<?xml version="1.0" encoding="UTF-8"?>
<FuGE xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
 xsi:schemaLocation="http://fuge.org/core C:\mage\mage_v2\2006_09_09_fuge_v1_candidate\FuGE-version1-schema-candidate.xml"
 xmlns="http://fuge.org/core"
 identifier="www.lab_xyz.com:FuGE:Investigation_C0001_2005_12_01" name="Investigation_C0001">
 
    <MaterialCollection>
    <!-- Direct Reference Example with Properties -->
      
      <GenericMaterial identifier="www.org_xyz.com:GenericMaterial:Investigation_C0001.rat_m">
        
        <_annotations OntologyTerm_ref="www.ncbi.nlm.nih.gov:OntologyIndividual:Rattus norvegicus"/>
        <_annotations OntologyTerm_ref="mged.sourceforge.net/ontologies:OntologyIndividual:Age"/>
        
      </GenericMaterial>
      
    <!-- Family Ontology Example -->
      
      <!-- loosely based on http://protege.cim3.net/file/pub/ontologies/family.swrl.owl/family.swrl.owl -->
      
      <GenericMaterial identifier="www.org_xyz.com:GenericMaterial:MARY_SMITH">
        
        <_annotations OntologyTerm_ref="www.org_xyz.com:OntologyIndividual:MARY_SMITH"/>
        
      </GenericMaterial>
      
      <GenericMaterial identifier="www.org_xyz.com:GenericMaterial:PAUL_SMITH">
        
        <_annotations OntologyTerm_ref="www.org_xyz.com:OntologyIndividual:PAUL_SMITH"/>
        
      </GenericMaterial>
      
      <GenericMaterial identifier="www.org_xyz.com:GenericMaterial:TRUDY_SMITH">
        
        <_annotations OntologyTerm_ref="www.org_xyz.com:OntologyIndividual:TRUDY_SMITH"/>
        
      </GenericMaterial>
      
    <!-- Observation Ontology Example -->
      <GenericMaterial identifier="www.lab_xyz.com:GenericMaterial:Investigation_C0001.rat_n">
        
        <_annotations OntologyTerm_ref="www.lab_xyz.com:ObjectProperty:Investigation_C0001.rat_n"/>
        
      </GenericMaterial>
      
    </MaterialCollection>
    
    <InvestigationCollection>
    <!-- Direct Reference MO Example -->
      <Investigation identifier="www.ebi.ac.uk/arrayexpress/:Investigation:E-MIMR-12">
        
        <_annotations OntologyTerm_ref="mged.sourceforge.net/ontologies:OntologyIndividual:compound_treatment_design"/>
        <_annotations OntologyTerm_ref="mged.sourceforge.net/ontologies:OntologyIndividual:time_series_design"/>
        
      </Investigation>
    </InvestigationCollection>
    
    <OntologyCollection>
      <!-- Direct Reference MO Example -->

			<OntologyIndividual term="compound_treatment_design" termAccession="#compound_treatment_design" 
											identifier="mged.sourceforge.net/ontologies:OntologyIndividual:compound_treatment_design"
											OntologySource_ref="mged.sourceforge.net/ontologies:OntologySource:MGEDOntology"/>

			<OntologyIndividual term="time_series_design" termAccession="#time_series_design" 
											identifier="mged.sourceforge.net/ontologies:OntologyIndividual:time_series_design"
											OntologySource_ref="mged.sourceforge.net/ontologies:OntologySource:MGEDOntology"/>
    
      <!-- Direct Reference Example with Properties -->
      
			<OntologyIndividual term="Rattus norvegicus" termAccession="#Rattus norvegicus" 
											identifier="www.ncbi.nlm.nih.gov:OntologyIndividual:Rattus norvegicus"
											OntologySource_ref="www.ncbi.nlm.nih.gov:OntologySource:Taxonomy"/>

			<OntologyIndividual term="Age" termAccession="#Age" 
											identifier="mged.sourceforge.net/ontologies:OntologyIndividual:Age"
											OntologySource_ref="mged.sourceforge.net/ontologies:OntologySource:MGEDOntology">
			
			  <ObjectProperty term="has_measurement" termAccession="#has_measurement" 
												identifier="mged.sourceforge.net/ontologies:ObjectProperty:has_measurement">

					<OntologyIndividual term="Measurement" termAccession="#Measurement" 
													identifier="mged.sourceforge.net/ontologies:Class:Measurement">

						<DataProperty term="has_value" termAccession="#has_value" value="2"
													identifier="mged.sourceforge.net/ontologies:has_value"/>                         

						<ObjectProperty term="has_units" termAccession="#has_units" 
															identifier="mged.sourceforge.net/ontologies:ObjectProperty:has_units">

							<OntologyIndividual term="days" termAccession="#days" 
														identifier="mged.sourceforge.net/ontologies:OntologyIndividual:days"/>

						</ObjectProperty>
						
					</OntologyIndividual>

				</ObjectProperty>
				
			  <ObjectProperty term="has_maximum_measurement" termAccession="#has_maximum_measurement" 
												identifier="mged.sourceforge.net/ontologies:ObjectProperty:has_maximum_measurement">

					<OntologyIndividual term="Measurement" termAccession="#Measurement" 
													identifier="mged.sourceforge.net/ontologies:Class:Measurement">

						<DataProperty term="has_value" termAccession="#has_value" value="3"
													identifier="mged.sourceforge.net/ontologies:has_value"/>                         

						<ObjectProperty term="has_units" termAccession="#has_units" 
															identifier="mged.sourceforge.net/ontologies:ObjectProperty:has_units">

							<OntologyIndividual term="days" termAccession="#days" 
														identifier="mged.sourceforge.net/ontologies:OntologyIndividual:days"/>

						</ObjectProperty>
						
					</OntologyIndividual>

				</ObjectProperty>
				
			  <ObjectProperty term="initial_time_point" termAccession="#initial_time_point" 
												identifier="mged.sourceforge.net/ontologies:ObjectProperty:initial_time_point">

					<OntologyIndividual term="birth" termAccession="#birth" 
													identifier="mged.sourceforge.net/ontologies:Class:birth"/>

				</ObjectProperty>
				
		  </OntologyIndividual>

      <!-- Family Ontology Example -->
    
			<OntologyIndividual term="PAUL_SMITH" termAccession="#PAUL_SMITH" 
												identifier="www.org_xyz.com:GenericMaterial:PAUL_SMITH"
												OntologySource_ref="www.org_xyz.com:OntologySource:www.org_xyz.com">
			
			  <ObjectProperty term="IS_A" termAccession="#IS_A" 
												identifier="fuge.sourceforge.net:ObjectProperty:IS_A">

					<OntologyIndividual term="Man" termAccession="#Man" 
													identifier="family.swrl.owl/ontologies:Class:Man"
													OntologySource_ref="family.swrl.owl/ontologies:OntologySource:family.swrl.owl" />

				</ObjectProperty>
				
				<ObjectProperty term="hasMother" termAccession="hasMother" 
													identifier="family.swrl.owl/ontologies:ObjectProperty:hasMother">

					<OntologyIndividual term="MARY_SMITH" termAccession="#MARY_SMITH" 
												identifier="www.org_xyz.com:GenericMaterial:MARY_SMITH"
												OntologySource_ref="www.org_xyz.com:OntologySource:www.org_xyz.com"/>

				</ObjectProperty>

		  </OntologyIndividual>

			<OntologyIndividual term="TRUDY_SMITH" termAccession="#TRUDY_SMITH" 
												identifier="www.org_xyz.com:GenericMaterial:TRUDY_SMITH"
												OntologySource_ref="www.org_xyz.com:OntologySource:www.org_xyz.com">
			
			  <ObjectProperty term="IS_A" termAccession="#IS_A" 
												identifier="fuge.sourceforge.net:ObjectProperty:IS_A">

					<OntologyIndividual term="Woman" termAccession="#Woman" 
													identifier="family.swrl.owl/ontologies:Class:Woman"
													OntologySource_ref="family.swrl.owl/ontologies:OntologySource:family.swrl.owl" />

				</ObjectProperty>
				
				<ObjectProperty term="hasConsort" termAccession="hasConsort" 
													identifier="family.swrl.owl/ontologies:ObjectProperty:hasConsort">

					<OntologyIndividual term="PAUL_SMITH" termAccession="#PAUL_SMITH" 
												identifier="www.org_xyz.com:GenericMaterial:PAUL_SMITH"
												OntologySource_ref="www.org_xyz.com:OntologySource:www.org_xyz.com"/>

				</ObjectProperty>

		  </OntologyIndividual>

			<OntologyIndividual term="MARY_SMITH" termAccession="#MARY_SMITH" 
												identifier="www.org_xyz.com:GenericMaterial:MARY_SMITH"
												OntologySource_ref="www.org_xyz.com:OntologySource:www.org_xyz.com">
			
			  <ObjectProperty term="IS_A" termAccession="#IS_A" 
												identifier="fuge.sourceforge.net:ObjectProperty:IS_A">

					<OntologyIndividual term="Woman" termAccession="#Woman" 
													identifier="family.swrl.owl/ontologies:Class:Woman"
													OntologySource_ref="family.swrl.owl/ontologies:OntologySource:family.swrl.owl" />

				</ObjectProperty>
				
				<ObjectProperty term="hasConsort" termAccession="hasConsort" 
													identifier="family.swrl.owl/ontologies:ObjectProperty:hasConsort">

					<OntologyIndividual term="TONY_SMITH" termAccession="#TONY_SMITH" 
												identifier="www.org_xyz.com:GenericMaterial:TONY_SMITH"
												OntologySource_ref="www.org_xyz.com:OntologySource:www.org_xyz.com"/>

				</ObjectProperty>

		  </OntologyIndividual>

	    <!-- Observation Ontology Example -->
			<!-- Would have instances of the following block, one for each rat that is part of the investigation -->
        <OntologyIndividual term="Investigation_C0001.rat_n" termAccession="Investigation_C0001.rat_n" 
                            identifier="www.lab_xyz.com:GenericMaterial:Investigation_C0001.rat_n"
                            OntologySource_ref="www.lab_xyz.com:OntologySource:www.lab_xyz.com">                      
            
				  <!-- link this individual to its class(es) of an external ontology -->
          <ObjectProperty term="IS_A" termAccession="#IS_A" 
                          identifier="www.ObservationOntology.net:ObjectProperty:IS_A">
                
				    <OntologyIndividual term="Subject" termAccession="#Subject" 
                            identifier="www.ObservationOntology.net:OntologyIndividual:Subject"
                            OntologySource_ref="www.ObservationOntology.net:OntologySource:ObservationOntology"/>
				  
				  </ObjectProperty>
				  
				  <!-- now the inherited restriction properties of the super ontology term can be used -->
          <ObjectProperty term="has_Observation" termAccession="#has_Observation" 
                          identifier="www.ObservationOntology.net:ObjectProperty:has_Observation">
                
				
						<OntologyIndividual term="Observation" termAccession="#Observation" 
																identifier="www.ObservationOntology.net:OntologyIndividual:Observation"
																OntologySource_ref="www.ObservationOntology.net:OntologySource:ObservationOntology">                      

							<ObjectProperty term="has_ObservationDay" termAccession="#has_ObservationDay" 
															identifier="www.ObservationOntology.net:ObjectProperty:has_ObservationDay">

								<OntologyIndividual term="ObservationDay" termAccession="#ObservationDay" 
																		identifier="www.ObservationOntology.net:OntologyIndividual:ObservationDay"> 

									<DataProperty term="has_date" termAccession="#has_date" value="2005-12-30"
																identifier="www.ObservationOntology.net:DataProperty:has_date"/>

									<ObjectProperty term="has_observation" termAccession="#has_observation" 
																	identifier="www.ObservationOntology.net:ObjectProperty:has_observation">

										<OntologyIndividual term="WeightMeasurement" termAccession="#WeightMeasurement" 
																				identifier="www.ObservationOntology.net:OntologyIndividual:WeightMeasurement">

											<ObjectProperty term="has_WeightMeasurementUnits" termAccession="#has_WeightMeasurementUnits" identifier="www.ObservationOntology.net:ObjectProperty:has_WeightMeasurementUnits">

												<OntologyIndividual term="grams" termAccession="#grams" 
																						identifier="www.MeasurementOntology.net:OntologyIndividual:grams" 
																						OntologySource_ref="www.MeasurementOntology.net:OntologySource:MeasurementOntology"/>

											</ObjectProperty>

											<DataProperty term="has_value" termAccession="#has_value" value="17.9"
																		identifier="www.lab_xyz.com:DataProperty.TABLE_FEED.AMOUNT_FEED:has_value"
																		OntologySource_ref="www.lab_xyz.com:OntologySource.TABLE_FEED.AMOUNT_FEED:www.lab_xyz.com"/>                         

										</OntologyIndividual>

										<OntologyIndividual term="wheat" termAccession="#wheat" 
																				identifier="www.someFoodOntology.net:OntologyIndividual:wheat" 
																				OntologySource_ref="www.someFoodOntology.net:OntologySource:SomeFoodOntology">

											<ObjectProperty term="IS_A" termAccession="#IS_A" identifier="www.ObservationOntology.net:ObjectProperty:IS_A">

												<OntologyIndividual term="Feed" termAccession="ObservationOntology" 
																						identifier="www.ObservationOntology.net:OntologyIndividual:Feed"  
																						OntologySource_ref="www.ObservationOntology.net:OntologySource:ObservationOntology"/>

											</ObjectProperty>

										</OntologyIndividual>                            

									</ObjectProperty>

								</OntologyIndividual>

							</ObjectProperty>                            

							<ObjectProperty term="has_ObservationDay" termAccession="#has_ObservationDay" 
															identifier="www.ObservationOntology.net:ObjectProperty:has_ObservationDay">

								<OntologyIndividual term="ObservationDay" termAccession="#ObservationDay" 
																		identifier="www.ObservationOntology.net:OntologyIndividual:ObservationDay"> 

									<DataProperty term="has_date" termAccession="#has_date" value="2005-12-31"
																identifier="www.ObservationOntology.net:DataProperty:has_date"/>

									<ObjectProperty term="has_Observation" termAccession="#has_Observation" 
																	identifier="www.ObservationOntology.net:ObjectProperty:has_Observation">

										<OntologyIndividual term="WeightMeasurement" termAccession="#WeightMeasurement" 
																				identifier="www.ObservationOntology.net:OntologyIndividual:WeightMeasurement">

											<ObjectProperty term="has_WeightMeasurementUnits" termAccession="#has_WeightMeasurementUnits" identifier="www.ObservationOntology.net:ObjectProperty:has_WeightMeasurementUnits">

												<OntologyIndividual term="grams" termAccession="#grams" 
																						identifier="www.MeasurementOntology.net:OntologyIndividual:grams" 
																						OntologySource_ref="www.MeasurementOntology.net:OntologySource:MeasurementOntology"/>

											</ObjectProperty>

											<DataProperty term="has_value" termAccession="#has_value" value="18.5"
																		identifier="www.lab_xyz.com:DataProperty.TABLE_FEED.AMOUNT_FEED:has_value"
																		OntologySource_ref="www.lab_xyz.com:OntologySource.TABLE_FEED.AMOUNT_FEED:www.lab_xyz.com"/>                         

										</OntologyIndividual>

										<OntologyIndividual term="corn" termAccession="#corn" 
																				identifier="www.someFoodOntology.net:OntologyIndividual:corn" 
																				OntologySource_ref="www.someFoodOntology.net:OntologySource:SomeFoodOntology">

											<ObjectProperty term="IS_A" termAccession="#IS_A" identifier="www.ObservationOntology.net:ObjectProperty:IS_A">

												<OntologyIndividual term="Feed" termAccession="ObservationOntology" 
																						identifier="www.ObservationOntology.net:OntologyIndividual:Feed"  
																						OntologySource_ref="www.ObservationOntology.net:OntologySource:ObservationOntology"/>

									    </ObjectProperty>

								    </OntologyIndividual>

									</ObjectProperty>

								</OntologyIndividual>

							</ObjectProperty>   
							
							<DataProperty term="has_SacrificeDate" termAccession="#has_SacrificeDate" value="2006-01-01"
							              identifier="www.ObservationOntology.net:ObjectProperty:has_SacrificeDate"/>
							
				    </OntologyIndividual>

          </ObjectProperty>            
        
        </OntologyIndividual>
                
				<!-- and so on -->
                
  
        <OntologySource ontologyURI="www.ObservationOntology.net" identifier="www.ObservationOntology.net:OntologySource:ObservationOntology"/>
        
        <OntologySource ontologyURI="www.someFoodOntology.net" identifier="www.someFoodOntology.net:OntologySource:SomeFoodOntology"/>
        
        <OntologySource ontologyURI="www.MeasurementOntology.net" identifier="www.MeasurementOntology.net:OntologySource:MeasurementOntology"/>
        
        <OntologySource ontologyURI="www.lab_xyz.com:OntologySource:www.lab_xyz.com" identifier="www.lab_xyz.com:OntologySource.TABLE_FEED.AMOUNT_FEED:www.lab_xyz.com">
          <_descriptions>
            <Description text = "A set of values specific to the provider of the document as specified in the local database column TABLE_FEED.AMOUNT_FEED"/>
          </_descriptions>
        </OntologySource>
        
        <OntologySource ontologyURI="www.lab_xyz.com:OntologySource:www.lab_xyz.com" identifier="www.lab_xyz.com:OntologySource.:www.lab_xyz.com">
          <_descriptions>
            <Description text = "A set of individuals specific to the provider of the document"/>
          </_descriptions>
        </OntologySource>
        
    </OntologyCollection>
    
    <Provider identifier="www.lab_xyz.com:Provider:department_01" name = "department_01">
    </Provider>
    
</FuGE>
