phyloXML 1.10

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.
Documentation phyloXML is an XML language to describe evolutionary trees and associated data. Version: 1.10. License: dual-licensed under the LGPL or Ruby's License. Copyright (c) 2008-2011 Christian M Zmasek.

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: Accession

Super-types: xs:token < Accession (by extension)
Sub-types: None
Name Accession
Used by (from the same schema document) Complex Type Sequence
Abstract no
Documentation Element Accession is used to capture the local part in a sequence identifier (e.g. 'P17304' in 'UniProtKB:P17304', in which case the 'source' attribute would be 'UniProtKB').
XML Instance Representation
<...
source=" xs:token [1]">
xs:token
</...>
Diagram
Schema Component Representation
<xs:complexType name="Accession">
<xs:simpleContent>
<xs:extension base=" xs:token ">
<xs:attribute name="source" type=" xs:token " use="required"/>
</xs:extension>
</xs:simpleContent>
</xs:complexType>
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Complex Type: Annotation

Super-types: None
Sub-types: None
Name Annotation
Used by (from the same schema document) Complex Type Sequence
Abstract no
Documentation The annotation of a molecular sequence. It is recommended to annotate by using the optional 'ref' attribute (some examples of acceptable values for the ref attribute: 'GO:0008270', 'KEGG:Tetrachloroethene degradation', 'EC:1.1.1.1'). Optional element 'desc' allows for a free text description. Optional element 'confidence' is used to state the type and value of support for a annotation. Similarly, optional attribute 'evidence' is used to describe the evidence for a annotation as free text (e.g. 'experimental'). Optional element 'property' allows for further, typed and referenced annotations from external resources.
XML Instance Representation
<...
ref=" phy:ref [0..1]"
source=" xs:token [0..1]"
evidence=" xs:token [0..1]"
type=" xs:token [0..1]">
<phy:desc> xs:token </phy:desc> [0..1]
<phy:confidence> phy:Confidence </phy:confidence> [0..1]
<phy:property> phy:Property </phy:property> [0..*]
<phy:uri> phy:Uri </phy:uri> [0..1]
</...>
Diagram
h-993584945 h158033242 h-676012345 h-675984882
Schema Component Representation
<xs:complexType name="Annotation">
<xs:sequence>
<xs:element name="desc" type=" xs:token " minOccurs="0"/>
<xs:element name="confidence" type=" phy:Confidence " minOccurs="0"/>
<xs:element name="property" type=" phy:Property " minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="uri" type=" phy:Uri " minOccurs="0"/>
</xs:sequence>
<xs:attribute name="ref" type=" phy:ref "/>
<xs:attribute name="source" type=" xs:token "/>
<xs:attribute name="evidence" type=" xs:token "/>
<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
Documentation The names and/or counts of binary characters present, gained, and lost at the root of a clade.
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
Documentation This indicates the color of a clade when rendered (the color applies to the whole clade unless overwritten by the color(s) of sub clades).
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
Documentation Element Clade is used in a recursive manner to describe the topology of a phylogenetic tree. The parent branch length of a clade can be described either with the 'branch_length' element or the 'branch_length' attribute (it is not recommended to use both at the same time, though). Usage of the 'branch_length' attribute allows for a less verbose description. Element 'confidence' is used to indicate the support for a clade/parent branch. Element 'events' is used to describe such events as gene-duplications at the root node/parent branch of a clade. Element 'width' is the branch width for this clade (including parent branch). Both 'color' and 'width' elements apply for the whole clade unless overwritten in-sub clades. Attribute 'id_source' is used to link other elements to a clade (on the xml-level).
XML Instance Representation
<...
branch_length=" xs:double [0..1]"
id_source=" phy:id_source [0..1]">
<phy:name> xs:token </phy:name> [0..1]
<phy:branch_length> xs:double </phy:branch_length> [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:events> phy:Events </phy:events> [0..1]
<phy:binary_characters> phy:BinaryCharacters </phy:binary_characters> [0..1]
<phy:distribution> phy:Distribution </phy:distribution> [0..*]
<phy:date> phy:Date </phy:date> [0..1]
<phy:reference> phy:Reference </phy:reference> [0..*]
<phy:property> phy:Property </phy:property> [0..*]
<phy:clade> phy:Clade </phy:clade> [0..*]
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-436501026 h-1514309680 h-979596407 h517931443 h401516646 h158033242 h-1482113798
Schema Component Representation
<xs:complexType name="Clade">
<xs:sequence>
<xs:element name="name" type=" xs:token " minOccurs="0"/>
<xs:element name="branch_length" 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="events" type=" phy:Events " minOccurs="0"/>
<xs:element name="binary_characters" type=" phy:BinaryCharacters " minOccurs="0"/>
<xs:element name="distribution" type=" phy:Distribution " minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="date" type=" phy:Date " minOccurs="0"/>
<xs:element name="reference" type=" phy:Reference " minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="property" type=" phy:Property " minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="clade" type=" phy:Clade " minOccurs="0" maxOccurs="unbounded"/>
<xs:any minOccurs="0" maxOccurs="unbounded" processContents="lax" namespace="##other"/>
</xs:sequence>
<xs:attribute name="branch_length" 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
Documentation This is used to express a typed relationship between two clades. For example it could be used to describe multiple parents of a clade.
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 Events , Complex Type Annotation , Complex Type SequenceRelation , Complex Type CladeRelation
Abstract no
Documentation A general purpose confidence element. For example this can be used to express the bootstrap support value of a clade (in which case the 'type' attribute is 'bootstrap').
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: Date

Super-types: None
Sub-types: None
Name Date
Used by (from the same schema document) Complex Type Clade
Abstract no
Documentation A date associated with a clade/node. Its value can be numerical by using the 'value' element and/or free text with the 'desc' element' (e.g. 'Silurian'). If a numerical value is used, it is recommended to employ the 'unit' attribute to indicate the type of the numerical value (e.g. 'mya' for 'million years ago'). The elements 'minimum' and 'maximum' are used the indicate a range/confidence interval
XML Instance Representation
<...
unit=" xs:token [0..1]">
<phy:desc> xs:token </phy:desc> [0..1]
<phy:value> xs:decimal </phy:value> [0..1]
<phy:minimum> xs:decimal </phy:minimum> [0..1]
<phy:maximum> xs:decimal </phy:maximum> [0..1]
</...>
Diagram
Schema Component Representation
<xs:complexType name="Date">
<xs:sequence>
<xs:element name="desc" type=" xs:token " minOccurs="0"/>
<xs:element name="value" type=" xs:decimal " minOccurs="0"/>
<xs:element name="minimum" type=" xs:decimal " minOccurs="0"/>
<xs:element name="maximum" type=" xs:decimal " minOccurs="0"/>
</xs:sequence>
<xs:attribute name="unit" type=" xs:token "/>
</xs:complexType>
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Complex Type: Distribution

Super-types: None
Sub-types: None
Name Distribution
Used by (from the same schema document) Complex Type Clade
Abstract no
Documentation The geographic distribution of the items of a clade (species, sequences), intended for phylogeographic applications. The location can be described either by free text in the 'desc' element and/or by the coordinates of one or more 'Points' (similar to the 'Point' element in Google's KML format) or by 'Polygons'.
XML Instance Representation
<...>
<phy:desc> xs:token </phy:desc> [0..1]
<phy:point> phy:Point </phy:point> [0..*]
<phy:polygon> phy:Polygon </phy:polygon> [0..*]
</...>
Diagram
h-1112505301 h332351765
Schema Component Representation
<xs:complexType name="Distribution">
<xs:sequence>
<xs:element name="desc" type=" xs:token " minOccurs="0"/>
<xs:element name="point" type=" phy:Point " minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="polygon" type=" phy:Polygon " minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</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
Documentation This is used describe the domain architecture of a protein. Attribute 'length' is the total length of the protein
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: Events

Super-types: None
Sub-types: None
Name Events
Used by (from the same schema document) Complex Type Clade
Abstract no
Documentation Events at the root node of a clade (e.g. one gene duplication).
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="Events">
<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
Abstract no
Documentation A general purpose identifier element. Allows to indicate the provider (or authority) of an identifier.
XML Instance Representation
<...
provider=" xs:token [0..1]">
xs:token
</...>
Diagram
Schema Component Representation
<xs:complexType name="Id">
<xs:simpleContent>
<xs:extension base=" xs:token ">
<xs:attribute name="provider" type=" xs:token "/>
</xs:extension>
</xs:simpleContent>
</xs:complexType>
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Complex Type: MolSeq

