identifier="ex003:Duration0">
					<fuge:AtomicValue value="1">
						<fuge:_unit OntologyTerm_ref="ex003:OntologyIndividual0"/>
					</fuge:AtomicValue>
					</gelml:Duration>
			</gelml:ElectrophoresisStep>
				<gelml:ElectrophoresisStep identifier="ex003:ElectrophoresisStep4">
					<gelml:ElectricalParameter identifier="ex003:ElectricalParameter2">
					<fuge:AtomicValue value="1000">
						<fuge:_unit OntologyTerm_ref="ex003:OntologyIndividual1"/>
					</fuge:AtomicValue>
						<gelml:_electricalSetting OntologyTerm_ref="ex003:OntologyIndividual19"/>
					</gelml:ElectricalParameter>
					<gelml:Duration identifier="ex003:Duration2">
					<fuge:AtomicValue value="1">
						<fuge:_unit OntologyTerm_ref="ex003:OntologyIndividual0"/>
					</fuge:AtomicValue>
					</gelml:Duration>
				</gelml:ElectrophoresisStep>
			<gelml:ElectrophoresisStep identifier="ex003:ElectrophoresisStep5" actionOrdinal="3">
				<gelml:ElectricalParameter identifier="ex003:ElectricalParameter3">
					<fuge:AtomicValue value="8000">
						<fuge:_unit OntologyTerm_ref="ex003:OntologyIndividual1"/>
					</fuge:AtomicValue>
					<gelml:_electricalSetting OntologyTerm_ref="ex003:OntologyIndividual18"/>
				</gelml:ElectricalParameter>
				<gelml:Duration identifier="ex003:Duration3">
					<fuge:AtomicValue value="0.034">
						<fuge:_unit OntologyTerm_ref="ex003:OntologyIndividual5"/>
					</fuge:AtomicValue>
				</gelml:Duration>
			</gelml:ElectrophoresisStep>
		</gelml:ElectrophoresisProtocol>
		<gelml:ElectrophoresisProtocol
			name="2nd dimension electrophoresis protocol (enter optional other name here)"
			identifier="ex003:ElectrophoresisProtocol1">
			<gelml:_electrophoresisEquipment GenericEquipment_ref="ex003:GenericEquipment0"/>
			<gelml:ElectrophoresisStep identifier="ex003:ElectrophoresisStep1" actionOrdinal="1">
				<gelml:ElectricalParameter identifier="ex003:ElectricalParameter4">
					<fuge:AtomicValue value="1.5">
						<fuge:_unit OntologyTerm_ref="ex003:OntologyIndividual23"/>
					</fuge:AtomicValue>
				</gelml:ElectricalParameter>
				<gelml:Duration identifier="ex003:Duration1">
					<fuge:AtomicValue value="Overnight"/>
				</gelml:Duration>
			</gelml:ElectrophoresisStep>
		</gelml:ElectrophoresisProtocol>
		<gelml:DetectionProtocol name="Sypro ruby staining for prep gels"
			identifier="ex003:DetectionProtocol0">
			<gelml:SubstanceAction identifier="ex003:SubstanceAction0" actionOrdinal="1"
				actionText="(Describe how stain or label was entered here and use Mass, concentration and or volume for the quantity below)">
				<gelml:_substanceType OntologyTerm_ref="ex003:OntologyIndividual2"/>
			</gelml:SubstanceAction>
		</gelml:DetectionProtocol>
		<gelml:Gel2DProtocol identifier="ex003:Gel2DProtocol0" name="Protocol for 2D prep gel">
				<gelml:SampleLoadingAction identifier="ex003:SampleLoadingAction0" actionOrdinal="1"
					SampleLoadingProtocol_ref="ex003:SampleLoadingProtocol0"/>			
				<gelml:FirstDimensionAction identifier="ex003:FirstDimensionAction0" actionOrdinal="2"
					ElectrophoresisProtocol_ref="ex003:ElectrophoresisProtocol1"/>				
				<gelml:SecondDimensionAction identifier="ex003:SecondDimensionAction0" actionOrdinal="4"
					ElectrophoresisProtocol_ref="ex003:ElectrophoresisProtocol1"/>				
				<gelml:InterDimensionAction identifier="ex003:InterDimensionAction0" actionOrdinal="3"
				preDimension="2" Protocol_ref="ex003:GenericProtocol1"/>
		</gelml:Gel2DProtocol>
		<gelml:SampleLoadingProtocol name="Sample loading protocol"
			identifier="ex003:SampleLoadingProtocol0"/>
		<fuge:GenericProtocol name="DIGE Image acquisition protocol" identifier="ex003:GenericProtocol0"
			protocolText="(describe image acquistion in here, optionally enter details of equipment, parameters, etc below)"/>
		<fuge:GenericProtocol name="Rehydration" identifier="ex003:GenericProtocol1"
			protocolText="rehydration for 10 h"/>
		<gelml:SampleLoadingProtocol name="Sample loading for prep gel"
			identifier="ex003:SampleLoadingProtocol1"/>
		<fuge:GenericProtocol name="Spot excision" identifier="ex003:GenericProtocol2"
			protocolText="One of the glass plates was treated with PlusOne™ Bind-Silane and spot location reference markers were attached to the right and left-hand sides of the glass plate. The gels were used for spot picking and subsequent mass spectrometry (MS) identification."/>
		<gelml:Gel2DProtocol name="Protocol for 2D prep gel" identifier="ex003:Gel2DProtocol1">
			<gelml:SampleLoadingAction identifier="ex003:SampleLoadingAction1" actionOrdinal="1"
					dimension="1" SampleLoadingProtocol_ref="ex003:SampleLoadingProtocol1"/>
			<gelml:FirstDimensionAction identifier="ex003:FirstDimensionAction1" actionOrdinal="2"
				ElectrophoresisProtocol_ref="ex003:ElectrophoresisProtocol0"/>
			<gelml:SecondDimensionAction identifier="ex003:SecondDimensionAction1" actionOrdinal="2"
				ElectrophoresisProtocol_ref="ex003:ElectrophoresisProtocol1"/>
		</gelml:Gel2DProtocol>
	</gelml:GelMLProtocolCollection>

	<gelml:Gel2DExperiment name="Description of DIGE gels" identifier="ex003:Gel2DExperiment0">
		<!-- Need to put in the 3 ref'd ImageAcquisition protocols -->
		<gelml:ImageAcquisitionApplication identifier="ex003:ImageAcquisitionApplication0"
			Image_ref="ex003:Image0" ImageAcquisitionProtocol_ref="ex003:GenericProtocol0"
			Material_ref="ex003:Gel2D0"/>
		<gelml:ImageAcquisitionApplication identifier="ex003:ImageAcquisitionApplication1"
			Image_ref="ex003:Image1" ImageAcquisitionProtocol_ref="ex003:GenericProtocol0"
			Material_ref="ex003:Gel2D0"/>
		<gelml:ImageAcquisitionApplication identifier="ex003:ImageAcquisitionApplication2"
			Image_ref="ex003:Image2" ImageAcquisitionProtocol_ref="ex003:GenericProtocol0"
			Material_ref="ex003:Gel2D0"/>
		<gelml:SampleLoadingApplication identifier="ex003:SampleLoadingApplication0"
			SampleLoadingProtocol_ref="ex003:SampleLoadingProtocol0" Gel_ref="ex003:Gel0">
			<fuge:GenericMaterialMeasurement Material_ref="ex003:GenericMaterial0">
				<fuge:AtomicValue value="30">
					<fuge:_unit OntologyTerm_ref=""/><!-- Millilitres? !!-->
				</fuge:AtomicValue>
			</fuge:GenericMaterialMeasurement>
			<fuge:GenericMaterialMeasurement Material_ref="ex003:GenericMaterial1">
				<fuge:AtomicValue value="30">
					<fuge:_unit OntologyTerm_ref=""/><!-- Millilitres? !!-->
				</fuge:AtomicValue>
			</fuge:GenericMaterialMeasurement>
			<fuge:GenericMaterialMeasurement Material_ref="ex003:GenericMaterial2">
				<fuge:AtomicValue value="30">
					<fuge:_unit OntologyTerm_ref=""/><!-- Millilitres? !!-->
				</fuge:AtomicValue>
			</fuge:GenericMaterialMeasurement>
		</gelml:SampleLoadingApplication>
		<gelml:_electrophoresisType OntologyTerm_ref="ex003:OntologyIndividual25"/>
		<gelml:Gel2DApplication
			name="(Enter optionally the activity date, operator using ContactRole, and details of gels used in first and second dimension)"
			identifier="ex003:Gel2DApplication0" Gel2DProtocol_ref="ex003:Gel2DProtocol0">
			<fuge:ActionApplication identifier="ex003:ActionApp4" ProtocolApplication_ref="ex003:SampleLoadingApplication0"
				Action_ref="ex003:SampleLoadingAction0"/>
			<fuge:ActionApplication identifier="ex003:ActionApp5" ProtocolApplication_ref="ex003:ElectrophoresisApplication0"
				Action_ref="ex003:FirstDimensionAction0"/>
			<fuge:ActionApplication identifier="ex003:ActionApp6" ProtocolApplication_ref="ex003:ElectrophoresisApplication1"
				Action_ref="ex003:SecondDimensionAction0"/>
				<gelml:Gel2D name="Main DIGE gel" identifier="ex003:Gel2D0">				
					<gelml:PHRange dimension="1">
					<fuge:Range lowerLimit="3" upperLimit="10"/>							
					</gelml:PHRange>
				</gelml:Gel2D>
				<gelml:_inputFirstDimension>
					<gelml:Gel name="IPG strip" identifier="ex003:Gel0" separationDimension="1">
						<!-- Note percent acrylamide and Acrylamide:crosslinker are not specified -->	
						<gelml:_model OntologyTerm_ref="ex003:OntologyIndividual24"/>			
						<gelml:Dimensions z="0" y="0" x="240">												
							<gelml:_dimensionUnit OntologyTerm_ref="ex003:OntologyIndividual3"/>						
						</gelml:Dimensions>
					</gelml:Gel>
				</gelml:_inputFirstDimension>
				<gelml:_inputSecondDimension>
					<gelml:Gel name="T SDS-PAGE" identifier="ex003:Gel1">
						<gelml:_percentAcrylamide>
						<fuge:AtomicValue value="12.5"/>
						</gelml:_percentAcrylamide>
					<!-- Other details not specified -->
					</gelml:Gel>
				</gelml:_inputSecondDimension>
		</gelml:Gel2DApplication>
		<gelml:ElectrophoresisApplication identifier="ex003:ElectrophoresisApplication0"
			ElectrophoresisProtocol_ref="ex003:ElectrophoresisProtocol0" Gel_ref="ex003:Gel0"></gelml:ElectrophoresisApplication>
			<gelml:ElectrophoresisApplication identifier="ex003:ElectrophoresisApplication1"
				ElectrophoresisProtocol_ref="ex003:ElectrophoresisProtocol1" Gel_ref="ex003:Gel1"></gelml:ElectrophoresisApplication>
	</gelml:Gel2DExperiment>

	<gelml:Gel2DExperiment name="Description of preparative gels for MS"
		identifier="ex003:Gel2DExperiment1">
		<gelml:ExcisionApplication identifier="ex003:ExcisionApplication0"
			ElectrophoresedGel_ref="ex003:Gel2D1" GenericProtocol_ref="ex003:GenericProtocol2">
			<gelml:_inputImageLocations>
				<gelml:LocationSet identifier="ex003:LocationSet1" Image_ref="ex003:Image3">
					<gelml:GelLocation name="example gel location (no genuine locations are known)"
						identifier="ex003:GelLocation0">
						<gelml:Circle centroidY="1" centroidX="1" pixelRadius="1"/>
					</gelml:GelLocation>
				</gelml:LocationSet>
			</gelml:_inputImageLocations>
			<gelml:ExcisedSample name="Details of excised samples would be entered here"
				identifier="ex003:ExcisedSample0" GelLocation_ref="ex003:GelLocation0"></gelml:ExcisedSample>
		</gelml:ExcisionApplication>
		<gelml:SampleLoadingApplication identifier="ex003:SampleLoadingApplication1"
			SampleLoadingProtocol_ref="ex003:SampleLoadingProtocol1" Gel_ref="ex003:Gel2"/>
		<gelml:_electrophoresisType OntologyTerm_ref="ex003:OntologyIndividual6"/>
		<gelml:Gel2DApplication identifier="ex003:Gel2DApplication1"
			Gel2DProtocol_ref="ex003:Gel2DProtocol1">
			<fuge:ActionApplication identifier="ex003:ActionApp1" ProtocolApplication_ref="ex003:SampleLoadingApplication1"
				Action_ref="ex003:SampleLoadingAction1"/>
			<fuge:ActionApplication identifier="ex003:ActionApp2" ProtocolApplication_ref="ex003:ElectrophoresisApplication2"
				Action_ref="ex003:FirstDimensionAction1"/>
			<fuge:ActionApplication identifier="ex003:ActionApp3" ProtocolApplication_ref="ex003:ElectrophoresisApplication3"
				Action_ref="ex003:SecondDimensionAction1"/>
			<gelml:Gel2D name="Main prep gel for MS" identifier="ex003:Gel2D1">
				<gelml:PHRange dimension="1">
					<fuge:Range upperLimit="10" lowerLimit="3"/>
				</gelml:PHRange>
			</gelml:Gel2D>
			<gelml:_inputFirstDimension>
				<gelml:Gel name="Immobiline DryStrip pH 3–10 NL" identifier="ex003:Gel2"
					separationDimension="1">
					<gelml:Dimensions z="0" y="0" x="240">
						<gelml:_dimensionUnit OntologyTerm_ref="ex003:OntologyIndividual3"/>
					</gelml:Dimensions>
				</gelml:Gel>
			</gelml:_inputFirstDimension>
			<gelml:_inputSecondDimension>
				<gelml:Gel name="Slab gel for preparing spots for MS" identifier="ex003:Gel4"
					separationDimension="2"/>
			</gelml:_inputSecondDimension>
		</gelml:Gel2DApplication>
		<gelml:ElectrophoresisApplication
			name="Application of electrophoresis on prep gel in 1st dimension"
			identifier="ex003:ElectrophoresisApplication2"
			ElectrophoresisProtocol_ref="ex003:ElectrophoresisProtocol0" Gel_ref="ex003:Gel2"></gelml:ElectrophoresisApplication>
		<gelml:ElectrophoresisApplication
			name="Application of electrophoresis protocol in 2nd dimension of prep gel"
			identifier="ex003:ElectrophoresisApplication3"
			ElectrophoresisProtocol_ref="ex003:ElectrophoresisProtocol1" Gel_ref="ex003:Gel4"></gelml:ElectrophoresisApplication>
	</gelml:Gel2DExperiment>

	<fuge:OntologyCollection>
		<fuge:OntologyIndividual identifier="ex003:OntologyIndividual0" term="hour"
			termAccession="UO:0000032"
			OntologySource_ref="ex003:OntologySource2"/>
		<fuge:OntologyIndividual identifier="ex003:OntologyIndividual1" term="volt"
			termAccession="UO:0000218"
			OntologySource_ref="ex003:OntologySource2"/>
 		<fuge:OntologyIndividual identifier="ex003:OntologyIndividual2" term="Sypro_ruby"
			termAccession="!! To come !!"
			OntologySource_ref="ex003:OntologySource1"/>
		<fuge:OntologyIndividual identifier="ex003:OntologyIndividual3" term="millimeter"
			termAccession="UO:0000016"
			OntologySource_ref="ex003:OntologySource2"/>
		<fuge:OntologyIndividual identifier="ex003:OntologyIndividual4" term="kilodalton"
			termAccession="UO:0000222"
			OntologySource_ref="ex003:OntologySource2"/>
		<fuge:OntologyIndividual identifier="ex003:OntologyIndividual5" term="volt-hour"
			termAccession="UO:0000229"
			OntologySource_ref="ex003:OntologySource2"/>
		<fuge:OntologyIndividual identifier="ex003:OntologyIndividual6"
			term="two dimensional gel electrophoresis"
			termAccession="sep:00155"
			OntologySource_ref="ex003:OntologySource1"/>
		<fuge:OntologyIndividual identifier="ex003:OntologyIndividual9" term="Cy3_labelled"
			termAccession="!!" OntologySource_ref="ex003:OntologySource1"/>
		<fuge:OntologyIndividual identifier="ex003:OntologyIndividual10" term="Cy5_labelled"
			termAccession="!!" OntologySource_ref="ex003:OntologySource1" />
		<fuge:OntologyIndividual identifier="ex003:OntologyIndividual11" term="Cy2_labelled"
			termAccession="!!" OntologySource_ref="ex003:OntologySource1"/>
		<fuge:OntologyIndividual identifier="ex003:OntologyIndividual12" term="Cy2_excitation_wavelength"
			termAccession="!!"/>
		<fuge:OntologyIndividual identifier="ex003:OntologyIndividual13" term="Cy3_excitation_wavelength"
			termAccession="!!"/>
		<fuge:OntologyIndividual identifier="ex003:OntologyIndividual14" term="Cy5_excitation_wavelength"
			termAccession="!!"/>
		<fuge:OntologyIndividual identifier="ex003:OntologyIndividual15" term="dots per inch"
			termAccession="UO:0000240" OntologySource_ref="ex003:OntologySource2"/>
		<fuge:OntologyIndividual identifier="ex003:OntologyIndividual16" term="Manufacturer"
			termAccession="uri to come" OntologySource_ref="ex003:OntologySource1"/>
		<fuge:OntologyIndividual identifier="ex003:OntologyIndividual17" term="linear distribution"
			termAccession="sep:00018" OntologySource_ref="ex003:OntologySource1"/>
		<fuge:OntologyIndividual identifier="ex003:OntologyIndividual18" term="logarithmic distribution"
			termAccession="sep:00019" OntologySource_ref="ex003:OntologySource1"/>
		<fuge:OntologyIndividual identifier="ex003:OntologyIndividual19" term="principal investigator"
			termAccession="sep:00035" OntologySource_ref="ex003:OntologySource1"/>
		<fuge:OntologyIndividual identifier="ex003:OntologyIndividual20" term="hold mode"
			termAccession="sep:00027" OntologySource_ref="ex003:OntologySource1"/>	
		<fuge:OntologyIndividual identifier="ex003:OntologyIndividual19" term="gradient"
			termAccession="accession to come" OntologySource_ref="ex003:OntologySource1"/>
		<fuge:OntologyIndividual identifier="ex003:OntologyIndividual22" term="celcius"
			termAccession="UO:0000027"
			OntologySource_ref="ex003:OntologySource2"/>
		<fuge:OntologyIndividual identifier="ex003:OntologyIndividual23" term="watt"
			termAccession="UO:0000114"
			OntologySource_ref="ex003:OntologySource2"/>		
		<fuge:OntologyIndividual identifier="ex003:OntologyIndividual24" term="immobiline dry strip"
			termAccession="sep:00131" OntologySource_ref="ex003:OntologySource1"/>
		<fuge:OntologyIndividual identifier="ex003:OntologyIndividual25"
			term="difference gel electrophoresis"
			termAccession="sep:00180"
			OntologySource_ref="ex003:OntologySource1"/>
		<!-- Possible change to reference OBO repository!! -->
		<fuge:OntologySource name="PSI-SEP CV" identifier="ex003:OntologySource1"
			ontologyURI="http://psidev.sourceforge.net/gps/CV/sep.obo"/>
		<fuge:OntologySource ontologyURI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo?view=log" identifier="ex003:OntologySource1" name="OBO-unit"/>
	</fuge:OntologyCollection>

	<fuge:ReferenceableCollection>
		<fuge:BibliographicReference
			name="(Note - info in volume should be moved to URI - Describable attributes are not implemented in Pedro)"
			identifier="ex003:BibliographicReference0"
			authors="J. Inagawa, J. Hirano, and S. Hattori"
			volume="http://www5.amershambiosciences.com/APTRIX/upp01077.nsf/Content/lsn_online_article_281004_f?OpenDocument&amp;hometitle=lsn_online"
			title="CyDye DIGE Fluor minimal dyes for tracking membrane protein abundance from epilepsy-induced rats : A clinical proteomic study"/>		
	</fuge:ReferenceableCollection>
</gelml:GelML>
