diff --git a/src/main/java/edu/ohsu/cmp/ecp/sds/SupplementalDataStorePartition.java b/src/main/java/edu/ohsu/cmp/ecp/sds/SupplementalDataStorePartition.java
index 8c59ea0..a62bee2 100644
--- a/src/main/java/edu/ohsu/cmp/ecp/sds/SupplementalDataStorePartition.java
+++ b/src/main/java/edu/ohsu/cmp/ecp/sds/SupplementalDataStorePartition.java
@@ -23,8 +23,6 @@
 @Component
 public class SupplementalDataStorePartition {
 
-	public static final String HEADER_PARTITION_NAME = "X-Partition-Name";
-
 	@Inject
 	SupplementalDataStoreProperties sdsProperties;
 
@@ -80,7 +78,8 @@ public RequestPartitionId partitionIdFromRequest(RequestDetails theRequestDetail
 	}
 
 	protected String partitionNameFromRequest(RequestDetails theRequestDetails) {
-		final String partitionNameHeaderValue = theRequestDetails.getHeader(HEADER_PARTITION_NAME);
+		final String httpHeader = sdsProperties.getPartition().getHttpHeader();
+		final String partitionNameHeaderValue = theRequestDetails.getHeader( httpHeader );
 		if (StringUtils.isNotBlank(partitionNameHeaderValue)) {
 			/*
 			 * later we want to recreate the partition name
diff --git a/src/main/java/edu/ohsu/cmp/ecp/sds/dstu3/SupplementalDataStoreLinkageDstu3.java b/src/main/java/edu/ohsu/cmp/ecp/sds/dstu3/SupplementalDataStoreLinkageDstu3.java
index a89ca78..d96cc27 100644
--- a/src/main/java/edu/ohsu/cmp/ecp/sds/dstu3/SupplementalDataStoreLinkageDstu3.java
+++ b/src/main/java/edu/ohsu/cmp/ecp/sds/dstu3/SupplementalDataStoreLinkageDstu3.java
@@ -1,9 +1,12 @@
 package edu.ohsu.cmp.ecp.sds.dstu3;
 
+import static java.util.stream.Collectors.toList;
+
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Optional;
 import java.util.Set;
+import java.util.function.Predicate;
 
 import javax.inject.Inject;
 
@@ -11,10 +14,12 @@
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.dstu3.model.RelatedPerson;
+import org.hl7.fhir.dstu3.model.Type;
 import org.hl7.fhir.dstu3.model.StringType;
 import org.hl7.fhir.dstu3.model.BooleanType;
 import org.hl7.fhir.dstu3.model.DomainResource;
 import org.hl7.fhir.dstu3.model.Extension;
+import org.hl7.fhir.dstu3.model.IdType;
 import org.hl7.fhir.dstu3.model.Linkage;
 import org.hl7.fhir.dstu3.model.Linkage.LinkageType;
 import org.hl7.fhir.dstu3.model.Patient;
@@ -27,6 +32,7 @@
 import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.starter.annotations.OnDSTU3Condition;
+import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.param.ReferenceParam;
 import edu.ohsu.cmp.ecp.sds.SupplementalDataStoreProperties;
@@ -52,9 +58,114 @@ public class SupplementalDataStoreLinkageDstu3 extends SupplementalDataStoreLink
 	@Inject
 	IFhirResourceDao<org.hl7.fhir.dstu3.model.RelatedPerson> daoRelatedPersonDstu3;
 
+	private static Predicate<IIdType> sameId( IIdType id ) {
+		return (i) -> {
+			if ( id.hasVersionIdPart() && i.hasVersionIdPart() && !id.getVersionIdPart().equals(i.getVersionIdPart()))
+				return false ;
+			if ( id.hasBaseUrl() && i.hasBaseUrl() && !id.getBaseUrl().equals(i.getBaseUrl()))
+				return false ;
+			if ( id.hasResourceType() && i.hasResourceType() && !id.getResourceType().equals(i.getResourceType()))
+				return false ;
+			if ( !id.hasIdPart() || !i.hasIdPart() )
+				return false ;
+			return id.getIdPart().equals( i.getIdPart() ) ;
+		};
+	}
+
+	private static Predicate<Linkage.LinkageItemComponent> refersTo( IQueryParameterType param ) {
+		if ( param instanceof ReferenceParam ) {
+			ReferenceParam refParam = (ReferenceParam)param ;
+			return refersTo( new IdType( refParam.getResourceType(), refParam.getIdPart() ) ) ;
+		} else {
+			return (i) -> false ;
+		}
+	}
+
+	private static Predicate<Linkage.LinkageItemComponent> refersTo( IIdType ref ) {
+		Predicate<IIdType> p = sameId( ref ) ;
+		return i -> i.hasResource() && i.getResource().hasReference() && p.test( referenceFromLinkage( i.getResource() ).getReferenceElement() );
+	}
+
+	private static Predicate<Linkage.LinkageItemComponent> sourceRefersTo( IQueryParameterType param ) {
+		if ( param instanceof ReferenceParam ) {
+			ReferenceParam refParam = (ReferenceParam)param ;
+			return sourceRefersTo( new IdType( refParam.getResourceType(), refParam.getIdPart() ) ) ;
+		} else {
+			return (i) -> false ;
+		}
+	}
+
+	private static Predicate<Linkage.LinkageItemComponent> sourceRefersTo( IIdType ref ) {
+		Predicate<Linkage.LinkageItemComponent> p1 = refersTo( ref ) ;
+		return i -> i.getType() == Linkage.LinkageType.SOURCE && p1.test(i) ;
+	}
+
+	private Predicate<IBaseResource> linkageItemFilter( List<List<IQueryParameterType>> parameterValue ) {
+		if ( null == parameterValue )
+			return r -> true ;
+		return r -> {
+			if ( !(r instanceof Linkage ) )
+				return false ;
+			Linkage linkage = (Linkage)r ;
+
+			return parameterValue.stream().allMatch( v1 -> v1.stream().anyMatch( v -> linkage.getItem().stream().anyMatch( refersTo( v ) ) ) ) ;
+		} ;
+	}
+
+	private Predicate<IBaseResource> linkageSourceFilter( List<List<IQueryParameterType>> parameterValue ) {
+		if ( null == parameterValue )
+			return r -> true ;
+			return r -> {
+				if ( !(r instanceof Linkage ) )
+					return false ;
+				Linkage linkage = (Linkage)r ;
+
+				return parameterValue.stream().allMatch( v1 -> v1.stream().anyMatch( v -> linkage.getItem().stream().anyMatch( sourceRefersTo( v ) ) ) ) ;
+			} ;
+	}
+
+	private IQueryParameterType convertQueryParameter( IQueryParameterType parameter ) {
+		if ( parameter instanceof ReferenceParam ) {
+			ReferenceParam refParam = (ReferenceParam)parameter ;
+			IdType id = new IdType( refParam.getValue() ).toUnqualifiedVersionless() ;
+			return new ReferenceParam( id ) ;
+		} else {
+			return parameter ;
+		}
+	}
+
+	private List<IQueryParameterType> convertQueryParameters( List<IQueryParameterType> parameters ) {
+		return parameters.stream().map( this::convertQueryParameter ).collect( toList() ) ;
+	}
+
+	private List<List<IQueryParameterType>> convertQueryParametersList( List<List<IQueryParameterType>> parameters ) {
+		return parameters.stream().map( this::convertQueryParameters ).collect( toList() ) ;
+	}
+
 	@Override
 	protected List<IBaseResource> searchLinkageResources( SearchParameterMap linkageSearchParamMap, RequestDetails theRequestDetails ) {
-		return daoLinkageDstu3.search(linkageSearchParamMap, theRequestDetails).getAllResources();
+		/*
+		 * server is returning LINKAGE resources while searching on SOURCE that match the id but are not SOURCE
+		 */
+		/*
+		 * item and source parameters must be relative (i.e. no baseUrl) in order to find these LINKAGE resources
+		 */
+
+		SearchParameterMap replacementSearchParameterMap = linkageSearchParamMap.clone() ;
+		List<List<IQueryParameterType>> itemQueryParameter = replacementSearchParameterMap.remove("item");
+		List<List<IQueryParameterType>> sourceQueryParameter = replacementSearchParameterMap.remove("source");
+		if ( null != itemQueryParameter ) {
+			replacementSearchParameterMap.put( "item", convertQueryParametersList( itemQueryParameter ) );
+		}
+		if ( null != sourceQueryParameter ) {
+			replacementSearchParameterMap.put( "source", convertQueryParametersList( sourceQueryParameter ) );
+		}
+		return daoLinkageDstu3.search(replacementSearchParameterMap, theRequestDetails).getAllResources()
+				.stream()
+				.filter( linkageItemFilter( itemQueryParameter ) )
+				.filter( linkageSourceFilter( sourceQueryParameter ) )
+				.collect( java.util.stream.Collectors.toList() )
+				;
 	}
 
 	@Override
@@ -64,8 +175,9 @@ protected List<IBaseResource> filterLinkageResourcesHavingAlternateItem( List<IB
 			if (res instanceof Linkage) {
 				Linkage linkage = (Linkage) res;
 				for (Linkage.LinkageItemComponent linkageItem : linkage.getItem()) {
-					if (linkageItem.getType() == LinkageType.ALTERNATE && linkageItem.hasResource() && linkageItem.getResource().hasReference() && nonLocalPatientId.equals(linkageItem.getResource().getReferenceElement())) {
+					if (linkageItem.getType() == LinkageType.ALTERNATE && linkageItem.hasResource() && linkageItem.getResource().hasReference() && nonLocalPatientId.equals( referenceFromLinkage( linkageItem.getResource() ).getReferenceElement())) {
 						linkageResources.add(res);
+						break;	// breaking to prevent re-adding res if there are multiple alternates
 					}
 				}
 			}
@@ -87,12 +199,37 @@ protected List<Reference> patientsFromLinkageResources(List<IBaseResource> linka
 		return linkedPatients;
 	}
 
+	private static Reference referenceFromLinkage( Reference ref ) {
+		if ( !ref.hasExtension(EXTENSION_URL_SDS_PARTITION_NAME) )
+			return ref ;
+		if ( !ref.hasReferenceElement() )
+			return ref ;
+		Type extValue = ref.getExtensionByUrl(EXTENSION_URL_SDS_PARTITION_NAME).getValue() ;
+		if ( !(extValue instanceof StringType) )
+			return ref ;
+		IIdType id = new IdType( ((StringType)extValue).getValue(), ref.getReferenceElement().getResourceType(), ref.getReferenceElement().getIdPart(), ref.getReferenceElement().getVersionIdPart() ) ;
+		return new Reference( id ) ;
+	}
+
+	private static Reference referenceForLinkage( IIdType id ) {
+		if ( id.hasBaseUrl() ) {
+			Reference ref = new Reference( id.toUnqualifiedVersionless() ) ;
+			ref.addExtension(EXTENSION_URL_SDS_PARTITION_NAME, new StringType( id.getBaseUrl() ) );
+			return ref ;
+		} else {
+			return new Reference(id) ;
+		}
+	}
+
 	@Override
 	protected void createLinkage( IIdType sourcePatientId, IIdType alternatePatientId, RequestDetails theRequestDetails ) {
 		Linkage linkage = new Linkage();
-		linkage.addItem().setType(LinkageType.SOURCE).setResource(new Reference(sourcePatientId));
-		linkage.addItem().setType(LinkageType.ALTERNATE).setResource(new Reference(alternatePatientId));
-		daoLinkageDstu3.create(linkage, theRequestDetails);
+		linkage.addItem().setType(LinkageType.SOURCE).setResource(referenceForLinkage(sourcePatientId));
+		linkage.addItem().setType(LinkageType.ALTERNATE).setResource(referenceForLinkage(alternatePatientId));
+		DaoMethodOutcome outcome = daoLinkageDstu3.create(linkage, theRequestDetails);
+		if ( Boolean.TRUE != outcome.getCreated() ) {
+			throw new RuntimeException( "failed to create linkage between " + sourcePatientId + " and " + alternatePatientId ) ;
+		}
 	}
 
 	@Override
@@ -104,6 +241,7 @@ protected Set<? extends IBaseReference> alternatePatientsFromLinkageResources(Li
 				.flatMap(k -> k.getItem().stream())
 				.filter(i -> i.getType() == LinkageType.ALTERNATE)
 				.map(i -> i.getResource())
+				.map( SupplementalDataStoreLinkageDstu3::referenceFromLinkage )
 				.collect(java.util.stream.Collectors.toList());
 		return FhirResourceComparison.references().createSet( sourceRefs ) ;
 	}
@@ -117,6 +255,7 @@ protected Set<? extends IBaseReference> sourcePatientsFromLinkageResources(List<
 				.flatMap(k -> k.getItem().stream())
 				.filter(i -> i.getType() == LinkageType.SOURCE)
 				.map(i -> i.getResource())
+				.map( SupplementalDataStoreLinkageDstu3::referenceFromLinkage )
 				.collect(java.util.stream.Collectors.toList());
 		return FhirResourceComparison.references().createSet( sourceRefs ) ;
 	}
diff --git a/src/main/java/edu/ohsu/cmp/ecp/sds/r4/SupplementalDataStoreLinkageR4.java b/src/main/java/edu/ohsu/cmp/ecp/sds/r4/SupplementalDataStoreLinkageR4.java
index b937765..fbb5f1a 100644
--- a/src/main/java/edu/ohsu/cmp/ecp/sds/r4/SupplementalDataStoreLinkageR4.java
+++ b/src/main/java/edu/ohsu/cmp/ecp/sds/r4/SupplementalDataStoreLinkageR4.java
@@ -1,5 +1,7 @@
 package edu.ohsu.cmp.ecp.sds.r4;
 
+import static java.util.stream.Collectors.toList;
+
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Optional;
@@ -31,7 +33,6 @@
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.starter.annotations.OnR4Condition;
 import ca.uhn.fhir.model.api.IQueryParameterType;
-import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.param.ReferenceParam;
 import edu.ohsu.cmp.ecp.sds.SupplementalDataStoreProperties;
@@ -70,7 +71,7 @@ private static Predicate<IIdType> sameId( IIdType id ) {
 			return id.getIdPart().equals( i.getIdPart() ) ;
 		};
 	}
-	
+
 	private static Predicate<Linkage.LinkageItemComponent> refersTo( IQueryParameterType param ) {
 		if ( param instanceof ReferenceParam ) {
 			ReferenceParam refParam = (ReferenceParam)param ;
@@ -79,7 +80,7 @@ private static Predicate<Linkage.LinkageItemComponent> refersTo( IQueryParameter
 			return (i) -> false ;
 		}
 	}
-	
+
 	private static Predicate<Linkage.LinkageItemComponent> refersTo( IIdType ref ) {
 		Predicate<IIdType> p = sameId( ref ) ;
 		return i -> i.hasResource() && i.getResource().hasReference() && p.test( referenceFromLinkage( i.getResource() ).getReferenceElement() );
@@ -93,13 +94,12 @@ private static Predicate<Linkage.LinkageItemComponent> sourceRefersTo( IQueryPar
 			return (i) -> false ;
 		}
 	}
-	
 
 	private static Predicate<Linkage.LinkageItemComponent> sourceRefersTo( IIdType ref ) {
 		Predicate<Linkage.LinkageItemComponent> p1 = refersTo( ref ) ;
 		return i -> i.getType() == Linkage.LinkageType.SOURCE && p1.test(i) ;
 	}
-	
+
 	private Predicate<IBaseResource> linkageItemFilter( List<List<IQueryParameterType>> parameterValue ) {
 		if ( null == parameterValue )
 			return r -> true ;
@@ -107,11 +107,11 @@ private Predicate<IBaseResource> linkageItemFilter( List<List<IQueryParameterTyp
 			if ( !(r instanceof Linkage ) )
 				return false ;
 			Linkage linkage = (Linkage)r ;
-			
+
 			return parameterValue.stream().allMatch( v1 -> v1.stream().anyMatch( v -> linkage.getItem().stream().anyMatch( refersTo( v ) ) ) ) ;
 		} ;
 	}
-	
+
 	private Predicate<IBaseResource> linkageSourceFilter( List<List<IQueryParameterType>> parameterValue ) {
 		if ( null == parameterValue )
 			return r -> true ;
@@ -119,28 +119,53 @@ private Predicate<IBaseResource> linkageSourceFilter( List<List<IQueryParameterT
 				if ( !(r instanceof Linkage ) )
 					return false ;
 				Linkage linkage = (Linkage)r ;
-				
+
 				return parameterValue.stream().allMatch( v1 -> v1.stream().anyMatch( v -> linkage.getItem().stream().anyMatch( sourceRefersTo( v ) ) ) ) ;
 			} ;
 	}
-	
+
+	private IQueryParameterType convertQueryParameter( IQueryParameterType parameter ) {
+		if ( parameter instanceof ReferenceParam ) {
+			ReferenceParam refParam = (ReferenceParam)parameter ;
+			IdType id = new IdType( refParam.getValue() ).toUnqualifiedVersionless() ;
+			return new ReferenceParam( id ) ;
+		} else {
+			return parameter ;
+		}
+	}
+
+	private List<IQueryParameterType> convertQueryParameters( List<IQueryParameterType> parameters ) {
+		return parameters.stream().map( this::convertQueryParameter ).collect( toList() ) ;
+	}
+
+	private List<List<IQueryParameterType>> convertQueryParametersList( List<List<IQueryParameterType>> parameters ) {
+		return parameters.stream().map( this::convertQueryParameters ).collect( toList() ) ;
+	}
+
 	@Override
 	protected List<IBaseResource> searchLinkageResources( SearchParameterMap linkageSearchParamMap, RequestDetails theRequestDetails ) {
 		/*
-		 * server is failing to find existing LINKAGE resources while searching on ITEM
-		 * 
-		return daoLinkageR4.search(linkageSearchParamMap, theRequestDetails).getAllResources();
+		 * server is returning LINKAGE resources while searching on SOURCE that match the id but are not SOURCE
+		 */
+		/*
+		 * item and source parameters must be relative (i.e. no baseUrl) in order to find these LINKAGE resources
 		 */
+
 		SearchParameterMap replacementSearchParameterMap = linkageSearchParamMap.clone() ;
-		Predicate<IBaseResource> itemFilter = linkageItemFilter( replacementSearchParameterMap.remove("item") ) ;
-		Predicate<IBaseResource> sourceFilter = linkageSourceFilter( replacementSearchParameterMap.remove("source") ) ;
+		List<List<IQueryParameterType>> itemQueryParameter = replacementSearchParameterMap.remove("item");
+		List<List<IQueryParameterType>> sourceQueryParameter = replacementSearchParameterMap.remove("source");
+		if ( null != itemQueryParameter ) {
+			replacementSearchParameterMap.put( "item", convertQueryParametersList( itemQueryParameter ) );
+		}
+		if ( null != sourceQueryParameter ) {
+			replacementSearchParameterMap.put( "source", convertQueryParametersList( sourceQueryParameter ) );
+		}
 		return daoLinkageR4.search(replacementSearchParameterMap, theRequestDetails).getAllResources()
 				.stream()
-				.filter( itemFilter )
-				.filter( sourceFilter )
+				.filter( linkageItemFilter( itemQueryParameter ) )
+				.filter( linkageSourceFilter( sourceQueryParameter ) )
 				.collect( java.util.stream.Collectors.toList() )
 				;
-		
 	}
 
 	@Override
diff --git a/src/main/java/edu/ohsu/cmp/ecp/sds/r4b/SupplementalDataStoreLinkageR4B.java b/src/main/java/edu/ohsu/cmp/ecp/sds/r4b/SupplementalDataStoreLinkageR4B.java
index 413e120..a578f5d 100644
--- a/src/main/java/edu/ohsu/cmp/ecp/sds/r4b/SupplementalDataStoreLinkageR4B.java
+++ b/src/main/java/edu/ohsu/cmp/ecp/sds/r4b/SupplementalDataStoreLinkageR4B.java
@@ -1,9 +1,12 @@
 package edu.ohsu.cmp.ecp.sds.r4b;
 
+import static java.util.stream.Collectors.toList;
+
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Optional;
 import java.util.Set;
+import java.util.function.Predicate;
 
 import javax.inject.Inject;
 
@@ -13,8 +16,10 @@
 import org.hl7.fhir.r4b.model.RelatedPerson;
 import org.hl7.fhir.r4b.model.UrlType;
 import org.hl7.fhir.r4b.model.BooleanType;
+import org.hl7.fhir.r4b.model.DataType;
 import org.hl7.fhir.r4b.model.DomainResource;
 import org.hl7.fhir.r4b.model.Extension;
+import org.hl7.fhir.r4b.model.IdType;
 import org.hl7.fhir.r4b.model.Linkage;
 import org.hl7.fhir.r4b.model.Linkage.LinkageType;
 import org.hl7.fhir.r4b.model.Patient;
@@ -27,6 +32,7 @@
 import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.starter.annotations.OnR4BCondition;
+import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.param.ReferenceParam;
 import edu.ohsu.cmp.ecp.sds.SupplementalDataStoreProperties;
@@ -52,9 +58,114 @@ public class SupplementalDataStoreLinkageR4B extends SupplementalDataStoreLinkag
 	@Inject
 	IFhirResourceDao<org.hl7.fhir.r4b.model.RelatedPerson> daoRelatedPersonR4B;
 
+	private static Predicate<IIdType> sameId( IIdType id ) {
+		return (i) -> {
+			if ( id.hasVersionIdPart() && i.hasVersionIdPart() && !id.getVersionIdPart().equals(i.getVersionIdPart()))
+				return false ;
+			if ( id.hasBaseUrl() && i.hasBaseUrl() && !id.getBaseUrl().equals(i.getBaseUrl()))
+				return false ;
+			if ( id.hasResourceType() && i.hasResourceType() && !id.getResourceType().equals(i.getResourceType()))
+				return false ;
+			if ( !id.hasIdPart() || !i.hasIdPart() )
+				return false ;
+			return id.getIdPart().equals( i.getIdPart() ) ;
+		};
+	}
+
+	private static Predicate<Linkage.LinkageItemComponent> refersTo( IQueryParameterType param ) {
+		if ( param instanceof ReferenceParam ) {
+			ReferenceParam refParam = (ReferenceParam)param ;
+			return refersTo( new IdType( refParam.getResourceType(), refParam.getIdPart() ) ) ;
+		} else {
+			return (i) -> false ;
+		}
+	}
+
+	private static Predicate<Linkage.LinkageItemComponent> refersTo( IIdType ref ) {
+		Predicate<IIdType> p = sameId( ref ) ;
+		return i -> i.hasResource() && i.getResource().hasReference() && p.test( referenceFromLinkage( i.getResource() ).getReferenceElement() );
+	}
+
+	private static Predicate<Linkage.LinkageItemComponent> sourceRefersTo( IQueryParameterType param ) {
+		if ( param instanceof ReferenceParam ) {
+			ReferenceParam refParam = (ReferenceParam)param ;
+			return sourceRefersTo( new IdType( refParam.getResourceType(), refParam.getIdPart() ) ) ;
+		} else {
+			return (i) -> false ;
+		}
+	}
+
+	private static Predicate<Linkage.LinkageItemComponent> sourceRefersTo( IIdType ref ) {
+		Predicate<Linkage.LinkageItemComponent> p1 = refersTo( ref ) ;
+		return i -> i.getType() == Linkage.LinkageType.SOURCE && p1.test(i) ;
+	}
+
+	private Predicate<IBaseResource> linkageItemFilter( List<List<IQueryParameterType>> parameterValue ) {
+		if ( null == parameterValue )
+			return r -> true ;
+		return r -> {
+			if ( !(r instanceof Linkage ) )
+				return false ;
+			Linkage linkage = (Linkage)r ;
+
+			return parameterValue.stream().allMatch( v1 -> v1.stream().anyMatch( v -> linkage.getItem().stream().anyMatch( refersTo( v ) ) ) ) ;
+		} ;
+	}
+
+	private Predicate<IBaseResource> linkageSourceFilter( List<List<IQueryParameterType>> parameterValue ) {
+		if ( null == parameterValue )
+			return r -> true ;
+			return r -> {
+				if ( !(r instanceof Linkage ) )
+					return false ;
+				Linkage linkage = (Linkage)r ;
+
+				return parameterValue.stream().allMatch( v1 -> v1.stream().anyMatch( v -> linkage.getItem().stream().anyMatch( sourceRefersTo( v ) ) ) ) ;
+			} ;
+	}
+
+	private IQueryParameterType convertQueryParameter( IQueryParameterType parameter ) {
+		if ( parameter instanceof ReferenceParam ) {
+			ReferenceParam refParam = (ReferenceParam)parameter ;
+			IdType id = new IdType( refParam.getValue() ).toUnqualifiedVersionless() ;
+			return new ReferenceParam( id ) ;
+		} else {
+			return parameter ;
+		}
+	}
+
+	private List<IQueryParameterType> convertQueryParameters( List<IQueryParameterType> parameters ) {
+		return parameters.stream().map( this::convertQueryParameter ).collect( toList() ) ;
+	}
+
+	private List<List<IQueryParameterType>> convertQueryParametersList( List<List<IQueryParameterType>> parameters ) {
+		return parameters.stream().map( this::convertQueryParameters ).collect( toList() ) ;
+	}
+
 	@Override
 	protected List<IBaseResource> searchLinkageResources( SearchParameterMap linkageSearchParamMap, RequestDetails theRequestDetails ) {
-		return daoLinkageR4B.search(linkageSearchParamMap, theRequestDetails).getAllResources();	
+		/*
+		 * server is returning LINKAGE resources while searching on SOURCE that match the id but are not SOURCE
+		 */
+		/*
+		 * item and source parameters must be relative (i.e. no baseUrl) in order to find these LINKAGE resources
+		 */
+
+		SearchParameterMap replacementSearchParameterMap = linkageSearchParamMap.clone() ;
+		List<List<IQueryParameterType>> itemQueryParameter = replacementSearchParameterMap.remove("item");
+		List<List<IQueryParameterType>> sourceQueryParameter = replacementSearchParameterMap.remove("source");
+		if ( null != itemQueryParameter ) {
+			replacementSearchParameterMap.put( "item", convertQueryParametersList( itemQueryParameter ) );
+		}
+		if ( null != sourceQueryParameter ) {
+			replacementSearchParameterMap.put( "source", convertQueryParametersList( sourceQueryParameter ) );
+		}
+		return daoLinkageR4B.search(replacementSearchParameterMap, theRequestDetails).getAllResources()
+				.stream()
+				.filter( linkageItemFilter( itemQueryParameter ) )
+				.filter( linkageSourceFilter( sourceQueryParameter ) )
+				.collect( java.util.stream.Collectors.toList() )
+				;
 	}
 
 	@Override
@@ -64,8 +175,9 @@ protected List<IBaseResource> filterLinkageResourcesHavingAlternateItem( List<IB
 			if (res instanceof Linkage) {
 				Linkage linkage = (Linkage) res;
 				for (Linkage.LinkageItemComponent linkageItem : linkage.getItem()) {
-					if (linkageItem.getType() == LinkageType.ALTERNATE && linkageItem.hasResource() && linkageItem.getResource().hasReference() && nonLocalPatientId.equals(linkageItem.getResource().getReferenceElement())) {
+					if (linkageItem.getType() == LinkageType.ALTERNATE && linkageItem.hasResource() && linkageItem.getResource().hasReference() && nonLocalPatientId.equals( referenceFromLinkage( linkageItem.getResource() ).getReferenceElement())) {
 						linkageResources.add(res);
+						break;	// breaking to prevent re-adding res if there are multiple alternates
 					}
 				}
 			}
@@ -87,12 +199,37 @@ protected List<Reference> patientsFromLinkageResources(List<IBaseResource> linka
 		return linkedPatients;
 	}
 
+	private static Reference referenceFromLinkage( Reference ref ) {
+		if ( !ref.hasExtension(EXTENSION_URL_SDS_PARTITION_NAME) )
+			return ref ;
+		if ( !ref.hasReferenceElement() )
+			return ref ;
+		DataType extValue = ref.getExtensionByUrl(EXTENSION_URL_SDS_PARTITION_NAME).getValue() ;
+		if ( !(extValue instanceof UrlType) )
+			return ref ;
+		IIdType id = new IdType( ((UrlType)extValue).getValue(), ref.getReferenceElement().getResourceType(), ref.getReferenceElement().getIdPart(), ref.getReferenceElement().getVersionIdPart() ) ;
+		return new Reference( id ) ;
+	}
+
+	private static Reference referenceForLinkage( IIdType id ) {
+		if ( id.hasBaseUrl() ) {
+			Reference ref = new Reference( id.toUnqualifiedVersionless() ) ;
+			ref.addExtension(EXTENSION_URL_SDS_PARTITION_NAME, new UrlType( id.getBaseUrl() ) );
+			return ref ;
+		} else {
+			return new Reference(id) ;
+		}
+	}
+
 	@Override
 	protected void createLinkage( IIdType sourcePatientId, IIdType alternatePatientId, RequestDetails theRequestDetails ) {
 		Linkage linkage = new Linkage();
-		linkage.addItem().setType(LinkageType.SOURCE).setResource(new Reference(sourcePatientId));
-		linkage.addItem().setType(LinkageType.ALTERNATE).setResource(new Reference(alternatePatientId));
-		daoLinkageR4B.create(linkage, theRequestDetails);
+		linkage.addItem().setType(LinkageType.SOURCE).setResource(referenceForLinkage(sourcePatientId));
+		linkage.addItem().setType(LinkageType.ALTERNATE).setResource(referenceForLinkage(alternatePatientId));
+		DaoMethodOutcome outcome = daoLinkageR4B.create(linkage, theRequestDetails);
+		if ( Boolean.TRUE != outcome.getCreated() ) {
+			throw new RuntimeException( "failed to create linkage between " + sourcePatientId + " and " + alternatePatientId ) ;
+		}
 	}
 
 	@Override
@@ -104,6 +241,7 @@ protected Set<? extends IBaseReference> alternatePatientsFromLinkageResources(Li
 				.flatMap(k -> k.getItem().stream())
 				.filter(i -> i.getType() == LinkageType.ALTERNATE)
 				.map(i -> i.getResource())
+				.map( SupplementalDataStoreLinkageR4B::referenceFromLinkage )
 				.collect(java.util.stream.Collectors.toList());
 		return FhirResourceComparison.references().createSet( sourceRefs ) ;
 	}
@@ -117,6 +255,7 @@ protected Set<? extends IBaseReference> sourcePatientsFromLinkageResources(List<
 				.flatMap(k -> k.getItem().stream())
 				.filter(i -> i.getType() == LinkageType.SOURCE)
 				.map(i -> i.getResource())
+				.map( SupplementalDataStoreLinkageR4B::referenceFromLinkage )
 				.collect(java.util.stream.Collectors.toList());
 		return FhirResourceComparison.references().createSet( sourceRefs ) ;
 	}
diff --git a/src/main/java/edu/ohsu/cmp/ecp/sds/r5/SupplementalDataStoreLinkageR5.java b/src/main/java/edu/ohsu/cmp/ecp/sds/r5/SupplementalDataStoreLinkageR5.java
index 512e238..bc8ee48 100644
--- a/src/main/java/edu/ohsu/cmp/ecp/sds/r5/SupplementalDataStoreLinkageR5.java
+++ b/src/main/java/edu/ohsu/cmp/ecp/sds/r5/SupplementalDataStoreLinkageR5.java
@@ -1,9 +1,12 @@
 package edu.ohsu.cmp.ecp.sds.r5;
 
+import static java.util.stream.Collectors.toList;
+
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Optional;
 import java.util.Set;
+import java.util.function.Predicate;
 
 import javax.inject.Inject;
 
@@ -13,8 +16,10 @@
 import org.hl7.fhir.r5.model.RelatedPerson;
 import org.hl7.fhir.r5.model.UrlType;
 import org.hl7.fhir.r5.model.BooleanType;
+import org.hl7.fhir.r5.model.DataType;
 import org.hl7.fhir.r5.model.DomainResource;
 import org.hl7.fhir.r5.model.Extension;
+import org.hl7.fhir.r5.model.IdType;
 import org.hl7.fhir.r5.model.Linkage;
 import org.hl7.fhir.r5.model.Linkage.LinkageType;
 import org.hl7.fhir.r5.model.Patient;
@@ -27,6 +32,7 @@
 import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.starter.annotations.OnR5Condition;
+import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.param.ReferenceParam;
 import edu.ohsu.cmp.ecp.sds.SupplementalDataStoreProperties;
@@ -52,9 +58,114 @@ public class SupplementalDataStoreLinkageR5 extends SupplementalDataStoreLinkage
 	@Inject
 	IFhirResourceDao<org.hl7.fhir.r5.model.RelatedPerson> daoRelatedPersonR5;
 
+	private static Predicate<IIdType> sameId( IIdType id ) {
+		return (i) -> {
+			if ( id.hasVersionIdPart() && i.hasVersionIdPart() && !id.getVersionIdPart().equals(i.getVersionIdPart()))
+				return false ;
+			if ( id.hasBaseUrl() && i.hasBaseUrl() && !id.getBaseUrl().equals(i.getBaseUrl()))
+				return false ;
+			if ( id.hasResourceType() && i.hasResourceType() && !id.getResourceType().equals(i.getResourceType()))
+				return false ;
+			if ( !id.hasIdPart() || !i.hasIdPart() )
+				return false ;
+			return id.getIdPart().equals( i.getIdPart() ) ;
+		};
+	}
+
+	private static Predicate<Linkage.LinkageItemComponent> refersTo( IQueryParameterType param ) {
+		if ( param instanceof ReferenceParam ) {
+			ReferenceParam refParam = (ReferenceParam)param ;
+			return refersTo( new IdType( refParam.getResourceType(), refParam.getIdPart() ) ) ;
+		} else {
+			return (i) -> false ;
+		}
+	}
+
+	private static Predicate<Linkage.LinkageItemComponent> refersTo( IIdType ref ) {
+		Predicate<IIdType> p = sameId( ref ) ;
+		return i -> i.hasResource() && i.getResource().hasReference() && p.test( referenceFromLinkage( i.getResource() ).getReferenceElement() );
+	}
+
+	private static Predicate<Linkage.LinkageItemComponent> sourceRefersTo( IQueryParameterType param ) {
+		if ( param instanceof ReferenceParam ) {
+			ReferenceParam refParam = (ReferenceParam)param ;
+			return sourceRefersTo( new IdType( refParam.getResourceType(), refParam.getIdPart() ) ) ;
+		} else {
+			return (i) -> false ;
+		}
+	}
+
+	private static Predicate<Linkage.LinkageItemComponent> sourceRefersTo( IIdType ref ) {
+		Predicate<Linkage.LinkageItemComponent> p1 = refersTo( ref ) ;
+		return i -> i.getType() == Linkage.LinkageType.SOURCE && p1.test(i) ;
+	}
+
+	private Predicate<IBaseResource> linkageItemFilter( List<List<IQueryParameterType>> parameterValue ) {
+		if ( null == parameterValue )
+			return r -> true ;
+		return r -> {
+			if ( !(r instanceof Linkage ) )
+				return false ;
+			Linkage linkage = (Linkage)r ;
+
+			return parameterValue.stream().allMatch( v1 -> v1.stream().anyMatch( v -> linkage.getItem().stream().anyMatch( refersTo( v ) ) ) ) ;
+		} ;
+	}
+
+	private Predicate<IBaseResource> linkageSourceFilter( List<List<IQueryParameterType>> parameterValue ) {
+		if ( null == parameterValue )
+			return r -> true ;
+			return r -> {
+				if ( !(r instanceof Linkage ) )
+					return false ;
+				Linkage linkage = (Linkage)r ;
+
+				return parameterValue.stream().allMatch( v1 -> v1.stream().anyMatch( v -> linkage.getItem().stream().anyMatch( sourceRefersTo( v ) ) ) ) ;
+			} ;
+	}
+
+	private IQueryParameterType convertQueryParameter( IQueryParameterType parameter ) {
+		if ( parameter instanceof ReferenceParam ) {
+			ReferenceParam refParam = (ReferenceParam)parameter ;
+			IdType id = new IdType( refParam.getValue() ).toUnqualifiedVersionless() ;
+			return new ReferenceParam( id ) ;
+		} else {
+			return parameter ;
+		}
+	}
+
+	private List<IQueryParameterType> convertQueryParameters( List<IQueryParameterType> parameters ) {
+		return parameters.stream().map( this::convertQueryParameter ).collect( toList() ) ;
+	}
+
+	private List<List<IQueryParameterType>> convertQueryParametersList( List<List<IQueryParameterType>> parameters ) {
+		return parameters.stream().map( this::convertQueryParameters ).collect( toList() ) ;
+	}
+
 	@Override
 	protected List<IBaseResource> searchLinkageResources( SearchParameterMap linkageSearchParamMap, RequestDetails theRequestDetails ) {
-		return daoLinkageR5.search(linkageSearchParamMap, theRequestDetails).getAllResources();
+		/*
+		 * server is returning LINKAGE resources while searching on SOURCE that match the id but are not SOURCE
+		 */
+		/*
+		 * item and source parameters must be relative (i.e. no baseUrl) in order to find these LINKAGE resources
+		 */
+
+		SearchParameterMap replacementSearchParameterMap = linkageSearchParamMap.clone() ;
+		List<List<IQueryParameterType>> itemQueryParameter = replacementSearchParameterMap.remove("item");
+		List<List<IQueryParameterType>> sourceQueryParameter = replacementSearchParameterMap.remove("source");
+		if ( null != itemQueryParameter ) {
+			replacementSearchParameterMap.put( "item", convertQueryParametersList( itemQueryParameter ) );
+		}
+		if ( null != sourceQueryParameter ) {
+			replacementSearchParameterMap.put( "source", convertQueryParametersList( sourceQueryParameter ) );
+		}
+		return daoLinkageR5.search(replacementSearchParameterMap, theRequestDetails).getAllResources()
+				.stream()
+				.filter( linkageItemFilter( itemQueryParameter ) )
+				.filter( linkageSourceFilter( sourceQueryParameter ) )
+				.collect( java.util.stream.Collectors.toList() )
+				;
 	}
 
 	@Override
@@ -64,8 +175,9 @@ protected List<IBaseResource> filterLinkageResourcesHavingAlternateItem( List<IB
 			if (res instanceof Linkage) {
 				Linkage linkage = (Linkage) res;
 				for (Linkage.LinkageItemComponent linkageItem : linkage.getItem()) {
-					if (linkageItem.getType() == LinkageType.ALTERNATE && linkageItem.hasResource() && linkageItem.getResource().hasReference() && nonLocalPatientId.equals(linkageItem.getResource().getReferenceElement())) {
+					if (linkageItem.getType() == LinkageType.ALTERNATE && linkageItem.hasResource() && linkageItem.getResource().hasReference() && nonLocalPatientId.equals( referenceFromLinkage( linkageItem.getResource() ).getReferenceElement())) {
 						linkageResources.add(res);
+						break;	// breaking to prevent re-adding res if there are multiple alternates
 					}
 				}
 			}
@@ -87,12 +199,37 @@ protected List<Reference> patientsFromLinkageResources(List<IBaseResource> linka
 		return linkedPatients;
 	}
 