Super-types: xs:token < MolSeq (by extension)
Sub-types: None
Name MolSeq
Used by (from the same schema document) Complex Type Sequence
Abstract no
Documentation Element 'mol_seq' is used to store molecular sequences. The 'is_aligned' attribute is used to indicated that this molecular sequence is aligned with all other sequences in the same phylogeny for which 'is aligned' is true as well (which, in most cases, means that gaps were introduced, and that all sequences for which 'is aligned' is true must have the same length).
XML Instance Representation
<...
is_aligned=" xs:boolean [0..1]">
xs:token
</...>
Diagram
Schema Component Representation
<xs:complexType name="MolSeq">
<xs:simpleContent>
<xs:extension base=" xs:token ">
<xs:attribute name="is_aligned" type=" xs:boolean "/>
</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
Documentation Element Phylogeny is used to represent a phylogeny. The required attribute 'rooted' is used to indicate whether the phylogeny is rooted or not. The attribute 'rerootable' can be used to indicate that the phylogeny is not allowed to be rooted differently (i.e. because it is associated with root dependent data, such as gene duplications). The attribute 'type' can be used to indicate the type of phylogeny (i.e. 'gene tree'). It is recommended to use the attribute 'branch_length_unit' if the phylogeny has branch lengths. Element clade is used in a recursive manner to describe the topology of a phylogenetic tree.
XML Instance Representation
<...
rooted=" xs:boolean [1]"
rerootable=" xs:boolean [0..1]"
branch_length_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:property> phy:Property </phy:property> [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 h158033242
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="property" type=" phy:Property " 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="branch_length_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
Documentation 'phyloxml' is the name of the root element. Phyloxml contains an arbitrary number of 'phylogeny' elements (each representing one phylogeny) possibly followed by elements from other namespaces.
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: Point

Super-types: None
Sub-types: None
Name Point
Used by (from the same schema document) Complex Type Distribution , Complex Type Polygon
Abstract no
Documentation The coordinates of a point with an optional altitude (used by element 'Distribution'). Required attributes are the 'geodetic_datum' used to indicate the geodetic datum (also called 'map datum', for example Google's KML uses 'WGS84'). Attribute 'alt_unit' is the unit for the altitude (e.g. 'meter').
XML Instance Representation
<...
geodetic_datum=" xs:token [1]"
alt_unit=" xs:token [0..1]">
<phy:lat> xs:decimal </phy:lat> [1]
<phy:long> xs:decimal </phy:long> [1]
<phy:alt> xs:decimal </phy:alt> [0..1]
</...>
Diagram
Schema Component Representation
<xs:complexType name="Point">
<xs:sequence>
<xs:element name="lat" type=" xs:decimal "/>
<xs:element name="long" type=" xs:decimal "/>
<xs:element name="alt" type=" xs:decimal " minOccurs="0"/>
</xs:sequence>
<xs:attribute name="geodetic_datum" type=" xs:token " use="required"/>
<xs:attribute name="alt_unit" type=" xs:token "/>
</xs:complexType>
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Complex Type: Polygon

Super-types: None
Sub-types: None
Name Polygon
Used by (from the same schema document) Complex Type Distribution
Abstract no
Documentation A polygon defined by a list of 'Points' (used by element 'Distribution').
XML Instance Representation
<...>
<phy:point> phy:Point </phy:point> [3..*]
</...>
Diagram
h-1112505301
Schema Component Representation
<xs:complexType name="Polygon">
<xs:sequence>
<xs:element name="point" type=" phy:Point " minOccurs="3" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
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Complex Type: Property

Super-types: None
Sub-types: None
Name Property
Used by (from the same schema document) Complex Type Phylogeny , Complex Type Clade , Complex Type Annotation
Abstract no
Documentation Property allows for typed and referenced properties from external resources to be attached to 'Phylogeny', 'Clade', and 'Annotation'. The value of a property is its mixed (free text) content. Attribute 'datatype' indicates the type of a property and is limited to xsd-datatypes (e.g. 'xsd:string', 'xsd:boolean', 'xsd:integer', 'xsd:decimal', 'xsd:float', 'xsd:double', 'xsd:date', 'xsd:anyURI'). Attribute 'applies_to' indicates the item to which a property applies to (e.g. 'node' for the parent node of a clade, 'parent_branch' for the parent branch of a clade). Attribute 'id_ref' allows to attached a property specifically to one element (on the xml-level). Optional attribute 'unit' is used to indicate the unit of the property. An example: <property datatype="xsd:integer" ref="NOAA:depth" applies_to="clade" unit="METRIC:m"> 200 </property>
XML Instance Representation
<...
ref=" phy:ref [1]"
unit=" phy:ref [0..1]"
datatype=" phy:PropertyDataType [1]"
applies_to=" phy:AppliesTo [1]"
id_ref=" phy:id_ref [0..1]"/>
Diagram
h-675984882 h-675984882 h-54338178 h-763252414 h577349652
Schema Component Representation
<xs:complexType name="Property" mixed="true">
<xs:attribute name="ref" type=" phy:ref " use="required"/>
<xs:attribute name="unit" type=" phy:ref "/>
<xs:attribute name="datatype" type=" phy:PropertyDataType " use="required"/>
<xs:attribute name="applies_to" type=" phy:AppliesTo " use="required"/>
<xs:attribute name="id_ref" type=" phy:id_ref "/>
</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
Documentation To represent an individual domain in a domain architecture. The name/unique identifier is described via the 'id' attribute. 'confidence' can be used to store (i.e.) E-values.
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: Reference

Super-types: None
Sub-types: None
Name Reference
Used by (from the same schema document) Complex Type Clade
Abstract no
Documentation A literature reference for a clade. It is recommended to use the 'doi' attribute instead of the free text 'desc' element whenever possible.
XML Instance Representation
<...
doi=" xs:token [0..1]">
<phy:desc> xs:token </phy:desc> [0..1]
</...>
Diagram
Schema Component Representation
<xs:complexType name="Reference">
<xs:sequence>
<xs:element name="desc" type=" xs:token " minOccurs="0"/>
</xs:sequence>
<xs:attribute name="doi" type=" xs:token "/>
</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
Documentation Element Sequence is used to represent a molecular sequence (Protein, DNA, RNA) associated with a node. 'symbol' is a short (maximal ten characters) symbol of the sequence (e.g. 'ACTM') whereas 'name' is used for the full name (e.g. 'muscle Actin'). 'location' is used for the location of a sequence on a genome/chromosome. The actual sequence can be stored with the 'mol_seq' element. Attribute 'type' is used to indicate the type of sequence ('dna', 'rna', or 'protein'). One intended use for 'id_ref' is to link a sequence to a taxonomy (via the taxonomy's 'id_source') in case of multiple sequences and taxonomies per node.
XML Instance Representation
<...
type=" phy:SequenceType [0..1]"
id_source=" phy:id_source [0..1]"
id_ref=" phy:id_ref [0..1]">
<phy:symbol> phy:SequenceSymbol </phy:symbol> [0..1]
<phy:accession> phy:Accession </phy:accession> [0..1]
<phy:name> xs:token </phy: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
h935679102 h-788356801 h-213750342 h-676012345 h917087604 h259010940 h1408823200 h-1482113798 h577349652
Schema Component Representation
<xs:complexType name="Sequence">
<xs:sequence>
<xs:element name="symbol" type=" phy:SequenceSymbol " minOccurs="0"/>
<xs:element name="accession" type=" phy:Accession " minOccurs="0"/>
<xs:element name="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="type" type=" phy:SequenceType "/>
<xs:attribute name="id_source" type=" phy:id_source "/>
<xs:attribute name="id_ref" type=" phy:id_ref "/>
</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
Documentation This is used to express a typed relationship between two sequences. For example it could be used to describe an orthology (in which case attribute 'type' is 'orthology').
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
Documentation Element Taxonomy is used to describe taxonomic information for a clade. Element 'code' is intended to store UniProt/Swiss-Prot style organism codes (e.g. 'APLCA' for the California sea hare 'Aplysia californica') or other styles of mnemonics (e.g. 'Aca'). Element 'authority' is used to keep the authority, such as 'J. G. Cooper, 1863', associated with the 'scientific_name'. Element 'id' is used for a unique identifier of a taxon (for example '6500' with 'ncbi_taxonomy' as 'provider' for the California sea hare). Attribute 'id_source' is used to link other elements to a taxonomy (on the xml-level).
XML Instance Representation
<...
id_source=" phy:id_source [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:authority> xs:token </phy:authority> [0..1]
<phy:common_name> xs:token </phy:common_name> [0..*]
<phy:synonym> xs:token </phy:synonym> [0..*]
<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 h-1482113798
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="authority" type=" xs:token " minOccurs="0"/>
<xs:element name="common_name" type=" xs:token " minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="synonym" type=" xs:token " minOccurs="0" maxOccurs="unbounded"/>
<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="id_source" type=" phy:id_source "/>
</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
Documentation A uniform resource identifier. In general, this is expected to be an URL (for example, to link to an image on a website, in which case the 'type' attribute might be 'image' and 'desc' might be 'image of a California sea hare').
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: AppliesTo

Super-types: xs:token < AppliesTo (by restriction)
Sub-types: None
Name AppliesTo
Used by (from the same schema document) Complex Type Property
Content
  • Base XSD Type: token
  • value comes from list: {'phylogeny'|'clade'|'node'|'annotation'|'parent_branch'|'other'}
Diagram
Schema Component Representation
<xs:simpleType name="AppliesTo">
<xs:restriction base=" xs:token ">
<xs:enumeration value="phylogeny"/>
<xs:enumeration value="clade"/>
<xs:enumeration value="node"/>
<xs:enumeration value="annotation"/>
<xs:enumeration value="parent_branch"/>
<xs:enumeration value="other"/>
</xs:restriction>
</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 Events
Content
  • Base XSD Type: token
  • value comes from list: {'transfer'|'fusion'|'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="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: PropertyDataType

Super-types: xs:token < PropertyDataType (by restriction)
Sub-types: None
Name PropertyDataType
Used by (from the same schema document) Complex Type Property
Content
  • Base XSD Type: token
  • value comes from list: {'xsd:string'|'xsd:boolean'|'xsd:decimal'|'xsd:float'|'xsd:double'|'xsd:duration'|'xsd:dateTime'|'xsd:time'|'xsd:date'|'xsd:gYearMonth'|'xsd:gYear'|'xsd:gMonthDay'|'xsd:gDay'|'xsd:gMonth'|'xsd:hexBinary'|'xsd:base64Binary'|'xsd:anyURI'|'xsd:normalizedString'|'xsd:token'|'xsd:integer'|'xsd:nonPositiveInteger'|'xsd:negativeInteger'|'xsd:long'|'xsd:int'|'xsd:short'|'xsd:byte'|'xsd:nonNegativeInteger'|'xsd:unsignedLong'|'xsd:unsignedInt'|'xsd:unsignedShort'|'xsd:unsignedByte'|'xsd:positiveInteger'}
Diagram
Schema Component Representation
<xs:simpleType name="PropertyDataType">
<xs:restriction base=" xs:token ">
<xs:enumeration value="xsd:string"/>
<xs:enumeration value="xsd:boolean"/>
<xs:enumeration value="xsd:decimal"/>
<xs:enumeration value="xsd:float"/>
<xs:enumeration value="xsd:double"/>
<xs:enumeration value="xsd:duration"/>
<xs:enumeration value="xsd:dateTime"/>
<xs:enumeration value="xsd:time"/>
<xs:enumeration value="xsd:date"/>
<xs:enumeration value="xsd:gYearMonth"/>
<xs:enumeration value="xsd:gYear"/>
<xs:enumeration value="xsd:gMonthDay"/>
<xs:enumeration value="xsd:gDay"/>
<xs:enumeration value="xsd:gMonth"/>
<xs:enumeration value="xsd:hexBinary"/>
<xs:enumeration value="xsd:base64Binary"/>
<xs:enumeration value="xsd:anyURI"/>
<xs:enumeration value="xsd:normalizedString"/>
<xs:enumeration value="xsd:token"/>
<xs:enumeration value="xsd:integer"/>
<xs:enumeration value="xsd:nonPositiveInteger"/>
<xs:enumeration value="xsd:negativeInteger"/>
<xs:enumeration value="xsd:long"/>
<xs:enumeration value="xsd:int"/>
<xs:enumeration value="xsd:short"/>
<xs:enumeration value="xsd:byte"/>
<xs:enumeration value="xsd:nonNegativeInteger"/>
<xs:enumeration value="xsd:unsignedLong"/>
<xs:enumeration value="xsd:unsignedInt"/>
<xs:enumeration value="xsd:unsignedShort"/>
<xs:enumeration value="xsd:unsignedByte"/>
<xs:enumeration value="xsd:positiveInteger"/>
</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'|'superkingdom'|'kingdom'|'subkingdom'|'branch'|'infrakingdom'|'superphylum'|'phylum'|'subphylum'|'infraphylum'|'microphylum'|'superdivision'|'division'|'subdivision'|'infradivision'|'superclass'|'class'|'subclass'|'infraclass'|'superlegion'|'legion'|'sublegion'|'infralegion'|'supercohort'|'cohort'|'subcohort'|'infracohort'|'superorder'|'order'|'suborder'|'superfamily'|'family'|'subfamily'|'supertribe'|'tribe'|'subtribe'|'infratribe'|'genus'|'subgenus'|'superspecies'|'species'|'subspecies'|'variety'|'subvariety'|'form'|'subform'|'cultivar'|'strain'|'unknown'|'other'}
Diagram
Schema Component Representation
<xs:simpleType name="Rank">
<xs:restriction base=" xs:token ">
<xs:enumeration value="domain"/>
<xs:enumeration value="superkingdom"/>
<xs:enumeration value="kingdom"/>
<xs:enumeration value="subkingdom"/>
<xs:enumeration value="branch"/>
<xs:enumeration value="infrakingdom"/>
<xs:enumeration value="superphylum"/>
<xs:enumeration value="phylum"/>
<xs:enumeration value="subphylum"/>
<xs:enumeration value="infraphylum"/>
<xs:enumeration value="microphylum"/>
<xs:enumeration value="superdivision"/>
<xs:enumeration value="division"/>
<xs:enumeration value="subdivision"/>
<xs:enumeration value="infradivision"/>
<xs:enumeration value="superclass"/>
<xs:enumeration value="class"/>
<xs:enumeration value="subclass"/>
<xs:enumeration value="infraclass"/>
<xs:enumeration value="superlegion"/>
<xs:enumeration value="legion"/>
<xs:enumeration value="sublegion"/>
<xs:enumeration value="infralegion"/>
<xs:enumeration value="supercohort"/>
<xs:enumeration value="cohort"/>
<xs:enumeration value="subcohort"/>
<xs:enumeration value="infracohort"/>
<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="supertribe"/>
<xs:enumeration value="tribe"/>
<xs:enumeration value="subtribe"/>
<xs:enumeration value="infratribe"/>
<xs:enumeration value="genus"/>
<xs:enumeration value="subgenus"/>
<xs:enumeration value="superspecies"/>
<xs:enumeration value="species"/>
<xs:enumeration value="subspecies"/>
<xs:enumeration value="variety"/>
<xs:enumeration value="subvariety"/>
<xs:enumeration value="form"/>
<xs:enumeration value="subform"/>
<xs:enumeration value="cultivar"/>
<xs:enumeration value="strain"/>
<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: SequenceSymbol

Super-types: xs:token < SequenceSymbol (by restriction)
Sub-types: None
Name SequenceSymbol
Used by (from the same schema document) Complex Type Sequence
Content
  • Base XSD Type: token
  • pattern = \S{1,20}
Diagram
Schema Component Representation
<xs:simpleType name="SequenceSymbol">
<xs:restriction base=" xs:token ">
<xs:pattern value="\S{1,20}"/>
</xs:restriction>
</xs:simpleType>
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Simple Type: SequenceType

Super-types: xs:token < SequenceType (by restriction)
Sub-types: None
Name SequenceType
Used by (from the same schema document) Complex Type Sequence
Content
  • Base XSD Type: token
  • value comes from list: {'rna'|'dna'|'protein'}
Diagram
Schema Component Representation
<xs:simpleType name="SequenceType">
<xs:restriction base=" xs:token ">
<xs:enumeration value="rna"/>
<xs:enumeration value="dna"/>
<xs:enumeration value="protein"/>
</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_]{2,10}
Diagram
Schema Component Representation
<xs:simpleType name="TaxonomyCode">
<xs:restriction base=" xs:token ">
<xs:pattern value="[a-zA-Z0-9_]{2,10}"/>
</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 Sequence , Complex Type Property , 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 Taxonomy , 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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Simple Type: ref

Super-types: xs:token < ref (by restriction)
Sub-types: None
Name ref
Used by (from the same schema document) Complex Type Annotation , Complex Type Property , Complex Type Property
Content
  • Base XSD Type: token
  • pattern = [a-zA-Z0-9_]+:[a-zA-Z0-9_\.\-\s]+
Diagram
Schema Component Representation
<xs:simpleType name="ref">
<xs:restriction base=" xs:token ">
<xs:pattern value="[a-zA-Z0-9_]+:[a-zA-Z0-9_\.\-\s]+"/>
</xs:restriction>
</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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