Vorba ID - Vamsas Object Request Broker Address ID (name needs to beworked on): Suggest it could be of the form documentRoot/datasetName/SequenceUID for adataset sequence. Alignment sequence: documentRoot/datasetName/AlignmentId/SequenceUIDfor an aligned form of a dataset sequence
Properties. Generally, these are mutable so an application should checkthem each time. This may change depending on the context of the property
Properties
attribute form default:
unqualified
element form default:
qualified
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:element name="Provenance"><xs:complexType><xs:annotation><xs:documentation>Defines the origin and series of operations applied directly to the object that references it.</xs:documentation></xs:annotation><xs:sequence><xs:element name="entry" maxOccurs="unbounded"><xs:complexType><xs:sequence><xs:element name="User" type="xs:string"><xs:annotation><xs:documentation>Who</xs:documentation></xs:annotation></xs:element><xs:element name="App" type="xs:string"><xs:annotation><xs:documentation>With which application</xs:documentation></xs:annotation></xs:element><xs:element name="Action" type="xs:string"><xs:annotation><xs:documentation>Did what</xs:documentation></xs:annotation></xs:element><xs:element name="Date" type="xs:dateTime"><xs:annotation><xs:documentation>When</xs:documentation></xs:annotation></xs:element><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:annotation><xs:documentation>parameter for the action</xs:documentation></xs:annotation></xs:element><xs:element ref="vamsas:input" minOccurs="0" maxOccurs="unbounded"><xs:annotation><xs:documentation>bioinformatic objects input to action</xs:documentation></xs:annotation></xs:element></xs:sequence><xs:attribute name="id" type="xs:ID" use="optional"><xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation></xs:attribute></xs:complexType></xs:element></xs:sequence></xs:complexType></xs:element>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
The type specifies how the property will be parsed.Empty property strings are allowed, and can be used to prototype theinput to a document. TODO: specify allowed types
Source
<xs:element name="property"><xs:complexType><xs:simpleContent><xs:annotation><xs:documentation>Named and typed property string</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:annotation><xs:documentation>The type specifies how the property will be parsed. Empty property strings are allowed, and can be used to prototype the input to a document. TODO: specify allowed types</xs:documentation></xs:annotation></xs:attribute></xs:extension></xs:simpleContent></xs:complexType></xs:element>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
The type specifies how the property will be parsed.Empty property strings are allowed, and can be used to prototype theinput to a document. TODO: specify allowed types
Source
<xs:element name="param"><xs:complexType><xs:annotation><xs:documentation>Specifies a named and typed value used to perform some data transformation.</xs:documentation><xs:documentation>LATER: experiment with xml validation of property set prototypes for services</xs:documentation></xs:annotation><xs:simpleContent><xs:annotation><xs:documentation>Named and typed property string</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:annotation><xs:documentation>The type specifies how the property will be parsed. Empty property strings are allowed, and can be used to prototype the input to a document. TODO: specify allowed types</xs:documentation></xs:annotation></xs:attribute></xs:extension></xs:simpleContent></xs:complexType></xs:element>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:element name="input"><xs:complexType><xs:annotation><xs:documentation>Selects all or part of a collection of vamsas objects as a named input to some transformation process. Many inputs with the same name imply a group input (such as a collection of sequences)</xs:documentation></xs:annotation><xs:complexContent><xs:extension base="vamsas:rangeType"><xs:attribute name="name" type="xs:string" use="required"/><xs:attribute name="objRef" type="xs:IDREFS" use="optional"><xs:annotation><xs:documentation>Reference Frame for rangeType specfication</xs:documentation></xs:annotation></xs:attribute></xs:extension></xs:complexContent></xs:complexType></xs:element>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:element name="pos" maxOccurs="unbounded"><xs:annotation><xs:documentation>a position within the associated object's coordinate system</xs:documentation></xs:annotation><xs:complexType><xs:attribute name="i" type="xs:int" use="required"/></xs:complexType></xs:element>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:element name="seg" maxOccurs="unbounded"><xs:annotation><xs:documentation>a region from start to end, with flag for inclusivity of terminii</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:annotation><xs:documentation>when false, a consecutive range like 'start=1, end=2' means the region lying after position 1 and before position 2</xs:documentation></xs:annotation></xs:attribute></xs:complexType></xs:element>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Element vamsas:VAMSAS
Namespace
http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Annotations
contains unassociated trees and a number of analysis sets
<xs:element name="VAMSAS"><xs:annotation><xs:documentation>contains unassociated trees and a number of analysis sets</xs:documentation></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:sequence><xs:attribute name="id" type="xs:ID" use="optional"><xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation></xs:attribute><xs:attribute name="modifiable" type="vamsas:locks" use="optional"/></xs:complexType></xs:element>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:element name="Tree"><xs:complexType><xs:annotation><xs:documentation>Contains a named collection of trees</xs:documentation><xs:documentation>TODO: define way of referencing leaves of global tree for any sequence/alignment object. SUggestion 1: Each named tree leafnode has a unique id (which may be unique in combination with trees own vorba ID). Dataset sequences can be tagged with a property "vamsas:tree_leaf"</xs:documentation></xs:annotation><xs:sequence><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:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation></xs:attribute><xs:attribute name="modifiable" type="vamsas:locks" use="optional"/></xs:extension></xs:simpleContent></xs:complexType></xs:element><xs:element name="treenode" minOccurs="0" maxOccurs="unbounded"><xs:annotation><xs:documentation>node identity and mapping data between tree representations and vamsas document objects</xs:documentation></xs:annotation><xs:complexType><xs:complexContent><xs:extension base="vamsas:nodeType"><xs:attribute name="treeId" type="xs:IDREFS"><xs:annotation><xs:documentation>reference to one or more trees containing the node being described.</xs:documentation></xs:annotation></xs:attribute><xs:attribute name="nodespec" type="xs:string"><xs:annotation><xs:documentation>String uniquely identifying a particular node in the referenced tree according to the format of the tree representation that is referenced.</xs:documentation></xs:annotation></xs:attribute></xs:extension></xs:complexContent></xs:complexType></xs:element><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><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation></xs:attribute><xs:attribute name="modifiable" type="vamsas:locks" use="optional"/></xs:complexType></xs:element>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
reference to one or more trees containingthe node being described.
Source
<xs:element name="treenode" minOccurs="0" maxOccurs="unbounded"><xs:annotation><xs:documentation>node identity and mapping data between tree representations and vamsas document objects</xs:documentation></xs:annotation><xs:complexType><xs:complexContent><xs:extension base="vamsas:nodeType"><xs:attribute name="treeId" type="xs:IDREFS"><xs:annotation><xs:documentation>reference to one or more trees containing the node being described.</xs:documentation></xs:annotation></xs:attribute><xs:attribute name="nodespec" type="xs:string"><xs:annotation><xs:documentation>String uniquely identifying a particular node in the referenced tree according to the format of the tree representation that is referenced.</xs:documentation></xs:annotation></xs:attribute></xs:extension></xs:complexContent></xs:complexType></xs:element>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:element name="name" type="xs:string" minOccurs="0" maxOccurs="1"><xs:annotation><xs:documentation>Short name for this node</xs:documentation></xs:annotation></xs:element>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:element name="description" type="xs:string" minOccurs="0" maxOccurs="1"><xs:annotation><xs:documentation>Descriptive text for this node</xs:documentation></xs:annotation></xs:element>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:element name="vref" type="vamsas:referenceType" minOccurs="0" maxOccurs="unbounded"><xs:annotation><xs:documentation>Direct associations between this node and any vamsas objects</xs:documentation></xs:annotation></xs:element>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:element name="DataSet"><xs:complexType><xs:annotation><xs:documentation>A collection of sequences, alignments, trees and other things.</xs:documentation><xs:documentation>TODO: Add a title field and properties for programs that can present the user with different distinct datasets For the moment, the program just presents them as a list and perhaps lets the user work out which dataset it wants based on the alignments that it contains. (Dominik and Jim 7th June 2007)</xs:documentation></xs:annotation><xs:sequence><xs:element name="Sequence" maxOccurs="unbounded"><xs:complexType><xs:annotation><xs:documentation>a primary or secondary sequence record from which all other sequences may be derived</xs:documentation></xs:annotation><xs:complexContent><xs:extension base="vamsas:SequenceType"><xs:sequence><xs:element name="dbRef" minOccurs="0" maxOccurs="unbounded"><xs:annotation><xs:documentation>Store a list of database references for this sequence record - with optional mapping from database sequence to the given sequence record</xs:documentation><xs:documentation/><xs:documentation/></xs:annotation><xs:complexType><xs:sequence><xs:element name="map" minOccurs="0" maxOccurs="unbounded"><xs:annotation><xs:documentation>the local mapType maps from the parent sequence coordinate frame to the reference frame defined by the dbRef element. The mapped mapType is the mapped range defined on the dbRef element's reference frame. Conventionally, the unit attribute defaults to 1, or will be inferred from the local sequence's dictionary type and any dictionary type associated with the database being mapped to. However, it may be used to avoid ambiguity.</xs:documentation></xs:annotation><xs:complexType><xs:complexContent><xs:extension base="vamsas:mapType"><xs:attribute name="id" type="xs:ID"/></xs:extension></xs:complexContent></xs:complexType></xs:element><xs:element ref="vamsas:link" 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:annotation><xs:documentation>TODO Database Naming Convention: either start using LSID (so change type to URI) or leave this as an uncontrolled/unspecified string ID</xs:documentation></xs:annotation></xs:attribute><xs:attribute name="version" type="xs:string" use="required"><xs:annotation><xs:documentation>Version must be specified -</xs:documentation></xs:annotation></xs:attribute><xs:attribute name="accessionId" type="xs:string" use="required"><xs:annotation><xs:documentation>TODO: make some specification of the database field from which this accessionId is taken from - should that be a special property of the dbRef object ?</xs:documentation></xs:annotation></xs:attribute><xs:attribute name="id" type="xs:ID" use="optional"><xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation></xs:attribute></xs:complexType></xs:element><xs:element name="vxref" type="vamsas:referenceType" minOccurs="0" maxOccurs="unbounded"><xs:annotation><xs:documentation>explicitly named cross reference to other objects in the document.</xs:documentation></xs:annotation></xs:element></xs:sequence><xs:attribute name="id" type="xs:ID" use="optional"><xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation></xs:attribute><xs:attribute name="dictionary" type="xs:string" use="required"><xs:annotation><xs:documentation>symbol class for sequence</xs:documentation></xs:annotation></xs:attribute></xs:extension></xs:complexContent></xs:complexType></xs:element><xs:element name="sequenceMapping" minOccurs="0" maxOccurs="unbounded"><xs:complexType><xs:annotation><xs:documentation>A mapping between the specified 'local' and 'mapped' sequence coordinate frames. The step size between each coordinate frame depends on the sequence dictionary types, or alternatively specified in the optional unit attribute on each range element.</xs:documentation></xs:annotation><xs:complexContent><xs:extension base="vamsas:mapType"><xs:sequence><xs:element ref="vamsas:Provenance"/></xs:sequence><xs:attribute name="loc" type="xs:IDREF" use="required"><xs:annotation><xs:documentation>Object on which the local range is defined.</xs:documentation></xs:annotation></xs:attribute><xs:attribute name="map" type="xs:IDREF" use="required"><xs:annotation><xs:documentation>Object on which the mapped range is defined.</xs:documentation></xs:annotation></xs:attribute><xs:attribute name="id" type="xs:ID" use="optional"/></xs:extension></xs:complexContent></xs:complexType></xs:element><xs:element name="DataSetAnnotations" minOccurs="0" maxOccurs="unbounded"><xs:complexType><xs:annotation><xs:documentation>Annotate over positions and regions of a dataset sequence</xs:documentation></xs:annotation><xs:complexContent><xs:extension base="vamsas:rangeAnnotation"><xs:sequence><xs:element ref="vamsas:Provenance"/></xs:sequence><xs:attribute name="seqRef" type="xs:IDREFS" use="required"><xs:annotation><xs:documentation>annotation is associated with a particular dataset sequence</xs:documentation></xs:annotation></xs:attribute></xs:extension></xs:complexContent></xs:complexType></xs:element><xs:element name="Alignment" minOccurs="0" maxOccurs="unbounded"><xs:complexType><xs:sequence><xs:element name="AlignmentAnnotation" minOccurs="0" maxOccurs="unbounded"><xs:annotation><xs:documentation>This is annotation over the coordinate frame defined by all the columns in the alignment.</xs:documentation></xs:annotation><xs:complexType><xs:complexContent><xs:extension base="vamsas:rangeAnnotation"><xs:sequence><xs:element ref="vamsas:Provenance"/></xs:sequence><xs:attribute name="graph" type="xs:boolean" use="required"><xs:annotation><xs:documentation>TODO: decide if this flag is redundant - when true it would suggest that the annotationElement values together form a graph</xs:documentation></xs:annotation></xs:attribute><xs:attribute name="seqrefs" type="xs:IDREFS" use="optional"><xs:annotation><xs:documentation>annotation is associated with a range on a particular group of alignment sequences</xs:documentation></xs:annotation></xs:attribute></xs:extension></xs:complexContent></xs:complexType></xs:element><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:sequence><xs:element name="AlignmentSequenceAnnotation" minOccurs="0" maxOccurs="unbounded"><xs:complexType><xs:annotation><xs:documentation>Annotate over positions and regions of the ungapped sequence in the context of the alignment</xs:documentation><xs:documentation/></xs:annotation><xs:complexContent><xs:extension base="vamsas:rangeAnnotation"><xs:sequence><xs:element ref="vamsas:Provenance"/></xs:sequence><xs:attribute name="graph" type="xs:boolean" use="required"><xs:annotation><xs:documentation>TODO: decide if this flag is redundant - when true it would suggest that the annotationElement values together form a graph</xs:documentation></xs:annotation></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>
<xs:documentation>Annotate over positions and regions of the alignment</xs:documentation>
</xs:annotation><xs:complexContent>
<xs:extension base="vamsas:rangeFeature">
<xs:attribute name="seqRef" type="xs:IDREF" use="optional">
<xs:annotation><xs:documentation>annotation may be associated with a particular sequence lying within the same reference frame as the rangeType's objRef</xs:documentation></xs:annotation>
</xs:attribute>
</xs:extension>
</xs:complexContent></xs:complexType></xs:element> --></xs:complexType></xs:element></xs:sequence><xs:attribute name="id" type="xs:ID" use="optional"><xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation></xs:attribute><xs:attribute name="refid" type="xs:IDREF" use="required"><xs:annotation><xs:documentation>Dataset Sequence from which this alignment sequence is taken from</xs:documentation></xs:annotation></xs:attribute></xs:extension></xs:complexContent></xs:complexType></xs:element><xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded"><xs:annotation><xs:documentation>typical properties may be additional alignment score objects</xs:documentation></xs:annotation></xs:element><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:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation></xs:attribute><xs:attribute name="modifiable" type="vamsas:locks" use="optional"/></xs:complexType></xs:element><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><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation></xs:attribute></xs:complexType></xs:element>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:element name="Sequence" maxOccurs="unbounded"><xs:complexType><xs:annotation><xs:documentation>a primary or secondary sequence record from which all other sequences may be derived</xs:documentation></xs:annotation><xs:complexContent><xs:extension base="vamsas:SequenceType"><xs:sequence><xs:element name="dbRef" minOccurs="0" maxOccurs="unbounded"><xs:annotation><xs:documentation>Store a list of database references for this sequence record - with optional mapping from database sequence to the given sequence record</xs:documentation><xs:documentation/><xs:documentation/></xs:annotation><xs:complexType><xs:sequence><xs:element name="map" minOccurs="0" maxOccurs="unbounded"><xs:annotation><xs:documentation>the local mapType maps from the parent sequence coordinate frame to the reference frame defined by the dbRef element. The mapped mapType is the mapped range defined on the dbRef element's reference frame. Conventionally, the unit attribute defaults to 1, or will be inferred from the local sequence's dictionary type and any dictionary type associated with the database being mapped to. However, it may be used to avoid ambiguity.</xs:documentation></xs:annotation><xs:complexType><xs:complexContent><xs:extension base="vamsas:mapType"><xs:attribute name="id" type="xs:ID"/></xs:extension></xs:complexContent></xs:complexType></xs:element><xs:element ref="vamsas:link" 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:annotation><xs:documentation>TODO Database Naming Convention: either start using LSID (so change type to URI) or leave this as an uncontrolled/unspecified string ID</xs:documentation></xs:annotation></xs:attribute><xs:attribute name="version" type="xs:string" use="required"><xs:annotation><xs:documentation>Version must be specified -</xs:documentation></xs:annotation></xs:attribute><xs:attribute name="accessionId" type="xs:string" use="required"><xs:annotation><xs:documentation>TODO: make some specification of the database field from which this accessionId is taken from - should that be a special property of the dbRef object ?</xs:documentation></xs:annotation></xs:attribute><xs:attribute name="id" type="xs:ID" use="optional"><xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation></xs:attribute></xs:complexType></xs:element><xs:element name="vxref" type="vamsas:referenceType" minOccurs="0" maxOccurs="unbounded"><xs:annotation><xs:documentation>explicitly named cross reference to other objects in the document.</xs:documentation></xs:annotation></xs:element></xs:sequence><xs:attribute name="id" type="xs:ID" use="optional"><xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation></xs:attribute><xs:attribute name="dictionary" type="xs:string" use="required"><xs:annotation><xs:documentation>symbol class for sequence</xs:documentation></xs:annotation></xs:attribute></xs:extension></xs:complexContent></xs:complexType></xs:element>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:element name="dbRef" minOccurs="0" maxOccurs="unbounded"><xs:annotation><xs:documentation>Store a list of database references for this sequence record - with optional mapping from database sequence to the given sequence record</xs:documentation><xs:documentation/><xs:documentation/></xs:annotation><xs:complexType><xs:sequence><xs:element name="map" minOccurs="0" maxOccurs="unbounded"><xs:annotation><xs:documentation>the local mapType maps from the parent sequence coordinate frame to the reference frame defined by the dbRef element. The mapped mapType is the mapped range defined on the dbRef element's reference frame. Conventionally, the unit attribute defaults to 1, or will be inferred from the local sequence's dictionary type and any dictionary type associated with the database being mapped to. However, it may be used to avoid ambiguity.</xs:documentation></xs:annotation><xs:complexType><xs:complexContent><xs:extension base="vamsas:mapType"><xs:attribute name="id" type="xs:ID"/></xs:extension></xs:complexContent></xs:complexType></xs:element><xs:element ref="vamsas:link" 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:annotation><xs:documentation>TODO Database Naming Convention: either start using LSID (so change type to URI) or leave this as an uncontrolled/unspecified string ID</xs:documentation></xs:annotation></xs:attribute><xs:attribute name="version" type="xs:string" use="required"><xs:annotation><xs:documentation>Version must be specified -</xs:documentation></xs:annotation></xs:attribute><xs:attribute name="accessionId" type="xs:string" use="required"><xs:annotation><xs:documentation>TODO: make some specification of the database field from which this accessionId is taken from - should that be a special property of the dbRef object ?</xs:documentation></xs:annotation></xs:attribute><xs:attribute name="id" type="xs:ID" use="optional"><xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation></xs:attribute></xs:complexType></xs:element>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
the local mapType maps from the parentsequence coordinate frame to the referenceframe defined by the dbRef element.The mapped mapType is the mapped range definedon the dbRef element's reference frame.Conventionally, the unit attribute defaults to 1, orwill be inferred from the local sequence'sdictionary type and any dictionary type associatedwith the database being mapped to.However, it may be used to avoid ambiguity.
<xs:element name="map" minOccurs="0" maxOccurs="unbounded"><xs:annotation><xs:documentation>the local mapType maps from the parent sequence coordinate frame to the reference frame defined by the dbRef element. The mapped mapType is the mapped range defined on the dbRef element's reference frame. Conventionally, the unit attribute defaults to 1, or will be inferred from the local sequence's dictionary type and any dictionary type associated with the database being mapped to. However, it may be used to avoid ambiguity.</xs:documentation></xs:annotation><xs:complexType><xs:complexContent><xs:extension base="vamsas:mapType"><xs:attribute name="id" type="xs:ID"/></xs:extension></xs:complexContent></xs:complexType></xs:element>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
number of dictionary symbol widths involved in eachmapped position on this sequence (for example, 3 for a dna sequence exonregion that is being mapped to a protein sequence). This is optional,since the unit can be usually be inferred from the dictionary type ofeach sequence involved in the mapping.
number of dictionary symbol widths involved in eachmapped position on this sequence (for example, 3 for a dna sequence exonregion that is being mapped to a protein sequence). This is optional,since the unit can be usually be inferred from the dictionary type ofeach sequence involved in the mapping.
<xs:element name="vxref" type="vamsas:referenceType" minOccurs="0" maxOccurs="unbounded"><xs:annotation><xs:documentation>explicitly named cross reference to other objects in the document.</xs:documentation></xs:annotation></xs:element>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:element name="sequenceMapping" minOccurs="0" maxOccurs="unbounded"><xs:complexType><xs:annotation><xs:documentation>A mapping between the specified 'local' and 'mapped' sequence coordinate frames. The step size between each coordinate frame depends on the sequence dictionary types, or alternatively specified in the optional unit attribute on each range element.</xs:documentation></xs:annotation><xs:complexContent><xs:extension base="vamsas:mapType"><xs:sequence><xs:element ref="vamsas:Provenance"/></xs:sequence><xs:attribute name="loc" type="xs:IDREF" use="required"><xs:annotation><xs:documentation>Object on which the local range is defined.</xs:documentation></xs:annotation></xs:attribute><xs:attribute name="map" type="xs:IDREF" use="required"><xs:annotation><xs:documentation>Object on which the mapped range is defined.</xs:documentation></xs:annotation></xs:attribute><xs:attribute name="id" type="xs:ID" use="optional"/></xs:extension></xs:complexContent></xs:complexType></xs:element>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
A Das Feature has both a type and a Type ID. We go theroute of requiring the type string to be taken from a controlledvocabulary if an application expects others to make sense of it. Thetype may qualified - so uniprot:CHAIN is a valid type name, andconsidered distinct from someotherDB:CHAIN
Source
<xs:element name="DataSetAnnotations" minOccurs="0" maxOccurs="unbounded"><xs:complexType><xs:annotation><xs:documentation>Annotate over positions and regions of a dataset sequence</xs:documentation></xs:annotation><xs:complexContent><xs:extension base="vamsas:rangeAnnotation"><xs:sequence><xs:element ref="vamsas:Provenance"/></xs:sequence><xs:attribute name="seqRef" type="xs:IDREFS" use="required"><xs:annotation><xs:documentation>annotation is associated with a particular dataset sequence</xs:documentation></xs:annotation></xs:attribute></xs:extension></xs:complexContent></xs:complexType></xs:element>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Short, meaningful name for the annotation - if thisis absent, then the type string should be used in its place.
Diagram
Type
xs:string
Properties
content:
simple
minOccurs:
0
Source
<xs:element name="label" type="xs:string" minOccurs="0"><xs:annotation><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>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:element name="description" type="xs:string" minOccurs="0"><xs:annotation><xs:documentation>Human readable description of the annotation</xs:documentation></xs:annotation></xs:element>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
TODO: specify this - we have considered taking the GOevidence codes as a model for assessing a measure of quality to anannotation.
Diagram
Type
xs:string
Properties
content:
simple
minOccurs:
0
Source
<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>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
position with respect to the coordinate frame defined by arangeType specification
Source
<xs:element name="annotationElement"><xs:complexType><xs:annotation><xs:documentation>per-site symbolic and/or quantitative annotation</xs:documentation><xs:documentation>SecondaryStructure and display character (from Jalview) have been subsumed into the glyph element</xs:documentation></xs:annotation><xs:sequence><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:annotation><xs:documentation>Discrete symbol - possibly graphically represented</xs:documentation></xs:annotation><xs:complexType><xs:simpleContent><xs:extension base="xs:string"><xs:attribute name="dict" type="xs:string" use="optional" default="utf8"><xs:annotation><xs:documentation>specifies the symbol dictionary for this glyph - eg utf8 (the default), aasecstr_3 or kd_hydrophobicity - the content is not validated so applications must ensure they gracefully deal with invalid entries here</xs:documentation><xs:documentation>TODO: specify a minimum list of glyph dictionaries to get us started and provide a way for the vamsasClient to validate their content if regexes are specified</xs:documentation></xs:annotation></xs:attribute></xs:extension></xs:simpleContent></xs:complexType></xs:element><xs:element name="value" type="xs:float" minOccurs="0" maxOccurs="unbounded"><xs:annotation><xs:documentation>Ordered set of float values - an application may treat the values together as a vector with common support for a set of annotation elements - but this is, again, not validated so applications should deal gracefully with varying numbers of dimensions</xs:documentation></xs:annotation></xs:element></xs:sequence><xs:attribute name="position" type="xs:integer" use="required"><xs:annotation><xs:documentation>position with respect to the coordinate frame defined by a rangeType specification</xs:documentation></xs:annotation></xs:attribute><xs:attribute name="after" type="xs:boolean" use="optional" default="false"><xs:annotation><xs:documentation>true means the annotation element appears between the specified position and the next</xs:documentation></xs:annotation></xs:attribute><xs:attribute name="id" type="xs:ID" use="optional"><xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation></xs:attribute></xs:complexType></xs:element>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:element name="description" type="xs:string" minOccurs="0"><xs:annotation><xs:documentation>Free text at this position</xs:documentation></xs:annotation></xs:element>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
specifies the symbol dictionary for thisglyph - eg utf8 (the default), aasecstr_3 orkd_hydrophobicity - the content is not validated soapplications must ensure they gracefully deal withinvalid entries here
TODO: specify a minimum list of glyphdictionaries to get us started and provide a way for thevamsasClient to validate their content if regexes arespecified
Source
<xs:element name="glyph" minOccurs="0" maxOccurs="unbounded"><xs:annotation><xs:documentation>Discrete symbol - possibly graphically represented</xs:documentation></xs:annotation><xs:complexType><xs:simpleContent><xs:extension base="xs:string"><xs:attribute name="dict" type="xs:string" use="optional" default="utf8"><xs:annotation><xs:documentation>specifies the symbol dictionary for this glyph - eg utf8 (the default), aasecstr_3 or kd_hydrophobicity - the content is not validated so applications must ensure they gracefully deal with invalid entries here</xs:documentation><xs:documentation>TODO: specify a minimum list of glyph dictionaries to get us started and provide a way for the vamsasClient to validate their content if regexes are specified</xs:documentation></xs:annotation></xs:attribute></xs:extension></xs:simpleContent></xs:complexType></xs:element>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Ordered set of float values - an application may treatthe values together as a vector with common support for a set ofannotation elements - but this is, again, not validated so applicationsshould deal gracefully with varying numbers of dimensions
Diagram
Type
xs:float
Properties
content:
simple
minOccurs:
0
maxOccurs:
unbounded
Source
<xs:element name="value" type="xs:float" minOccurs="0" maxOccurs="unbounded"><xs:annotation><xs:documentation>Ordered set of float values - an application may treat the values together as a vector with common support for a set of annotation elements - but this is, again, not validated so applications should deal gracefully with varying numbers of dimensions</xs:documentation></xs:annotation></xs:element>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:element name="score" minOccurs="0" maxOccurs="unbounded"><xs:annotation><xs:documentation>Ordered set of optionally named float values for the whole annotation</xs:documentation></xs:annotation><xs:complexType><xs:simpleContent><xs:extension base="xs:float"><xs:attribute name="name" type="xs:string" use="optional" default="score"/></xs:extension></xs:simpleContent></xs:complexType></xs:element>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:element name="Alignment" minOccurs="0" maxOccurs="unbounded"><xs:complexType><xs:sequence><xs:element name="AlignmentAnnotation" minOccurs="0" maxOccurs="unbounded"><xs:annotation><xs:documentation>This is annotation over the coordinate frame defined by all the columns in the alignment.</xs:documentation></xs:annotation><xs:complexType><xs:complexContent><xs:extension base="vamsas:rangeAnnotation"><xs:sequence><xs:element ref="vamsas:Provenance"/></xs:sequence><xs:attribute name="graph" type="xs:boolean" use="required"><xs:annotation><xs:documentation>TODO: decide if this flag is redundant - when true it would suggest that the annotationElement values together form a graph</xs:documentation></xs:annotation></xs:attribute><xs:attribute name="seqrefs" type="xs:IDREFS" use="optional"><xs:annotation><xs:documentation>annotation is associated with a range on a particular group of alignment sequences</xs:documentation></xs:annotation></xs:attribute></xs:extension></xs:complexContent></xs:complexType></xs:element><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:sequence><xs:element name="AlignmentSequenceAnnotation" minOccurs="0" maxOccurs="unbounded"><xs:complexType><xs:annotation><xs:documentation>Annotate over positions and regions of the ungapped sequence in the context of the alignment</xs:documentation><xs:documentation/></xs:annotation><xs:complexContent><xs:extension base="vamsas:rangeAnnotation"><xs:sequence><xs:element ref="vamsas:Provenance"/></xs:sequence><xs:attribute name="graph" type="xs:boolean" use="required"><xs:annotation><xs:documentation>TODO: decide if this flag is redundant - when true it would suggest that the annotationElement values together form a graph</xs:documentation></xs:annotation></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>
<xs:documentation>Annotate over positions and regions of the alignment</xs:documentation>
</xs:annotation><xs:complexContent>
<xs:extension base="vamsas:rangeFeature">
<xs:attribute name="seqRef" type="xs:IDREF" use="optional">
<xs:annotation><xs:documentation>annotation may be associated with a particular sequence lying within the same reference frame as the rangeType's objRef</xs:documentation></xs:annotation>
</xs:attribute>
</xs:extension>
</xs:complexContent></xs:complexType></xs:element> --></xs:complexType></xs:element></xs:sequence><xs:attribute name="id" type="xs:ID" use="optional"><xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation></xs:attribute><xs:attribute name="refid" type="xs:IDREF" use="required"><xs:annotation><xs:documentation>Dataset Sequence from which this alignment sequence is taken from</xs:documentation></xs:annotation></xs:attribute></xs:extension></xs:complexContent></xs:complexType></xs:element><xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded"><xs:annotation><xs:documentation>typical properties may be additional alignment score objects</xs:documentation></xs:annotation></xs:element><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:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation></xs:attribute><xs:attribute name="modifiable" type="vamsas:locks" use="optional"/></xs:complexType></xs:element>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
A Das Feature has both a type and a Type ID. We go theroute of requiring the type string to be taken from a controlledvocabulary if an application expects others to make sense of it. Thetype may qualified - so uniprot:CHAIN is a valid type name, andconsidered distinct from someotherDB:CHAIN
Source
<xs:element name="AlignmentAnnotation" minOccurs="0" maxOccurs="unbounded"><xs:annotation><xs:documentation>This is annotation over the coordinate frame defined by all the columns in the alignment.</xs:documentation></xs:annotation><xs:complexType><xs:complexContent><xs:extension base="vamsas:rangeAnnotation"><xs:sequence><xs:element ref="vamsas:Provenance"/></xs:sequence><xs:attribute name="graph" type="xs:boolean" use="required"><xs:annotation><xs:documentation>TODO: decide if this flag is redundant - when true it would suggest that the annotationElement values together form a graph</xs:documentation></xs:annotation></xs:attribute><xs:attribute name="seqrefs" type="xs:IDREFS" use="optional"><xs:annotation><xs:documentation>annotation is associated with a range on a particular group of alignment sequences</xs:documentation></xs:annotation></xs:attribute></xs:extension></xs:complexContent></xs:complexType></xs:element>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:element name="alignmentSequence" maxOccurs="unbounded"><xs:complexType><xs:complexContent><xs:extension base="vamsas:SequenceType"><xs:sequence><xs:element name="AlignmentSequenceAnnotation" minOccurs="0" maxOccurs="unbounded"><xs:complexType><xs:annotation><xs:documentation>Annotate over positions and regions of the ungapped sequence in the context of the alignment</xs:documentation><xs:documentation/></xs:annotation><xs:complexContent><xs:extension base="vamsas:rangeAnnotation"><xs:sequence><xs:element ref="vamsas:Provenance"/></xs:sequence><xs:attribute name="graph" type="xs:boolean" use="required"><xs:annotation><xs:documentation>TODO: decide if this flag is redundant - when true it would suggest that the annotationElement values together form a graph</xs:documentation></xs:annotation></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>
<xs:documentation>Annotate over positions and regions of the alignment</xs:documentation>
</xs:annotation><xs:complexContent>
<xs:extension base="vamsas:rangeFeature">
<xs:attribute name="seqRef" type="xs:IDREF" use="optional">
<xs:annotation><xs:documentation>annotation may be associated with a particular sequence lying within the same reference frame as the rangeType's objRef</xs:documentation></xs:annotation>
</xs:attribute>
</xs:extension>
</xs:complexContent></xs:complexType></xs:element> --></xs:complexType></xs:element></xs:sequence><xs:attribute name="id" type="xs:ID" use="optional"><xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation></xs:attribute><xs:attribute name="refid" type="xs:IDREF" use="required"><xs:annotation><xs:documentation>Dataset Sequence from which this alignment sequence is taken from</xs:documentation></xs:annotation></xs:attribute></xs:extension></xs:complexContent></xs:complexType></xs:element>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
A Das Feature has both a type and a Type ID. We go theroute of requiring the type string to be taken from a controlledvocabulary if an application expects others to make sense of it. Thetype may qualified - so uniprot:CHAIN is a valid type name, andconsidered distinct from someotherDB:CHAIN
Source
<xs:element name="AlignmentSequenceAnnotation" minOccurs="0" maxOccurs="unbounded"><xs:complexType><xs:annotation><xs:documentation>Annotate over positions and regions of the ungapped sequence in the context of the alignment</xs:documentation><xs:documentation/></xs:annotation><xs:complexContent><xs:extension base="vamsas:rangeAnnotation"><xs:sequence><xs:element ref="vamsas:Provenance"/></xs:sequence><xs:attribute name="graph" type="xs:boolean" use="required"><xs:annotation><xs:documentation>TODO: decide if this flag is redundant - when true it would suggest that the annotationElement values together form a graph</xs:documentation></xs:annotation></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>
<xs:documentation>Annotate over positions and regions of the alignment</xs:documentation>
</xs:annotation><xs:complexContent>
<xs:extension base="vamsas:rangeFeature">
<xs:attribute name="seqRef" type="xs:IDREF" use="optional">
<xs:annotation><xs:documentation>annotation may be associated with a particular sequence lying within the same reference frame as the rangeType's objRef</xs:documentation></xs:annotation>
</xs:attribute>
</xs:extension>
</xs:complexContent></xs:complexType></xs:element> --></xs:complexType></xs:element>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Version string describing the application specificdata storage version used
Source
<xs:element name="ApplicationData"><xs:complexType><xs:annotation><xs:documentation>Data specific to a particular type and version of vamsas application</xs:documentation></xs:annotation><xs:complexContent><xs:extension base="vamsas:appData"><xs:sequence><xs:element name="User" minOccurs="0" maxOccurs="unbounded"><xs:complexType><xs:complexContent><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:extension></xs:complexContent></xs:complexType></xs:element><xs:element name="Common" minOccurs="0"><xs:complexType><xs:complexContent><xs:extension base="vamsas:appData"/></xs:complexContent></xs:complexType></xs:element><xs:element name="Instance" minOccurs="0" maxOccurs="unbounded"><xs:complexType><xs:complexContent><xs:extension base="vamsas:appData"><xs:annotation><xs:documentation>Data available to just a specific instance of the application</xs:documentation><xs:documentation>VAMSAS/Pierre: Is this data volatile ? Application instances may not be accessible after the session has closed - the user may have to be presented with the option of picking up the data in that instance</xs:documentation></xs:annotation><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>Canonical name of application</xs:documentation></xs:annotation></xs:attribute></xs:extension></xs:complexContent></xs:complexType></xs:element>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:element name="User" minOccurs="0" maxOccurs="unbounded"><xs:complexType><xs:complexContent><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:extension></xs:complexContent></xs:complexType></xs:element>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:element name="Instance" minOccurs="0" maxOccurs="unbounded"><xs:complexType><xs:complexContent><xs:extension base="vamsas:appData"><xs:annotation><xs:documentation>Data available to just a specific instance of the application</xs:documentation><xs:documentation>VAMSAS/Pierre: Is this data volatile ? Application instances may not be accessible after the session has closed - the user may have to be presented with the option of picking up the data in that instance</xs:documentation></xs:annotation><xs:attribute name="urn" type="xs:string" use="required"/></xs:extension></xs:complexContent></xs:complexType></xs:element>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Type of arbitrary data - TODO: decide format - use(extended) MIME types ?
Source
<xs:element name="Attachment"><xs:complexType><xs:complexContent><xs:extension base="vamsas:appData"><xs:annotation><xs:documentation>General data container to attach a typed data object to any vamsas object</xs:documentation></xs:annotation><xs:attribute name="compressed" type="xs:boolean" use="optional" default="false"><xs:annotation><xs:documentation>true implies data will be decompresses with Zip before presenting to application</xs:documentation></xs:annotation></xs:attribute><xs:attribute name="type" type="xs:string" use="required"><xs:annotation><xs:documentation>Type of arbitrary data - TODO: decide format - use (extended) MIME types ?</xs:documentation></xs:annotation></xs:attribute><xs:attribute name="objectref" type="xs:IDREF" use="required"><xs:annotation><xs:documentation>Object the arbitrary data is associated with</xs:documentation></xs:annotation></xs:attribute><xs:attribute name="id" type="xs:ID" use="optional"><xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation></xs:attribute></xs:extension></xs:complexContent></xs:complexType></xs:element>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Complex Type vamsas:rangeType
Namespace
http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Annotations
Specify an ordered set of positions and/or regions on the principledimension of some associated vamsas object
Keeping to jaxb-1.0 specification for the moment - this choice shouldbecome a substitution group when we use jaxb-2.0 capable bindings
<xs:complexType name="rangeType" abstract="true"><xs:annotation><xs:documentation>Specify an ordered set of positions and/or regions on the principle dimension of some associated vamsas object</xs:documentation><xs:documentation>Keeping to jaxb-1.0 specification for the moment - this choice should become a substitution group when we use jaxb-2.0 capable bindings</xs:documentation></xs:annotation><xs:choice><xs:element name="pos" maxOccurs="unbounded"><xs:annotation><xs:documentation>a position within the associated object's coordinate system</xs:documentation></xs:annotation><xs:complexType><xs:attribute name="i" type="xs:int" use="required"/></xs:complexType></xs:element><xs:element name="seg" maxOccurs="unbounded"><xs:annotation><xs:documentation>a region from start to end, with flag for inclusivity of terminii</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:annotation><xs:documentation>when false, a consecutive range like 'start=1, end=2' means the region lying after position 1 and before position 2</xs:documentation></xs:annotation></xs:attribute></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>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Simple Type vamsas:locks
Namespace
http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Annotations
Contains lock information: locktype:ApplicationHandle locktype is'local' or 'full' A lock is only valid if the ApplicationHandle resolves to a livingapplication in the vamsas session. A local lock means that the application haslocked changes to all local properties on the object. A full lock means that theapplication has locked changes to all properties on the object, and any objects thatit holds references to.
<xs:simpleType name="locks"><xs:annotation><xs:documentation>Contains lock information: locktype:ApplicationHandle locktype is 'local' or 'full' A lock is only valid if the ApplicationHandle resolves to a living application in the vamsas session. A local lock means that the application has locked changes to all local properties on the object. A full lock means that the application has locked changes to all properties on the object, and any objects that it holds references to.</xs:documentation></xs:annotation><xs:restriction base="xs:string"/></xs:simpleType>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:complexType name="nodeType"><xs:sequence><xs:element name="name" type="xs:string" minOccurs="0" maxOccurs="1"><xs:annotation><xs:documentation>Short name for this node</xs:documentation></xs:annotation></xs:element><xs:element name="description" type="xs:string" minOccurs="0" maxOccurs="1"><xs:annotation><xs:documentation>Descriptive text for this node</xs:documentation></xs:annotation></xs:element><xs:element name="vref" type="vamsas:referenceType" minOccurs="0" maxOccurs="unbounded"><xs:annotation><xs:documentation>Direct associations between this node and any vamsas objects</xs:documentation></xs:annotation></xs:element><xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded"/></xs:sequence><xs:attribute name="id" type="xs:ID" use="optional"><xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation></xs:attribute><xs:attribute name="modifiable" type="vamsas:locks" use="optional"/></xs:complexType>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Complex Type vamsas:referenceType
Namespace
http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Annotations
base type for citing arbitrary links between vamsas objects
<xs:complexType name="referenceType"><xs:annotation><xs:documentation>base type for citing arbitrary links between vamsas objects</xs:documentation></xs:annotation><xs:simpleContent><xs:extension base="xs:string"><xs:annotation><xs:documentation>Optional human readable description of the relationship</xs:documentation></xs:annotation><xs:attribute name="id" type="xs:ID" use="optional"><xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation></xs:attribute><xs:attribute name="refs" type="xs:IDREFS"><xs:annotation><xs:documentation>List of one or more vamsas object references</xs:documentation></xs:annotation></xs:attribute></xs:extension></xs:simpleContent></xs:complexType>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:complexType name="mapType"><xs:annotation><xs:documentation>Two sets of ranges defined between objects - usually sequences, indicating which regions on each are mapped.</xs:documentation></xs:annotation><xs:sequence><xs:element name="local" type="vamsas:mapRangeType"><xs:annotation><xs:documentation></xs:documentation></xs:annotation></xs:element><xs:element name="mapped" type="vamsas:mapRangeType"><xs:annotation><xs:documentation></xs:documentation></xs:annotation></xs:element></xs:sequence></xs:complexType>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
number of dictionary symbol widths involved in eachmapped position on this sequence (for example, 3 for a dna sequence exonregion that is being mapped to a protein sequence). This is optional,since the unit can be usually be inferred from the dictionary type ofeach sequence involved in the mapping.
Source
<xs:complexType name="mapRangeType"><xs:complexContent><xs:extension base="vamsas:rangeType"><xs:attribute name="unit" type="xs:positiveInteger" use="optional"><xs:annotation><xs:documentation>number of dictionary symbol widths involved in each mapped position on this sequence (for example, 3 for a dna sequence exon region that is being mapped to a protein sequence). This is optional, since the unit can be usually be inferred from the dictionary type of each sequence involved in the mapping.</xs:documentation></xs:annotation></xs:attribute></xs:extension></xs:complexContent></xs:complexType>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
Complex Type vamsas:rangeAnnotation
Namespace
http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
Annotations
Annotation for a rangeSpec - values can be attached for the wholespecification, and to each position within the spec. following the orientationspecified by the ordered set of rangeSpec (pos, seg) elements.
A Das Feature has both a type and a Type ID. We go theroute of requiring the type string to be taken from a controlledvocabulary if an application expects others to make sense of it. Thetype may qualified - so uniprot:CHAIN is a valid type name, andconsidered distinct from someotherDB:CHAIN
Source
<xs:complexType name="rangeAnnotation"><xs:annotation><xs:documentation>Annotation for a rangeSpec - values can be attached for the whole specification, and to each position within the spec. following the orientation specified by the ordered set of rangeSpec (pos, seg) elements.</xs:documentation></xs:annotation><xs:complexContent><xs:extension base="vamsas:rangeType"><xs:sequence><xs:element name="label" type="xs:string" minOccurs="0"><xs:annotation><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:annotation><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>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:annotation><xs:documentation>Annotation Element position maps to ordered positions defined by the sequence of rangeType pos positions or concatenated seg start/end segments.</xs:documentation></xs:annotation></xs:element><xs:element name="score" minOccurs="0" maxOccurs="unbounded"><xs:annotation><xs:documentation>Ordered set of optionally named float values for the whole annotation</xs:documentation></xs:annotation><xs:complexType><xs:simpleContent><xs:extension base="xs:float"><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:annotation><xs:documentation>Note:These are mutable so an application should check them each time.</xs:documentation></xs:annotation></xs:element></xs:sequence><xs:attribute name="id" type="xs:ID" use="optional"><xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation></xs:attribute><xs:attribute name="modifiable" type="vamsas:locks" use="optional"/><xs:attribute name="group" type="xs:string" use="optional" default=""><xs:annotation><xs:documentation>Annotation with the same non-empty group name are grouped together</xs:documentation></xs:annotation></xs:attribute><xs:attribute name="type" type="xs:string" use="required"><xs:annotation><xs:documentation>A Das Feature has both a type and a Type ID. We go the route of requiring the type string to be taken from a controlled vocabulary if an application expects others to make sense of it. The type may qualified - so uniprot:CHAIN is a valid type name, and considered distinct from someotherDB:CHAIN</xs:documentation></xs:annotation></xs:attribute></xs:extension></xs:complexContent></xs:complexType>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
The type specifies how the property will be parsed.Empty property strings are allowed, and can be used to prototype theinput to a document. TODO: specify allowed types
<xs:attribute name="type" type="xs:string" use="required"><xs:annotation><xs:documentation>The type specifies how the property will be parsed. Empty property strings are allowed, and can be used to prototype the input to a document. TODO: specify allowed types</xs:documentation></xs:annotation></xs:attribute>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
The type specifies how the property will be parsed.Empty property strings are allowed, and can be used to prototype theinput to a document. TODO: specify allowed types
<xs:attribute name="type" type="xs:string" use="required"><xs:annotation><xs:documentation>The type specifies how the property will be parsed. Empty property strings are allowed, and can be used to prototype the input to a document. TODO: specify allowed types</xs:documentation></xs:annotation></xs:attribute>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:attribute name="inclusive" type="xs:boolean" use="required"><xs:annotation><xs:documentation>when false, a consecutive range like 'start=1, end=2' means the region lying after position 1 and before position 2</xs:documentation></xs:annotation></xs:attribute>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:attribute name="refs" type="xs:IDREFS"><xs:annotation><xs:documentation>List of one or more vamsas object references</xs:documentation></xs:annotation></xs:attribute>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:attribute name="treeId" type="xs:IDREFS"><xs:annotation><xs:documentation>reference to one or more trees containing the node being described.</xs:documentation></xs:annotation></xs:attribute>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:attribute name="nodespec" type="xs:string"><xs:annotation><xs:documentation>String uniquely identifying a particular node in the referenced tree according to the format of the tree representation that is referenced.</xs:documentation></xs:annotation></xs:attribute>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
number of dictionary symbol widths involved in eachmapped position on this sequence (for example, 3 for a dna sequence exonregion that is being mapped to a protein sequence). This is optional,since the unit can be usually be inferred from the dictionary type ofeach sequence involved in the mapping.
<xs:attribute name="unit" type="xs:positiveInteger" use="optional"><xs:annotation><xs:documentation>number of dictionary symbol widths involved in each mapped position on this sequence (for example, 3 for a dna sequence exon region that is being mapped to a protein sequence). This is optional, since the unit can be usually be inferred from the dictionary type of each sequence involved in the mapping.</xs:documentation></xs:annotation></xs:attribute>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:attribute name="source" type="xs:string" use="required"><xs:annotation><xs:documentation>TODO Database Naming Convention: either start using LSID (so change type to URI) or leave this as an uncontrolled/unspecified string ID</xs:documentation></xs:annotation></xs:attribute>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:attribute name="version" type="xs:string" use="required"><xs:annotation><xs:documentation>Version must be specified -</xs:documentation></xs:annotation></xs:attribute>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:attribute name="accessionId" type="xs:string" use="required"><xs:annotation><xs:documentation>TODO: make some specification of the database field from which this accessionId is taken from - should that be a special property of the dbRef object ?</xs:documentation></xs:annotation></xs:attribute>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:attribute name="dictionary" type="xs:string" use="required"><xs:annotation><xs:documentation>symbol class for sequence</xs:documentation></xs:annotation></xs:attribute>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:attribute name="loc" type="xs:IDREF" use="required"><xs:annotation><xs:documentation>Object on which the local range is defined.</xs:documentation></xs:annotation></xs:attribute>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:attribute name="map" type="xs:IDREF" use="required"><xs:annotation><xs:documentation>Object on which the mapped range is defined.</xs:documentation></xs:annotation></xs:attribute>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
specifies the symbol dictionary for thisglyph - eg utf8 (the default), aasecstr_3 orkd_hydrophobicity - the content is not validated soapplications must ensure they gracefully deal withinvalid entries here
TODO: specify a minimum list of glyphdictionaries to get us started and provide a way for thevamsasClient to validate their content if regexes arespecified
<xs:attribute name="dict" type="xs:string" use="optional" default="utf8"><xs:annotation><xs:documentation>specifies the symbol dictionary for this glyph - eg utf8 (the default), aasecstr_3 or kd_hydrophobicity - the content is not validated so applications must ensure they gracefully deal with invalid entries here</xs:documentation><xs:documentation>TODO: specify a minimum list of glyph dictionaries to get us started and provide a way for the vamsasClient to validate their content if regexes are specified</xs:documentation></xs:annotation></xs:attribute>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:attribute name="position" type="xs:integer" use="required"><xs:annotation><xs:documentation>position with respect to the coordinate frame defined by a rangeType specification</xs:documentation></xs:annotation></xs:attribute>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:attribute name="after" type="xs:boolean" use="optional" default="false"><xs:annotation><xs:documentation>true means the annotation element appears between the specified position and the next</xs:documentation></xs:annotation></xs:attribute>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:attribute name="group" type="xs:string" use="optional" default=""><xs:annotation><xs:documentation>Annotation with the same non-empty group name are grouped together</xs:documentation></xs:annotation></xs:attribute>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
A Das Feature has both a type and a Type ID. We go theroute of requiring the type string to be taken from a controlledvocabulary if an application expects others to make sense of it. Thetype may qualified - so uniprot:CHAIN is a valid type name, andconsidered distinct from someotherDB:CHAIN
<xs:attribute name="type" type="xs:string" use="required"><xs:annotation><xs:documentation>A Das Feature has both a type and a Type ID. We go the route of requiring the type string to be taken from a controlled vocabulary if an application expects others to make sense of it. The type may qualified - so uniprot:CHAIN is a valid type name, and considered distinct from someotherDB:CHAIN</xs:documentation></xs:annotation></xs:attribute>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:attribute name="seqRef" type="xs:IDREFS" use="required"><xs:annotation><xs:documentation>annotation is associated with a particular dataset sequence</xs:documentation></xs:annotation></xs:attribute>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:attribute name="graph" type="xs:boolean" use="required"><xs:annotation><xs:documentation>TODO: decide if this flag is redundant - when true it would suggest that the annotationElement values together form a graph</xs:documentation></xs:annotation></xs:attribute>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:attribute name="seqrefs" type="xs:IDREFS" use="optional"><xs:annotation><xs:documentation>annotation is associated with a range on a particular group of alignment sequences</xs:documentation></xs:annotation></xs:attribute>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:attribute name="graph" type="xs:boolean" use="required"><xs:annotation><xs:documentation>TODO: decide if this flag is redundant - when true it would suggest that the annotationElement values together form a graph</xs:documentation></xs:annotation></xs:attribute>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:attribute name="refid" type="xs:IDREF" use="required"><xs:annotation><xs:documentation>Dataset Sequence from which this alignment sequence is taken from</xs:documentation></xs:annotation></xs:attribute>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<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>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:attribute name="name" type="xs:string" use="required"><xs:annotation><xs:documentation>Canonical name of application</xs:documentation></xs:annotation></xs:attribute>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:attribute name="compressed" type="xs:boolean" use="optional" default="false"><xs:annotation><xs:documentation>true implies data will be decompresses with Zip before presenting to application</xs:documentation></xs:annotation></xs:attribute>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:attribute name="type" type="xs:string" use="required"><xs:annotation><xs:documentation>Type of arbitrary data - TODO: decide format - use (extended) MIME types ?</xs:documentation></xs:annotation></xs:attribute>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd
<xs:attribute name="objectref" type="xs:IDREF" use="required"><xs:annotation><xs:documentation>Object the arbitrary data is associated with</xs:documentation></xs:annotation></xs:attribute>
Schema location
file:/C:/Documents and Settings/JimP/workspace-3.4/VamsasClient/schemas/vamsas.xsd