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: