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Annotations
Attributes
Diagrams
Facets
Instances
Model
Properties
Source
Used by
Main schema phyloxml.xsd
Namespace http://www.phyloxml.org
Annotations
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.
Properties
attribute form default unqualified
element form default qualified
Element phy:phyloxml
Namespace http://www.phyloxml.org
Diagram
Diagram phyloxml_xsd.tmp#http___www.phyloxml.org_Phyloxml_phylogeny phyloxml_xsd.tmp#http___www.phyloxml.org_Phyloxml
Type phy:Phyloxml
Properties
content complex
Model
phy:phylogeny* , ANY element from ANY namespace OTHER than 'http://www.phyloxml.org'
Children phy:phylogeny
Instance
<phy:phyloxml xmlns:phy="http://www.phyloxml.org">
  <phy:phylogeny branch_length_unit="" rerootable="" rooted="" type="">{0,unbounded}</phy:phylogeny>
</phy:phyloxml>
Source
<xs:element name="phyloxml" type="phy:Phyloxml"/>
Element phy:Phyloxml / phy:phylogeny
Namespace http://www.phyloxml.org
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 phyloxml_xsd.tmp#Phylogeny
Type phy:Phylogeny
Properties
content complex
minOccurs 0
maxOccurs unbounded
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'
Children phy:clade, phy:clade_relation, phy:confidence, phy:date, phy:description, phy:id, phy:name, phy:property, phy:sequence_relation
Instance
<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>
Attributes
QName Type Use
branch_length_unit xs:token optional
rerootable xs:boolean optional
rooted xs:boolean required
type xs:token optional
Source
<xs:element name="phylogeny" type="phy:Phylogeny" minOccurs="0" maxOccurs="unbounded"/>
Element phy:Phylogeny / phy:name
Namespace http://www.phyloxml.org
Diagram
Diagram
Type xs:token
Properties
content simple
minOccurs 0
Source
<xs:element name="name" type="xs:token" minOccurs="0"/>
Element phy:Phylogeny / phy:id
Namespace http://www.phyloxml.org
Diagram
Diagram phyloxml_xsd.tmp#Id_provider phyloxml_xsd.tmp#Id
Type phy:Id
Properties
content complex
minOccurs 0
Attributes
QName Type Use
provider xs:token optional
Source
<xs:element name="id" type="phy:Id" minOccurs="0"/>
Element phy:Phylogeny / phy:description
Namespace http://www.phyloxml.org
Diagram
Diagram
Type xs:token
Properties
content simple
minOccurs 0
Source
<xs:element name="description" type="xs:token" minOccurs="0"/>
Element phy:Phylogeny / phy:date
Namespace http://www.phyloxml.org
Diagram
Diagram
Type xs:dateTime
Properties
content simple
minOccurs 0
Source
<xs:element name="date" type="xs:dateTime" minOccurs="0"/>
Element phy:Phylogeny / phy:confidence
Namespace http://www.phyloxml.org
Diagram
Diagram phyloxml_xsd.tmp#Confidence_type phyloxml_xsd.tmp#Confidence_stddev phyloxml_xsd.tmp#Confidence
Type phy:Confidence
Properties
content complex
minOccurs 0
maxOccurs unbounded
Attributes
QName Type Use
stddev xs:double optional
type xs:token required
Source
<xs:element name="confidence" type="phy:Confidence" minOccurs="0" maxOccurs="unbounded"/>
Element phy:Phylogeny / phy:clade
Namespace http://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
Type phy:Clade
Properties
content complex
minOccurs 0
Model
Children phy: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
QName Type Use
branch_length xs:double optional
collapse xs:boolean optional
id_source phy:id_source optional
Source
<xs:element name="clade" type="phy:Clade" minOccurs="0"/>
Element phy:Clade / phy:name
Namespace http://www.phyloxml.org
Diagram
Diagram
Type xs:token
Properties
content simple
minOccurs 0
Source
<xs:element name="name" type="xs:token" minOccurs="0"/>
Element phy:Clade / phy:branch_length
Namespace http://www.phyloxml.org
Diagram
Diagram
Type xs:double
Properties
content simple
minOccurs 0
Source
<xs:element name="branch_length" type="xs:double" minOccurs="0"/>
Element phy:Clade / phy:confidence
Namespace http://www.phyloxml.org
Diagram
Diagram phyloxml_xsd.tmp#Confidence_type phyloxml_xsd.tmp#Confidence_stddev phyloxml_xsd.tmp#Confidence
Type phy:Confidence
Properties
content complex
minOccurs 0
maxOccurs unbounded
Attributes
QName Type Use
stddev xs:double optional
type xs:token required
Source
<xs:element name="confidence" type="phy:Confidence" minOccurs="0" maxOccurs="unbounded"/>
Element phy:Clade / phy:width
Namespace http://www.phyloxml.org
Diagram
Diagram
Type xs:double
Properties
content simple
minOccurs 0
Source
<xs:element name="width" type="xs:double" minOccurs="0"/>
Element phy:Clade / phy:color
Namespace http://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
Type phy:BranchColor
Properties
content complex
minOccurs 0
Model
Children phy: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
Namespace http://www.phyloxml.org
Diagram
Diagram
Type xs:unsignedByte
Properties
content simple
Source
<xs:element name="red" type="xs:unsignedByte"/>
Element phy:BranchColor / phy:green
Namespace http://www.phyloxml.org
Diagram
Diagram
Type xs:unsignedByte
Properties
content simple
Source
<xs:element name="green" type="xs:unsignedByte"/>
Element phy:BranchColor / phy:blue
Namespace http://www.phyloxml.org
Diagram
Diagram
Type xs:unsignedByte
Properties
content simple
Source
<xs:element name="blue" type="xs:unsignedByte"/>
Element phy:BranchColor / phy:alpha
Namespace http://www.phyloxml.org
Diagram
Diagram
Type xs:unsignedByte
Properties
content simple
minOccurs 0
Source
<xs:element name="alpha" type="xs:unsignedByte" minOccurs="0"/>
Element phy:Clade / phy:taxonomy
Namespace http://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
Type phy:Taxonomy
Properties
content complex
minOccurs 0
maxOccurs unbounded
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'
Children phy: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
QName Type Use
id_source phy:id_source optional
Source
<xs:element name="taxonomy" type="phy:Taxonomy" minOccurs="0" maxOccurs="unbounded"/>
Element phy:Taxonomy / phy:id
Namespace http://www.phyloxml.org
Diagram
Diagram phyloxml_xsd.tmp#Id_provider phyloxml_xsd.tmp#Id
Type phy:Id
Properties
content complex
minOccurs 0
Attributes
QName Type Use
provider xs:token optional
Source
<xs:element name="id" type="phy:Id" minOccurs="0"/>
Element phy:Taxonomy / phy:code
Namespace http://www.phyloxml.org
Diagram
Diagram phyloxml_xsd.tmp#TaxonomyCode
Type phy:TaxonomyCode
Properties
content simple
minOccurs 0
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
Namespace http://www.phyloxml.org
Diagram
Diagram
Type xs:token
Properties
content simple
minOccurs 0
Source
<xs:element name="scientific_name" type="xs:token" minOccurs="0"/>
Element phy:Taxonomy / phy:authority
Namespace http://www.phyloxml.org
Diagram
Diagram
Type xs:token
Properties
content simple
minOccurs 0
Source
<xs:element name="authority" type="xs:token" minOccurs="0"/>
Element phy:Taxonomy / phy:common_name
Namespace http://www.phyloxml.org
Diagram
Diagram
Type xs:token
Properties
content simple
minOccurs 0
Source
<xs:element name="common_name" type="xs:token" minOccurs="0"/>
Element phy:Taxonomy / phy:synonym
Namespace http://www.phyloxml.org
Diagram
Diagram
Type xs:token
Properties
content simple
minOccurs 0
maxOccurs unbounded
Source
<xs:element name="synonym" type="xs:token" minOccurs="0" maxOccurs="unbounded"/>
Element phy:Taxonomy / phy:rank
Namespace http://www.phyloxml.org
Diagram
Diagram phyloxml_xsd.tmp#Rank
Type phy:Rank
Properties
content simple
minOccurs 0
Facets
enumeration domain
enumeration superkingdom
enumeration kingdom
enumeration subkingdom
enumeration branch
enumeration infrakingdom
enumeration superphylum
enumeration phylum
enumeration subphylum
enumeration infraphylum
enumeration microphylum
enumeration superdivision
enumeration division
enumeration subdivision
enumeration infradivision
enumeration superclass
enumeration class
enumeration subclass
enumeration infraclass
enumeration superlegion
enumeration legion
enumeration sublegion
enumeration infralegion
enumeration supercohort
enumeration cohort
enumeration subcohort
enumeration infracohort
enumeration magnorder
enumeration superorder
enumeration order
enumeration suborder
enumeration infraorder
enumeration superfamily
enumeration family
enumeration subfamily
enumeration supertribe
enumeration tribe
enumeration subtribe
enumeration infratribe
enumeration genus
enumeration subgenus
enumeration superspecies
enumeration species
enumeration subspecies
enumeration variety
enumeration varietas
enumeration subvariety
enumeration form
enumeration subform
enumeration cultivar
enumeration strain
enumeration section
enumeration subsection
enumeration unknown
enumeration other
Source
<xs:element name="rank" type="phy:Rank" minOccurs="0"/>
Element phy:Taxonomy / phy:uri
Namespace http://www.phyloxml.org
Diagram
Diagram phyloxml_xsd.tmp#Uri_desc phyloxml_xsd.tmp#Uri_type phyloxml_xsd.tmp#Uri
Type phy:Uri
Properties
content complex
minOccurs 0
maxOccurs unbounded
Attributes
QName Type Use
desc xs:token optional
type xs:token optional
Source
<xs:element name="uri" type="phy:Uri" minOccurs="0" maxOccurs="unbounded"/>
Element phy:Clade / phy:sequence
Namespace http://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
Type phy:Sequence
Properties
content complex
minOccurs 0
maxOccurs unbounded
Model
Children phy: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
QName Type Use
id_ref phy:id_ref optional
id_source phy:id_source optional
type phy:SequenceType optional
Source
<xs:element name="sequence" type="phy:Sequence" minOccurs="0" maxOccurs="unbounded"/>
Element phy:Sequence / phy:symbol
Namespace http://www.phyloxml.org
Diagram
Diagram phyloxml_xsd.tmp#SequenceSymbol
Type phy:SequenceSymbol
Properties
content simple
minOccurs 0
Facets
pattern \S{1,20}
Source
<xs:element name="symbol" type="phy:SequenceSymbol" minOccurs="0"/>
Element phy:Sequence / phy:accession
Namespace http://www.phyloxml.org
Diagram
Diagram phyloxml_xsd.tmp#Accession_source phyloxml_xsd.tmp#Accession_comment phyloxml_xsd.tmp#Accession
Type phy:Accession
Properties
content complex
minOccurs 0
Attributes
QName Type Use
comment xs:token optional
source xs:token required
Source
<xs:element name="accession" type="phy:Accession" minOccurs="0"/>
Element phy:Sequence / phy:name
Namespace http://www.phyloxml.org
Diagram
Diagram
Type xs:token
Properties
content simple
minOccurs 0
Source
<xs:element name="name" type="xs:token" minOccurs="0"/>
Element phy:Sequence / phy:gene_name
Namespace http://www.phyloxml.org
Diagram
Diagram
Type xs:token
Properties
content simple
minOccurs 0
Source
<xs:element name="gene_name" type="xs:token" minOccurs="0"/>
Element phy:Sequence / phy:location
Namespace http://www.phyloxml.org
Diagram
Diagram
Type xs:token
Properties
content simple
minOccurs 0
Source
<xs:element name="location" type="xs:token" minOccurs="0"/>
Element phy:Sequence / phy:mol_seq
Namespace http://www.phyloxml.org
Diagram
Diagram phyloxml_xsd.tmp#MolSeq_is_aligned phyloxml_xsd.tmp#MolSeq
Type phy:MolSeq
Properties
content complex
minOccurs 0
Attributes
QName Type Use
is_aligned xs:boolean optional
Source
<xs:element name="mol_seq" type="phy:MolSeq" minOccurs="0"/>
Element phy:Sequence / phy:uri
Namespace http://www.phyloxml.org
Diagram
Diagram phyloxml_xsd.tmp#Uri_desc phyloxml_xsd.tmp#Uri_type phyloxml_xsd.tmp#Uri
Type phy:Uri
Properties
content complex
minOccurs 0
maxOccurs unbounded
Attributes
QName Type Use
desc xs:token optional
type xs:token optional
Source
<xs:element name="uri" type="phy:Uri" minOccurs="0" maxOccurs="unbounded"/>
Element phy:Sequence / phy:annotation
Namespace http://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
Type phy:Annotation
Properties
content complex
minOccurs 0
maxOccurs unbounded
Model
Children phy: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
QName Type Use
evidence xs:token optional
ref phy:ref optional
source xs:token optional
type xs:token optional
Source
<xs:element name="annotation" type="phy:Annotation" minOccurs="0" maxOccurs="unbounded"/>
Element phy:Annotation / phy:desc
Namespace http://www.phyloxml.org
Diagram
Diagram
Type xs:token
Properties
content simple
minOccurs 0
Source
<xs:element name="desc" type="xs:token" minOccurs="0"/>
Element phy:Annotation / phy:confidence
Namespace http://www.phyloxml.org
Diagram
Diagram phyloxml_xsd.tmp#Confidence_type phyloxml_xsd.tmp#Confidence_stddev phyloxml_xsd.tmp#Confidence
Type phy:Confidence
Properties
content complex
minOccurs 0
Attributes
QName Type Use
stddev xs:double optional
type xs:token required
Source
<xs:element name="confidence" type="phy:Confidence" minOccurs="0"/>
Element phy:Annotation / phy:property
Namespace http://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
Type phy:Property
Properties
content complex
minOccurs 0
maxOccurs unbounded
mixed true
Model
Attributes
QName Type Use
applies_to phy:AppliesTo required
datatype phy:PropertyDataType required
id_ref phy:id_ref optional
ref phy:ref required
unit phy:ref optional
Source
<xs:element name="property" type="phy:Property" minOccurs="0" maxOccurs="unbounded"/>
Element phy:Annotation / phy:uri
Namespace http://www.phyloxml.org
Diagram
Diagram phyloxml_xsd.tmp#Uri_desc phyloxml_xsd.tmp#Uri_type phyloxml_xsd.tmp#Uri
Type phy:Uri
Properties
content complex
minOccurs 0
maxOccurs unbounded
Attributes
QName Type Use
desc xs:token optional
type xs:token optional
Source
<xs:element name="uri" type="phy:Uri" minOccurs="0" maxOccurs="unbounded"/>
Element phy:Sequence / phy:cross_references
Namespace http://www.phyloxml.org
Diagram
Diagram phyloxml_xsd.tmp#CrossReferences_accession phyloxml_xsd.tmp#CrossReferences
Type phy:CrossReferences
Properties
content complex
minOccurs 0
Model
Children phy: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
Namespace http://www.phyloxml.org
Diagram
Diagram phyloxml_xsd.tmp#Accession_source phyloxml_xsd.tmp#Accession_comment phyloxml_xsd.tmp#Accession
Type phy:Accession
Properties
content complex
minOccurs 1
maxOccurs unbounded
Attributes
QName Type Use
comment xs:token optional
source xs:token required
Source
<xs:element name="accession" type="phy:Accession" minOccurs="1" maxOccurs="unbounded"/>
Element phy:Sequence / phy:domain_architecture
Namespace http://www.phyloxml.org
Diagram
Diagram phyloxml_xsd.tmp#DomainArchitecture_length phyloxml_xsd.tmp#DomainArchitecture_domain phyloxml_xsd.tmp#DomainArchitecture
Type phy:DomainArchitecture
Properties
content complex
minOccurs 0
Model
Children phy: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
QName Type Use
length xs:nonNegativeInteger optional
Source
<xs:element name="domain_architecture" type="phy:DomainArchitecture" minOccurs="0"/>
Element phy:DomainArchitecture / phy:domain
Namespace http://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
Type phy:ProteinDomain
Properties
content complex
minOccurs 1
maxOccurs unbounded
Attributes
QName Type Use
confidence xs:double optional
from xs:nonNegativeInteger required
id xs:token optional
to xs:nonNegativeInteger required
Source
<xs:element name="domain" type="phy:ProteinDomain" minOccurs="1" maxOccurs="unbounded"/>
Element phy:Clade / phy:events
Namespace http://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
Type phy:Events
Properties
content complex
minOccurs 0
Model
Children phy: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
Namespace http://www.phyloxml.org
Diagram
Diagram phyloxml_xsd.tmp#EventType
Type phy:EventType
Properties
content simple
minOccurs 0
Facets
enumeration transfer
enumeration fusion
enumeration speciation_or_duplication
enumeration other
enumeration mixed
enumeration unassigned
Source
<xs:element name="type" type="phy:EventType" minOccurs="0"/>
Element phy:Events / phy:duplications
Namespace http://www.phyloxml.org
Diagram
Diagram
Type xs:nonNegativeInteger
Properties
content simple
minOccurs 0
Source
<xs:element name="duplications" type="xs:nonNegativeInteger" minOccurs="0"/>
Element phy:Events / phy:speciations
Namespace http://www.phyloxml.org
Diagram
Diagram
Type xs:nonNegativeInteger
Properties
content simple
minOccurs 0
Source
<xs:element name="speciations" type="xs:nonNegativeInteger" minOccurs="0"/>
Element phy:Events / phy:losses
Namespace http://www.phyloxml.org
Diagram
Diagram
Type xs:nonNegativeInteger
Properties
content simple
minOccurs 0
Source
<xs:element name="losses" type="xs:nonNegativeInteger" minOccurs="0"/>
Element phy:Events / phy:confidence
Namespace http://www.phyloxml.org
Diagram
Diagram phyloxml_xsd.tmp#Confidence_type phyloxml_xsd.tmp#Confidence_stddev phyloxml_xsd.tmp#Confidence
Type phy:Confidence
Properties
content complex
minOccurs 0
Attributes
QName Type Use
stddev xs:double optional
type xs:token required
Source
<xs:element name="confidence" type="phy:Confidence" minOccurs="0"/>
Element phy:Clade / phy:binary_characters
Namespace http://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
Type phy:BinaryCharacters
Properties
content complex
minOccurs 0
Model
Children phy: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
QName Type Use
absent_count xs:nonNegativeInteger optional
gained_count xs:nonNegativeInteger optional
lost_count xs:nonNegativeInteger optional
present_count xs:nonNegativeInteger optional
type xs:token optional
Source
<xs:element name="binary_characters" type="phy:BinaryCharacters" minOccurs="0"/>
Element phy:BinaryCharacters / phy:gained
Namespace http://www.phyloxml.org
Diagram
Diagram phyloxml_xsd.tmp#BinaryCharacterList_bc phyloxml_xsd.tmp#BinaryCharacterList
Type phy:BinaryCharacterList
Properties
content complex
minOccurs 0
Model
Children phy: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
Namespace http://www.phyloxml.org
Diagram
Diagram
Type xs:token
Properties
content simple
maxOccurs unbounded
Source
<xs:element name="bc" type="xs:token" maxOccurs="unbounded"/>
Element phy:BinaryCharacters / phy:lost
Namespace http://www.phyloxml.org
Diagram
Diagram phyloxml_xsd.tmp#BinaryCharacterList_bc phyloxml_xsd.tmp#BinaryCharacterList
Type phy:BinaryCharacterList
Properties
content complex
minOccurs 0
Model
Children phy: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
Namespace http://www.phyloxml.org
Diagram
Diagram phyloxml_xsd.tmp#BinaryCharacterList_bc phyloxml_xsd.tmp#BinaryCharacterList
Type phy:BinaryCharacterList
Properties
content complex
minOccurs 0
Model
Children phy: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
Namespace http://www.phyloxml.org
Diagram
Diagram phyloxml_xsd.tmp#BinaryCharacterList_bc phyloxml_xsd.tmp#BinaryCharacterList
Type phy:BinaryCharacterList
Properties
content complex
minOccurs 0
Model
Children phy: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
Namespace http://www.phyloxml.org
Diagram
Diagram phyloxml_xsd.tmp#Distribution_desc phyloxml_xsd.tmp#Distribution_point phyloxml_xsd.tmp#Distribution_polygon phyloxml_xsd.tmp#Distribution
Type phy:Distribution
Properties
content complex
minOccurs 0
maxOccurs unbounded
Model
Children phy: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
Namespace http://www.phyloxml.org
Diagram
Diagram
Type xs:token
Properties
content simple
minOccurs 0
Source
<xs:element name="desc" type="xs:token" minOccurs="0"/>
Element phy:Distribution / phy:point
Namespace http://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
Type phy:Point
Properties
content complex
minOccurs 0
maxOccurs unbounded
Model
Children phy: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
QName Type Use
alt_unit xs:token optional
geodetic_datum xs:token required
Source
<xs:element name="point" type="phy:Point" minOccurs="0" maxOccurs="unbounded"/>
Element phy:Point / phy:lat
Namespace http://www.phyloxml.org
Diagram
Diagram
Type xs:decimal
Properties
content simple
Source
<xs:element name="lat" type="xs:decimal"/>
Element phy:Point / phy:long
Namespace http://www.phyloxml.org
Diagram
Diagram
Type xs:decimal
Properties
content simple
Source
<xs:element name="long" type="xs:decimal"/>
Element phy:Point / phy:alt
Namespace http://www.phyloxml.org
Diagram
Diagram
Type xs:decimal
Properties
content simple
minOccurs 0
Source
<xs:element name="alt" type="xs:decimal" minOccurs="0"/>
Element phy:Distribution / phy:polygon
Namespace http://www.phyloxml.org
Diagram
Diagram phyloxml_xsd.tmp#Polygon_point phyloxml_xsd.tmp#Polygon
Type phy:Polygon
Properties
content complex
minOccurs 0
maxOccurs unbounded
Model
Children phy: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
Namespace http://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
Type phy:Point
Properties
content complex
minOccurs 3
maxOccurs unbounded
Model
Children phy: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
QName Type Use
alt_unit xs:token optional
geodetic_datum xs:token required
Source
<xs:element name="point" type="phy:Point" minOccurs="3" maxOccurs="unbounded"/>
Element phy:Clade / phy:date
Namespace http://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
Type phy:Date
Properties
content complex
minOccurs 0
Model
Children phy: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
QName Type Use
unit xs:token optional
Source
<xs:element name="date" type="phy:Date" minOccurs="0"/>
Element phy:Date / phy:desc
Namespace http://www.phyloxml.org
Diagram
Diagram
Type xs:token
Properties
content simple
minOccurs 0
Source
<xs:element name="desc" type="xs:token" minOccurs="0"/>
Element phy:Date / phy:value
Namespace http://www.phyloxml.org
Diagram
Diagram
Type xs:decimal
Properties
content simple
minOccurs 0
Source
<xs:element name="value" type="xs:decimal" minOccurs="0"/>
Element phy:Date / phy:minimum
Namespace http://www.phyloxml.org
Diagram
Diagram
Type xs:decimal
Properties
content simple
minOccurs 0
Source
<xs:element name="minimum" type="xs:decimal" minOccurs="0"/>
Element phy:Date / phy:maximum
Namespace http://www.phyloxml.org
Diagram
Diagram
Type xs:decimal
Properties
content simple
minOccurs 0
Source
<xs:element name="maximum" type="xs:decimal" minOccurs="0"/>
Element phy:Clade / phy:reference
Namespace http://www.phyloxml.org
Diagram
Diagram phyloxml_xsd.tmp#Reference_doi phyloxml_xsd.tmp#Reference_desc phyloxml_xsd.tmp#Reference
Type phy:Reference
Properties
content complex
minOccurs 0
maxOccurs unbounded
Model
Children phy:desc
Instance
<phy:reference doi="" xmlns:phy="http://www.phyloxml.org">
  <phy:desc>{0,1}</phy:desc>
</phy:reference>
Attributes
QName Type Use
doi xs:token optional
Source
<xs:element name="reference" type="phy:Reference" minOccurs="0" maxOccurs="unbounded"/>
Element phy:Reference / phy:desc
Namespace http://www.phyloxml.org
Diagram
Diagram
Type xs:token
Properties
content simple
minOccurs 0
Source
<xs:element name="desc" type="xs:token" minOccurs="0"/>
Element phy:Clade / phy:property
Namespace http://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
Type phy:Property
Properties
content complex
minOccurs 0
maxOccurs unbounded
mixed true
Model
Attributes
QName Type Use
applies_to phy:AppliesTo required
datatype phy:PropertyDataType required
id_ref phy:id_ref optional
ref phy:ref required
unit phy:ref optional
Source
<xs:element name="property" type="phy:Property" minOccurs="0" maxOccurs="unbounded"/>
Element phy:Clade / phy:clade
Namespace http://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
Type phy:Clade
Properties
content complex
minOccurs 0
maxOccurs unbounded
Model
Children phy: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
QName Type Use
branch_length xs:double optional
collapse xs:boolean optional
id_source phy:id_source optional
Source
<xs:element name="clade" type="phy:Clade" minOccurs="0" maxOccurs="unbounded"/>
Element phy:Phylogeny / phy:clade_relation
Namespace http://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
Type phy:CladeRelation
Properties
content complex
minOccurs 0
maxOccurs unbounded
Model
Children phy: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
QName Type Use
distance xs:double optional
id_ref_0 phy:id_ref required
id_ref_1 phy:id_ref required
type xs:token required
Source
<xs:element name="clade_relation" type="phy:CladeRelation" minOccurs="0" maxOccurs="unbounded"/>
Element phy:CladeRelation / phy:confidence
Namespace http://www.phyloxml.org
Diagram
Diagram phyloxml_xsd.tmp#Confidence_type phyloxml_xsd.tmp#Confidence_stddev phyloxml_xsd.tmp#Confidence
Type phy:Confidence
Properties
content complex
minOccurs 0
Attributes
QName Type Use
stddev xs:double optional
type xs:token required
Source
<xs:element name="confidence" type="phy:Confidence" minOccurs="0"/>
Element phy:Phylogeny / phy:sequence_relation
Namespace http://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
Type phy:SequenceRelation
Properties
content complex
minOccurs 0
maxOccurs unbounded
Model
Children phy: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
QName Type Use
distance xs:double optional
id_ref_0 phy:id_ref required
id_ref_1 phy:id_ref required
type phy:SequenceRelationType required
Source
<xs:element name="sequence_relation" type="phy:SequenceRelation" minOccurs="0" maxOccurs="unbounded"/>
Element phy:SequenceRelation / phy:confidence
Namespace http://www.phyloxml.org
Diagram
Diagram phyloxml_xsd.tmp#Confidence_type phyloxml_xsd.tmp#Confidence_stddev phyloxml_xsd.tmp#Confidence
Type phy:Confidence
Properties
content complex
minOccurs 0
Attributes
QName Type Use
stddev xs:double optional
type xs:token required
Source
<xs:element name="confidence" type="phy:Confidence" minOccurs="0"/>
Element phy:Phylogeny / phy:property
Namespace http://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
Type phy:Property
Properties
content complex
minOccurs 0
maxOccurs unbounded
mixed true
Model
Attributes
QName Type Use
applies_to phy:AppliesTo required
datatype phy:PropertyDataType required
id_ref phy:id_ref optional
ref phy:ref required
unit phy:ref optional
Source
<xs:element name="property" type="phy:Property" minOccurs="0" maxOccurs="unbounded"/>
Complex Type phy:Phyloxml
Namespace http://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'
Children phy: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
Namespace http://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
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'
Children phy:clade, phy:clade_relation, phy:confidence, phy:date, phy:description, phy:id, phy:name, phy:property, phy:sequence_relation
Attributes
QName Type Use
branch_length_unit xs:token optional
rerootable xs:boolean optional
rooted xs:boolean required
type xs:token optional
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
Namespace http://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
Type extension of xs:token
Used by
Attributes
QName Type Use
provider xs:token optional
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
Namespace http://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
Type extension of xs:double
Used by
Attributes
QName Type Use
stddev xs:double optional
type xs:token required
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
Namespace http://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
Children phy: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
QName Type Use
branch_length xs:double optional
collapse xs:boolean optional
id_source phy:id_source optional
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
Namespace http://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
Model
Children phy: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
Namespace http://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
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'
Children phy:authority, phy:code, phy:common_name, phy:id, phy:rank, phy:scientific_name, phy:synonym, phy:uri
Attributes
QName Type Use
id_source phy:id_source optional
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
Namespace http://www.phyloxml.org
Diagram
Diagram
Type restriction of xs:token
Facets
pattern ([A-Z9][A-Z]{2}[A-Z0-9]{2})|RAT|PIG|PEA
Used by
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
Namespace http://www.phyloxml.org
Diagram
Diagram
Type restriction of xs:token
Facets
enumeration domain
enumeration superkingdom
enumeration kingdom
enumeration subkingdom
enumeration branch
enumeration infrakingdom
enumeration superphylum
enumeration phylum
enumeration subphylum
enumeration infraphylum
enumeration microphylum
enumeration superdivision
enumeration division
enumeration subdivision
enumeration infradivision
enumeration superclass
enumeration class
enumeration subclass
enumeration infraclass
enumeration superlegion
enumeration legion
enumeration sublegion
enumeration infralegion
enumeration supercohort
enumeration cohort
enumeration subcohort
enumeration infracohort
enumeration magnorder
enumeration superorder
enumeration order
enumeration suborder
enumeration infraorder
enumeration superfamily
enumeration family
enumeration subfamily
enumeration supertribe
enumeration tribe
enumeration subtribe
enumeration infratribe
enumeration genus
enumeration subgenus
enumeration superspecies
enumeration species
enumeration subspecies
enumeration variety
enumeration varietas
enumeration subvariety
enumeration form
enumeration subform
enumeration cultivar
enumeration strain
enumeration section
enumeration subsection
enumeration unknown
enumeration other
Used by
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
Namespace http://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
Type extension of xs:anyURI
Used by
Attributes
QName Type Use
desc xs:token optional
type xs:token optional
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
Namespace http://www.phyloxml.org
Diagram
Diagram
Type xs:ID
Used by
Source
<xs:simpleType name="id_source">
  <xs:restriction base="xs:ID"/>
</xs:simpleType>
Complex Type phy:Sequence
Namespace http://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
Model
Children phy:accession, phy:annotation, phy:cross_references, phy:domain_architecture, phy:gene_name, phy:location, phy:mol_seq, phy:name, phy:symbol, phy:uri
Attributes
QName Type Use
id_ref phy:id_ref optional
id_source phy:id_source optional
type phy:SequenceType optional
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
Namespace http://www.phyloxml.org
Diagram
Diagram
Type restriction of xs:token
Facets
pattern \S{1,20}
Used by
Source
<xs:simpleType name="SequenceSymbol">
  <xs:restriction base="xs:token">
    <xs:pattern value="\S{1,20}"/>
  </xs:restriction>
</xs:simpleType>
Complex Type phy:Accession
Namespace http://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
Type extension of xs:token
Used by
Attributes
QName Type Use
comment xs:token optional
source xs:token required
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
Namespace http://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
Type extension of xs:token
Used by
Attributes
QName Type Use
is_aligned xs:boolean optional
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
Namespace http://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
Model
Children phy:confidence, phy:desc, phy:property, phy:uri
Attributes
QName Type Use
evidence xs:token optional
ref phy:ref optional
source xs:token optional
type xs:token optional
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
Namespace http://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
mixed true
Used by
Model
Attributes
QName Type Use
applies_to phy:AppliesTo required
datatype phy:PropertyDataType required
id_ref phy:id_ref optional
ref phy:ref required
unit phy:ref optional
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
Namespace http://www.phyloxml.org
Diagram
Diagram
Type restriction 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
Namespace http://www.phyloxml.org
Diagram
Diagram
Type restriction of xs:token
Facets
enumeration xsd:string
enumeration xsd:boolean
enumeration xsd:decimal
enumeration xsd:float
enumeration xsd:double
enumeration xsd:duration
enumeration xsd:dateTime
enumeration xsd:time
enumeration xsd:date
enumeration xsd:gYearMonth
enumeration xsd:gYear
enumeration xsd:gMonthDay
enumeration xsd:gDay
enumeration xsd:gMonth
enumeration xsd:hexBinary
enumeration xsd:base64Binary
enumeration xsd:anyURI
enumeration xsd:normalizedString
enumeration xsd:token
enumeration xsd:integer
enumeration xsd:nonPositiveInteger
enumeration xsd:negativeInteger
enumeration xsd:long
enumeration xsd:int
enumeration xsd:short
enumeration xsd:byte
enumeration xsd:nonNegativeInteger
enumeration xsd:unsignedLong
enumeration xsd:unsignedInt
enumeration xsd:unsignedShort
enumeration xsd:unsignedByte
enumeration xsd:positiveInteger
Used by
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
Namespace http://www.phyloxml.org
Diagram
Diagram
Type restriction of xs:token
Facets
enumeration phylogeny
enumeration clade
enumeration node
enumeration annotation
enumeration parent_branch
enumeration other
Used by
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
Namespace http://www.phyloxml.org
Diagram
Diagram
Type xs:IDREF
Used by
Source
<xs:simpleType name="id_ref">
  <xs:restriction base="xs:IDREF"/>
</xs:simpleType>
Complex Type phy:CrossReferences
Namespace http://www.phyloxml.org
Annotations
Used to store accessions to additional resources.
Diagram
Diagram phyloxml_xsd.tmp#CrossReferences_accession
Used by
Model
Children phy: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
Namespace http://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
Model
Children phy:domain
Attributes
QName Type Use
length xs:nonNegativeInteger optional
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
Namespace http://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
Type extension of xs:token
Used by
Attributes
QName Type Use
confidence xs:double optional
from xs:nonNegativeInteger required
id xs:token optional
to xs:nonNegativeInteger required
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
Namespace http://www.phyloxml.org
Diagram
Diagram
Type restriction of xs:token
Facets
enumeration rna
enumeration dna
enumeration protein
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
Namespace http://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
Model
Children phy: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
Namespace http://www.phyloxml.org
Diagram
Diagram
Type restriction of xs:token
Facets
enumeration transfer
enumeration fusion
enumeration speciation_or_duplication
enumeration other
enumeration mixed
enumeration unassigned
Used by
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
Namespace http://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
Model
Children phy:absent, phy:gained, phy:lost, phy:present
Attributes
QName Type Use
absent_count xs:nonNegativeInteger optional
gained_count xs:nonNegativeInteger optional
lost_count xs:nonNegativeInteger optional
present_count xs:nonNegativeInteger optional
type xs:token optional
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
Namespace http://www.phyloxml.org
Diagram
Diagram phyloxml_xsd.tmp#BinaryCharacterList_bc
Used by
Model
Children phy: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
Namespace http://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
Model
Children phy: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
Namespace http://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
Children phy:alt, phy:lat, phy:long
Attributes
QName Type Use
alt_unit xs:token optional
geodetic_datum xs:token required
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
Namespace http://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
Model
Children phy:point
Source