X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2Fvamsas.xsd;h=5a74d58715db89497a3ab1e947c25545b4251346;hb=787f8da0fbb39ad5b6acfecf5bf9dc9e0750317e;hp=996c187ffc343a439fbb6ac541057e3b32d6ac9d;hpb=69cfd66548e4aec0de74b70b81ccd83c5b38de47;p=vamsas.git

diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd
index 996c187..5a74d58 100644
--- a/schemas/vamsas.xsd
+++ b/schemas/vamsas.xsd
@@ -1,10 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!-- edited with XMLSPY v5 rel. 4 U (http://www.xmlspy.com) by MSD (EMBL OUTSTATION THE EBI WELLCOME TRUST GENOME CAMPUS) -->
-<!-- edited with XMLSpy v2005 rel. 3 U (http://www.altova.com) by lj (jl) -->
-<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"
-	xmlns:vamsas="http://www.vamsas.org"
-	targetNamespace="http://www.vamsas.org" elementFormDefault="qualified"
-	attributeFormDefault="unqualified">
+<!-- edited with XMLSpy v2006 sp1 U (http://www.altova.com) by ioh[ (o[ih[oh) -->
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="http://www.vamsas.org" targetNamespace="http://www.vamsas.org" elementFormDefault="qualified" attributeFormDefault="unqualified">
 	<xs:annotation>
 		<xs:documentation>
 			Vorba ID - Vamsas Object Request Broker Address ID (name
@@ -25,10 +22,8 @@
 		</xs:annotation>
 		<xs:complexType>
 			<xs:sequence>
-				<xs:element ref="vamsas:Tree" minOccurs="0"
-					maxOccurs="unbounded" />
-				<xs:element ref="vamsas:DataSet" minOccurs="0"
-					maxOccurs="unbounded" />
+				<xs:element ref="vamsas:Tree" minOccurs="0" maxOccurs="unbounded"/>
+				<xs:element ref="vamsas:DataSet" minOccurs="0" maxOccurs="unbounded"/>
 			</xs:sequence>
 			<xs:attribute name="id" type="xs:ID" use="optional">
 				<xs:annotation>
@@ -37,8 +32,7 @@
 					</xs:documentation>
 				</xs:annotation>
 			</xs:attribute>
-			<xs:attribute name="modifiable" type="xs:boolean"
-				default="true" use="optional">
+			<xs:attribute name="modifiable" type="xs:boolean" use="optional" default="true">
 				<xs:annotation>
 					<xs:documentation>
 						objects with modifiable=false will not be
@@ -70,15 +64,13 @@
 				</xs:documentation>
 			</xs:annotation>
 			<xs:sequence>
-				<xs:element name="title" type="xs:string" minOccurs="0" />
+				<xs:element name="title" type="xs:string" minOccurs="0"/>
 				<xs:element name="newick" maxOccurs="unbounded">
 					<xs:complexType>
 						<xs:simpleContent>
 							<xs:extension base="xs:string">
-								<xs:attribute name="title"
-									type="xs:string" use="optional" />
-								<xs:attribute name="id" type="xs:ID"
-									use="optional">
+								<xs:attribute name="title" type="xs:string" use="optional"/>
+								<xs:attribute name="id" type="xs:ID" use="optional">
 									<xs:annotation>
 										<xs:documentation>
 											Primary Key for vamsas
@@ -86,8 +78,7 @@
 										</xs:documentation>
 									</xs:annotation>
 								</xs:attribute>
-								<xs:attribute name="modifiable"
-									type="xs:boolean" default="true" use="optional">
+								<xs:attribute name="modifiable" type="xs:boolean" use="optional" default="true">
 									<xs:annotation>
 										<xs:documentation>
 											objects with
@@ -101,9 +92,8 @@
 						</xs:simpleContent>
 					</xs:complexType>
 				</xs:element>
-				<xs:element ref="vamsas:property" maxOccurs="unbounded"
-					minOccurs="0" />
-				<xs:element ref="vamsas:Provenance" />
+				<xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded"/>
+				<xs:element ref="vamsas:Provenance"/>
 			</xs:sequence>
 			<xs:attribute name="id" type="xs:ID" use="optional">
 				<xs:annotation>
@@ -112,8 +102,7 @@
 					</xs:documentation>
 				</xs:annotation>
 			</xs:attribute>
-			<xs:attribute name="modifiable" type="xs:boolean"
-				default="true" use="optional">
+			<xs:attribute name="modifiable" type="xs:boolean" use="optional" default="true">
 				<xs:annotation>
 					<xs:documentation>
 						objects with modifiable=false will not be
@@ -132,10 +121,8 @@
 					</xs:documentation>
 				</xs:annotation>
 				<xs:extension base="xs:string">
-					<xs:attribute name="name" type="xs:string"
-						use="required" />
-					<xs:attribute name="type" type="xs:string"
-						use="required">
+					<xs:attribute name="name" type="xs:string" use="required"/>
+					<xs:attribute name="type" type="xs:string" use="required">
 						<xs:annotation>
 							<xs:documentation>
 								The type specifies how the property will
@@ -151,22 +138,22 @@
 		</xs:complexType>
 	</xs:element>
 	<xs:element name="link">
-	<xs:complexType>
-		<xs:annotation>
-			<xs:documentation>
+		<xs:complexType>
+			<xs:annotation>
+				<xs:documentation>
 				Primitive labelled URI object
 			</xs:documentation>
-		</xs:annotation>
-		<xs:simpleContent>
-			<xs:extension base="xs:string">
-				<xs:attribute name="href" type="xs:anyURI">
-					<xs:annotation>
-						<xs:documentation>The URI</xs:documentation>
-					</xs:annotation>
-				</xs:attribute>
-			</xs:extension>
-		</xs:simpleContent>
-	</xs:complexType>
+			</xs:annotation>
+			<xs:simpleContent>
+				<xs:extension base="xs:string">
+					<xs:attribute name="href" type="xs:anyURI">
+						<xs:annotation>
+							<xs:documentation>The URI</xs:documentation>
+						</xs:annotation>
+					</xs:attribute>
+				</xs:extension>
+			</xs:simpleContent>
+		</xs:complexType>
 	</xs:element>
 	<xs:complexType name="rangeType" abstract="true">
 		<xs:annotation>
@@ -180,10 +167,8 @@
 				jaxb-2.0 capable bindings
 			</xs:documentation>
 		</xs:annotation>
-		<!--  Do we really need this - a position could be just a seg with start=end and inclusive=true -->
 		<xs:choice>
-			<xs:element name="pos" maxOccurs="unbounded"
-				minOccurs="1">
+			<xs:element name="pos" maxOccurs="unbounded">
 				<xs:annotation>
 					<xs:documentation>
 						a position within the associated object's
@@ -191,11 +176,10 @@
 					</xs:documentation>
 				</xs:annotation>
 				<xs:complexType>
-					<xs:attribute name="i" type="xs:int" use="required" />
+					<xs:attribute name="i" type="xs:int" use="required"/>
 				</xs:complexType>
 			</xs:element>
-			<xs:element name="seg" maxOccurs="unbounded"
-				minOccurs="1">
+			<xs:element name="seg" maxOccurs="unbounded">
 				<xs:annotation>
 					<xs:documentation>
 						a region from start to end, with flag for
@@ -203,12 +187,9 @@
 					</xs:documentation>
 				</xs:annotation>
 				<xs:complexType>
-					<xs:attribute name="start" type="xs:int"
-						use="required" />
-					<xs:attribute name="end" type="xs:int"
-						use="required" />
-					<xs:attribute name="inclusive" type="xs:boolean"
-						use="required">
+					<xs:attribute name="start" type="xs:int" use="required"/>
+					<xs:attribute name="end" type="xs:int" use="required"/>
+					<xs:attribute name="inclusive" type="xs:boolean" use="required">
 						<xs:annotation>
 							<xs:documentation>
 								when false, a consecutive range like
@@ -220,6 +201,7 @@
 				</xs:complexType>
 			</xs:element>
 		</xs:choice>
+		<!--  Do we really need this - a position could be just a seg with start=end and inclusive=true -->
 	</xs:complexType>
 	<xs:complexType name="rangeAnnotation">
 		<xs:annotation>
@@ -230,30 +212,28 @@
 		<xs:complexContent>
 			<xs:extension base="vamsas:rangeType">
 				<xs:sequence>
-					<xs:element name="label" type="xs:string"
-						minOccurs="0" >
+					<xs:element name="label" type="xs:string" minOccurs="0">
 						<xs:annotation>
-						<xs:documentation>
+							<xs:documentation>
 							Short, meaningful name for the annotation - if this is absent, then the type string should be used in its place.
 						</xs:documentation>
 						</xs:annotation>
-						</xs:element>
-					<xs:element name="description" type="xs:string"
-						minOccurs="0" >
+					</xs:element>
+					<xs:element name="description" type="xs:string" minOccurs="0">
 						<xs:annotation>
-						<xs:documentation>
+							<xs:documentation>
 							Human readable description of the annotation
 						</xs:documentation>
 						</xs:annotation>
-						</xs:element>
-					<xs:element name="status" type="xs:string"
-						minOccurs="0" >
-						<xs:annotation><xs:documentation>
+					</xs:element>
+					<xs:element name="status" type="xs:string" minOccurs="0">
+						<xs:annotation>
+							<xs:documentation>
 							TODO: specify this - we have considered taking the GO evidence codes as a model for assessing a measure of quality to an annotation.
-						</xs:documentation></xs:annotation>
-						</xs:element>
-					<xs:element ref="vamsas:annotationElement"
-						minOccurs="0" maxOccurs="unbounded">
+						</xs:documentation>
+						</xs:annotation>
+					</xs:element>
+					<xs:element ref="vamsas:annotationElement" minOccurs="0" maxOccurs="unbounded">
 						<xs:annotation>
 							<xs:documentation>
 								Annotation Element position maps to
@@ -263,8 +243,7 @@
 							</xs:documentation>
 						</xs:annotation>
 					</xs:element>
-					<xs:element name="score" minOccurs="0"
-						maxOccurs="unbounded">
+					<xs:element name="score" minOccurs="0" maxOccurs="unbounded">
 						<xs:annotation>
 							<xs:documentation>
 								Ordered set of optionally named float
@@ -274,16 +253,13 @@
 						<xs:complexType>
 							<xs:simpleContent>
 								<xs:extension base="xs:float">
-									<xs:attribute name="name"
-										type="xs:string" use="optional" default="score">
-									</xs:attribute>
+									<xs:attribute name="name" type="xs:string" use="optional" default="score"/>
 								</xs:extension>
 							</xs:simpleContent>
 						</xs:complexType>
 					</xs:element>
-					<xs:element ref="vamsas:link" minOccurs="0" maxOccurs="unbounded" />
-					<xs:element ref="vamsas:property" minOccurs="0"
-						maxOccurs="unbounded">
+					<xs:element ref="vamsas:link" minOccurs="0" maxOccurs="unbounded"/>
+					<xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded">
 						<xs:annotation>
 							<xs:documentation>
 								Note:These are mutable so an application
@@ -299,8 +275,7 @@
 						</xs:documentation>
 					</xs:annotation>
 				</xs:attribute>
-				<xs:attribute name="modifiable" type="xs:boolean"
-					default="true" use="optional">
+				<xs:attribute name="modifiable" type="xs:boolean" use="optional" default="true">
 					<xs:annotation>
 						<xs:documentation>
 							objects with modifiable=false will not be
@@ -308,8 +283,7 @@
 						</xs:documentation>
 					</xs:annotation>
 				</xs:attribute>
-				<xs:attribute name="group" type="xs:string"
-					use="optional" default="">
+				<xs:attribute name="group" type="xs:string" use="optional" default="">
 					<xs:annotation>
 						<xs:documentation>
 							Annotation with the same non-empty group
@@ -317,8 +291,7 @@
 						</xs:documentation>
 					</xs:annotation>
 				</xs:attribute>
-				<xs:attribute name="type" type="xs:string"
-					use="required">
+				<xs:attribute name="type" type="xs:string" use="required">
 					<xs:annotation>
 						<xs:documentation>
 							A Das Feature has both a type and a Type ID.
@@ -353,10 +326,8 @@
 					</xs:documentation>
 				</xs:annotation>
 				<xs:extension base="xs:string">
-					<xs:attribute name="name" type="xs:string"
-						use="required" />
-					<xs:attribute name="type" type="xs:string"
-						use="required">
+					<xs:attribute name="name" type="xs:string" use="required"/>
+					<xs:attribute name="type" type="xs:string" use="required">
 						<xs:annotation>
 							<xs:documentation>
 								The type specifies how the property will
@@ -382,13 +353,9 @@
 				</xs:documentation>
 			</xs:annotation>
 			<xs:complexContent>
-
 				<xs:extension base="vamsas:rangeType">
-					<xs:attribute name="name" type="xs:string"
-						use="required">
-					</xs:attribute>
-					<xs:attribute name="objRef" type="xs:IDREF"
-						use="optional">
+					<xs:attribute name="name" type="xs:string" use="required"/>
+					<xs:attribute name="objRef" type="xs:IDREF" use="optional">
 						<xs:annotation>
 							<xs:documentation>
 								Reference Frame for rangeType
@@ -400,7 +367,6 @@
 			</xs:complexContent>
 		</xs:complexType>
 	</xs:element>
-
 	<xs:element name="Provenance">
 		<xs:complexType>
 			<xs:annotation>
@@ -427,8 +393,7 @@
 									</xs:documentation>
 								</xs:annotation>
 							</xs:element>
-							<xs:element name="Action"
-								type="xs:string">
+							<xs:element name="Action" type="xs:string">
 								<xs:annotation>
 									<xs:documentation>
 										Did what
@@ -442,24 +407,21 @@
 									</xs:documentation>
 								</xs:annotation>
 							</xs:element>
-							<xs:element ref="vamsas:property"
-								minOccurs="0" maxOccurs="unbounded">
+							<xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded">
 								<xs:annotation>
 									<xs:documentation>
 										additional information
 									</xs:documentation>
 								</xs:annotation>
 							</xs:element>
-							<xs:element ref="vamsas:param" minOccurs="0"
-								maxOccurs="unbounded">
+							<xs:element ref="vamsas:param" minOccurs="0" maxOccurs="unbounded">
 								<xs:annotation>
 									<xs:documentation>
 										parameter for the action
 									</xs:documentation>
 								</xs:annotation>
 							</xs:element>
-							<xs:element ref="vamsas:input" minOccurs="0"
-								maxOccurs="unbounded">
+							<xs:element ref="vamsas:input" minOccurs="0" maxOccurs="unbounded">
 								<xs:annotation>
 									<xs:documentation>
 										bioinformatic objects input to
@@ -468,8 +430,7 @@
 								</xs:annotation>
 							</xs:element>
 						</xs:sequence>
-						<xs:attribute name="id" type="xs:ID"
-							use="optional">
+						<xs:attribute name="id" type="xs:ID" use="optional">
 							<xs:annotation>
 								<xs:documentation>
 									Primary Key for vamsas object
@@ -503,8 +464,7 @@
 						<xs:complexContent>
 							<xs:extension base="vamsas:SequenceType">
 								<xs:sequence>
-									<xs:element name="dbRef"
-										minOccurs="0" maxOccurs="unbounded">
+									<xs:element name="dbRef" minOccurs="0" maxOccurs="unbounded">
 										<xs:annotation>
 											<xs:documentation>
 												Store a list of database
@@ -514,17 +474,14 @@
 												database sequence to the
 												given sequence record
 											</xs:documentation>
-											<xs:documentation></xs:documentation>
-											<xs:documentation></xs:documentation>
+											<xs:documentation/>
+											<xs:documentation/>
 										</xs:annotation>
 										<xs:complexType>
 											<xs:sequence>
-												<xs:element name="map"
-													minOccurs="0" maxOccurs="unbounded">
+												<xs:element name="map" minOccurs="0" maxOccurs="unbounded">
 													<xs:complexType>
-														<xs:attribute
-															name="from" type="xs:integer" default="0"
-															use="optional">
+														<xs:attribute name="from" type="xs:integer" use="optional" default="0">
 															<xs:annotation>
 																<xs:documentation>
 																	Offset
@@ -544,8 +501,7 @@
 																</xs:documentation>
 															</xs:annotation>
 														</xs:attribute>
-														<xs:attribute
-															name="to" type="xs:integer" default="0" use="optional">
+														<xs:attribute name="to" type="xs:integer" use="optional" default="0">
 															<xs:annotation>
 																<xs:documentation>
 																	Offset
@@ -565,10 +521,9 @@
 																</xs:documentation>
 															</xs:annotation>
 														</xs:attribute>
-														<xs:attribute
-															name="start" type="xs:integer" use="required">
-														<xs:annotation>
-															<xs:documentation>
+														<xs:attribute name="start" type="xs:integer" use="required">
+															<xs:annotation>
+																<xs:documentation>
 																Offset
 																to first
 																last
@@ -585,12 +540,11 @@
 																sequence
 																maps to
 															</xs:documentation>
-														</xs:annotation>
+															</xs:annotation>
 														</xs:attribute>
-														<xs:attribute
-															name="end" type="xs:integer" use="required">
-														<xs:annotation>
-															<xs:documentation>
+														<xs:attribute name="end" type="xs:integer" use="required">
+															<xs:annotation>
+																<xs:documentation>
 																Offset
 																to last
 																position
@@ -605,16 +559,14 @@
 																sequence
 																maps to
 															</xs:documentation>
-														</xs:annotation>
+															</xs:annotation>
 														</xs:attribute>
 													</xs:complexType>
 												</xs:element>
 												<xs:element ref="vamsas:link" minOccurs="0" maxOccurs="unbounded"/>
-												<xs:element
-													ref="vamsas:property" minOccurs="0" maxOccurs="unbounded" />
+												<xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded"/>
 											</xs:sequence>
-											<xs:attribute name="source"
-												type="xs:string" use="required">
+											<xs:attribute name="source" type="xs:string" use="required">
 												<xs:annotation>
 													<xs:documentation>
 														TODO Database
@@ -630,8 +582,7 @@
 													</xs:documentation>
 												</xs:annotation>
 											</xs:attribute>
-											<xs:attribute name="version"
-												type="xs:string" use="required">
+											<xs:attribute name="version" type="xs:string" use="required">
 												<xs:annotation>
 													<xs:documentation>
 														Version must be
@@ -639,8 +590,7 @@
 													</xs:documentation>
 												</xs:annotation>
 											</xs:attribute>
-											<xs:attribute
-												name="accessionId" type="xs:string" use="required">
+											<xs:attribute name="accessionId" type="xs:string" use="required">
 												<xs:annotation>
 													<xs:documentation>
 														TODO: make some
@@ -656,8 +606,7 @@
 													</xs:documentation>
 												</xs:annotation>
 											</xs:attribute>
-											<xs:attribute name="id"
-												type="xs:ID" use="optional">
+											<xs:attribute name="id" type="xs:ID" use="optional">
 												<xs:annotation>
 													<xs:documentation>
 														Primary Key for
@@ -669,8 +618,7 @@
 										</xs:complexType>
 									</xs:element>
 								</xs:sequence>
-								<xs:attribute name="id" type="xs:ID"
-									use="optional">
+								<xs:attribute name="id" type="xs:ID" use="optional">
 									<xs:annotation>
 										<xs:documentation>
 											Primary Key for vamsas
@@ -678,8 +626,7 @@
 										</xs:documentation>
 									</xs:annotation>
 								</xs:attribute>
-								<xs:attribute name="dictionary"
-									type="xs:string" use="required">
+								<xs:attribute name="dictionary" type="xs:string" use="required">
 									<xs:annotation>
 										<xs:documentation>
 											symbol class for sequence
@@ -690,8 +637,7 @@
 						</xs:complexContent>
 					</xs:complexType>
 				</xs:element>
-				<xs:element name="DataSetAnnotations" minOccurs="0"
-					maxOccurs="unbounded">
+				<xs:element name="DataSetAnnotations" minOccurs="0" maxOccurs="unbounded">
 					<xs:complexType>
 						<xs:annotation>
 							<xs:documentation>
@@ -700,14 +646,11 @@
 							</xs:documentation>
 						</xs:annotation>
 						<xs:complexContent>
-							<xs:extension
-								base="vamsas:rangeAnnotation">
+							<xs:extension base="vamsas:rangeAnnotation">
 								<xs:sequence>
-									<xs:element ref="vamsas:Provenance"
-										maxOccurs="1" minOccurs="1" />
+									<xs:element ref="vamsas:Provenance"/>
 								</xs:sequence>
-								<xs:attribute name="seqRef"
-									type="xs:IDREF" use="required">
+								<xs:attribute name="seqRef" type="xs:IDREF" use="required">
 									<xs:annotation>
 										<xs:documentation>
 											annotation is associated
@@ -720,12 +663,10 @@
 						</xs:complexContent>
 					</xs:complexType>
 				</xs:element>
-				<xs:element name="Alignment" minOccurs="0"
-					maxOccurs="unbounded">
+				<xs:element name="Alignment" minOccurs="0" maxOccurs="unbounded">
 					<xs:complexType>
 						<xs:sequence>
-							<xs:element name="AlignmentAnnotation"
-								minOccurs="0" maxOccurs="unbounded">
+							<xs:element name="AlignmentAnnotation" minOccurs="0" maxOccurs="unbounded">
 								<xs:annotation>
 									<xs:documentation>
 										This is annotation over the
@@ -735,14 +676,11 @@
 								</xs:annotation>
 								<xs:complexType>
 									<xs:complexContent>
-										<xs:extension
-											base="vamsas:rangeAnnotation">
+										<xs:extension base="vamsas:rangeAnnotation">
 											<xs:sequence>
-												<xs:element
-													ref="vamsas:Provenance" minOccurs="1" maxOccurs="1" />
+												<xs:element ref="vamsas:Provenance"/>
 											</xs:sequence>
-											<xs:attribute name="graph"
-												type="xs:boolean" use="required">
+											<xs:attribute name="graph" type="xs:boolean" use="required">
 												<xs:annotation>
 													<xs:documentation>
 														TODO: decide if
@@ -760,18 +698,13 @@
 									</xs:complexContent>
 								</xs:complexType>
 							</xs:element>
-							<xs:element ref="vamsas:Tree" minOccurs="0"
-								maxOccurs="unbounded" />
-							<xs:element name="alignmentSequence"
-								maxOccurs="unbounded">
+							<xs:element ref="vamsas:Tree" minOccurs="0" maxOccurs="unbounded"/>
+							<xs:element name="alignmentSequence" maxOccurs="unbounded">
 								<xs:complexType>
 									<xs:complexContent>
-										<xs:extension
-											base="vamsas:SequenceType">
+										<xs:extension base="vamsas:SequenceType">
 											<xs:sequence>
-												<xs:element
-													name="AlignmentSequenceAnnotation" minOccurs="0"
-													maxOccurs="unbounded">
+												<xs:element name="AlignmentSequenceAnnotation" minOccurs="0" maxOccurs="unbounded">
 													<xs:complexType>
 														<xs:annotation>
 															<xs:documentation>
@@ -788,17 +721,14 @@
 																of the
 																alignment
 															</xs:documentation>
-															<xs:documentation></xs:documentation>
+															<xs:documentation/>
 														</xs:annotation>
 														<xs:complexContent>
-															<xs:extension
-																base="vamsas:rangeAnnotation">
+															<xs:extension base="vamsas:rangeAnnotation">
 																<xs:sequence>
-																	<xs:element
-																		ref="vamsas:Provenance" minOccurs="1" maxOccurs="1" />
+																	<xs:element ref="vamsas:Provenance"/>
 																</xs:sequence>
-																<xs:attribute
-																	name="graph" type="xs:boolean" use="required">
+																<xs:attribute name="graph" type="xs:boolean" use="required">
 																	<xs:annotation>
 																		<xs:documentation>
 																			TODO:
@@ -827,7 +757,6 @@
 																</xs:attribute>
 															</xs:extension>
 														</xs:complexContent>
-
 														<!--  								
 															This replaces the flat list of sequenceFeatures.
 															<xs:element name="AlignmentFeatures" minOccurs="0" maxOccurs="unbounded"><xs:complexType><xs:annotation>
@@ -842,8 +771,7 @@
 													</xs:complexType>
 												</xs:element>
 											</xs:sequence>
-											<xs:attribute name="id"
-												type="xs:ID" use="optional">
+											<xs:attribute name="id" type="xs:ID" use="optional">
 												<xs:annotation>
 													<xs:documentation>
 														Primary Key for
@@ -852,8 +780,7 @@
 													</xs:documentation>
 												</xs:annotation>
 											</xs:attribute>
-											<xs:attribute name="refid"
-												type="xs:IDREF" use="required">
+											<xs:attribute name="refid" type="xs:IDREF" use="required">
 												<xs:annotation>
 													<xs:documentation>
 														Dataset Sequence
@@ -868,8 +795,7 @@
 									</xs:complexContent>
 								</xs:complexType>
 							</xs:element>
-							<xs:element ref="vamsas:property"
-								minOccurs="0" maxOccurs="unbounded">
+							<xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded">
 								<xs:annotation>
 									<xs:documentation>
 										typical properties may be
@@ -878,14 +804,11 @@
 									</xs:documentation>
 								</xs:annotation>
 							</xs:element>
-							<xs:element ref="vamsas:Provenance" />
+							<xs:element ref="vamsas:Provenance"/>
 						</xs:sequence>
-						<xs:attribute name="gapChar" type="xs:string"
-							use="required" />
-						<xs:attribute name="aligned" type="xs:boolean"
-							use="optional" />
-						<xs:attribute name="id" type="xs:ID"
-							use="optional">
+						<xs:attribute name="gapChar" type="xs:string" use="required"/>
+						<xs:attribute name="aligned" type="xs:boolean" use="optional"/>
+						<xs:attribute name="id" type="xs:ID" use="optional">
 							<xs:annotation>
 								<xs:documentation>
 									Primary Key for vamsas object
@@ -893,8 +816,7 @@
 								</xs:documentation>
 							</xs:annotation>
 						</xs:attribute>
-						<xs:attribute name="modifiable"
-							type="xs:boolean" default="true" use="optional">
+						<xs:attribute name="modifiable" type="xs:boolean" use="optional" default="true">
 							<xs:annotation>
 								<xs:documentation>
 									objects with modifiable=false will
@@ -905,9 +827,8 @@
 						</xs:attribute>
 					</xs:complexType>
 				</xs:element>
-				<xs:element ref="vamsas:Tree" minOccurs="0"
-					maxOccurs="unbounded" />
-				<xs:element ref="vamsas:Provenance" />
+				<xs:element ref="vamsas:Tree" minOccurs="0" maxOccurs="unbounded"/>
+				<xs:element ref="vamsas:Provenance"/>
 			</xs:sequence>
 			<xs:attribute name="id" type="xs:ID" use="optional">
 				<xs:annotation>
@@ -930,17 +851,14 @@
 				</xs:documentation>
 			</xs:annotation>
 			<xs:sequence>
-
-				<xs:element name="description" type="xs:string"
-					minOccurs="0">
+				<xs:element name="description" type="xs:string" minOccurs="0">
 					<xs:annotation>
 						<xs:documentation>
 							Free text at this position
 						</xs:documentation>
 					</xs:annotation>
 				</xs:element>
-				<xs:element name="glyph" minOccurs="0"
-					maxOccurs="unbounded">
+				<xs:element name="glyph" minOccurs="0" maxOccurs="unbounded">
 					<xs:annotation>
 						<xs:documentation>
 							Discrete symbol - possibly graphically
@@ -950,8 +868,7 @@
 					<xs:complexType>
 						<xs:simpleContent>
 							<xs:extension base="xs:string">
-								<xs:attribute name="dict"
-									type="xs:string" default="utf8" use="optional">
+								<xs:attribute name="dict" type="xs:string" use="optional" default="utf8">
 									<xs:annotation>
 										<xs:documentation>
 											specifies the symbol
@@ -978,8 +895,7 @@
 						</xs:simpleContent>
 					</xs:complexType>
 				</xs:element>
-				<xs:element name="value" type="xs:float" minOccurs="0"
-					maxOccurs="unbounded">
+				<xs:element name="value" type="xs:float" minOccurs="0" maxOccurs="unbounded">
 					<xs:annotation>
 						<xs:documentation>
 							Ordered set of float values - an application
@@ -992,8 +908,7 @@
 					</xs:annotation>
 				</xs:element>
 			</xs:sequence>
-			<xs:attribute name="position" type="xs:integer"
-				use="required">
+			<xs:attribute name="position" type="xs:integer" use="required">
 				<xs:annotation>
 					<xs:documentation>
 						position with respect to the coordinate frame
@@ -1001,8 +916,7 @@
 					</xs:documentation>
 				</xs:annotation>
 			</xs:attribute>
-			<xs:attribute name="after" type="xs:boolean" use="optional"
-				default="false">
+			<xs:attribute name="after" type="xs:boolean" use="optional" default="false">
 				<xs:annotation>
 					<xs:documentation>
 						true means the annotation element appears
@@ -1021,23 +935,20 @@
 	</xs:element>
 	<xs:complexType name="SequenceType">
 		<xs:sequence>
-			<xs:element name="sequence" type="xs:string" minOccurs="1"
-				maxOccurs="1" />
-			<xs:element name="name" type="xs:string" minOccurs="1"
-				maxOccurs="1" />
-			<xs:element name="description" type="xs:string"
-				minOccurs="0" maxOccurs="1" />
-			<xs:element ref="vamsas:property" minOccurs="0"
-				maxOccurs="unbounded">
+			<xs:element name="sequence" type="xs:string"/>
+			<xs:element name="name" type="xs:string"/>
+			<xs:element name="description" type="xs:string" minOccurs="0"/>
+			<xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded">
 				<xs:annotation>
 					<xs:documentation>
 						additional typed properties
 					</xs:documentation>
 				</xs:annotation>
 			</xs:element>
+			<xs:element ref="vamsas:mapping" minOccurs="0" maxOccurs="unbounded"/>
 		</xs:sequence>
-		<xs:attribute name="start" type="xs:integer" use="required" />
-		<xs:attribute name="end" type="xs:integer" use="required" />
+		<xs:attribute name="start" type="xs:integer" use="required"/>
+		<xs:attribute name="end" type="xs:integer" use="required"/>
 	</xs:complexType>
 	<xs:element name="ApplicationData">
 		<xs:complexType>
@@ -1050,42 +961,33 @@
 			<xs:complexContent>
 				<xs:extension base="vamsas:appData">
 					<xs:sequence>
-						<xs:element name="User" maxOccurs="unbounded"
-							minOccurs="0">
+						<xs:element name="User" minOccurs="0" maxOccurs="unbounded">
 							<xs:complexType>
 								<xs:complexContent>
-									<xs:extension
-										base="vamsas:appData">
+									<xs:extension base="vamsas:appData">
 										<xs:annotation>
 											<xs:documentation>
 												Data available to just a
 												particular user
 											</xs:documentation>
 										</xs:annotation>
-										<xs:attribute name="fullname"
-											type="xs:string" use="required" />
-										<xs:attribute
-											name="organization" type="xs:string" use="required" />
+										<xs:attribute name="fullname" type="xs:string" use="required"/>
+										<xs:attribute name="organization" type="xs:string" use="required"/>
 									</xs:extension>
 								</xs:complexContent>
 							</xs:complexType>
 						</xs:element>
-						<xs:element name="Common" maxOccurs="1"
-							minOccurs="0">
+						<xs:element name="Common" minOccurs="0">
 							<xs:complexType>
 								<xs:complexContent>
-									<xs:extension
-										base="vamsas:appData">
-									</xs:extension>
+									<xs:extension base="vamsas:appData"/>
 								</xs:complexContent>
 							</xs:complexType>
 						</xs:element>
-						<xs:element name="Instance"
-							maxOccurs="unbounded" minOccurs="0">
+						<xs:element name="Instance" minOccurs="0" maxOccurs="unbounded">
 							<xs:complexType>
 								<xs:complexContent>
-									<xs:extension
-										base="vamsas:appData">
+									<xs:extension base="vamsas:appData">
 										<xs:annotation>
 											<xs:documentation>
 												Data available to just a
@@ -1105,23 +1007,25 @@
 												that instance
 											</xs:documentation>
 										</xs:annotation>
-										<xs:attribute name="urn"
-											type="xs:string" use="required" />
+										<xs:attribute name="urn" type="xs:string" use="required"/>
 									</xs:extension>
 								</xs:complexContent>
 							</xs:complexType>
 						</xs:element>
 					</xs:sequence>
-					<xs:attribute name="version" type="xs:string"
-						use="required" ><xs:annotation><xs:documentation>
-							Version string describing the application specific data storage version used</xs:documentation></xs:annotation></xs:attribute>
-					<xs:attribute name="name" type="xs:string"
-						use="required" >
-						<xs:annotation><xs:documentation>
+					<xs:attribute name="version" type="xs:string" use="required">
+						<xs:annotation>
+							<xs:documentation>
+							Version string describing the application specific data storage version used</xs:documentation>
+						</xs:annotation>
+					</xs:attribute>
+					<xs:attribute name="name" type="xs:string" use="required">
+						<xs:annotation>
+							<xs:documentation>
 							Canonical name of application
 						</xs:documentation>
 						</xs:annotation>
-						</xs:attribute>
+					</xs:attribute>
 				</xs:extension>
 			</xs:complexContent>
 		</xs:complexType>
@@ -1136,8 +1040,7 @@
 							data object to any vamsas object
 						</xs:documentation>
 					</xs:annotation>
-					<xs:attribute name="compressed" type="xs:boolean"
-						use="optional" default="false">
+					<xs:attribute name="compressed" type="xs:boolean" use="optional" default="false">
 						<xs:annotation>
 							<xs:documentation>
 								true implies data will be decompresses
@@ -1146,8 +1049,7 @@
 							</xs:documentation>
 						</xs:annotation>
 					</xs:attribute>
-					<xs:attribute name="type" type="xs:string"
-						use="required">
+					<xs:attribute name="type" type="xs:string" use="required">
 						<xs:annotation>
 							<xs:documentation>
 								Type of arbitrary data - TODO: decide
@@ -1155,8 +1057,7 @@
 							</xs:documentation>
 						</xs:annotation>
 					</xs:attribute>
-					<xs:attribute name="objectref" type="xs:IDREF"
-						use="required">
+					<xs:attribute name="objectref" type="xs:IDREF" use="required">
 						<xs:annotation>
 							<xs:documentation>
 								Object the arbitrary data is associated
@@ -1164,8 +1065,7 @@
 							</xs:documentation>
 						</xs:annotation>
 					</xs:attribute>
-					<xs:attribute name="id" type="xs:ID"
-						use="optional">
+					<xs:attribute name="id" type="xs:ID" use="optional">
 						<xs:annotation>
 							<xs:documentation>
 								Primary Key for vamsas object
@@ -1179,8 +1079,32 @@
 	</xs:element>
 	<xs:complexType name="appData">
 		<xs:choice>
-			<xs:element name="data" type="xs:base64Binary" />
-			<xs:element name="dataReference" type="xs:string" />
+			<xs:element name="data" type="xs:base64Binary"/>
+			<xs:element name="dataReference" type="xs:string"/>
 		</xs:choice>
 	</xs:complexType>
+	<xs:element name="mapping">
+		<xs:complexType>
+			<xs:sequence>
+				<xs:element name="objectA">
+					<xs:complexType>
+						<xs:complexContent>
+							<xs:extension base="vamsas:rangeType">
+								<xs:attribute name="objRefA" type="xs:IDREF" use="required"/>
+							</xs:extension>
+						</xs:complexContent>
+					</xs:complexType>
+				</xs:element>
+				<xs:element name="objectB">
+					<xs:complexType>
+						<xs:complexContent>
+							<xs:extension base="vamsas:rangeType">
+								<xs:attribute name="objRefB" type="xs:IDREF" use="required"/>
+							</xs:extension>
+						</xs:complexContent>
+					</xs:complexType>
+				</xs:element>
+			</xs:sequence>
+		</xs:complexType>
+	</xs:element>
 </xs:schema>