Documentation for phyloXML 1.00

Table of Contents

top

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 phylogenies and associated data. Version: 1.00. License: LGPL. Copyright (c) 2008-2009 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>
top

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 "/>
top

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>
top

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>
top

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>
top

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>
top

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>
top

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>
top

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>
top

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>
top

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').
XML Instance Representation
<...
unit=" xs:token [0..1]"
range=" xs:decimal [0..1]">
<phy:desc> xs:token </phy:desc> [0..1]
<phy:value> xs:decimal </phy:value> [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:sequence>
<xs:attribute name="unit" type=" xs:token "/>
<xs:attribute name="range" type=" xs:decimal "/>
</xs:complexType>
top

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>
top

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