+	private static Reference referenceFromLinkage( Reference ref ) {
+		if ( !ref.hasExtension(EXTENSION_URL_SDS_PARTITION_NAME) )
+			return ref ;
+		if ( !ref.hasReferenceElement() )
+			return ref ;
+		DataType extValue = ref.getExtensionByUrl(EXTENSION_URL_SDS_PARTITION_NAME).getValue() ;
+		if ( !(extValue instanceof UrlType) )
+			return ref ;
+		IIdType id = new IdType( ((UrlType)extValue).getValue(), ref.getReferenceElement().getResourceType(), ref.getReferenceElement().getIdPart(), ref.getReferenceElement().getVersionIdPart() ) ;
+		return new Reference( id ) ;
+	}
+
+	private static Reference referenceForLinkage( IIdType id ) {
+		if ( id.hasBaseUrl() ) {
+			Reference ref = new Reference( id.toUnqualifiedVersionless() ) ;
+			ref.addExtension(EXTENSION_URL_SDS_PARTITION_NAME, new UrlType( id.getBaseUrl() ) );
+			return ref ;
+		} else {
+			return new Reference(id) ;
+		}
+	}
+
 	@Override
 	protected void createLinkage( IIdType sourcePatientId, IIdType alternatePatientId, RequestDetails theRequestDetails ) {
 		Linkage linkage = new Linkage();
-		linkage.addItem().setType(LinkageType.SOURCE).setResource(new Reference(sourcePatientId));
-		linkage.addItem().setType(LinkageType.ALTERNATE).setResource(new Reference(alternatePatientId));
-		daoLinkageR5.create(linkage, theRequestDetails);
+		linkage.addItem().setType(LinkageType.SOURCE).setResource(referenceForLinkage(sourcePatientId));
+		linkage.addItem().setType(LinkageType.ALTERNATE).setResource(referenceForLinkage(alternatePatientId));
+		DaoMethodOutcome outcome = daoLinkageR5.create(linkage, theRequestDetails);
+		if ( Boolean.TRUE != outcome.getCreated() ) {
+			throw new RuntimeException( "failed to create linkage between " + sourcePatientId + " and " + alternatePatientId ) ;
+		}
 	}
 
 	@Override
@@ -104,6 +241,7 @@ protected Set<? extends IBaseReference> alternatePatientsFromLinkageResources(Li
 				.flatMap(k -> k.getItem().stream())
 				.filter(i -> i.getType() == LinkageType.ALTERNATE)
 				.map(i -> i.getResource())
+				.map( SupplementalDataStoreLinkageR5::referenceFromLinkage )
 				.collect(java.util.stream.Collectors.toList());
 		return FhirResourceComparison.references().createSet( sourceRefs ) ;
 	}
@@ -117,6 +255,7 @@ protected Set<? extends IBaseReference> sourcePatientsFromLinkageResources(List<
 				.flatMap(k -> k.getItem().stream())
 				.filter(i -> i.getType() == LinkageType.SOURCE)
 				.map(i -> i.getResource())
+				.map( SupplementalDataStoreLinkageR5::referenceFromLinkage )
 				.collect(java.util.stream.Collectors.toList());
 		return FhirResourceComparison.references().createSet( sourceRefs ) ;
 	}
diff --git a/src/test/java/edu/ohsu/cmp/ecp/sds/BaseSuppplementalDataStoreTest.java b/src/test/java/edu/ohsu/cmp/ecp/sds/BaseSuppplementalDataStoreTest.java
index 7fc0970..c4db806 100644
--- a/src/test/java/edu/ohsu/cmp/ecp/sds/BaseSuppplementalDataStoreTest.java
+++ b/src/test/java/edu/ohsu/cmp/ecp/sds/BaseSuppplementalDataStoreTest.java
@@ -51,6 +51,9 @@ public abstract class BaseSuppplementalDataStoreTest {
 	@LocalServerPort
 	private int port;
 
+	@Autowired
+	private SupplementalDataStoreProperties sdsProperties ;
+
 	@Autowired
 	private ModelConfig myModelConfig;
 
@@ -101,7 +104,7 @@ public void resetTestSpecificIdComponents(TestInfo testInfo) {
 	
 	protected IGenericClient clientTargetingPartition( String partitionName ) {
 		IGenericClient client = client() ;
-		client.registerInterceptor( new PartitionNameHeaderClientInterceptor( partitionName ) );
+		client.registerInterceptor( new PartitionNameHeaderClientInterceptor( sdsProperties.getPartition().getHttpHeader(), partitionName ) );
 		return client ;
 
 	}
@@ -114,7 +117,7 @@ protected IGenericClient authenticatingClient( String token ) {
 
 	protected IGenericClient authenticatingClientTargetingPartition( String token, String partitionName ) {
 		IGenericClient client = client() ;
-		client.registerInterceptor( new PartitionNameHeaderClientInterceptor( partitionName ) );
+		client.registerInterceptor( new PartitionNameHeaderClientInterceptor( sdsProperties.getPartition().getHttpHeader(), partitionName ) );
 		client.registerInterceptor( new BearerTokenAuthInterceptor( token ) );
 		return client ;
 	}
diff --git a/src/test/java/edu/ohsu/cmp/ecp/sds/PartitionNameHeaderClientInterceptor.java b/src/test/java/edu/ohsu/cmp/ecp/sds/PartitionNameHeaderClientInterceptor.java
index 809b142..3da3136 100644
--- a/src/test/java/edu/ohsu/cmp/ecp/sds/PartitionNameHeaderClientInterceptor.java
+++ b/src/test/java/edu/ohsu/cmp/ecp/sds/PartitionNameHeaderClientInterceptor.java
@@ -8,15 +8,17 @@
 
 class PartitionNameHeaderClientInterceptor implements IClientInterceptor {
 
+	private final String httpHeader;
 	private final String partitionName;
 
-	public PartitionNameHeaderClientInterceptor(String partitionName) {
+	public PartitionNameHeaderClientInterceptor(String httpHeader, String partitionName) {
+		this.httpHeader = httpHeader ;
 		this.partitionName = partitionName;
 	}
 
 	@Override
 	public void interceptRequest(IHttpRequest theRequest) {
-		theRequest.addHeader( SupplementalDataStorePartition.HEADER_PARTITION_NAME, partitionName );
+		theRequest.addHeader( httpHeader, partitionName );
 	}
 
 	@Override
diff --git a/src/test/resources/application.yaml b/src/test/resources/application.yaml
index d0e1848..9bbbf79 100644
--- a/src/test/resources/application.yaml
+++ b/src/test/resources/application.yaml
@@ -2,6 +2,7 @@ sds:
   require-base-url: false
   partition:
     local-name: SDS-LOCAL
+    http-header: X-Partition-Name
     multiple-linked-local-patients: WARN
 spring:
   main: