From: cmzmasek Date: Fri, 15 Jul 2016 17:53:51 +0000 (-0700) Subject: v1.20 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e98e95cf04f54612516fea4dd1494d105a86ee19;p=jalview.git v1.20 --- diff --git a/forester/phyloxml/oxygen/phyloxml_to_html_xslt.xml b/forester/phyloxml/accessories/phyloxml_to_html_xslt.xml similarity index 100% rename from forester/phyloxml/oxygen/phyloxml_to_html_xslt.xml rename to forester/phyloxml/accessories/phyloxml_to_html_xslt.xml diff --git a/forester/phyloxml/docs/version_1.20/docHtml.css b/forester/phyloxml/docs/version_1.20/docHtml.css new file mode 100644 index 0000000..969603e --- /dev/null +++ b/forester/phyloxml/docs/version_1.20/docHtml.css @@ -0,0 +1,605 @@ +/*---------------------------------------- + Global +-----------------------------------------*/ + +body{ +} +body, table { + font-family:arial, helvetica, sans-serif; + font-size:12px; +} + +@media print{ + body, table { + font-size:10px; + } +} + +/*-------------------------------------------- + Source code in the instance, source or + annotations. +--------------------------------------------*/ +span.tEl { + color: #000096; + background-color:inherit; +} +span.tXSLEl { + color: #0064C8; + background-color:inherit; +} +span.tAN { + color: #F5844C; + background-color:inherit; +} +span.tAV { + color: #993300; + background-color:inherit; +} +span.tI { + color: #000000; + background-color:inherit; +} +span.tT { + color: #000000; + background-color:inherit; +} +span.tC { + color: #006400; + background-color:inherit; +} +span.tCD { + color: #008C00; + background-color:inherit; +} +span.tPI { + color: #8B26C9; + background-color:inherit; +} +span.tEn { + color: #969600; + background-color:inherit; +} +span.qname{ + color:#000096; + background-color:inherit; +} + +/*----------------------------------------- + Documentation sections. +------------------------------------------*/ + +div.componentTitle, p.sHierarchyTitle { + font-size:1.4em; + font-weight:bold; + text-align:left; + margin-top:1.4em; + margin-bottom:0.7em; +} +div.componentTitle{ +/* color:rgb(255, 160, 100);*/ + color:#333333; + background-color:inherit; 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phyloxml.xsd

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http://www.phyloxml.org

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Showing:

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Annotations
Attributes
Diagrams
Facets
Instances
Model
Properties
Source
Used by
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Main schema phyloxml.xsd
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Namespacehttp://www.phyloxml.org
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Annotations
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phyloXML is an XML language to describe evolutionary trees and associated
+data. Version: 1.20. License: dual-licensed under the LGPL or Ruby's License. Copyright (c)
+2008-2016 Christian M Zmasek.
+
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Properties
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attribute form defaultunqualified
element form defaultqualified
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Element phy:phyloxml
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Namespacehttp://www.phyloxml.org
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Diagram
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Diagram + phyloxml_xsd.tmp#http___www.phyloxml.org_Phyloxml_phylogeny + phyloxml_xsd.tmp#http___www.phyloxml.org_Phyloxml
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Typephy:Phyloxml
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Properties
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contentcomplex
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Model
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phy:phylogeny* , ANY element from ANY namespace OTHER than 'http://www.phyloxml.org'
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Childrenphy:phylogeny
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Instance
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<phy:phyloxml xmlns:phy="http://www.phyloxml.org">
+  <phy:phylogeny branch_length_unit="" rerootable="" rooted="" type="">{0,unbounded}</phy:phylogeny>
+</phy:phyloxml>
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Source
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<xs:element name="phyloxml" type="phy:Phyloxml"/>
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Element phy:Phyloxml / phy:phylogeny
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Namespacehttp://www.phyloxml.org
+
Diagram
+
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+
Diagram + phyloxml_xsd.tmp#Phylogeny_rooted + phyloxml_xsd.tmp#Phylogeny_rerootable + phyloxml_xsd.tmp#Phylogeny_branch_length_unit + phyloxml_xsd.tmp#Phylogeny_type + phyloxml_xsd.tmp#Phylogeny_name + phyloxml_xsd.tmp#Phylogeny_id + phyloxml_xsd.tmp#Phylogeny_description + phyloxml_xsd.tmp#Phylogeny_date + phyloxml_xsd.tmp#Phylogeny_confidence + phyloxml_xsd.tmp#Phylogeny_clade + phyloxml_xsd.tmp#Phylogeny_clade_relation + phyloxml_xsd.tmp#Phylogeny_sequence_relation + phyloxml_xsd.tmp#Phylogeny_property + phyloxml_xsd.tmp#Phylogeny
+
Typephy:Phylogeny
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Properties
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contentcomplex
minOccurs0
maxOccursunbounded
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Model
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phy:name{0,1} , phy:id{0,1} , phy:description{0,1} , phy:date{0,1} , phy:confidence* , phy:clade{0,1} , phy:clade_relation* , phy:sequence_relation* , phy:property* , ANY element from ANY namespace OTHER than 'http://www.phyloxml.org'
+
Childrenphy:clade, phy:clade_relation, phy:confidence, phy:date, phy:description, phy:id, phy:name, phy:property, phy:sequence_relation
+
Instance
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<phy:phylogeny branch_length_unit="" rerootable="" rooted="" type="" xmlns:phy="http://www.phyloxml.org">
+  <phy:name>{0,1}</phy:name>
+  <phy:id provider="">{0,1}</phy:id>
+  <phy:description>{0,1}</phy:description>
+  <phy:date>{0,1}</phy:date>
+  <phy:confidence stddev="" type="">{0,unbounded}</phy:confidence>
+  <phy:clade branch_length="" collapse="" id_source="">{0,1}</phy:clade>
+  <phy:clade_relation distance="" id_ref_0="" id_ref_1="" type="">{0,unbounded}</phy:clade_relation>
+  <phy:sequence_relation distance="" id_ref_0="" id_ref_1="" type="">{0,unbounded}</phy:sequence_relation>
+  <phy:property applies_to="" datatype="" id_ref="" ref="" unit="">{0,unbounded}</phy:property>
+</phy:phylogeny>
+
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Attributes
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QNameTypeUse
branch_length_unitxs:tokenoptional +
+
rerootablexs:booleanoptional +
+
rootedxs:booleanrequired +
+
typexs:tokenoptional +
+
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Source
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<xs:element name="phylogeny" type="phy:Phylogeny" minOccurs="0" maxOccurs="unbounded"/>
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Element phy:Phylogeny / phy:name
+ + + + + + + + + + + + + + + + +
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Namespacehttp://www.phyloxml.org
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Diagram
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Diagram
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Typexs:token
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Properties
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contentsimple
minOccurs0
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Source
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<xs:element name="name" type="xs:token" minOccurs="0"/>
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Element phy:Phylogeny / phy:id
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Namespacehttp://www.phyloxml.org
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Diagram
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Diagram + phyloxml_xsd.tmp#Id_provider + phyloxml_xsd.tmp#Id
+
Typephy:Id
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Properties
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contentcomplex
minOccurs0
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Attributes
+
+
+
+ + + + + + + + + + + + + + + +
QNameTypeUse
providerxs:tokenoptional +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="id" type="phy:Id" minOccurs="0"/>
+
+
+
Element phy:Phylogeny / phy:description
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram
+
Typexs:token
+
Properties
+
+
+
+ + + + + + + + + +
contentsimple
minOccurs0
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="description" type="xs:token" minOccurs="0"/>
+
+
+
Element phy:Phylogeny / phy:date
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram
+
Typexs:dateTime
+
Properties
+
+
+
+ + + + + + + + + +
contentsimple
minOccurs0
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="date" type="xs:dateTime" minOccurs="0"/>
+
+
+
Element phy:Phylogeny / phy:confidence
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#Confidence_type + phyloxml_xsd.tmp#Confidence_stddev + phyloxml_xsd.tmp#Confidence
+
Typephy:Confidence
+
Properties
+
+
+
+ + + + + + + + + + + + + +
contentcomplex
minOccurs0
maxOccursunbounded
+
+
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + + + + + + + +
QNameTypeUse
stddevxs:doubleoptional +
+
typexs:tokenrequired +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="confidence" type="phy:Confidence" minOccurs="0" maxOccurs="unbounded"/>
+
+
+
Element phy:Phylogeny / phy:clade
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#NO_NAMESPACE_Clade_branch_length + phyloxml_xsd.tmp#Clade_id_source + phyloxml_xsd.tmp#Clade_collapse + phyloxml_xsd.tmp#Clade_name + phyloxml_xsd.tmp#Clade_branch_length + phyloxml_xsd.tmp#Clade_confidence + phyloxml_xsd.tmp#Clade_width + phyloxml_xsd.tmp#Clade_color + phyloxml_xsd.tmp#Clade_taxonomy + phyloxml_xsd.tmp#Clade_sequence + phyloxml_xsd.tmp#Clade_events + phyloxml_xsd.tmp#Clade_binary_characters + phyloxml_xsd.tmp#Clade_distribution + phyloxml_xsd.tmp#Clade_date + phyloxml_xsd.tmp#Clade_reference + phyloxml_xsd.tmp#Clade_property + phyloxml_xsd.tmp#Clade_clade + phyloxml_xsd.tmp#Clade
+
Typephy:Clade
+
Properties
+
+
+
+ + + + + + + + + +
contentcomplex
minOccurs0
+
+
Model
+
+ +
Childrenphy:binary_characters, phy:branch_length, phy:clade, phy:color, phy:confidence, phy:date, phy:distribution, phy:events, phy:name, phy:property, phy:reference, phy:sequence, phy:taxonomy, phy:width
+
Instance
+
+
+
+ + + + +
<phy:clade branch_length="" collapse="" id_source="" xmlns:phy="http://www.phyloxml.org">
+  <phy:name>{0,1}</phy:name>
+  <phy:branch_length>{0,1}</phy:branch_length>
+  <phy:confidence stddev="" type="">{0,unbounded}</phy:confidence>
+  <phy:width>{0,1}</phy:width>
+  <phy:color>{0,1}</phy:color>
+  <phy:taxonomy id_source="">{0,unbounded}</phy:taxonomy>
+  <phy:sequence id_ref="" id_source="" type="">{0,unbounded}</phy:sequence>
+  <phy:events>{0,1}</phy:events>
+  <phy:binary_characters absent_count="" gained_count="" lost_count="" present_count="" type="">{0,1}</phy:binary_characters>
+  <phy:distribution>{0,unbounded}</phy:distribution>
+  <phy:date unit="">{0,1}</phy:date>
+  <phy:reference doi="">{0,unbounded}</phy:reference>
+  <phy:property applies_to="" datatype="" id_ref="" ref="" unit="">{0,unbounded}</phy:property>
+  <phy:clade branch_length="" collapse="" id_source="">{0,unbounded}</phy:clade>
+</phy:clade>
+
+
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeUse
branch_lengthxs:doubleoptional +
+
collapsexs:booleanoptional +
+
id_sourcephy:id_sourceoptional +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="clade" type="phy:Clade" minOccurs="0"/>
+
+
+
Element phy:Clade / phy:name
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram
+
Typexs:token
+
Properties
+
+
+
+ + + + + + + + + +
contentsimple
minOccurs0
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="name" type="xs:token" minOccurs="0"/>
+
+
+
Element phy:Clade / phy:branch_length
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram
+
Typexs:double
+
Properties
+
+
+
+ + + + + + + + + +
contentsimple
minOccurs0
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="branch_length" type="xs:double" minOccurs="0"/>
+
+
+
Element phy:Clade / phy:confidence
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#Confidence_type + phyloxml_xsd.tmp#Confidence_stddev + phyloxml_xsd.tmp#Confidence
+
Typephy:Confidence
+
Properties
+
+
+
+ + + + + + + + + + + + + +
contentcomplex
minOccurs0
maxOccursunbounded
+
+
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + + + + + + + +
QNameTypeUse
stddevxs:doubleoptional +
+
typexs:tokenrequired +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="confidence" type="phy:Confidence" minOccurs="0" maxOccurs="unbounded"/>
+
+
+
Element phy:Clade / phy:width
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram
+
Typexs:double
+
Properties
+
+
+
+ + + + + + + + + +
contentsimple
minOccurs0
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="width" type="xs:double" minOccurs="0"/>
+
+
+
Element phy:Clade / phy:color
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#BranchColor_red + phyloxml_xsd.tmp#BranchColor_green + phyloxml_xsd.tmp#BranchColor_blue + phyloxml_xsd.tmp#BranchColor_alpha + phyloxml_xsd.tmp#BranchColor
+
Typephy:BranchColor
+
Properties
+
+
+
+ + + + + + + + + +
contentcomplex
minOccurs0
+
+
Model
+
+ +
Childrenphy:alpha, phy:blue, phy:green, phy:red
+
Instance
+
+
+
+ + + + +
<phy:color xmlns:phy="http://www.phyloxml.org">
+  <phy:red>{1,1}</phy:red>
+  <phy:green>{1,1}</phy:green>
+  <phy:blue>{1,1}</phy:blue>
+  <phy:alpha>{0,1}</phy:alpha>
+</phy:color>
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="color" type="phy:BranchColor" minOccurs="0"/>
+
+
+
Element phy:BranchColor / phy:red
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram
+
Typexs:unsignedByte
+
Properties
+
+
+
+ + + + + +
contentsimple
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="red" type="xs:unsignedByte"/>
+
+
+
Element phy:BranchColor / phy:green
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram
+
Typexs:unsignedByte
+
Properties
+
+
+
+ + + + + +
contentsimple
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="green" type="xs:unsignedByte"/>
+
+
+
Element phy:BranchColor / phy:blue
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram
+
Typexs:unsignedByte
+
Properties
+
+
+
+ + + + + +
contentsimple
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="blue" type="xs:unsignedByte"/>
+
+
+
Element phy:BranchColor / phy:alpha
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram
+
Typexs:unsignedByte
+
Properties
+
+
+
+ + + + + + + + + +
contentsimple
minOccurs0
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="alpha" type="xs:unsignedByte" minOccurs="0"/>
+
+
+
Element phy:Clade / phy:taxonomy
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#Taxonomy_id_source + phyloxml_xsd.tmp#Taxonomy_id + phyloxml_xsd.tmp#Taxonomy_code + phyloxml_xsd.tmp#Taxonomy_scientific_name + phyloxml_xsd.tmp#Taxonomy_authority + phyloxml_xsd.tmp#Taxonomy_common_name + phyloxml_xsd.tmp#Taxonomy_synonym + phyloxml_xsd.tmp#Taxonomy_rank + phyloxml_xsd.tmp#Taxonomy_uri + phyloxml_xsd.tmp#Taxonomy
+
Typephy:Taxonomy
+
Properties
+
+
+
+ + + + + + + + + + + + + +
contentcomplex
minOccurs0
maxOccursunbounded
+
+
Model
+
+
phy:id{0,1} , phy:code{0,1} , phy:scientific_name{0,1} , phy:authority{0,1} , phy:common_name{0,1} , phy:synonym* , phy:rank{0,1} , phy:uri* , ANY element from ANY namespace OTHER than 'http://www.phyloxml.org'
+
Childrenphy:authority, phy:code, phy:common_name, phy:id, phy:rank, phy:scientific_name, phy:synonym, phy:uri
+
Instance
+
+
+
+ + + + +
<phy:taxonomy id_source="" xmlns:phy="http://www.phyloxml.org">
+  <phy:id provider="">{0,1}</phy:id>
+  <phy:code>{0,1}</phy:code>
+  <phy:scientific_name>{0,1}</phy:scientific_name>
+  <phy:authority>{0,1}</phy:authority>
+  <phy:common_name>{0,1}</phy:common_name>
+  <phy:synonym>{0,unbounded}</phy:synonym>
+  <phy:rank>{0,1}</phy:rank>
+  <phy:uri desc="" type="">{0,unbounded}</phy:uri>
+</phy:taxonomy>
+
+
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + +
QNameTypeUse
id_sourcephy:id_sourceoptional +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="taxonomy" type="phy:Taxonomy" minOccurs="0" maxOccurs="unbounded"/>
+
+
+
Element phy:Taxonomy / phy:id
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#Id_provider + phyloxml_xsd.tmp#Id
+
Typephy:Id
+
Properties
+
+
+
+ + + + + + + + + +
contentcomplex
minOccurs0
+
+
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + +
QNameTypeUse
providerxs:tokenoptional +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="id" type="phy:Id" minOccurs="0"/>
+
+
+
Element phy:Taxonomy / phy:code
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#TaxonomyCode
+
Typephy:TaxonomyCode
+
Properties
+
+
+
+ + + + + + + + + +
contentsimple
minOccurs0
+
+
+
Facets
+
+
+
+ + + + + + +
pattern([A-Z9][A-Z]{2}[A-Z0-9]{2})|RAT|PIG|PEA +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="code" type="phy:TaxonomyCode" minOccurs="0"/>
+
+
+
Element phy:Taxonomy / phy:scientific_name
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram
+
Typexs:token
+
Properties
+
+
+
+ + + + + + + + + +
contentsimple
minOccurs0
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="scientific_name" type="xs:token" minOccurs="0"/>
+
+
+
Element phy:Taxonomy / phy:authority
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram
+
Typexs:token
+
Properties
+
+
+
+ + + + + + + + + +
contentsimple
minOccurs0
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="authority" type="xs:token" minOccurs="0"/>
+
+
+
Element phy:Taxonomy / phy:common_name
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram
+
Typexs:token
+
Properties
+
+
+
+ + + + + + + + + +
contentsimple
minOccurs0
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="common_name" type="xs:token" minOccurs="0"/>
+
+
+
Element phy:Taxonomy / phy:synonym
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram
+
Typexs:token
+
Properties
+
+
+
+ + + + + + + + + + + + + +
contentsimple
minOccurs0
maxOccursunbounded
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="synonym" type="xs:token" minOccurs="0" maxOccurs="unbounded"/>
+
+
+
Element phy:Taxonomy / phy:rank
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#Rank
+
Typephy:Rank
+
Properties
+
+
+
+ + + + + + + + + +
contentsimple
minOccurs0
+
+
+
Facets
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
enumerationdomain +
+
enumerationsuperkingdom +
+
enumerationkingdom +
+
enumerationsubkingdom +
+
enumerationbranch +
+
enumerationinfrakingdom +
+
enumerationsuperphylum +
+
enumerationphylum +
+
enumerationsubphylum +
+
enumerationinfraphylum +
+
enumerationmicrophylum +
+
enumerationsuperdivision +
+
enumerationdivision +
+
enumerationsubdivision +
+
enumerationinfradivision +
+
enumerationsuperclass +
+
enumerationclass +
+
enumerationsubclass +
+
enumerationinfraclass +
+
enumerationsuperlegion +
+
enumerationlegion +
+
enumerationsublegion +
+
enumerationinfralegion +
+
enumerationsupercohort +
+
enumerationcohort +
+
enumerationsubcohort +
+
enumerationinfracohort +
+
enumerationmagnorder +
+
enumerationsuperorder +
+
enumerationorder +
+
enumerationsuborder +
+
enumerationinfraorder +
+
enumerationsuperfamily +
+
enumerationfamily +
+
enumerationsubfamily +
+
enumerationsupertribe +
+
enumerationtribe +
+
enumerationsubtribe +
+
enumerationinfratribe +
+
enumerationgenus +
+
enumerationsubgenus +
+
enumerationsuperspecies +
+
enumerationspecies +
+
enumerationsubspecies +
+
enumerationvariety +
+
enumerationvarietas +
+
enumerationsubvariety +
+
enumerationform +
+
enumerationsubform +
+
enumerationcultivar +
+
enumerationstrain +
+
enumerationsection +
+
enumerationsubsection +
+
enumerationunknown +
+
enumerationother +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="rank" type="phy:Rank" minOccurs="0"/>
+
+
+
Element phy:Taxonomy / phy:uri
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#Uri_desc + phyloxml_xsd.tmp#Uri_type + phyloxml_xsd.tmp#Uri
+
Typephy:Uri
+
Properties
+
+
+
+ + + + + + + + + + + + + +
contentcomplex
minOccurs0
maxOccursunbounded
+
+
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + + + + + + + +
QNameTypeUse
descxs:tokenoptional +
+
typexs:tokenoptional +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="uri" type="phy:Uri" minOccurs="0" maxOccurs="unbounded"/>
+
+
+
Element phy:Clade / phy:sequence
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#Sequence_type + phyloxml_xsd.tmp#Sequence_id_source + phyloxml_xsd.tmp#Sequence_id_ref + phyloxml_xsd.tmp#Sequence_symbol + phyloxml_xsd.tmp#Sequence_accession + phyloxml_xsd.tmp#Sequence_name + phyloxml_xsd.tmp#Sequence_gene_name + phyloxml_xsd.tmp#Sequence_location + phyloxml_xsd.tmp#Sequence_mol_seq + phyloxml_xsd.tmp#Sequence_uri + phyloxml_xsd.tmp#Sequence_annotation + phyloxml_xsd.tmp#Sequence_cross_references + phyloxml_xsd.tmp#Sequence_domain_architecture + phyloxml_xsd.tmp#Sequence
+
Typephy:Sequence
+
Properties
+
+
+
+ + + + + + + + + + + + + +
contentcomplex
minOccurs0
maxOccursunbounded
+
+
Model
+
+ +
Childrenphy:accession, phy:annotation, phy:cross_references, phy:domain_architecture, phy:gene_name, phy:location, phy:mol_seq, phy:name, phy:symbol, phy:uri
+
Instance
+
+
+
+ + + + +
<phy:sequence id_ref="" id_source="" type="" xmlns:phy="http://www.phyloxml.org">
+  <phy:symbol>{0,1}</phy:symbol>
+  <phy:accession comment="" source="">{0,1}</phy:accession>
+  <phy:name>{0,1}</phy:name>
+  <phy:gene_name>{0,1}</phy:gene_name>
+  <phy:location>{0,1}</phy:location>
+  <phy:mol_seq is_aligned="">{0,1}</phy:mol_seq>
+  <phy:uri desc="" type="">{0,unbounded}</phy:uri>
+  <phy:annotation evidence="" ref="" source="" type="">{0,unbounded}</phy:annotation>
+  <phy:cross_references>{0,1}</phy:cross_references>
+  <phy:domain_architecture length="">{0,1}</phy:domain_architecture>
+</phy:sequence>
+
+
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeUse
id_refphy:id_refoptional +
+
id_sourcephy:id_sourceoptional +
+
typephy:SequenceTypeoptional +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="sequence" type="phy:Sequence" minOccurs="0" maxOccurs="unbounded"/>
+
+
+
Element phy:Sequence / phy:symbol
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#SequenceSymbol
+
Typephy:SequenceSymbol
+
Properties
+
+
+
+ + + + + + + + + +
contentsimple
minOccurs0
+
+
+
Facets
+
+
+
+ + + + + + +
pattern\S{1,20} +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="symbol" type="phy:SequenceSymbol" minOccurs="0"/>
+
+
+
Element phy:Sequence / phy:accession
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#Accession_source + phyloxml_xsd.tmp#Accession_comment + phyloxml_xsd.tmp#Accession
+
Typephy:Accession
+
Properties
+
+
+
+ + + + + + + + + +
contentcomplex
minOccurs0
+
+
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + + + + + + + +
QNameTypeUse
commentxs:tokenoptional +
+
sourcexs:tokenrequired +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="accession" type="phy:Accession" minOccurs="0"/>
+
+
+
Element phy:Sequence / phy:name
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram
+
Typexs:token
+
Properties
+
+
+
+ + + + + + + + + +
contentsimple
minOccurs0
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="name" type="xs:token" minOccurs="0"/>
+
+
+
Element phy:Sequence / phy:gene_name
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram
+
Typexs:token
+
Properties
+
+
+
+ + + + + + + + + +
contentsimple
minOccurs0
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="gene_name" type="xs:token" minOccurs="0"/>
+
+
+
Element phy:Sequence / phy:location
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram
+
Typexs:token
+
Properties
+
+
+
+ + + + + + + + + +
contentsimple
minOccurs0
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="location" type="xs:token" minOccurs="0"/>
+
+
+
Element phy:Sequence / phy:mol_seq
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#MolSeq_is_aligned + phyloxml_xsd.tmp#MolSeq
+
Typephy:MolSeq
+
Properties
+
+
+
+ + + + + + + + + +
contentcomplex
minOccurs0
+
+
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + +
QNameTypeUse
is_alignedxs:booleanoptional +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="mol_seq" type="phy:MolSeq" minOccurs="0"/>
+
+
+
Element phy:Sequence / phy:uri
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#Uri_desc + phyloxml_xsd.tmp#Uri_type + phyloxml_xsd.tmp#Uri
+
Typephy:Uri
+
Properties
+
+
+
+ + + + + + + + + + + + + +
contentcomplex
minOccurs0
maxOccursunbounded
+
+
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + + + + + + + +
QNameTypeUse
descxs:tokenoptional +
+
typexs:tokenoptional +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="uri" type="phy:Uri" minOccurs="0" maxOccurs="unbounded"/>
+
+
+
Element phy:Sequence / phy:annotation
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#Annotation_ref + phyloxml_xsd.tmp#Annotation_source + phyloxml_xsd.tmp#Annotation_evidence + phyloxml_xsd.tmp#Annotation_type + phyloxml_xsd.tmp#Annotation_desc + phyloxml_xsd.tmp#Annotation_confidence + phyloxml_xsd.tmp#Annotation_property + phyloxml_xsd.tmp#Annotation_uri + phyloxml_xsd.tmp#Annotation
+
Typephy:Annotation
+
Properties
+
+
+
+ + + + + + + + + + + + + +
contentcomplex
minOccurs0
maxOccursunbounded
+
+
Model
+
+ +
Childrenphy:confidence, phy:desc, phy:property, phy:uri
+
Instance
+
+
+
+ + + + +
<phy:annotation evidence="" ref="" source="" type="" xmlns:phy="http://www.phyloxml.org">
+  <phy:desc>{0,1}</phy:desc>
+  <phy:confidence stddev="" type="">{0,1}</phy:confidence>
+  <phy:property applies_to="" datatype="" id_ref="" ref="" unit="">{0,unbounded}</phy:property>
+  <phy:uri desc="" type="">{0,unbounded}</phy:uri>
+</phy:annotation>
+
+
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeUse
evidencexs:tokenoptional +
+
refphy:refoptional +
+
sourcexs:tokenoptional +
+
typexs:tokenoptional +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="annotation" type="phy:Annotation" minOccurs="0" maxOccurs="unbounded"/>
+
+
+
Element phy:Annotation / phy:desc
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram
+
Typexs:token
+
Properties
+
+
+
+ + + + + + + + + +
contentsimple
minOccurs0
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="desc" type="xs:token" minOccurs="0"/>
+
+
+
Element phy:Annotation / phy:confidence
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#Confidence_type + phyloxml_xsd.tmp#Confidence_stddev + phyloxml_xsd.tmp#Confidence
+
Typephy:Confidence
+
Properties
+
+
+
+ + + + + + + + + +
contentcomplex
minOccurs0
+
+
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + + + + + + + +
QNameTypeUse
stddevxs:doubleoptional +
+
typexs:tokenrequired +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="confidence" type="phy:Confidence" minOccurs="0"/>
+
+
+
Element phy:Annotation / phy:property
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#Property_ref + phyloxml_xsd.tmp#Property_unit + phyloxml_xsd.tmp#Property_datatype + phyloxml_xsd.tmp#Property_applies_to + phyloxml_xsd.tmp#Property_id_ref + phyloxml_xsd.tmp#Property
+
Typephy:Property
+
Properties
+
+
+
+ + + + + + + + + + + + + + + + + +
contentcomplex
minOccurs0
maxOccursunbounded
mixedtrue
+
+
Model
+
+
+
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeUse
applies_tophy:AppliesTorequired +
+
datatypephy:PropertyDataTyperequired +
+
id_refphy:id_refoptional +
+
refphy:refrequired +
+
unitphy:refoptional +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="property" type="phy:Property" minOccurs="0" maxOccurs="unbounded"/>
+
+
+
Element phy:Annotation / phy:uri
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#Uri_desc + phyloxml_xsd.tmp#Uri_type + phyloxml_xsd.tmp#Uri
+
Typephy:Uri
+
Properties
+
+
+
+ + + + + + + + + + + + + +
contentcomplex
minOccurs0
maxOccursunbounded
+
+
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + + + + + + + +
QNameTypeUse
descxs:tokenoptional +
+
typexs:tokenoptional +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="uri" type="phy:Uri" minOccurs="0" maxOccurs="unbounded"/>
+
+
+
Element phy:Sequence / phy:cross_references
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#CrossReferences_accession + phyloxml_xsd.tmp#CrossReferences
+
Typephy:CrossReferences
+
Properties
+
+
+
+ + + + + + + + + +
contentcomplex
minOccurs0
+
+
Model
+
+ +
Childrenphy:accession
+
Instance
+
+
+
+ + + + +
<phy:cross_references xmlns:phy="http://www.phyloxml.org">
+  <phy:accession comment="" source="">{1,unbounded}</phy:accession>
+</phy:cross_references>
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="cross_references" type="phy:CrossReferences" minOccurs="0"/>
+
+
+
Element phy:CrossReferences / phy:accession
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#Accession_source + phyloxml_xsd.tmp#Accession_comment + phyloxml_xsd.tmp#Accession
+
Typephy:Accession
+
Properties
+
+
+
+ + + + + + + + + + + + + +
contentcomplex
minOccurs1
maxOccursunbounded
+
+
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + + + + + + + +
QNameTypeUse
commentxs:tokenoptional +
+
sourcexs:tokenrequired +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="accession" type="phy:Accession" minOccurs="1" maxOccurs="unbounded"/>
+
+
+
Element phy:Sequence / phy:domain_architecture
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#DomainArchitecture_length + phyloxml_xsd.tmp#DomainArchitecture_domain + phyloxml_xsd.tmp#DomainArchitecture
+
Typephy:DomainArchitecture
+
Properties
+
+
+
+ + + + + + + + + +
contentcomplex
minOccurs0
+
+
Model
+
+ +
Childrenphy:domain
+
Instance
+
+
+
+ + + + +
<phy:domain_architecture length="" xmlns:phy="http://www.phyloxml.org">
+  <phy:domain confidence="" from="" id="" to="">{1,unbounded}</phy:domain>
+</phy:domain_architecture>
+
+
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + +
QNameTypeUse
lengthxs:nonNegativeIntegeroptional +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="domain_architecture" type="phy:DomainArchitecture" minOccurs="0"/>
+
+
+
Element phy:DomainArchitecture / phy:domain
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#ProteinDomain_from + phyloxml_xsd.tmp#ProteinDomain_to + phyloxml_xsd.tmp#ProteinDomain_confidence + phyloxml_xsd.tmp#ProteinDomain_id + phyloxml_xsd.tmp#ProteinDomain
+
Typephy:ProteinDomain
+
Properties
+
+
+
+ + + + + + + + + + + + + +
contentcomplex
minOccurs1
maxOccursunbounded
+
+
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeUse
confidencexs:doubleoptional +
+
fromxs:nonNegativeIntegerrequired +
+
idxs:tokenoptional +
+
toxs:nonNegativeIntegerrequired +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="domain" type="phy:ProteinDomain" minOccurs="1" maxOccurs="unbounded"/>
+
+
+
Element phy:Clade / phy:events
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#Events_type + phyloxml_xsd.tmp#Events_duplications + phyloxml_xsd.tmp#Events_speciations + phyloxml_xsd.tmp#Events_losses + phyloxml_xsd.tmp#Events_confidence + phyloxml_xsd.tmp#Events
+
Typephy:Events
+
Properties
+
+
+
+ + + + + + + + + +
contentcomplex
minOccurs0
+
+
Model
+
+ +
Childrenphy:confidence, phy:duplications, phy:losses, phy:speciations, phy:type
+
Instance
+
+
+
+ + + + +
<phy:events xmlns:phy="http://www.phyloxml.org">
+  <phy:type>{0,1}</phy:type>
+  <phy:duplications>{0,1}</phy:duplications>
+  <phy:speciations>{0,1}</phy:speciations>
+  <phy:losses>{0,1}</phy:losses>
+  <phy:confidence stddev="" type="">{0,1}</phy:confidence>
+</phy:events>
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="events" type="phy:Events" minOccurs="0"/>
+
+
+
Element phy:Events / phy:type
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#EventType
+
Typephy:EventType
+
Properties
+
+
+
+ + + + + + + + + +
contentsimple
minOccurs0
+
+
+
Facets
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
enumerationtransfer +
+
enumerationfusion +
+
enumerationspeciation_or_duplication +
+
enumerationother +
+
enumerationmixed +
+
enumerationunassigned +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="type" type="phy:EventType" minOccurs="0"/>
+
+
+
Element phy:Events / phy:duplications
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram
+
Typexs:nonNegativeInteger
+
Properties
+
+
+
+ + + + + + + + + +
contentsimple
minOccurs0
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="duplications" type="xs:nonNegativeInteger" minOccurs="0"/>
+
+
+
Element phy:Events / phy:speciations
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram
+
Typexs:nonNegativeInteger
+
Properties
+
+
+
+ + + + + + + + + +
contentsimple
minOccurs0
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="speciations" type="xs:nonNegativeInteger" minOccurs="0"/>
+
+
+
Element phy:Events / phy:losses
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram
+
Typexs:nonNegativeInteger
+
Properties
+
+
+
+ + + + + + + + + +
contentsimple
minOccurs0
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="losses" type="xs:nonNegativeInteger" minOccurs="0"/>
+
+
+
Element phy:Events / phy:confidence
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#Confidence_type + phyloxml_xsd.tmp#Confidence_stddev + phyloxml_xsd.tmp#Confidence
+
Typephy:Confidence
+
Properties
+
+
+
+ + + + + + + + + +
contentcomplex
minOccurs0
+
+
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + + + + + + + +
QNameTypeUse
stddevxs:doubleoptional +
+
typexs:tokenrequired +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="confidence" type="phy:Confidence" minOccurs="0"/>
+
+
+
Element phy:Clade / phy:binary_characters
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#BinaryCharacters_type + phyloxml_xsd.tmp#BinaryCharacters_gained_count + phyloxml_xsd.tmp#BinaryCharacters_lost_count + phyloxml_xsd.tmp#BinaryCharacters_present_count + phyloxml_xsd.tmp#BinaryCharacters_absent_count + phyloxml_xsd.tmp#BinaryCharacters_gained + phyloxml_xsd.tmp#BinaryCharacters_lost + phyloxml_xsd.tmp#BinaryCharacters_present + phyloxml_xsd.tmp#BinaryCharacters_absent + phyloxml_xsd.tmp#BinaryCharacters
+
Typephy:BinaryCharacters
+
Properties
+
+
+
+ + + + + + + + + +
contentcomplex
minOccurs0
+
+
Model
+
+ +
Childrenphy:absent, phy:gained, phy:lost, phy:present
+
Instance
+
+
+
+ + + + +
<phy:binary_characters absent_count="" gained_count="" lost_count="" present_count="" type="" xmlns:phy="http://www.phyloxml.org">
+  <phy:gained>{0,1}</phy:gained>
+  <phy:lost>{0,1}</phy:lost>
+  <phy:present>{0,1}</phy:present>
+  <phy:absent>{0,1}</phy:absent>
+</phy:binary_characters>
+
+
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeUse
absent_countxs:nonNegativeIntegeroptional +
+
gained_countxs:nonNegativeIntegeroptional +
+
lost_countxs:nonNegativeIntegeroptional +
+
present_countxs:nonNegativeIntegeroptional +
+
typexs:tokenoptional +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="binary_characters" type="phy:BinaryCharacters" minOccurs="0"/>
+
+
+
Element phy:BinaryCharacters / phy:gained
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#BinaryCharacterList_bc + phyloxml_xsd.tmp#BinaryCharacterList
+
Typephy:BinaryCharacterList
+
Properties
+
+
+
+ + + + + + + + + +
contentcomplex
minOccurs0
+
+
Model
+
+ +
Childrenphy:bc
+
Instance
+
+
+
+ + + + +
<phy:gained xmlns:phy="http://www.phyloxml.org">
+  <phy:bc>{1,unbounded}</phy:bc>
+</phy:gained>
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="gained" type="phy:BinaryCharacterList" minOccurs="0"/>
+
+
+
Element phy:BinaryCharacterList / phy:bc
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram
+
Typexs:token
+
Properties
+
+
+
+ + + + + + + + + +
contentsimple
maxOccursunbounded
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="bc" type="xs:token" maxOccurs="unbounded"/>
+
+
+
Element phy:BinaryCharacters / phy:lost
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#BinaryCharacterList_bc + phyloxml_xsd.tmp#BinaryCharacterList
+
Typephy:BinaryCharacterList
+
Properties
+
+
+
+ + + + + + + + + +
contentcomplex
minOccurs0
+
+
Model
+
+ +
Childrenphy:bc
+
Instance
+
+
+
+ + + + +
<phy:lost xmlns:phy="http://www.phyloxml.org">
+  <phy:bc>{1,unbounded}</phy:bc>
+</phy:lost>
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="lost" type="phy:BinaryCharacterList" minOccurs="0"/>
+
+
+
Element phy:BinaryCharacters / phy:present
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#BinaryCharacterList_bc + phyloxml_xsd.tmp#BinaryCharacterList
+
Typephy:BinaryCharacterList
+
Properties
+
+
+
+ + + + + + + + + +
contentcomplex
minOccurs0
+
+
Model
+
+ +
Childrenphy:bc
+
Instance
+
+
+
+ + + + +
<phy:present xmlns:phy="http://www.phyloxml.org">
+  <phy:bc>{1,unbounded}</phy:bc>
+</phy:present>
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="present" type="phy:BinaryCharacterList" minOccurs="0"/>
+
+
+
Element phy:BinaryCharacters / phy:absent
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#BinaryCharacterList_bc + phyloxml_xsd.tmp#BinaryCharacterList
+
Typephy:BinaryCharacterList
+
Properties
+
+
+
+ + + + + + + + + +
contentcomplex
minOccurs0
+
+
Model
+
+ +
Childrenphy:bc
+
Instance
+
+
+
+ + + + +
<phy:absent xmlns:phy="http://www.phyloxml.org">
+  <phy:bc>{1,unbounded}</phy:bc>
+</phy:absent>
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="absent" type="phy:BinaryCharacterList" minOccurs="0"/>
+
+
+
Element phy:Clade / phy:distribution
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#Distribution_desc + phyloxml_xsd.tmp#Distribution_point + phyloxml_xsd.tmp#Distribution_polygon + phyloxml_xsd.tmp#Distribution
+
Typephy:Distribution
+
Properties
+
+
+
+ + + + + + + + + + + + + +
contentcomplex
minOccurs0
maxOccursunbounded
+
+
Model
+
+ +
Childrenphy:desc, phy:point, phy:polygon
+
Instance
+
+
+
+ + + + +
<phy:distribution xmlns:phy="http://www.phyloxml.org">
+  <phy:desc>{0,1}</phy:desc>
+  <phy:point alt_unit="" geodetic_datum="">{0,unbounded}</phy:point>
+  <phy:polygon>{0,unbounded}</phy:polygon>
+</phy:distribution>
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="distribution" type="phy:Distribution" minOccurs="0" maxOccurs="unbounded"/>
+
+
+
Element phy:Distribution / phy:desc
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram
+
Typexs:token
+
Properties
+
+
+
+ + + + + + + + + +
contentsimple
minOccurs0
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="desc" type="xs:token" minOccurs="0"/>
+
+
+
Element phy:Distribution / phy:point
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#Point_geodetic_datum + phyloxml_xsd.tmp#Point_alt_unit + phyloxml_xsd.tmp#Point_lat + phyloxml_xsd.tmp#Point_long + phyloxml_xsd.tmp#Point_alt + phyloxml_xsd.tmp#Point
+
Typephy:Point
+
Properties
+
+
+
+ + + + + + + + + + + + + +
contentcomplex
minOccurs0
maxOccursunbounded
+
+
Model
+
+ +
Childrenphy:alt, phy:lat, phy:long
+
Instance
+
+
+
+ + + + +
<phy:point alt_unit="" geodetic_datum="" xmlns:phy="http://www.phyloxml.org">
+  <phy:lat>{1,1}</phy:lat>
+  <phy:long>{1,1}</phy:long>
+  <phy:alt>{0,1}</phy:alt>
+</phy:point>
+
+
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + + + + + + + +
QNameTypeUse
alt_unitxs:tokenoptional +
+
geodetic_datumxs:tokenrequired +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="point" type="phy:Point" minOccurs="0" maxOccurs="unbounded"/>
+
+
+
Element phy:Point / phy:lat
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram
+
Typexs:decimal
+
Properties
+
+
+
+ + + + + +
contentsimple
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="lat" type="xs:decimal"/>
+
+
+
Element phy:Point / phy:long
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram
+
Typexs:decimal
+
Properties
+
+
+
+ + + + + +
contentsimple
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="long" type="xs:decimal"/>
+
+
+
Element phy:Point / phy:alt
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram
+
Typexs:decimal
+
Properties
+
+
+
+ + + + + + + + + +
contentsimple
minOccurs0
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="alt" type="xs:decimal" minOccurs="0"/>
+
+
+
Element phy:Distribution / phy:polygon
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#Polygon_point + phyloxml_xsd.tmp#Polygon
+
Typephy:Polygon
+
Properties
+
+
+
+ + + + + + + + + + + + + +
contentcomplex
minOccurs0
maxOccursunbounded
+
+
Model
+
+ +
Childrenphy:point
+
Instance
+
+
+
+ + + + +
<phy:polygon xmlns:phy="http://www.phyloxml.org">
+  <phy:point alt_unit="" geodetic_datum="">{3,unbounded}</phy:point>
+</phy:polygon>
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="polygon" type="phy:Polygon" minOccurs="0" maxOccurs="unbounded"/>
+
+
+
Element phy:Polygon / phy:point
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#Point_geodetic_datum + phyloxml_xsd.tmp#Point_alt_unit + phyloxml_xsd.tmp#Point_lat + phyloxml_xsd.tmp#Point_long + phyloxml_xsd.tmp#Point_alt + phyloxml_xsd.tmp#Point
+
Typephy:Point
+
Properties
+
+
+
+ + + + + + + + + + + + + +
contentcomplex
minOccurs3
maxOccursunbounded
+
+
Model
+
+ +
Childrenphy:alt, phy:lat, phy:long
+
Instance
+
+
+
+ + + + +
<phy:point alt_unit="" geodetic_datum="" xmlns:phy="http://www.phyloxml.org">
+  <phy:lat>{1,1}</phy:lat>
+  <phy:long>{1,1}</phy:long>
+  <phy:alt>{0,1}</phy:alt>
+</phy:point>
+
+
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + + + + + + + +
QNameTypeUse
alt_unitxs:tokenoptional +
+
geodetic_datumxs:tokenrequired +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="point" type="phy:Point" minOccurs="3" maxOccurs="unbounded"/>
+
+
+
Element phy:Clade / phy:date
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#Date_unit + phyloxml_xsd.tmp#Date_desc + phyloxml_xsd.tmp#Date_value + phyloxml_xsd.tmp#Date_minimum + phyloxml_xsd.tmp#Date_maximum + phyloxml_xsd.tmp#Date
+
Typephy:Date
+
Properties
+
+
+
+ + + + + + + + + +
contentcomplex
minOccurs0
+
+
Model
+
+ +
Childrenphy:desc, phy:maximum, phy:minimum, phy:value
+
Instance
+
+
+
+ + + + +
<phy:date unit="" xmlns:phy="http://www.phyloxml.org">
+  <phy:desc>{0,1}</phy:desc>
+  <phy:value>{0,1}</phy:value>
+  <phy:minimum>{0,1}</phy:minimum>
+  <phy:maximum>{0,1}</phy:maximum>
+</phy:date>
+
+
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + +
QNameTypeUse
unitxs:tokenoptional +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="date" type="phy:Date" minOccurs="0"/>
+
+
+
Element phy:Date / phy:desc
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram
+
Typexs:token
+
Properties
+
+
+
+ + + + + + + + + +
contentsimple
minOccurs0
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="desc" type="xs:token" minOccurs="0"/>
+
+
+
Element phy:Date / phy:value
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram
+
Typexs:decimal
+
Properties
+
+
+
+ + + + + + + + + +
contentsimple
minOccurs0
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="value" type="xs:decimal" minOccurs="0"/>
+
+
+
Element phy:Date / phy:minimum
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram
+
Typexs:decimal
+
Properties
+
+
+
+ + + + + + + + + +
contentsimple
minOccurs0
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="minimum" type="xs:decimal" minOccurs="0"/>
+
+
+
Element phy:Date / phy:maximum
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram
+
Typexs:decimal
+
Properties
+
+
+
+ + + + + + + + + +
contentsimple
minOccurs0
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="maximum" type="xs:decimal" minOccurs="0"/>
+
+
+
Element phy:Clade / phy:reference
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#Reference_doi + phyloxml_xsd.tmp#Reference_desc + phyloxml_xsd.tmp#Reference
+
Typephy:Reference
+
Properties
+
+
+
+ + + + + + + + + + + + + +
contentcomplex
minOccurs0
maxOccursunbounded
+
+
Model
+
+ +
Childrenphy:desc
+
Instance
+
+
+
+ + + + +
<phy:reference doi="" xmlns:phy="http://www.phyloxml.org">
+  <phy:desc>{0,1}</phy:desc>
+</phy:reference>
+
+
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + +
QNameTypeUse
doixs:tokenoptional +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="reference" type="phy:Reference" minOccurs="0" maxOccurs="unbounded"/>
+
+
+
Element phy:Reference / phy:desc
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram
+
Typexs:token
+
Properties
+
+
+
+ + + + + + + + + +
contentsimple
minOccurs0
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="desc" type="xs:token" minOccurs="0"/>
+
+
+
Element phy:Clade / phy:property
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#Property_ref + phyloxml_xsd.tmp#Property_unit + phyloxml_xsd.tmp#Property_datatype + phyloxml_xsd.tmp#Property_applies_to + phyloxml_xsd.tmp#Property_id_ref + phyloxml_xsd.tmp#Property
+
Typephy:Property
+
Properties
+
+
+
+ + + + + + + + + + + + + + + + + +
contentcomplex
minOccurs0
maxOccursunbounded
mixedtrue
+
+
Model
+
+
+
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeUse
applies_tophy:AppliesTorequired +
+
datatypephy:PropertyDataTyperequired +
+
id_refphy:id_refoptional +
+
refphy:refrequired +
+
unitphy:refoptional +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="property" type="phy:Property" minOccurs="0" maxOccurs="unbounded"/>
+
+
+
Element phy:Clade / phy:clade
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#NO_NAMESPACE_Clade_branch_length + phyloxml_xsd.tmp#Clade_id_source + phyloxml_xsd.tmp#Clade_collapse + phyloxml_xsd.tmp#Clade_name + phyloxml_xsd.tmp#Clade_branch_length + phyloxml_xsd.tmp#Clade_confidence + phyloxml_xsd.tmp#Clade_width + phyloxml_xsd.tmp#Clade_color + phyloxml_xsd.tmp#Clade_taxonomy + phyloxml_xsd.tmp#Clade_sequence + phyloxml_xsd.tmp#Clade_events + phyloxml_xsd.tmp#Clade_binary_characters + phyloxml_xsd.tmp#Clade_distribution + phyloxml_xsd.tmp#Clade_date + phyloxml_xsd.tmp#Clade_reference + phyloxml_xsd.tmp#Clade_property + phyloxml_xsd.tmp#Clade_clade + phyloxml_xsd.tmp#Clade
+
Typephy:Clade
+
Properties
+
+
+
+ + + + + + + + + + + + + +
contentcomplex
minOccurs0
maxOccursunbounded
+
+
Model
+
+ +
Childrenphy:binary_characters, phy:branch_length, phy:clade, phy:color, phy:confidence, phy:date, phy:distribution, phy:events, phy:name, phy:property, phy:reference, phy:sequence, phy:taxonomy, phy:width
+
Instance
+
+
+
+ + + + +
<phy:clade branch_length="" collapse="" id_source="" xmlns:phy="http://www.phyloxml.org">
+  <phy:name>{0,1}</phy:name>
+  <phy:branch_length>{0,1}</phy:branch_length>
+  <phy:confidence stddev="" type="">{0,unbounded}</phy:confidence>
+  <phy:width>{0,1}</phy:width>
+  <phy:color>{0,1}</phy:color>
+  <phy:taxonomy id_source="">{0,unbounded}</phy:taxonomy>
+  <phy:sequence id_ref="" id_source="" type="">{0,unbounded}</phy:sequence>
+  <phy:events>{0,1}</phy:events>
+  <phy:binary_characters absent_count="" gained_count="" lost_count="" present_count="" type="">{0,1}</phy:binary_characters>
+  <phy:distribution>{0,unbounded}</phy:distribution>
+  <phy:date unit="">{0,1}</phy:date>
+  <phy:reference doi="">{0,unbounded}</phy:reference>
+  <phy:property applies_to="" datatype="" id_ref="" ref="" unit="">{0,unbounded}</phy:property>
+  <phy:clade branch_length="" collapse="" id_source="">{0,unbounded}</phy:clade>
+</phy:clade>
+
+
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeUse
branch_lengthxs:doubleoptional +
+
collapsexs:booleanoptional +
+
id_sourcephy:id_sourceoptional +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="clade" type="phy:Clade" minOccurs="0" maxOccurs="unbounded"/>
+
+
+
Element phy:Phylogeny / phy:clade_relation
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#CladeRelation_id_ref_0 + phyloxml_xsd.tmp#CladeRelation_id_ref_1 + phyloxml_xsd.tmp#CladeRelation_distance + phyloxml_xsd.tmp#CladeRelation_type + phyloxml_xsd.tmp#CladeRelation_confidence + phyloxml_xsd.tmp#CladeRelation
+
Typephy:CladeRelation
+
Properties
+
+
+
+ + + + + + + + + + + + + +
contentcomplex
minOccurs0
maxOccursunbounded
+
+
Model
+
+ +
Childrenphy:confidence
+
Instance
+
+
+
+ + + + +
<phy:clade_relation distance="" id_ref_0="" id_ref_1="" type="" xmlns:phy="http://www.phyloxml.org">
+  <phy:confidence stddev="" type="">{0,1}</phy:confidence>
+</phy:clade_relation>
+
+
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeUse
distancexs:doubleoptional +
+
id_ref_0phy:id_refrequired +
+
id_ref_1phy:id_refrequired +
+
typexs:tokenrequired +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="clade_relation" type="phy:CladeRelation" minOccurs="0" maxOccurs="unbounded"/>
+
+
+
Element phy:CladeRelation / phy:confidence
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#Confidence_type + phyloxml_xsd.tmp#Confidence_stddev + phyloxml_xsd.tmp#Confidence
+
Typephy:Confidence
+
Properties
+
+
+
+ + + + + + + + + +
contentcomplex
minOccurs0
+
+
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + + + + + + + +
QNameTypeUse
stddevxs:doubleoptional +
+
typexs:tokenrequired +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="confidence" type="phy:Confidence" minOccurs="0"/>
+
+
+
Element phy:Phylogeny / phy:sequence_relation
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#SequenceRelation_id_ref_0 + phyloxml_xsd.tmp#SequenceRelation_id_ref_1 + phyloxml_xsd.tmp#SequenceRelation_distance + phyloxml_xsd.tmp#SequenceRelation_type + phyloxml_xsd.tmp#SequenceRelation_confidence + phyloxml_xsd.tmp#SequenceRelation
+
Typephy:SequenceRelation
+
Properties
+
+
+
+ + + + + + + + + + + + + +
contentcomplex
minOccurs0
maxOccursunbounded
+
+
Model
+
+ +
Childrenphy:confidence
+
Instance
+
+
+
+ + + + +
<phy:sequence_relation distance="" id_ref_0="" id_ref_1="" type="" xmlns:phy="http://www.phyloxml.org">
+  <phy:confidence stddev="" type="">{0,1}</phy:confidence>
+</phy:sequence_relation>
+
+
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeUse
distancexs:doubleoptional +
+
id_ref_0phy:id_refrequired +
+
id_ref_1phy:id_refrequired +
+
typephy:SequenceRelationTyperequired +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="sequence_relation" type="phy:SequenceRelation" minOccurs="0" maxOccurs="unbounded"/>
+
+
+
Element phy:SequenceRelation / phy:confidence
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#Confidence_type + phyloxml_xsd.tmp#Confidence_stddev + phyloxml_xsd.tmp#Confidence
+
Typephy:Confidence
+
Properties
+
+
+
+ + + + + + + + + +
contentcomplex
minOccurs0
+
+
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + + + + + + + +
QNameTypeUse
stddevxs:doubleoptional +
+
typexs:tokenrequired +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="confidence" type="phy:Confidence" minOccurs="0"/>
+
+
+
Element phy:Phylogeny / phy:property
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#Property_ref + phyloxml_xsd.tmp#Property_unit + phyloxml_xsd.tmp#Property_datatype + phyloxml_xsd.tmp#Property_applies_to + phyloxml_xsd.tmp#Property_id_ref + phyloxml_xsd.tmp#Property
+
Typephy:Property
+
Properties
+
+
+
+ + + + + + + + + + + + + + + + + +
contentcomplex
minOccurs0
maxOccursunbounded
mixedtrue
+
+
Model
+
+
+
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeUse
applies_tophy:AppliesTorequired +
+
datatypephy:PropertyDataTyperequired +
+
id_refphy:id_refoptional +
+
refphy:refrequired +
+
unitphy:refoptional +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:element name="property" type="phy:Property" minOccurs="0" maxOccurs="unbounded"/>
+
+
+
Complex Type phy:Phyloxml
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Annotations
+
+
+
+
+ + + + +
'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.
+
+
+
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#http___www.phyloxml.org_Phyloxml_phylogeny
+
+
Used by
+
+
+
+ + + + + +
Element phy:phyloxml
+
+
Model
+
+
phy:phylogeny* , ANY element from ANY namespace OTHER than 'http://www.phyloxml.org'
+
Childrenphy:phylogeny
+
Source
+
+
+
+ + + + +
<xs:complexType name="Phyloxml">
+  <xs:annotation>
+    <xs: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.</xs:documentation>
+  </xs:annotation>
+  <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>
+
+
+
Complex Type phy:Phylogeny
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Annotations
+
+
+
+
+ + + + +
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.
+
+
+
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#Phylogeny_rooted + phyloxml_xsd.tmp#Phylogeny_rerootable + phyloxml_xsd.tmp#Phylogeny_branch_length_unit + phyloxml_xsd.tmp#Phylogeny_type + phyloxml_xsd.tmp#Phylogeny_name + phyloxml_xsd.tmp#Phylogeny_id + phyloxml_xsd.tmp#Phylogeny_description + phyloxml_xsd.tmp#Phylogeny_date + phyloxml_xsd.tmp#Phylogeny_confidence + phyloxml_xsd.tmp#Phylogeny_clade + phyloxml_xsd.tmp#Phylogeny_clade_relation + phyloxml_xsd.tmp#Phylogeny_sequence_relation + phyloxml_xsd.tmp#Phylogeny_property
+
+
Used by
+
+
+
+ + + + + +
Element phy:Phyloxml/phy:phylogeny
+
+
Model
+
+
phy:name{0,1} , phy:id{0,1} , phy:description{0,1} , phy:date{0,1} , phy:confidence* , phy:clade{0,1} , phy:clade_relation* , phy:sequence_relation* , phy:property* , ANY element from ANY namespace OTHER than 'http://www.phyloxml.org'
+
Childrenphy:clade, phy:clade_relation, phy:confidence, phy:date, phy:description, phy:id, phy:name, phy:property, phy:sequence_relation
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeUse
branch_length_unitxs:tokenoptional +
+
rerootablexs:booleanoptional +
+
rootedxs:booleanrequired +
+
typexs:tokenoptional +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:complexType name="Phylogeny">
+  <xs:annotation>
+    <xs: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.</xs:documentation>
+  </xs:annotation>
+  <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>
+
+
+
Complex Type phy:Id
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Annotations
+
+
+
+
+ + + + +
A general purpose identifier element. Allows to indicate the provider
+(or authority) of an identifier.
+
+
+
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#Id_provider
+
Typeextension of xs:token
+
Used by
+
+
+
+ + + + + +
Elements phy:Phylogeny/phy:id, phy:Taxonomy/phy:id
+
+
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + +
QNameTypeUse
providerxs:tokenoptional +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:complexType name="Id">
+  <xs:annotation>
+    <xs:documentation>A general purpose identifier element. Allows to indicate the provider (or authority) of an identifier.</xs:documentation>
+  </xs:annotation>
+  <xs:simpleContent>
+    <xs:extension base="xs:token">
+      <xs:attribute name="provider" type="xs:token"/>
+    </xs:extension>
+  </xs:simpleContent>
+</xs:complexType>
+
+
+
Complex Type phy:Confidence
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Annotations
+
+
+
+
+ + + + +
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').
+
+
+
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#Confidence_type + phyloxml_xsd.tmp#Confidence_stddev
+
Typeextension of xs:double
+
Used by
+
+
+ +
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + + + + + + + +
QNameTypeUse
stddevxs:doubleoptional +
+
typexs:tokenrequired +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:complexType name="Confidence">
+  <xs:annotation>
+    <xs: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').</xs:documentation>
+  </xs:annotation>
+  <xs:simpleContent>
+    <xs:extension base="xs:double">
+      <xs:attribute name="type" type="xs:token" use="required"/>
+      <xs:attribute name="stddev" type="xs:double"/>
+    </xs:extension>
+  </xs:simpleContent>
+</xs:complexType>
+
+
+
Complex Type phy:Clade
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Annotations
+
+
+
+
+ + + + +
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).
+
+
+
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#NO_NAMESPACE_Clade_branch_length + phyloxml_xsd.tmp#Clade_id_source + phyloxml_xsd.tmp#Clade_collapse + phyloxml_xsd.tmp#Clade_name + phyloxml_xsd.tmp#Clade_branch_length + phyloxml_xsd.tmp#Clade_confidence + phyloxml_xsd.tmp#Clade_width + phyloxml_xsd.tmp#Clade_color + phyloxml_xsd.tmp#Clade_taxonomy + phyloxml_xsd.tmp#Clade_sequence + phyloxml_xsd.tmp#Clade_events + phyloxml_xsd.tmp#Clade_binary_characters + phyloxml_xsd.tmp#Clade_distribution + phyloxml_xsd.tmp#Clade_date + phyloxml_xsd.tmp#Clade_reference + phyloxml_xsd.tmp#Clade_property + phyloxml_xsd.tmp#Clade_clade
+
+
Used by
+
+
+ +
Model
+
+ +
Childrenphy:binary_characters, phy:branch_length, phy:clade, phy:color, phy:confidence, phy:date, phy:distribution, phy:events, phy:name, phy:property, phy:reference, phy:sequence, phy:taxonomy, phy:width
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeUse
branch_lengthxs:doubleoptional +
+
collapsexs:booleanoptional +
+
id_sourcephy:id_sourceoptional +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:complexType name="Clade">
+  <xs:annotation>
+    <xs: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).</xs:documentation>
+  </xs:annotation>
+  <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="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:attribute name="collapse" type="xs:boolean"/>
+</xs:complexType>
+
+
+
Complex Type phy:BranchColor
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Annotations
+
+
+
+
+ + + + +
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).
+
+
+
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#BranchColor_red + phyloxml_xsd.tmp#BranchColor_green + phyloxml_xsd.tmp#BranchColor_blue + phyloxml_xsd.tmp#BranchColor_alpha
+
+
Used by
+
+
+
+ + + + + +
Element phy:Clade/phy:color
+
+
Model
+
+ +
Childrenphy:alpha, phy:blue, phy:green, phy:red
+
Source
+
+
+
+ + + + +
<xs:complexType name="BranchColor">
+  <xs:annotation>
+    <xs: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).</xs:documentation>
+  </xs:annotation>
+  <xs:sequence>
+    <xs:element name="red" type="xs:unsignedByte"/>
+    <xs:element name="green" type="xs:unsignedByte"/>
+    <xs:element name="blue" type="xs:unsignedByte"/>
+    <xs:element name="alpha" type="xs:unsignedByte" minOccurs="0"/>
+  </xs:sequence>
+</xs:complexType>
+
+
+
Complex Type phy:Taxonomy
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Annotations
+
+
+
+
+ + + + +
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'). 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).
+
+
+
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#Taxonomy_id_source + phyloxml_xsd.tmp#Taxonomy_id + phyloxml_xsd.tmp#Taxonomy_code + phyloxml_xsd.tmp#Taxonomy_scientific_name + phyloxml_xsd.tmp#Taxonomy_authority + phyloxml_xsd.tmp#Taxonomy_common_name + phyloxml_xsd.tmp#Taxonomy_synonym + phyloxml_xsd.tmp#Taxonomy_rank + phyloxml_xsd.tmp#Taxonomy_uri
+
+
Used by
+
+
+
+ + + + + +
Element phy:Clade/phy:taxonomy
+
+
Model
+
+
phy:id{0,1} , phy:code{0,1} , phy:scientific_name{0,1} , phy:authority{0,1} , phy:common_name{0,1} , phy:synonym* , phy:rank{0,1} , phy:uri* , ANY element from ANY namespace OTHER than 'http://www.phyloxml.org'
+
Childrenphy:authority, phy:code, phy:common_name, phy:id, phy:rank, phy:scientific_name, phy:synonym, phy:uri
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + +
QNameTypeUse
id_sourcephy:id_sourceoptional +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:complexType name="Taxonomy">
+  <xs:annotation>
+    <xs: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'). 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).</xs:documentation>
+  </xs:annotation>
+  <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"/>
+    <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" maxOccurs="unbounded"/>
+    <xs:any minOccurs="0" maxOccurs="unbounded" processContents="lax" namespace="##other"/>
+  </xs:sequence>
+  <xs:attribute name="id_source" type="phy:id_source"/>
+</xs:complexType>
+
+
+
Simple Type phy:TaxonomyCode
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram
+
Typerestriction of xs:token
+
Facets
+
+
+
+ + + + + + +
pattern([A-Z9][A-Z]{2}[A-Z0-9]{2})|RAT|PIG|PEA +
+
+
+
+
Used by
+
+
+
+ + + + + +
Element phy:Taxonomy/phy:code
+
+
+
Source
+
+
+
+ + + + +
<xs:simpleType name="TaxonomyCode">
+  <xs:restriction base="xs:token">
+    <xs:pattern value="([A-Z9][A-Z]{2}[A-Z0-9]{2})|RAT|PIG|PEA"/>
+  </xs:restriction>
+</xs:simpleType>
+
+
+
Simple Type phy:Rank
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram
+
Typerestriction of xs:token
+
Facets
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
enumerationdomain +
+
enumerationsuperkingdom +
+
enumerationkingdom +
+
enumerationsubkingdom +
+
enumerationbranch +
+
enumerationinfrakingdom +
+
enumerationsuperphylum +
+
enumerationphylum +
+
enumerationsubphylum +
+
enumerationinfraphylum +
+
enumerationmicrophylum +
+
enumerationsuperdivision +
+
enumerationdivision +
+
enumerationsubdivision +
+
enumerationinfradivision +
+
enumerationsuperclass +
+
enumerationclass +
+
enumerationsubclass +
+
enumerationinfraclass +
+
enumerationsuperlegion +
+
enumerationlegion +
+
enumerationsublegion +
+
enumerationinfralegion +
+
enumerationsupercohort +
+
enumerationcohort +
+
enumerationsubcohort +
+
enumerationinfracohort +
+
enumerationmagnorder +
+
enumerationsuperorder +
+
enumerationorder +
+
enumerationsuborder +
+
enumerationinfraorder +
+
enumerationsuperfamily +
+
enumerationfamily +
+
enumerationsubfamily +
+
enumerationsupertribe +
+
enumerationtribe +
+
enumerationsubtribe +
+
enumerationinfratribe +
+
enumerationgenus +
+
enumerationsubgenus +
+
enumerationsuperspecies +
+
enumerationspecies +
+
enumerationsubspecies +
+
enumerationvariety +
+
enumerationvarietas +
+
enumerationsubvariety +
+
enumerationform +
+
enumerationsubform +
+
enumerationcultivar +
+
enumerationstrain +
+
enumerationsection +
+
enumerationsubsection +
+
enumerationunknown +
+
enumerationother +
+
+
+
+
Used by
+
+
+
+ + + + + +
Element phy:Taxonomy/phy:rank
+
+
+
Source
+
+
+
+ + + + +
<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="magnorder"/>
+    <xs:enumeration value="superorder"/>
+    <xs:enumeration value="order"/>
+    <xs:enumeration value="suborder"/>
+    <xs:enumeration value="infraorder"/>
+    <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="varietas"/>
+    <xs:enumeration value="subvariety"/>
+    <xs:enumeration value="form"/>
+    <xs:enumeration value="subform"/>
+    <xs:enumeration value="cultivar"/>
+    <xs:enumeration value="strain"/>
+    <xs:enumeration value="section"/>
+    <xs:enumeration value="subsection"/>
+    <xs:enumeration value="unknown"/>
+    <xs:enumeration value="other"/>
+  </xs:restriction>
+</xs:simpleType>
+
+
+
Complex Type phy:Uri
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Annotations
+
+
+
+
+ + + + +
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').
+
+
+
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#Uri_desc + phyloxml_xsd.tmp#Uri_type
+
Typeextension of xs:anyURI
+
Used by
+
+
+ +
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + + + + + + + +
QNameTypeUse
descxs:tokenoptional +
+
typexs:tokenoptional +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:complexType name="Uri">
+  <xs:annotation>
+    <xs: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').</xs:documentation>
+  </xs:annotation>
+  <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>
+
+
+
Simple Type phy:id_source
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram
+
Typexs:ID
+
Used by
+
+
+ +
+
Source
+
+
+
+ + + + +
<xs:simpleType name="id_source">
+  <xs:restriction base="xs:ID"/>
+</xs:simpleType>
+
+
+
Complex Type phy:Sequence
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Annotations
+
+
+
+
+ + + + +
Element Sequence is used to represent a molecular sequence (Protein,
+DNA, RNA) associated with a node. 'symbol' is a short (maximal 20 characters) symbol of
+the sequence (e.g. 'ACTM') whereas 'name' is used for the full name (e.g. 'muscle
+Actin'). 'gene_name' can be used when protein and gene names differ. '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.
+
+
+
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#Sequence_type + phyloxml_xsd.tmp#Sequence_id_source + phyloxml_xsd.tmp#Sequence_id_ref + phyloxml_xsd.tmp#Sequence_symbol + phyloxml_xsd.tmp#Sequence_accession + phyloxml_xsd.tmp#Sequence_name + phyloxml_xsd.tmp#Sequence_gene_name + phyloxml_xsd.tmp#Sequence_location + phyloxml_xsd.tmp#Sequence_mol_seq + phyloxml_xsd.tmp#Sequence_uri + phyloxml_xsd.tmp#Sequence_annotation + phyloxml_xsd.tmp#Sequence_cross_references + phyloxml_xsd.tmp#Sequence_domain_architecture
+
+
Used by
+
+
+
+ + + + + +
Element phy:Clade/phy:sequence
+
+
Model
+
+ +
Childrenphy:accession, phy:annotation, phy:cross_references, phy:domain_architecture, phy:gene_name, phy:location, phy:mol_seq, phy:name, phy:symbol, phy:uri
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeUse
id_refphy:id_refoptional +
+
id_sourcephy:id_sourceoptional +
+
typephy:SequenceTypeoptional +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:complexType name="Sequence">
+  <xs:annotation>
+    <xs:documentation>Element Sequence is used to represent a molecular sequence (Protein, DNA, RNA) associated with a node. 'symbol' is a short (maximal 20 characters) symbol of the sequence (e.g. 'ACTM') whereas 'name' is used for the full name (e.g. 'muscle Actin'). 'gene_name' can be used when protein and gene names differ. '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.</xs:documentation>
+  </xs:annotation>
+  <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="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" maxOccurs="unbounded"/>
+    <xs:element name="annotation" type="phy:Annotation" minOccurs="0" maxOccurs="unbounded"/>
+    <xs:element name="cross_references" type="phy:CrossReferences" minOccurs="0"/>
+    <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>
+
+
+
Simple Type phy:SequenceSymbol
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram
+
Typerestriction of xs:token
+
Facets
+
+
+
+ + + + + + +
pattern\S{1,20} +
+
+
+
+
Used by
+
+
+
+ + + + + +
Element phy:Sequence/phy:symbol
+
+
+
Source
+
+
+
+ + + + +
<xs:simpleType name="SequenceSymbol">
+  <xs:restriction base="xs:token">
+    <xs:pattern value="\S{1,20}"/>
+  </xs:restriction>
+</xs:simpleType>
+
+
+
Complex Type phy:Accession
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Annotations
+
+
+
+
+ + + + +
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').
+
+
+
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#Accession_source + phyloxml_xsd.tmp#Accession_comment
+
Typeextension of xs:token
+
Used by
+
+
+ +
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + + + + + + + +
QNameTypeUse
commentxs:tokenoptional +
+
sourcexs:tokenrequired +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:complexType name="Accession">
+  <xs:annotation>
+    <xs: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').</xs:documentation>
+  </xs:annotation>
+  <xs:simpleContent>
+    <xs:extension base="xs:token">
+      <xs:attribute name="source" type="xs:token" use="required"/>
+      <xs:attribute name="comment" type="xs:token"/>
+    </xs:extension>
+  </xs:simpleContent>
+</xs:complexType>
+
+
+
Complex Type phy:MolSeq
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Annotations
+
+
+
+
+ + + + +
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).
+
+
+
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#MolSeq_is_aligned
+
Typeextension of xs:token
+
Used by
+
+
+
+ + + + + +
Element phy:Sequence/phy:mol_seq
+
+
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + +
QNameTypeUse
is_alignedxs:booleanoptional +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:complexType name="MolSeq">
+  <xs:annotation>
+    <xs: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).</xs:documentation>
+  </xs:annotation>
+  <xs:simpleContent>
+    <xs:extension base="xs:token">
+      <xs:attribute name="is_aligned" type="xs:boolean"/>
+    </xs:extension>
+  </xs:simpleContent>
+</xs:complexType>
+
+
+
Complex Type phy:Annotation
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Annotations
+
+
+
+
+ + + + +
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.
+
+
+
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#Annotation_ref + phyloxml_xsd.tmp#Annotation_source + phyloxml_xsd.tmp#Annotation_evidence + phyloxml_xsd.tmp#Annotation_type + phyloxml_xsd.tmp#Annotation_desc + phyloxml_xsd.tmp#Annotation_confidence + phyloxml_xsd.tmp#Annotation_property + phyloxml_xsd.tmp#Annotation_uri
+
+
Used by
+
+
+
+ + + + + +
Element phy:Sequence/phy:annotation
+
+
Model
+
+ +
Childrenphy:confidence, phy:desc, phy:property, phy:uri
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeUse
evidencexs:tokenoptional +
+
refphy:refoptional +
+
sourcexs:tokenoptional +
+
typexs:tokenoptional +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:complexType name="Annotation">
+  <xs:annotation>
+    <xs: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.</xs:documentation>
+  </xs: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" maxOccurs="unbounded"/>
+  </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>
+
+
+
Complex Type phy:Property
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Annotations
+
+
+
+
+ + + + +
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>
+
+
+
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#Property_ref + phyloxml_xsd.tmp#Property_unit + phyloxml_xsd.tmp#Property_datatype + phyloxml_xsd.tmp#Property_applies_to + phyloxml_xsd.tmp#Property_id_ref
+
+
Properties
+
+
+
+ + + + + +
mixedtrue
+
+
+
Used by
+
+
+ +
Model
+
+
+
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeUse
applies_tophy:AppliesTorequired +
+
datatypephy:PropertyDataTyperequired +
+
id_refphy:id_refoptional +
+
refphy:refrequired +
+
unitphy:refoptional +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:complexType name="Property" mixed="true">
+  <xs:annotation>
+    <xs: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></xs:documentation>
+  </xs:annotation>
+  <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>
+
+
+
Simple Type phy:ref
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram
+
Typerestriction of xs:token
+
Facets
+
+
+
+ + + + + + +
pattern[a-zA-Z0-9_]+:\S+ +
+
+
+
+
Used by
+
+
+ +
+
Source
+
+
+
+ + + + +
<xs:simpleType name="ref">
+  <xs:restriction base="xs:token">
+    <xs:pattern value="[a-zA-Z0-9_]+:\S+"/>
+  </xs:restriction>
+</xs:simpleType>
+
+
+
Simple Type phy:PropertyDataType
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram
+
Typerestriction of xs:token
+
Facets
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
enumerationxsd:string +
+
enumerationxsd:boolean +
+
enumerationxsd:decimal +
+
enumerationxsd:float +
+
enumerationxsd:double +
+
enumerationxsd:duration +
+
enumerationxsd:dateTime +
+
enumerationxsd:time +
+
enumerationxsd:date +
+
enumerationxsd:gYearMonth +
+
enumerationxsd:gYear +
+
enumerationxsd:gMonthDay +
+
enumerationxsd:gDay +
+
enumerationxsd:gMonth +
+
enumerationxsd:hexBinary +
+
enumerationxsd:base64Binary +
+
enumerationxsd:anyURI +
+
enumerationxsd:normalizedString +
+
enumerationxsd:token +
+
enumerationxsd:integer +
+
enumerationxsd:nonPositiveInteger +
+
enumerationxsd:negativeInteger +
+
enumerationxsd:long +
+
enumerationxsd:int +
+
enumerationxsd:short +
+
enumerationxsd:byte +
+
enumerationxsd:nonNegativeInteger +
+
enumerationxsd:unsignedLong +
+
enumerationxsd:unsignedInt +
+
enumerationxsd:unsignedShort +
+
enumerationxsd:unsignedByte +
+
enumerationxsd:positiveInteger +
+
+
+
+
Used by
+
+
+
+ + + + + +
Attribute phy:Property/@datatype
+
+
+
Source
+
+
+
+ + + + +
<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>
+
+
+
Simple Type phy:AppliesTo
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram
+
Typerestriction of xs:token
+
Facets
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
enumerationphylogeny +
+
enumerationclade +
+
enumerationnode +
+
enumerationannotation +
+
enumerationparent_branch +
+
enumerationother +
+
+
+
+
Used by
+
+
+
+ + + + + +
Attribute phy:Property/@applies_to
+
+
+
Source
+
+
+
+ + + + +
<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>
+
+
+
Simple Type phy:id_ref
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram
+
Typexs:IDREF
+
Used by
+
+
+ +
+
Source
+
+
+
+ + + + +
<xs:simpleType name="id_ref">
+  <xs:restriction base="xs:IDREF"/>
+</xs:simpleType>
+
+
+
Complex Type phy:CrossReferences
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Annotations
+
+
+
+
+ + + + +
Used to store accessions to additional resources.
+
+
+
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#CrossReferences_accession
+
+
Used by
+
+
+
+ + + + + +
Element phy:Sequence/phy:cross_references
+
+
Model
+
+ +
Childrenphy:accession
+
Source
+
+
+
+ + + + +
<xs:complexType name="CrossReferences">
+  <xs:annotation>
+    <xs:documentation>Used to store accessions to additional resources.</xs:documentation>
+  </xs:annotation>
+  <xs:sequence>
+    <xs:element name="accession" type="phy:Accession" minOccurs="1" maxOccurs="unbounded"/>
+  </xs:sequence>
+</xs:complexType>
+
+
+
Complex Type phy:DomainArchitecture
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Annotations
+
+
+
+
+ + + + +
This is used describe the domain architecture of a protein. Attribute
+'length' is the total length of the protein
+
+
+
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#DomainArchitecture_length + phyloxml_xsd.tmp#DomainArchitecture_domain
+
+
Used by
+
+
+
+ + + + + +
Element phy:Sequence/phy:domain_architecture
+
+
Model
+
+ +
Childrenphy:domain
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + +
QNameTypeUse
lengthxs:nonNegativeIntegeroptional +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:complexType name="DomainArchitecture">
+  <xs:annotation>
+    <xs:documentation>This is used describe the domain architecture of a protein. Attribute 'length' is the total length of the protein</xs:documentation>
+  </xs:annotation>
+  <xs:sequence>
+    <xs:element name="domain" type="phy:ProteinDomain" minOccurs="1" maxOccurs="unbounded"/>
+  </xs:sequence>
+  <xs:attribute name="length" type="xs:nonNegativeInteger"/>
+</xs:complexType>
+
+
+
Complex Type phy:ProteinDomain
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Annotations
+
+
+
+
+ + + + +
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.
+
+
+
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#ProteinDomain_from + phyloxml_xsd.tmp#ProteinDomain_to + phyloxml_xsd.tmp#ProteinDomain_confidence + phyloxml_xsd.tmp#ProteinDomain_id
+
Typeextension of xs:token
+
Used by
+
+
+
+ + + + + +
Element phy:DomainArchitecture/phy:domain
+
+
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeUse
confidencexs:doubleoptional +
+
fromxs:nonNegativeIntegerrequired +
+
idxs:tokenoptional +
+
toxs:nonNegativeIntegerrequired +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:complexType name="ProteinDomain">
+  <xs:annotation>
+    <xs: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.</xs:documentation>
+  </xs:annotation>
+  <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>
+
+
+
Simple Type phy:SequenceType
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram
+
Typerestriction of xs:token
+
Facets
+
+
+
+ + + + + + + + + + + + + + + + +
enumerationrna +
+
enumerationdna +
+
enumerationprotein +
+
+
+
+
Used by
+
+
+
+ + + + + +
Attribute phy:Sequence/@type
+
+
+
Source
+
+
+
+ + + + +
<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>
+
+
+
Complex Type phy:Events
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Annotations
+
+
+
+
+ + + + +
Events at the root node of a clade (e.g. one gene duplication).
+
+
+
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#Events_type + phyloxml_xsd.tmp#Events_duplications + phyloxml_xsd.tmp#Events_speciations + phyloxml_xsd.tmp#Events_losses + phyloxml_xsd.tmp#Events_confidence
+
+
Used by
+
+
+
+ + + + + +
Element phy:Clade/phy:events
+
+
Model
+
+ +
Childrenphy:confidence, phy:duplications, phy:losses, phy:speciations, phy:type
+
Source
+
+
+
+ + + + +
<xs:complexType name="Events">
+  <xs:annotation>
+    <xs:documentation>Events at the root node of a clade (e.g. one gene duplication).</xs:documentation>
+  </xs:annotation>
+  <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>
+
+
+
Simple Type phy:EventType
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram
+
Typerestriction of xs:token
+
Facets
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
enumerationtransfer +
+
enumerationfusion +
+
enumerationspeciation_or_duplication +
+
enumerationother +
+
enumerationmixed +
+
enumerationunassigned +
+
+
+
+
Used by
+
+
+
+ + + + + +
Element phy:Events/phy:type
+
+
+
Source
+
+
+
+ + + + +
<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>
+
+
+
Complex Type phy:BinaryCharacters
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Annotations
+
+
+
+
+ + + + +
The names and/or counts of binary characters present, gained, and lost
+at the root of a clade.
+
+
+
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#BinaryCharacters_type + phyloxml_xsd.tmp#BinaryCharacters_gained_count + phyloxml_xsd.tmp#BinaryCharacters_lost_count + phyloxml_xsd.tmp#BinaryCharacters_present_count + phyloxml_xsd.tmp#BinaryCharacters_absent_count + phyloxml_xsd.tmp#BinaryCharacters_gained + phyloxml_xsd.tmp#BinaryCharacters_lost + phyloxml_xsd.tmp#BinaryCharacters_present + phyloxml_xsd.tmp#BinaryCharacters_absent
+
+
Used by
+
+
+
+ + + + + +
Element phy:Clade/phy:binary_characters
+
+
Model
+
+ +
Childrenphy:absent, phy:gained, phy:lost, phy:present
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeUse
absent_countxs:nonNegativeIntegeroptional +
+
gained_countxs:nonNegativeIntegeroptional +
+
lost_countxs:nonNegativeIntegeroptional +
+
present_countxs:nonNegativeIntegeroptional +
+
typexs:tokenoptional +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:complexType name="BinaryCharacters">
+  <xs:annotation>
+    <xs:documentation>The names and/or counts of binary characters present, gained, and lost at the root of a clade.</xs:documentation>
+  </xs:annotation>
+  <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>
+
+
+
Complex Type phy:BinaryCharacterList
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#BinaryCharacterList_bc
+
+
Used by
+
+
+ +
Model
+
+ +
Childrenphy:bc
+
Source
+
+
+
+ + + + +
<xs:complexType name="BinaryCharacterList">
+  <xs:sequence>
+    <xs:element name="bc" type="xs:token" maxOccurs="unbounded"/>
+  </xs:sequence>
+</xs:complexType>
+
+
+
Complex Type phy:Distribution
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Annotations
+
+
+
+
+ + + + +
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'.
+
+
+
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#Distribution_desc + phyloxml_xsd.tmp#Distribution_point + phyloxml_xsd.tmp#Distribution_polygon
+
+
Used by
+
+
+
+ + + + + +
Element phy:Clade/phy:distribution
+
+
Model
+
+ +
Childrenphy:desc, phy:point, phy:polygon
+
Source
+
+
+
+ + + + +
<xs:complexType name="Distribution">
+  <xs:annotation>
+    <xs: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'.</xs:documentation>
+  </xs:annotation>
+  <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>
+
+
+
Complex Type phy:Point
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Annotations
+
+
+
+
+ + + + +
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').
+
+
+
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#Point_geodetic_datum + phyloxml_xsd.tmp#Point_alt_unit + phyloxml_xsd.tmp#Point_lat + phyloxml_xsd.tmp#Point_long + phyloxml_xsd.tmp#Point_alt
+
+
Used by
+
+
+ +
Model
+
+ +
Childrenphy:alt, phy:lat, phy:long
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + + + + + + + +
QNameTypeUse
alt_unitxs:tokenoptional +
+
geodetic_datumxs:tokenrequired +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:complexType name="Point">
+  <xs:annotation>
+    <xs: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').</xs:documentation>
+  </xs:annotation>
+  <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>
+
+
+
Complex Type phy:Polygon
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Annotations
+
+
+
+
+ + + + +
A polygon defined by a list of 'Points' (used by element
+'Distribution').
+
+
+
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#Polygon_point
+
+
Used by
+
+
+
+ + + + + +
Element phy:Distribution/phy:polygon
+
+
Model
+
+ +
Childrenphy:point
+
Source
+
+
+
+ + + + +
<xs:complexType name="Polygon">
+  <xs:annotation>
+    <xs:documentation>A polygon defined by a list of 'Points' (used by element 'Distribution').</xs:documentation>
+  </xs:annotation>
+  <xs:sequence>
+    <xs:element name="point" type="phy:Point" minOccurs="3" maxOccurs="unbounded"/>
+  </xs:sequence>
+</xs:complexType>
+
+
+
Complex Type phy:Date
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Annotations
+
+
+
+
+ + + + +
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
+
+
+
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#Date_unit + phyloxml_xsd.tmp#Date_desc + phyloxml_xsd.tmp#Date_value + phyloxml_xsd.tmp#Date_minimum + phyloxml_xsd.tmp#Date_maximum
+
+
Used by
+
+
+
+ + + + + +
Element phy:Clade/phy:date
+
+
Model
+
+ +
Childrenphy:desc, phy:maximum, phy:minimum, phy:value
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + +
QNameTypeUse
unitxs:tokenoptional +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:complexType name="Date">
+  <xs:annotation>
+    <xs: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</xs:documentation>
+  </xs:annotation>
+  <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>
+
+
+
Complex Type phy:Reference
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Annotations
+
+
+
+
+ + + + +
A literature reference for a clade. It is recommended to use the 'doi'
+attribute instead of the free text 'desc' element whenever possible.
+
+
+
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#Reference_doi + phyloxml_xsd.tmp#Reference_desc
+
+
Used by
+
+
+
+ + + + + +
Element phy:Clade/phy:reference
+
+
Model
+
+ +
Childrenphy:desc
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + +
QNameTypeUse
doixs:tokenoptional +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:complexType name="Reference">
+  <xs:annotation>
+    <xs:documentation>A literature reference for a clade. It is recommended to use the 'doi' attribute instead of the free text 'desc' element whenever possible.</xs:documentation>
+  </xs:annotation>
+  <xs:sequence>
+    <xs:element name="desc" type="xs:token" minOccurs="0"/>
+  </xs:sequence>
+  <xs:attribute name="doi" type="xs:token"/>
+</xs:complexType>
+
+
+
Complex Type phy:CladeRelation
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Annotations
+
+
+
+
+ + + + +
This is used to express a typed relationship between two clades. For
+example it could be used to describe multiple parents of a clade.
+
+
+
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#CladeRelation_id_ref_0 + phyloxml_xsd.tmp#CladeRelation_id_ref_1 + phyloxml_xsd.tmp#CladeRelation_distance + phyloxml_xsd.tmp#CladeRelation_type + phyloxml_xsd.tmp#CladeRelation_confidence
+
+
Used by
+
+
+
+ + + + + +
Element phy:Phylogeny/phy:clade_relation
+
+
Model
+
+ +
Childrenphy:confidence
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeUse
distancexs:doubleoptional +
+
id_ref_0phy:id_refrequired +
+
id_ref_1phy:id_refrequired +
+
typexs:tokenrequired +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:complexType name="CladeRelation">
+  <xs:annotation>
+    <xs: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.</xs:documentation>
+  </xs:annotation>
+  <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>
+
+
+
Complex Type phy:SequenceRelation
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Annotations
+
+
+
+
+ + + + +
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').
+
+
+
+
Diagram
+
+
+
Diagram + phyloxml_xsd.tmp#SequenceRelation_id_ref_0 + phyloxml_xsd.tmp#SequenceRelation_id_ref_1 + phyloxml_xsd.tmp#SequenceRelation_distance + phyloxml_xsd.tmp#SequenceRelation_type + phyloxml_xsd.tmp#SequenceRelation_confidence
+
+
Used by
+
+
+
+ + + + + +
Element phy:Phylogeny/phy:sequence_relation
+
+
Model
+
+ +
Childrenphy:confidence
+
Attributes
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
QNameTypeUse
distancexs:doubleoptional +
+
id_ref_0phy:id_refrequired +
+
id_ref_1phy:id_refrequired +
+
typephy:SequenceRelationTyperequired +
+
+
+
+
Source
+
+
+
+ + + + +
<xs:complexType name="SequenceRelation">
+  <xs:annotation>
+    <xs: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').</xs:documentation>
+  </xs:annotation>
+  <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>
+
+
+
Simple Type phy:SequenceRelationType
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
Namespacehttp://www.phyloxml.org
+
Diagram
+
+
+
Diagram
+
Typerestriction of xs:token
+
Facets
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
enumerationorthology +
+
enumerationone_to_one_orthology +
+
enumerationsuper_orthology +
+
enumerationparalogy +
+
enumerationultra_paralogy +
+
enumerationxenology +
+
enumerationunknown +
+
enumerationother +
+
+
+
+
Used by
+
+
+
+ + + + + +
Attribute phy:SequenceRelation/@type
+
+
+
Source
+
+
+
+ + + + +
<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>
+
+
+
Attribute phy:Id / @provider
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:token
+
Properties
+
+
+
+ + + + + +
contentsimple
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:Id
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="provider" type="xs:token"/>
+
+
+
Attribute phy:Confidence / @type
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:token
+
Properties
+
+
+
+ + + + + +
userequired
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:Confidence
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="type" type="xs:token" use="required"/>
+
+
+
Attribute phy:Confidence / @stddev
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:double
+
Properties
+
+
+
+ + + + + +
contentsimple
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:Confidence
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="stddev" type="xs:double"/>
+
+
+
Attribute phy:Uri / @desc
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:token
+
Properties
+
+
+
+ + + + + +
contentsimple
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:Uri
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="desc" type="xs:token"/>
+
+
+
Attribute phy:Uri / @type
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:token
+
Properties
+
+
+
+ + + + + +
contentsimple
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:Uri
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="type" type="xs:token"/>
+
+
+
Attribute phy:Taxonomy / @id_source
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typephy:id_source
+
Properties
+
+
+
+ + + + + +
contentsimple
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:Taxonomy
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="id_source" type="phy:id_source"/>
+
+
+
Attribute phy:Accession / @source
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:token
+
Properties
+
+
+
+ + + + + +
userequired
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:Accession
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="source" type="xs:token" use="required"/>
+
+
+
Attribute phy:Accession / @comment
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:token
+
Properties
+
+
+
+ + + + + +
contentsimple
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:Accession
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="comment" type="xs:token"/>
+
+
+
Attribute phy:MolSeq / @is_aligned
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:boolean
+
Properties
+
+
+
+ + + + + +
contentsimple
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:MolSeq
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="is_aligned" type="xs:boolean"/>
+
+
+
Attribute phy:Property / @ref
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typephy:ref
+
Properties
+
+
+
+ + + + + +
userequired
+
+
+
Facets
+
+
+
+ + + + + + +
pattern[a-zA-Z0-9_]+:\S+ +
+
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:Property
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="ref" type="phy:ref" use="required"/>
+
+
+
Attribute phy:Property / @unit
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typephy:ref
+
Properties
+
+
+
+ + + + + +
contentsimple
+
+
+
Facets
+
+
+
+ + + + + + +
pattern[a-zA-Z0-9_]+:\S+ +
+
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:Property
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="unit" type="phy:ref"/>
+
+
+
Attribute phy:Property / @datatype
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typephy:PropertyDataType
+
Properties
+
+
+
+ + + + + +
userequired
+
+
+
Facets
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
enumerationxsd:string +
+
enumerationxsd:boolean +
+
enumerationxsd:decimal +
+
enumerationxsd:float +
+
enumerationxsd:double +
+
enumerationxsd:duration +
+
enumerationxsd:dateTime +
+
enumerationxsd:time +
+
enumerationxsd:date +
+
enumerationxsd:gYearMonth +
+
enumerationxsd:gYear +
+
enumerationxsd:gMonthDay +
+
enumerationxsd:gDay +
+
enumerationxsd:gMonth +
+
enumerationxsd:hexBinary +
+
enumerationxsd:base64Binary +
+
enumerationxsd:anyURI +
+
enumerationxsd:normalizedString +
+
enumerationxsd:token +
+
enumerationxsd:integer +
+
enumerationxsd:nonPositiveInteger +
+
enumerationxsd:negativeInteger +
+
enumerationxsd:long +
+
enumerationxsd:int +
+
enumerationxsd:short +
+
enumerationxsd:byte +
+
enumerationxsd:nonNegativeInteger +
+
enumerationxsd:unsignedLong +
+
enumerationxsd:unsignedInt +
+
enumerationxsd:unsignedShort +
+
enumerationxsd:unsignedByte +
+
enumerationxsd:positiveInteger +
+
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:Property
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="datatype" type="phy:PropertyDataType" use="required"/>
+
+
+
Attribute phy:Property / @applies_to
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typephy:AppliesTo
+
Properties
+
+
+
+ + + + + +
userequired
+
+
+
Facets
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
enumerationphylogeny +
+
enumerationclade +
+
enumerationnode +
+
enumerationannotation +
+
enumerationparent_branch +
+
enumerationother +
+
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:Property
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="applies_to" type="phy:AppliesTo" use="required"/>
+
+
+
Attribute phy:Property / @id_ref
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typephy:id_ref
+
Properties
+
+
+
+ + + + + +
contentsimple
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:Property
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="id_ref" type="phy:id_ref"/>
+
+
+
Attribute phy:Annotation / @ref
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typephy:ref
+
Properties
+
+
+
+ + + + + +
contentsimple
+
+
+
Facets
+
+
+
+ + + + + + +
pattern[a-zA-Z0-9_]+:\S+ +
+
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:Annotation
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="ref" type="phy:ref"/>
+
+
+
Attribute phy:Annotation / @source
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:token
+
Properties
+
+
+
+ + + + + +
contentsimple
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:Annotation
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="source" type="xs:token"/>
+
+
+
Attribute phy:Annotation / @evidence
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:token
+
Properties
+
+
+
+ + + + + +
contentsimple
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:Annotation
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="evidence" type="xs:token"/>
+
+
+
Attribute phy:Annotation / @type
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:token
+
Properties
+
+
+
+ + + + + +
contentsimple
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:Annotation
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="type" type="xs:token"/>
+
+
+
Attribute phy:ProteinDomain / @from
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:nonNegativeInteger
+
Properties
+
+
+
+ + + + + +
userequired
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:ProteinDomain
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="from" type="xs:nonNegativeInteger" use="required"/>
+
+
+
Attribute phy:ProteinDomain / @to
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:nonNegativeInteger
+
Properties
+
+
+
+ + + + + +
userequired
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:ProteinDomain
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="to" type="xs:nonNegativeInteger" use="required"/>
+
+
+
Attribute phy:ProteinDomain / @confidence
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:double
+
Properties
+
+
+
+ + + + + +
contentsimple
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:ProteinDomain
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="confidence" type="xs:double"/>
+
+
+
Attribute phy:ProteinDomain / @id
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:token
+
Properties
+
+
+
+ + + + + +
contentsimple
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:ProteinDomain
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="id" type="xs:token"/>
+
+
+
Attribute phy:DomainArchitecture / @length
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:nonNegativeInteger
+
Properties
+
+
+
+ + + + + +
contentsimple
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:DomainArchitecture
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="length" type="xs:nonNegativeInteger"/>
+
+
+
Attribute phy:Sequence / @type
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typephy:SequenceType
+
Properties
+
+
+
+ + + + + +
contentsimple
+
+
+
Facets
+
+
+
+ + + + + + + + + + + + + + + + +
enumerationrna +
+
enumerationdna +
+
enumerationprotein +
+
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:Sequence
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="type" type="phy:SequenceType"/>
+
+
+
Attribute phy:Sequence / @id_source
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typephy:id_source
+
Properties
+
+
+
+ + + + + +
contentsimple
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:Sequence
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="id_source" type="phy:id_source"/>
+
+
+
Attribute phy:Sequence / @id_ref
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typephy:id_ref
+
Properties
+
+
+
+ + + + + +
contentsimple
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:Sequence
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="id_ref" type="phy:id_ref"/>
+
+
+
Attribute phy:BinaryCharacters / @type
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:token
+
Properties
+
+
+
+ + + + + +
contentsimple
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:BinaryCharacters
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="type" type="xs:token"/>
+
+
+
Attribute phy:BinaryCharacters / @gained_count
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:nonNegativeInteger
+
Properties
+
+
+
+ + + + + +
contentsimple
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:BinaryCharacters
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="gained_count" type="xs:nonNegativeInteger"/>
+
+
+
Attribute phy:BinaryCharacters / @lost_count
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:nonNegativeInteger
+
Properties
+
+
+
+ + + + + +
contentsimple
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:BinaryCharacters
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="lost_count" type="xs:nonNegativeInteger"/>
+
+
+
Attribute phy:BinaryCharacters / @present_count
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:nonNegativeInteger
+
Properties
+
+
+
+ + + + + +
contentsimple
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:BinaryCharacters
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="present_count" type="xs:nonNegativeInteger"/>
+
+
+
Attribute phy:BinaryCharacters / @absent_count
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:nonNegativeInteger
+
Properties
+
+
+
+ + + + + +
contentsimple
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:BinaryCharacters
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="absent_count" type="xs:nonNegativeInteger"/>
+
+
+
Attribute phy:Point / @geodetic_datum
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:token
+
Properties
+
+
+
+ + + + + +
userequired
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:Point
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="geodetic_datum" type="xs:token" use="required"/>
+
+
+
Attribute phy:Point / @alt_unit
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:token
+
Properties
+
+
+
+ + + + + +
contentsimple
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:Point
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="alt_unit" type="xs:token"/>
+
+
+
Attribute phy:Date / @unit
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:token
+
Properties
+
+
+
+ + + + + +
contentsimple
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:Date
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="unit" type="xs:token"/>
+
+
+
Attribute phy:Reference / @doi
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:token
+
Properties
+
+
+
+ + + + + +
contentsimple
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:Reference
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="doi" type="xs:token"/>
+
+
+
Attribute phy:Clade / @branch_length
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:double
+
Properties
+
+
+
+ + + + + +
contentsimple
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:Clade
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="branch_length" type="xs:double"/>
+
+
+
Attribute phy:Clade / @id_source
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typephy:id_source
+
Properties
+
+
+
+ + + + + +
contentsimple
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:Clade
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="id_source" type="phy:id_source"/>
+
+
+
Attribute phy:Clade / @collapse
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:boolean
+
Properties
+
+
+
+ + + + + +
contentsimple
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:Clade
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="collapse" type="xs:boolean"/>
+
+
+
Attribute phy:CladeRelation / @id_ref_0
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typephy:id_ref
+
Properties
+
+
+
+ + + + + +
userequired
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:CladeRelation
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="id_ref_0" type="phy:id_ref" use="required"/>
+
+
+
Attribute phy:CladeRelation / @id_ref_1
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typephy:id_ref
+
Properties
+
+
+
+ + + + + +
userequired
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:CladeRelation
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="id_ref_1" type="phy:id_ref" use="required"/>
+
+
+
Attribute phy:CladeRelation / @distance
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:double
+
Properties
+
+
+
+ + + + + +
contentsimple
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:CladeRelation
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="distance" type="xs:double"/>
+
+
+
Attribute phy:CladeRelation / @type
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:token
+
Properties
+
+
+
+ + + + + +
userequired
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:CladeRelation
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="type" type="xs:token" use="required"/>
+
+
+
Attribute phy:SequenceRelation / @id_ref_0
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typephy:id_ref
+
Properties
+
+
+
+ + + + + +
userequired
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:SequenceRelation
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="id_ref_0" type="phy:id_ref" use="required"/>
+
+
+
Attribute phy:SequenceRelation / @id_ref_1
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typephy:id_ref
+
Properties
+
+
+
+ + + + + +
userequired
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:SequenceRelation
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="id_ref_1" type="phy:id_ref" use="required"/>
+
+
+
Attribute phy:SequenceRelation / @distance
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:double
+
Properties
+
+
+
+ + + + + +
contentsimple
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:SequenceRelation
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="distance" type="xs:double"/>
+
+
+
Attribute phy:SequenceRelation / @type
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typephy:SequenceRelationType
+
Properties
+
+
+
+ + + + + +
userequired
+
+
+
Facets
+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
enumerationorthology +
+
enumerationone_to_one_orthology +
+
enumerationsuper_orthology +
+
enumerationparalogy +
+
enumerationultra_paralogy +
+
enumerationxenology +
+
enumerationunknown +
+
enumerationother +
+
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:SequenceRelation
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="type" type="phy:SequenceRelationType" use="required"/>
+
+
+
Attribute phy:Phylogeny / @rooted
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:boolean
+
Properties
+
+
+
+ + + + + +
userequired
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:Phylogeny
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="rooted" type="xs:boolean" use="required"/>
+
+
+
Attribute phy:Phylogeny / @rerootable
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:boolean
+
Properties
+
+
+
+ + + + + +
contentsimple
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:Phylogeny
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="rerootable" type="xs:boolean"/>
+
+
+
Attribute phy:Phylogeny / @branch_length_unit
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:token
+
Properties
+
+
+
+ + + + + +
contentsimple
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:Phylogeny
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="branch_length_unit" type="xs:token"/>
+
+
+
Attribute phy:Phylogeny / @type
+ + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + +
NamespaceNo namespace
Typexs:token
+
Properties
+
+
+
+ + + + + +
contentsimple
+
+
+
Used by
+
+
+
+ + + + + +
Complex Type phy:Phylogeny
+
+
+
Source
+
+
+
+ + + + +
<xs:attribute name="type" type="xs:token"/>
+
+
+
+ + \ No newline at end of file diff --git a/forester/phyloxml/oxygen/phyloxml_oxygen_project.xpr b/forester/phyloxml/oxygen/phyloxml_oxygen_project.xpr deleted file mode 100644 index 49f03e7..0000000 --- a/forester/phyloxml/oxygen/phyloxml_oxygen_project.xpr +++ /dev/null @@ -1,369 +0,0 @@ - - - - - - - - - scenario.associations - - - - phyloxml_test_document_2 - - - XSL - - - phyloxml_test_document_2.xml - - - - - - scenarios - - - - Execute DDXQuery - - - - - - - - - - - - - - - - - - ${currentFileURL} - - - - - - false - - - false - - - DD_XQUERY - - - true - - - false - - - - - - false - - - - - - false - - - false - - - true - - - false - - - true - - - - - - - - - DataDirect - - - - - - - - Execute SQL - - - - - - - - - - - - - - - - - - ${currentFileURL} - - - - - - false - - - false - - - SQL - - - true - - - false - - - - - - false - - - - - - false - - - false - - - false - - - false - - - true - - - - - - - - - JDBC - - - - - - - - Execute XQuery - - - - - - - - - - - - - - - - - - ${currentFileURL} - - - - - - false - - - false - - - XQUERY - - - true - - - false - - - - - - false - - - - - - false - - - false - - - true - - - false - - - true - - - - - - - - - Saxon9B XQuery - - - - - - - - phyloxml_test_document_2 - - - - - - - - - pdf - - - Built-in (Apache FOP) - - - - - - - - - ${currentFileURL} - - - true - - - false - - - XSL - - - true - - - false - - - - - - false - - - - - - false - - - false - - - true - - - false - - - true - - - - - - - - - Saxon6.5.5 - - - - - - - - - scenarios.load.from.project - true - - - - - - - - - - - - - - - - - - - - - - - - - - - - -