phyloXML 0.90

Table of Contents

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Schema Document Properties

Target Namespace http://www.phyloxml.org
Element and Attribute Namespaces
  • Global element and attribute declarations belong to this schema's target namespace.
  • By default, local element declarations belong to this schema's target namespace.
  • By default, local attribute declarations have no namespace.

Declared Namespaces

Prefix Namespace
xml http://www.w3.org/XML/1998/namespace
phy http://www.phyloxml.org
xs http://www.w3.org/2001/XMLSchema
Schema Component Representation
<xs:schema targetNamespace="http://www.phyloxml.org" elementFormDefault="qualified" attributeFormDefault="unqualified">
...
</xs:schema>
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Global Declarations

Element: phyloxml

Name phyloxml
Type phy:Phyloxml
Nillable no
Abstract no
Logical Diagram
XML Instance Representation
<phy:phyloxml>
Start Sequence [1..*]
<phy:phylogeny> phy:Phylogeny </phy:phylogeny> [0..*]
Allow any elements from a namespace other than this schema's namespace (lax validation). [0..*]
End Sequence
</phy:phyloxml>
Diagram
h535307528
Schema Component Representation
<xs:element name="phyloxml" type=" phy:Phyloxml "/>
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Global Definitions

Complex Type: Annotation

Super-types: None
Sub-types: None
Name Annotation
Used by (from the same schema document) Complex Type Sequence
Abstract no
XML Instance Representation
<...
type=" xs:token [0..1]">
<!-- Mixed content -->
<phy:id> phy:Id </phy:id> [0..1]
<phy:confidence> phy:Confidence </phy:confidence> [0..1]
<phy:uri> phy:Uri </phy:uri> [0..1]
</...>
Diagram
h-853091232 h-993584945 h-676012345
Schema Component Representation
<xs:complexType name="Annotation" mixed="true">
<xs:sequence>
<xs:element name="id" type=" phy:Id " minOccurs="0"/>
<xs:element name="confidence" type=" phy:Confidence " minOccurs="0"/>
<xs:element name="uri" type=" phy:Uri " minOccurs="0"/>
</xs:sequence>
<xs:attribute name="type" type=" xs:token "/>
</xs:complexType>
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Complex Type: BinaryCharacterList

Super-types: None
Sub-types: None
Name BinaryCharacterList
Used by (from the same schema document) Complex Type BinaryCharacters , Complex Type BinaryCharacters , Complex Type BinaryCharacters , Complex Type BinaryCharacters
Abstract no
XML Instance Representation
<...>
<phy:bc> xs:token </phy:bc> [1..*]
</...>
Diagram
Schema Component Representation
<xs:complexType name="BinaryCharacterList">
<xs:sequence>
<xs:element name="bc" type=" xs:token " maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
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Complex Type: BinaryCharacters

Super-types: None
Sub-types: None
Name BinaryCharacters
Used by (from the same schema document) Complex Type Clade
Abstract no
XML Instance Representation
<...
type=" xs:token [0..1]"
gained_count=" xs:nonNegativeInteger [0..1]"
lost_count=" xs:nonNegativeInteger [0..1]"
present_count=" xs:nonNegativeInteger [0..1]"
absent_count=" xs:nonNegativeInteger [0..1]">
<phy:gained> phy:BinaryCharacterList </phy:gained> [0..1]
<phy:lost> phy:BinaryCharacterList </phy:lost> [0..1]
<phy:present> phy:BinaryCharacterList </phy:present> [0..1]
<phy:absent> phy:BinaryCharacterList </phy:absent> [0..1]
</...>
Diagram
h1535743041 h1535743041 h1535743041 h1535743041
Schema Component Representation
<xs:complexType name="BinaryCharacters">
<xs:sequence>
<xs:element name="gained" type=" phy:BinaryCharacterList " minOccurs="0"/>
<xs:element name="lost" type=" phy:BinaryCharacterList " minOccurs="0"/>
<xs:element name="present" type=" phy:BinaryCharacterList " minOccurs="0"/>
<xs:element name="absent" type=" phy:BinaryCharacterList " minOccurs="0"/>
</xs:sequence>
<xs:attribute name="type" type=" xs:token "/>
<xs:attribute name="gained_count" type=" xs:nonNegativeInteger "/>
<xs:attribute name="lost_count" type=" xs:nonNegativeInteger "/>
<xs:attribute name="present_count" type=" xs:nonNegativeInteger "/>
<xs:attribute name="absent_count" type=" xs:nonNegativeInteger "/>
</xs:complexType>
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Complex Type: BranchColor

Super-types: None
Sub-types: None
Name BranchColor
Used by (from the same schema document) Complex Type Clade
Abstract no
XML Instance Representation
<...>
<phy:red> xs:unsignedByte </phy:red> [1]
<phy:green> xs:unsignedByte </phy:green> [1]
<phy:blue> xs:unsignedByte </phy:blue> [1]
</...>
Diagram
Schema Component Representation
<xs:complexType name="BranchColor">
<xs:sequence>
<xs:element name="red" type=" xs:unsignedByte "/>
<xs:element name="green" type=" xs:unsignedByte "/>
<xs:element name="blue" type=" xs:unsignedByte "/>
</xs:sequence>
</xs:complexType>
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Complex Type: Clade

Super-types: None
Sub-types: None
Name Clade
Used by (from the same schema document) Complex Type Phylogeny , Complex Type Clade
Abstract no
XML Instance Representation
<...
distance=" xs:double [0..1]"
id_source=" phy:id_source [0..1]">
<phy:name> xs:token </phy:name> [0..1]
<phy:distance> xs:double </phy:distance> [0..1]
<phy:confidence> phy:Confidence </phy:confidence> [0..*]
<phy:width> xs:double </phy:width> [0..1]
<phy:color> phy:BranchColor </phy:color> [0..1]
<phy:node_id> phy:Id </phy:node_id> [0..1]
<phy:taxonomy> phy:Taxonomy </phy:taxonomy> [0..*]
<phy:sequence> phy:Sequence </phy:sequence> [0..*]
<phy:event> phy:Event </phy:event> [0..1]
<phy:binary_characters> phy:BinaryCharacters </phy:binary_characters> [0..1]
<phy:distribution> xs:token </phy:distribution> [0..1]
<phy:date> xs:token </phy:date> [0..1]
<phy:clade> phy:Clade </phy:clade> [0..*]
<phy:custom> phy:Custom </phy:custom> [0..1]
Allow any elements from a namespace other than this schema's namespace (lax validation). [0..*]
</...>
Diagram
h-993584945 h-1691165380 h-853091232 h888650454 h-1794244794 h-1122459339 h-1514309680 h-494260170 h-1482113798
Schema Component Representation
<xs:complexType name="Clade">
<xs:sequence>
<xs:element name="name" type=" xs:token " minOccurs="0"/>
<xs:element name="distance" type=" xs:double " minOccurs="0"/>
<xs:element name="confidence" type=" phy:Confidence " minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="width" type=" xs:double " minOccurs="0"/>
<xs:element name="color" type=" phy:BranchColor " minOccurs="0"/>
<xs:element name="node_id" type=" phy:Id " minOccurs="0"/>
<xs:element name="taxonomy" type=" phy:Taxonomy " minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="sequence" type=" phy:Sequence " minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="event" type=" phy:Event " minOccurs="0"/>
<xs:element name="binary_characters" type=" phy:BinaryCharacters " minOccurs="0"/>
<xs:element name="distribution" type=" xs:token " minOccurs="0"/>
<xs:element name="date" type=" xs:token " minOccurs="0"/>
<xs:element name="clade" type=" phy:Clade " minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="custom" type=" phy:Custom " minOccurs="0"/>
<xs:any minOccurs="0" maxOccurs="unbounded" processContents="lax" namespace="##other"/>
</xs:sequence>
<xs:attribute name="distance" type=" xs:double "/>
<xs:attribute name="id_source" type=" phy:id_source "/>
</xs:complexType>
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Complex Type: CladeRelation

Super-types: None
Sub-types: None
Name CladeRelation
Used by (from the same schema document) Complex Type Phylogeny
Abstract no
XML Instance Representation
<...
id_ref_0=" phy:id_ref [1]"
id_ref_1=" phy:id_ref [1]"
distance=" xs:double [0..1]"
type=" xs:token [1]">
<phy:confidence> phy:Confidence </phy:confidence> [0..1]
</...>
Diagram
h-993584945 h577349652 h577349652
Schema Component Representation
<xs:complexType name="CladeRelation">
<xs:sequence>
<xs:element name="confidence" type=" phy:Confidence " minOccurs="0"/>
</xs:sequence>
<xs:attribute name="id_ref_0" type=" phy:id_ref " use="required"/>
<xs:attribute name="id_ref_1" type=" phy:id_ref " use="required"/>
<xs:attribute name="distance" type=" xs:double "/>
<xs:attribute name="type" type=" xs:token " use="required"/>
</xs:complexType>
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Complex Type: Confidence

Super-types: xs:double < Confidence (by extension)
Sub-types: None
Name Confidence
Used by (from the same schema document) Complex Type Phylogeny , Complex Type Clade , Complex Type Event , Complex Type Annotation , Complex Type SequenceRelation , Complex Type CladeRelation
Abstract no
XML Instance Representation
<...
type=" xs:token [1]">
xs:double
</...>
Diagram
Schema Component Representation
<xs:complexType name="Confidence">
<xs:simpleContent>
<xs:extension base=" xs:double ">
<xs:attribute name="type" type=" xs:token " use="required"/>
</xs:extension>
</xs:simpleContent>
</xs:complexType>
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Complex Type: Custom

Super-types: None
Sub-types: None
Name Custom
Used by (from the same schema document) Complex Type Phylogeny , Complex Type Clade
Abstract no
XML Instance Representation
<...
unit=" xs:token [0..1]"
custom_type=" phy:CustomType [1]"
custom_property=" phy:CustomProperty [1]"
id_ref=" phy:id_ref [0..1]">
<phy:name> xs:token </phy:name> [1]
<phy:value> xs:token </phy:value> [1]
</...>
Diagram
h890448016 h-1670259669 h577349652
Schema Component Representation
<xs:complexType name="Custom">
<xs:sequence>
<xs:element name="name" type=" xs:token "/>
<xs:element name="value" type=" xs:token "/>
</xs:sequence>
<xs:attribute name="unit" type=" xs:token "/>
<xs:attribute name="custom_type" type=" phy:CustomType " use="required"/>
<xs:attribute name="custom_property" type=" phy:CustomProperty " use="required"/>
<xs:attribute name="id_ref" type=" phy:id_ref "/>
</xs:complexType>
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Complex Type: DomainArchitecture

Super-types: None
Sub-types: None
Name DomainArchitecture
Used by (from the same schema document) Complex Type Sequence
Abstract no
XML Instance Representation
<...
length=" xs:nonNegativeInteger [0..1]">
<phy:domain> phy:ProteinDomain </phy:domain> [1..*]
</...>
Diagram
h-1389097534
Schema Component Representation
<xs:complexType name="DomainArchitecture">
<xs:sequence>
<xs:element name="domain" type=" phy:ProteinDomain " minOccurs="1" maxOccurs="unbounded"/>
</xs:sequence>
<xs:attribute name="length" type=" xs:nonNegativeInteger "/>
</xs:complexType>
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Complex Type: Event

Super-types: None
Sub-types: None
Name Event
Used by (from the same schema document) Complex Type Clade
Abstract no
XML Instance Representation
<...>
<phy:type> phy:EventType </phy:type> [0..1]
<phy:duplications> xs:nonNegativeInteger </phy:duplications> [0..1]
<phy:speciations> xs:nonNegativeInteger </phy:speciations> [0..1]
<phy:losses> xs:nonNegativeInteger </phy:losses> [0..1]
<phy:confidence> phy:Confidence </phy:confidence> [0..1]
</...>
Diagram
h1358103055 h-993584945
Schema Component Representation
<xs:complexType name="Event">
<xs:sequence>
<xs:element name="type" type=" phy:EventType " minOccurs="0"/>
<xs:element name="duplications" type=" xs:nonNegativeInteger " minOccurs="0"/>
<xs:element name="speciations" type=" xs:nonNegativeInteger " minOccurs="0"/>
<xs:element name="losses" type=" xs:nonNegativeInteger " minOccurs="0"/>
<xs:element name="confidence" type=" phy:Confidence " minOccurs="0"/>
</xs:sequence>
</xs:complexType>
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Complex Type: Id

Super-types: xs:token < Id (by extension)
Sub-types: None
Name Id
Used by (from the same schema document) Complex Type Phylogeny , Complex Type Clade , Complex Type Taxonomy , Complex Type Sequence , Complex Type Annotation
Abstract no
XML Instance Representation
<...
type=" xs:token [0..1]">
xs:token
</...>
Diagram
Schema Component Representation
<xs:complexType name="Id">
<xs:simpleContent>
<xs:extension base=" xs:token ">
<xs:attribute name="type" type=" xs:token "/>
</xs:extension>
</xs:simpleContent>
</xs:complexType>
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Complex Type: Phylogeny

Super-types: None
Sub-types: None
Name Phylogeny
Used by (from the same schema document) Complex Type Phyloxml
Abstract no
XML Instance Representation
<...
rooted=" xs:boolean [1]"
rerootable=" xs:boolean [0..1]"
distance_unit=" xs:token [0..1]"
type=" xs:token [0..1]">
<phy:name> xs:token </phy:name> [0..1]
<phy:id> phy:Id </phy:id> [0..1]
<phy:description> xs:token </phy:description> [0..1]
<phy:date> xs:dateTime </phy:date> [0..1]
<phy:confidence> phy:Confidence </phy:confidence> [0..*]
<phy:clade> phy:Clade </phy:clade> [0..1]
<phy:clade_relation> phy:CladeRelation </phy:clade_relation> [0..*]
<phy:sequence_relation> phy:SequenceRelation </phy:sequence_relation> [0..*]
<phy:custom> phy:Custom </phy:custom> [0..*]
Allow any elements from a namespace other than this schema's namespace (lax validation). [0..*]
</...>
Diagram
h-853091232 h-993584945 h-1124608460 h192331856 h-802965662 h-494260170
Schema Component Representation
<xs:complexType name="Phylogeny">
<xs:sequence>
<xs:element name="name" type=" xs:token " minOccurs="0"/>
<xs:element name="id" type=" phy:Id " minOccurs="0"/>
<xs:element name="description" type=" xs:token " minOccurs="0"/>
<xs:element name="date" type=" xs:dateTime " minOccurs="0"/>
<xs:element name="confidence" type=" phy:Confidence " minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="clade" type=" phy:Clade " minOccurs="0"/>
<xs:element name="clade_relation" type=" phy:CladeRelation " minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="sequence_relation" type=" phy:SequenceRelation " minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="custom" type=" phy:Custom " minOccurs="0" maxOccurs="unbounded"/>
<xs:any minOccurs="0" maxOccurs="unbounded" processContents="lax" namespace="##other"/>
</xs:sequence>
<xs:attribute name="rooted" type=" xs:boolean " use="required"/>
<xs:attribute name="rerootable" type=" xs:boolean "/>
<xs:attribute name="distance_unit" type=" xs:token "/>
<xs:attribute name="type" type=" xs:token "/>
</xs:complexType>
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Complex Type: Phyloxml

Super-types: None
Sub-types: None
Name Phyloxml
Used by (from the same schema document) Element phyloxml
Abstract no
XML Instance Representation
<...>
Start Sequence [1..*]
<phy:phylogeny> phy:Phylogeny </phy:phylogeny> [0..*]
Allow any elements from a namespace other than this schema's namespace (lax validation). [0..*]
End Sequence
</...>
Diagram
h535307528
Schema Component Representation
<xs:complexType name="Phyloxml">
<xs:sequence maxOccurs="unbounded">
<xs:element name="phylogeny" type=" phy:Phylogeny " minOccurs="0" maxOccurs="unbounded"/>
<xs:any minOccurs="0" maxOccurs="unbounded" processContents="lax" namespace="##other"/>
</xs:sequence>
</xs:complexType>
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Complex Type: ProteinDomain

Super-types: xs:token < ProteinDomain (by extension)
Sub-types: None
Name ProteinDomain
Used by (from the same schema document) Complex Type DomainArchitecture
Abstract no
XML Instance Representation
<...
from=" xs:nonNegativeInteger [1]"
to=" xs:nonNegativeInteger [1]"
confidence=" xs:double [0..1]"
id=" xs:token [0..1]">
xs:token
</...>
Diagram
Schema Component Representation
<xs:complexType name="ProteinDomain">
<xs:simpleContent>
<xs:extension base=" xs:token ">
<xs:attribute name="from" type=" xs:nonNegativeInteger " use="required"/>
<xs:attribute name="to" type=" xs:nonNegativeInteger " use="required"/>
<xs:attribute name="confidence" type=" xs:double "/>
<xs:attribute name="id" type=" xs:token "/>
</xs:extension>
</xs:simpleContent>
</xs:complexType>
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Complex Type: Sequence

Super-types: None
Sub-types: None
Name Sequence
Used by (from the same schema document) Complex Type Clade
Abstract no
XML Instance Representation
<...
id_source=" phy:id_source [0..1]"
type=" xs:token [0..1]">
<phy:id> phy:Id </phy:id> [0..1]
<phy:accession> xs:token </phy:accession> [0..1]
<phy:gene_name> xs:token </phy:gene_name> [0..1]
<phy:location> xs:token </phy:location> [0..1]
<phy:mol_seq> phy:MolSeq </phy:mol_seq> [0..1]
<phy:uri> phy:Uri </phy:uri> [0..1]
<phy:annotation> phy:Annotation </phy:annotation> [0..*]
<phy:domain_architecture> phy:DomainArchitecture </phy:domain_architecture> [0..1]
Allow any elements from a namespace other than this schema's namespace (lax validation). [0..*]
</...>
Diagram
h-853091232 h-213750342 h-676012345 h917087604 h259010940 h-1482113798
Schema Component Representation
<xs:complexType name="Sequence">
<xs:sequence>
<xs:element name="id" type=" phy:Id " minOccurs="0"/>
<xs:element name="accession" type=" xs:token " minOccurs="0"/>
<xs:element name="gene_name" type=" xs:token " minOccurs="0"/>
<xs:element name="location" type=" xs:token " minOccurs="0"/>
<xs:element name="mol_seq" type=" phy:MolSeq " minOccurs="0"/>
<xs:element name="uri" type=" phy:Uri " minOccurs="0"/>
<xs:element name="annotation" type=" phy:Annotation " minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="domain_architecture" type=" phy:DomainArchitecture " minOccurs="0"/>
<xs:any minOccurs="0" maxOccurs="unbounded" processContents="lax" namespace="##other"/>
</xs:sequence>
<xs:attribute name="id_source" type=" phy:id_source "/>
<xs:attribute name="type" type=" xs:token "/>
</xs:complexType>
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Complex Type: SequenceRelation

Super-types: None
Sub-types: None
Name SequenceRelation
Used by (from the same schema document) Complex Type Phylogeny
Abstract no
XML Instance Representation
<...
id_ref_0=" phy:id_ref [1]"
id_ref_1=" phy:id_ref [1]"
distance=" xs:double [0..1]"
type=" phy:SequenceRelationType [1]">
<phy:confidence> phy:Confidence </phy:confidence> [0..1]
</...>
Diagram
h-993584945 h577349652 h577349652 h519911868
Schema Component Representation
<xs:complexType name="SequenceRelation">
<xs:sequence>
<xs:element name="confidence" type=" phy:Confidence " minOccurs="0"/>
</xs:sequence>
<xs:attribute name="id_ref_0" type=" phy:id_ref " use="required"/>
<xs:attribute name="id_ref_1" type=" phy:id_ref " use="required"/>
<xs:attribute name="distance" type=" xs:double "/>
<xs:attribute name="type" type=" phy:SequenceRelationType " use="required"/>
</xs:complexType>
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Complex Type: Taxonomy

Super-types: None
Sub-types: None
Name Taxonomy
Used by (from the same schema document) Complex Type Clade
Abstract no
XML Instance Representation
<...
type=" xs:token [0..1]">
<phy:id> phy:Id </phy:id> [0..1]
<phy:code> phy:TaxonomyCode </phy:code> [0..1]
<phy:scientific_name> xs:token </phy:scientific_name> [0..1]
<phy:common_name> xs:token </phy:common_name> [0..1]
<phy:rank> phy:Rank </phy:rank> [0..1]
<phy:uri> phy:Uri </phy:uri> [0..1]
Allow any elements from a namespace other than this schema's namespace (lax validation). [0..*]
</...>
Diagram
h-853091232 h712147427 h518348337 h-676012345
Schema Component Representation
<xs:complexType name="Taxonomy">
<xs:sequence>
<xs:element name="id" type=" phy:Id " minOccurs="0"/>
<xs:element name="code" type=" phy:TaxonomyCode " minOccurs="0"/>
<xs:element name="scientific_name" type=" xs:token " minOccurs="0"/>
<xs:element name="common_name" type=" xs:token " minOccurs="0"/>
<xs:element name="rank" type=" phy:Rank " minOccurs="0"/>
<xs:element name="uri" type=" phy:Uri " minOccurs="0"/>
<xs:any minOccurs="0" maxOccurs="unbounded" processContents="lax" namespace="##other"/>
</xs:sequence>
<xs:attribute name="type" type=" xs:token "/>
</xs:complexType>
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Complex Type: Uri

Super-types: xs:anyURI < Uri (by extension)
Sub-types: None
Name Uri
Used by (from the same schema document) Complex Type Taxonomy , Complex Type Sequence , Complex Type Annotation
Abstract no
XML Instance Representation
<...
desc=" xs:token [0..1]"
type=" xs:token [0..1]">
xs:anyURI
</...>
Diagram
Schema Component Representation
<xs:complexType name="Uri">
<xs:simpleContent>
<xs:extension base=" xs:anyURI ">
<xs:attribute name="desc" type=" xs:token "/>
<xs:attribute name="type" type=" xs:token "/>
</xs:extension>
</xs:simpleContent>
</xs:complexType>
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Simple Type: CustomProperty

Super-types: xs:token < CustomProperty (by restriction)
Sub-types: None
Name CustomProperty
Used by (from the same schema document) Complex Type Custom
Content
  • Base XSD Type: token
  • value comes from list: {'phylogeny'|'clade'|'node'|'sequence'|'taxonomy'|'other'}
Diagram
Schema Component Representation
<xs:simpleType name="CustomProperty">
<xs:restriction base=" xs:token ">
<xs:enumeration value="phylogeny"/>
<xs:enumeration value="clade"/>
<xs:enumeration value="node"/>
<xs:enumeration value="sequence"/>
<xs:enumeration value="taxonomy"/>
<xs:enumeration value="other"/>
</xs:restriction>
</xs:simpleType>
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Simple Type: CustomType

Super-types: xs:token < CustomType (by restriction)
Sub-types: None
Name CustomType
Used by (from the same schema document) Complex Type Custom
Content
  • Base XSD Type: token
  • value comes from list: {'string'|'character'|'decimal'|'integer'|'byte'|'boolean'|'uri'|'other'}
Diagram
Schema Component Representation
<xs:simpleType name="CustomType">
<xs:restriction base=" xs:token ">
<xs:enumeration value="string"/>
<xs:enumeration value="character"/>
<xs:enumeration value="decimal"/>
<xs:enumeration value="integer"/>
<xs:enumeration value="byte"/>
<xs:enumeration value="boolean"/>
<xs:enumeration value="uri"/>
<xs:enumeration value="other"/>
</xs:restriction>
</xs:simpleType>
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Simple Type: Distribution

Super-types: xs:token < Distribution (by restriction)
Sub-types: None
Name Distribution
Content
  • Base XSD Type: token
Diagram
Schema Component Representation
<xs:simpleType name="Distribution">
<xs:restriction base=" xs:token "/>
</xs:simpleType>
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Simple Type: EventType

Super-types: xs:token < EventType (by restriction)
Sub-types: None
Name EventType
Used by (from the same schema document) Complex Type Event
Content
  • Base XSD Type: token
  • value comes from list: {'transfer'|'fusion'|'root'|'speciation_or_duplication'|'other'|'mixed'|'unassigned'}
Diagram
Schema Component Representation
<xs:simpleType name="EventType">
<xs:restriction base=" xs:token ">
<xs:enumeration value="transfer"/>
<xs:enumeration value="fusion"/>
<xs:enumeration value="root"/>
<xs:enumeration value="speciation_or_duplication"/>
<xs:enumeration value="other"/>
<xs:enumeration value="mixed"/>
<xs:enumeration value="unassigned"/>
</xs:restriction>
</xs:simpleType>
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Simple Type: MolSeq

Super-types: xs:token < MolSeq (by restriction)
Sub-types: None
Name MolSeq
Used by (from the same schema document) Complex Type Sequence
Content
  • Base XSD Type: token
  • pattern = [a-zA-Z\.\-\?\*_]+
Diagram
Schema Component Representation
<xs:simpleType name="MolSeq">
<xs:restriction base=" xs:token ">
<xs:pattern value="[a-zA-Z\.\-\?\*_]+"/>
</xs:restriction>
</xs:simpleType>
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Simple Type: Rank

Super-types: xs:token < Rank (by restriction)
Sub-types: None
Name Rank
Used by (from the same schema document) Complex Type Taxonomy
Content
  • Base XSD Type: token
  • value comes from list: {'domain'|'kingdom'|'branch'|'phylum'|'subphylum'|'division'|'superclass'|'class'|'subclass'|'superorder'|'order'|'suborder'|'superfamily'|'family'|'subfamily'|'genus'|'subgenus'|'species'|'subspecies'|'variety'|'form'|'cultivar'|'unknown'|'other'}
Diagram
Schema Component Representation
<xs:simpleType name="Rank">
<xs:restriction base=" xs:token ">
<xs:enumeration value="domain"/>
<xs:enumeration value="kingdom"/>
<xs:enumeration value="branch"/>
<xs:enumeration value="phylum"/>
<xs:enumeration value="subphylum"/>
<xs:enumeration value="division"/>
<xs:enumeration value="superclass"/>
<xs:enumeration value="class"/>
<xs:enumeration value="subclass"/>
<xs:enumeration value="superorder"/>
<xs:enumeration value="order"/>
<xs:enumeration value="suborder"/>
<xs:enumeration value="superfamily"/>
<xs:enumeration value="family"/>
<xs:enumeration value="subfamily"/>
<xs:enumeration value="genus"/>
<xs:enumeration value="subgenus"/>
<xs:enumeration value="species"/>
<xs:enumeration value="subspecies"/>
<xs:enumeration value="variety"/>
<xs:enumeration value="form"/>
<xs:enumeration value="cultivar"/>
<xs:enumeration value="unknown"/>
<xs:enumeration value="other"/>
</xs:restriction>
</xs:simpleType>
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Simple Type: SequenceRelationType

Super-types: xs:token < SequenceRelationType (by restriction)
Sub-types: None
Name SequenceRelationType
Used by (from the same schema document) Complex Type SequenceRelation
Content
  • Base XSD Type: token
  • value comes from list: {'orthology'|'one_to_one_orthology'|'super_orthology'|'paralogy'|'ultra_paralogy'|'xenology'|'unknown'|'other'}
Diagram
Schema Component Representation
<xs:simpleType name="SequenceRelationType">
<xs:restriction base=" xs:token ">
<xs:enumeration value="orthology"/>
<xs:enumeration value="one_to_one_orthology"/>
<xs:enumeration value="super_orthology"/>
<xs:enumeration value="paralogy"/>
<xs:enumeration value="ultra_paralogy"/>
<xs:enumeration value="xenology"/>
<xs:enumeration value="unknown"/>
<xs:enumeration value="other"/>
</xs:restriction>
</xs:simpleType>
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Simple Type: TaxonomyCode

Super-types: xs:token < TaxonomyCode (by restriction)
Sub-types: None
Name TaxonomyCode
Used by (from the same schema document) Complex Type Taxonomy
Content
  • Base XSD Type: token
  • pattern = [a-zA-Z0-9_]{2,20}
Diagram
Schema Component Representation
<xs:simpleType name="TaxonomyCode">
<xs:restriction base=" xs:token ">
<xs:pattern value="[a-zA-Z0-9_]{2,20}"/>
</xs:restriction>
</xs:simpleType>
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Simple Type: id_ref

Super-types: xs:IDREF < id_ref (by restriction)
Sub-types: None
Name id_ref
Used by (from the same schema document) Complex Type Custom , Complex Type SequenceRelation , Complex Type SequenceRelation , Complex Type CladeRelation , Complex Type CladeRelation
Content
  • Base XSD Type: IDREF
Diagram
Schema Component Representation
<xs:simpleType name="id_ref">
<xs:restriction base=" xs:IDREF "/>
</xs:simpleType>
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Simple Type: id_source

Super-types: xs:ID < id_source (by restriction)
Sub-types: None
Name id_source
Used by (from the same schema document) Complex Type Clade , Complex Type Sequence
Content
  • Base XSD Type: ID
Diagram
Schema Component Representation
<xs:simpleType name="id_source">
<xs:restriction base=" xs:ID "/>
</xs:simpleType>
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Legend

Complex Type:

Schema Component Type

AusAddress

Schema Component Name
Super-types: Address < AusAddress (by extension)
Sub-types:
  • QLDAddress (by restriction)
If this schema component is a type definition, its type hierarchy is shown in a gray-bordered box.
Name AusAddress
Abstract no
The table above displays the properties of this schema component.
XML Instance Representation
<... country="Australia" >
<unitNo> string </unitNo> [0..1]
<houseNo> string </houseNo> [1]
<street> string </street> [1]
Start Choice [1]
<city> string </city> [1]
<town> string </town> [1]
End Choice
<state> AusStates </state> [1]
<postcode> string <<pattern = [1-9][0-9]{3}>> </postcode> [1] ?
</...>

The XML Instance Representation table above shows the schema component's content as an XML instance.

Schema Component Representation
<complexType name="AusAddress">
<complexContent>
<extension base=" Address ">
<sequence>
<element name="state" type=" AusStates "/>
<element name="postcode">
<simpleType>
<restriction base=" string ">
<pattern value="[1-9][0-9]{3}"/>
</restriction>
</simpleType>
</element>
</sequence>
<attribute name="country" type=" string " fixed="Australia"/>
</extension>
</complexContent>
</complexType>
The Schema Component Representation table above displays the underlying XML representation of the schema component. (Annotations are not shown.)
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Glossary

Abstract (Applies to complex type definitions and element declarations). An abstract element or complex type cannot used to validate an element instance. If there is a reference to an abstract element, only element declarations that can substitute the abstract element can be used to validate the instance. For references to abstract type definitions, only derived types can be used.

All Model Group Child elements can be provided in any order in instances. See: http://www.w3.org/TR/xmlschema-1/#element-all.

Choice Model Group Only one from the list of child elements and model groups can be provided in instances. See: http://www.w3.org/TR/xmlschema-1/#element-choice.

Collapse Whitespace Policy Replace tab, line feed, and carriage return characters with space character (Unicode character 32). Then, collapse contiguous sequences of space characters into single space character, and remove leading and trailing space characters.

Disallowed Substitutions (Applies to element declarations). If substitution is specified, then substitution group members cannot be used in place of the given element declaration to validate element instances. If derivation methods, e.g. extension, restriction, are specified, then the given element declaration will not validate element instances that have types derived from the element declaration's type using the specified derivation methods. Normally, element instances can override their declaration's type by specifying an xsi:type attribute.

Key Constraint Like Uniqueness Constraint, but additionally requires that the specified value(s) must be provided. See: http://www.w3.org/TR/xmlschema-1/#cIdentity-constraint_Definitions.

Key Reference Constraint Ensures that the specified value(s) must match value(s) from a Key Constraint or Uniqueness Constraint. See: http://www.w3.org/TR/xmlschema-1/#cIdentity-constraint_Definitions.

Model Group Groups together element content, specifying the order in which the element content can occur and the number of times the group of element content may be repeated. See: http://www.w3.org/TR/xmlschema-1/#Model_Groups.

Nillable (Applies to element declarations). If an element declaration is nillable, instances can use the xsi:nil attribute. The xsi:nil attribute is the boolean attribute, nil, from the http://www.w3.org/2001/XMLSchema-instance namespace. If an element instance has an xsi:nil attribute set to true, it can be left empty, even though its element declaration may have required content.

Notation A notation is used to identify the format of a piece of data. Values of elements and attributes that are of type, NOTATION, must come from the names of declared notations. See: http://www.w3.org/TR/xmlschema-1/#cNotation_Declarations.

Preserve Whitespace Policy Preserve whitespaces exactly as they appear in instances.

Prohibited Derivations (Applies to type definitions). Derivation methods that cannot be used to create sub-types from a given type definition.

Prohibited Substitutions (Applies to complex type definitions). Prevents sub-types that have been derived using the specified derivation methods from validating element instances in place of the given type definition.

Replace Whitespace Policy Replace tab, line feed, and carriage return characters with space character (Unicode character 32).

Sequence Model Group Child elements and model groups must be provided in the specified order in instances. See: http://www.w3.org/TR/xmlschema-1/#element-sequence.

Substitution Group Elements that are members of a substitution group can be used wherever the head element of the substitution group is referenced.

Substitution Group Exclusions (Applies to element declarations). Prohibits element declarations from nominating themselves as being able to substitute a given element declaration, if they have types that are derived from the original element's type using the specified derivation methods.

Target Namespace The target namespace identifies the namespace that components in this schema belongs to. If no target namespace is provided, then the schema components do not belong to any namespace.

Uniqueness Constraint Ensures uniqueness of an element/attribute value, or a combination of values, within a specified scope. See: http://www.w3.org/TR/xmlschema-1/#cIdentity-constraint_Definitions.

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Generated by <oXygen/> XML Editor using a modified version of xs3p that adds schema diagrams and chunking support. Last modified: