bio-phyloxml 0.9.0

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+ <?xml version="1.0" encoding="UTF-8"?>
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+ <!-- -->
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+ <!-- phyloXML -->
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+ <!-- -->
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+ <!-- schema in XMLSchema -->
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+ <!-- -->
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+ <!-- License: The phyloXML XML Schema Definition is -->
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+ <!-- dual-licensed under the LGPL or Ruby's -->
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+ <!-- License. -->
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+ <!-- You can redistribute and/or modify -->
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+ <!-- it under either the terms of the LGPL, -->
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+ <!-- or Ruby's License. -->
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+ <!-- see: http://www.ruby-lang.org/en/about/license.txt -->
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+ <!-- -->
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+ <!-- Copyright (c) 2008-2009 Christian M Zmasek -->
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+ <!-- -->
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+ <!-- www.phyloxml.org -->
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+ <!-- Version: 1.10 -->
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+ <!-- Last modified: 2009.11.17 by Christian M Zmasek -->
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+ <!-- -->
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+ <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:phy="http://www.phyloxml.org"
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+ targetNamespace="http://www.phyloxml.org" elementFormDefault="qualified" attributeFormDefault="unqualified">
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+ <xs:annotation>
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+ <xs:documentation> phyloXML is an XML language to describe evolutionary trees and associated data. Version: 1.10.
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+ License: dual-licensed under the LGPL or Ruby's License. Copyright (c) 2008-2009 Christian M Zmasek.</xs:documentation>
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+ </xs:annotation>
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+ <!-- phyloxml is the root element:-->
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+ <xs:element name="phyloxml" type="phy:Phyloxml"/>
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+ <!-- phyloXML definition:-->
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+ <xs:complexType name="Phyloxml">
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+ <xs:annotation>
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+ <xs:documentation> 'phyloxml' is the name of the root element. Phyloxml contains an arbitrary number of
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+ 'phylogeny' elements (each representing one phylogeny) possibly followed by elements from other namespaces.
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+ </xs:documentation>
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+ </xs:annotation>
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+ <xs:sequence maxOccurs="unbounded">
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+ <xs:element name="phylogeny" type="phy:Phylogeny" minOccurs="0" maxOccurs="unbounded"/>
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+ <xs:any minOccurs="0" maxOccurs="unbounded" processContents="lax" namespace="##other"/>
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+ </xs:sequence>
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+ </xs:complexType>
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+ <!-- Phylogeny:-->
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+ <xs:complexType name="Phylogeny">
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+ <xs:annotation>
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+ <xs:documentation> Element Phylogeny is used to represent a phylogeny. The required attribute 'rooted' is used
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+ to indicate whether the phylogeny is rooted or not. The attribute 'rerootable' can be used to indicate that
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+ the phylogeny is not allowed to be rooted differently (i.e. because it is associated with root dependent
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+ data, such as gene duplications). The attribute 'type' can be used to indicate the type of phylogeny (i.e.
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+ 'gene tree'). It is recommended to use the attribute 'branch_length_unit' if the phylogeny has branch
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+ lengths. Element clade is used in a recursive manner to describe the topology of a phylogenetic
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+ tree.</xs:documentation>
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+ </xs:annotation>
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+ <xs:sequence>
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+ <xs:element name="name" type="xs:token" minOccurs="0"/>
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+ <xs:element name="id" type="phy:Id" minOccurs="0"/>
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+ <xs:element name="description" type="xs:token" minOccurs="0"/>
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+ <xs:element name="date" type="xs:dateTime" minOccurs="0"/>
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+ <xs:element name="confidence" type="phy:Confidence" minOccurs="0" maxOccurs="unbounded"/>
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+ <xs:element name="clade" type="phy:Clade" minOccurs="0"/>
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+ <xs:element name="clade_relation" type="phy:CladeRelation" minOccurs="0" maxOccurs="unbounded"/>
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+ <xs:element name="sequence_relation" type="phy:SequenceRelation" minOccurs="0" maxOccurs="unbounded"/>
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+ <xs:element name="property" type="phy:Property" minOccurs="0" maxOccurs="unbounded"/>
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+ <xs:any minOccurs="0" maxOccurs="unbounded" processContents="lax" namespace="##other"/>
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+ </xs:sequence>
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+ <xs:attribute name="rooted" type="xs:boolean" use="required"/>
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+ <xs:attribute name="rerootable" type="xs:boolean"/>
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+ <xs:attribute name="branch_length_unit" type="xs:token"/>
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+ <xs:attribute name="type" type="xs:token"/>
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+ </xs:complexType>
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+ <!-- Clade:-->
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+ <xs:complexType name="Clade">
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+ <xs:annotation>
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+ <xs:documentation> Element Clade is used in a recursive manner to describe the topology of a phylogenetic tree.
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+ The parent branch length of a clade can be described either with the 'branch_length' element or the
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+ 'branch_length' attribute (it is not recommended to use both at the same time, though). Usage of the
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+ 'branch_length' attribute allows for a less verbose description. Element 'confidence' is used to indicate
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+ the support for a clade/parent branch. Element 'events' is used to describe such events as gene-duplications
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+ at the root node/parent branch of a clade. Element 'width' is the branch width for this clade (including
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+ parent branch). Both 'color' and 'width' elements apply for the whole clade unless overwritten in-sub
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+ clades. Attribute 'id_source' is used to link other elements to a clade (on the xml-level).
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+ </xs:documentation>
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+ </xs:annotation>
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+ <xs:sequence>
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+ <xs:element name="name" type="xs:token" minOccurs="0"/>
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+ <xs:element name="branch_length" type="xs:double" minOccurs="0"/>
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+ <xs:element name="confidence" type="phy:Confidence" minOccurs="0" maxOccurs="unbounded"/>
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+ <xs:element name="width" type="xs:double" minOccurs="0"/>
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+ <xs:element name="color" type="phy:BranchColor" minOccurs="0"/>
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+ <xs:element name="node_id" type="phy:Id" minOccurs="0"/>
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+ <xs:element name="taxonomy" type="phy:Taxonomy" minOccurs="0" maxOccurs="unbounded"/>
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+ <xs:element name="sequence" type="phy:Sequence" minOccurs="0" maxOccurs="unbounded"/>
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+ <xs:element name="events" type="phy:Events" minOccurs="0"/>
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+ <xs:element name="binary_characters" type="phy:BinaryCharacters" minOccurs="0"/>
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+ <xs:element name="distribution" type="phy:Distribution" minOccurs="0" maxOccurs="unbounded"/>
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+ <xs:element name="date" type="phy:Date" minOccurs="0"/>
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+ <xs:element name="reference" type="phy:Reference" minOccurs="0" maxOccurs="unbounded"/>
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+ <xs:element name="property" type="phy:Property" minOccurs="0" maxOccurs="unbounded"/>
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+ <xs:element name="clade" type="phy:Clade" minOccurs="0" maxOccurs="unbounded"/>
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+ <xs:any minOccurs="0" maxOccurs="unbounded" processContents="lax" namespace="##other"/>
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+ </xs:sequence>
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+ <xs:attribute name="branch_length" type="xs:double"/>
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+ <xs:attribute name="id_source" type="phy:id_source"/>
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+ </xs:complexType>
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+ <!-- Taxonomy:-->
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+ <xs:complexType name="Taxonomy">
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+ <xs:annotation>
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+ <xs:documentation> Element Taxonomy is used to describe taxonomic information for a clade. Element 'code' is
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+ intended to store UniProt/Swiss-Prot style organism codes (e.g. 'APLCA' for the California sea hare 'Aplysia
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+ californica') or other styles of mnemonics (e.g. 'Aca'). Element 'authority' is used to keep the authority,
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+ such as 'J. G. Cooper, 1863', associated with the 'scientific_name'. Element 'id' is used for a unique
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+ identifier of a taxon (for example '6500' with 'ncbi_taxonomy' as 'provider' for the California sea hare).
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+ Attribute 'id_source' is used to link other elements to a taxonomy (on the xml-level).</xs:documentation>
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+ </xs:annotation>
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+ <xs:sequence>
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+ <xs:element name="id" type="phy:Id" minOccurs="0"/>
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+ <xs:element name="code" type="phy:TaxonomyCode" minOccurs="0"/>
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+ <xs:element name="scientific_name" type="xs:token" minOccurs="0"/>
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+ <xs:element name="authority" type="xs:token" minOccurs="0"/>
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+ <xs:element name="common_name" type="xs:token" minOccurs="0" maxOccurs="unbounded"/>
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+ <xs:element name="synonym" type="xs:token" minOccurs="0" maxOccurs="unbounded"/>
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+ <xs:element name="rank" type="phy:Rank" minOccurs="0"/>
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+ <xs:element name="uri" type="phy:Uri" minOccurs="0"/>
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+ <xs:any minOccurs="0" maxOccurs="unbounded" processContents="lax" namespace="##other"/>
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+ </xs:sequence>
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+ <xs:attribute name="id_source" type="phy:id_source"/>
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+ </xs:complexType>
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+ <xs:simpleType name="TaxonomyCode">
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+ <xs:restriction base="xs:token">
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+ <xs:pattern value="[a-zA-Z0-9_]{2,10}"/>
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+ </xs:restriction>
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+ </xs:simpleType>
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+ <xs:simpleType name="Rank">
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+ <xs:restriction base="xs:token">
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+ <xs:enumeration value="domain"/>
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+ <xs:enumeration value="kingdom"/>
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+ <xs:enumeration value="subkingdom"/>
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+ <xs:enumeration value="branch"/>
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+ <xs:enumeration value="infrakingdom"/>
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+ <xs:enumeration value="superphylum"/>
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+ <xs:enumeration value="phylum"/>
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+ <xs:enumeration value="subphylum"/>
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+ <xs:enumeration value="infraphylum"/>
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+ <xs:enumeration value="microphylum"/>
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+ <xs:enumeration value="superdivision"/>
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+ <xs:enumeration value="division"/>
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+ <xs:enumeration value="subdivision"/>
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+ <xs:enumeration value="infradivision"/>
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+ <xs:enumeration value="superclass"/>
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+ <xs:enumeration value="class"/>
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+ <xs:enumeration value="subclass"/>
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+ <xs:enumeration value="infraclass"/>
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+ <xs:enumeration value="superlegion"/>
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+ <xs:enumeration value="legion"/>
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+ <xs:enumeration value="sublegion"/>
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+ <xs:enumeration value="infralegion"/>
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+ <xs:enumeration value="supercohort"/>
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+ <xs:enumeration value="cohort"/>
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+ <xs:enumeration value="subcohort"/>
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+ <xs:enumeration value="infracohort"/>
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+ <xs:enumeration value="superorder"/>
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+ <xs:enumeration value="order"/>
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+ <xs:enumeration value="suborder"/>
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+ <xs:enumeration value="superfamily"/>
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+ <xs:enumeration value="family"/>
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+ <xs:enumeration value="subfamily"/>
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+ <xs:enumeration value="supertribe"/>
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+ <xs:enumeration value="tribe"/>
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+ <xs:enumeration value="subtribe"/>
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+ <xs:enumeration value="infratribe"/>
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+ <xs:enumeration value="genus"/>
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+ <xs:enumeration value="subgenus"/>
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+ <xs:enumeration value="superspecies"/>
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+ <xs:enumeration value="species"/>
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+ <xs:enumeration value="subspecies"/>
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+ <xs:enumeration value="variety"/>
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+ <xs:enumeration value="subvariety"/>
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+ <xs:enumeration value="form"/>
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+ <xs:enumeration value="subform"/>
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+ <xs:enumeration value="cultivar"/>
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+ <xs:enumeration value="unknown"/>
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+ <xs:enumeration value="other"/>
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+ </xs:restriction>
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+ </xs:simpleType>
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+ <!-- Sequence:-->
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+ <xs:complexType name="Sequence">
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+ <xs:annotation>
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+ <xs:documentation> Element Sequence is used to represent a molecular sequence (Protein, DNA, RNA) associated
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+ with a node. 'symbol' is a short (maximal ten characters) symbol of the sequence (e.g. 'ACTM') whereas
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+ 'name' is used for the full name (e.g. 'muscle Actin'). 'location' is used for the location of a sequence on
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+ a genome/chromosome. The actual sequence can be stored with the 'mol_seq' element. Attribute 'type' is used
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+ to indicate the type of sequence ('dna', 'rna', or 'protein'). One intended use for 'id_ref' is to link a
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+ sequence to a taxonomy (via the taxonomy's 'id_source') in case of multiple sequences and taxonomies per
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+ node. </xs:documentation>
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+ </xs:annotation>
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+ <xs:sequence>
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+ <xs:element name="symbol" type="phy:SequenceSymbol" minOccurs="0"/>
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+ <xs:element name="accession" type="phy:Accession" minOccurs="0"/>
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+ <xs:element name="name" type="xs:token" minOccurs="0"/>
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+ <xs:element name="location" type="xs:token" minOccurs="0"/>
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+ <xs:element name="mol_seq" type="phy:MolSeq" minOccurs="0"/>
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+ <xs:element name="uri" type="phy:Uri" minOccurs="0"/>
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+ <xs:element name="annotation" type="phy:Annotation" minOccurs="0" maxOccurs="unbounded"/>
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+ <xs:element name="domain_architecture" type="phy:DomainArchitecture" minOccurs="0"/>
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+ <xs:any minOccurs="0" maxOccurs="unbounded" processContents="lax" namespace="##other"/>
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+ </xs:sequence>
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+ <xs:attribute name="type" type="phy:SequenceType"/>
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+ <xs:attribute name="id_source" type="phy:id_source"/>
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+ <xs:attribute name="id_ref" type="phy:id_ref"/>
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+ </xs:complexType>
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+ <xs:simpleType name="SequenceSymbol">
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+ <xs:restriction base="xs:token">
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+ <xs:pattern value="\S{1,10}"/>
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+ </xs:restriction>
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+ </xs:simpleType>
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+ <xs:complexType name="MolSeq">
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+ <xs:annotation>
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+ <xs:documentation> Element 'mol_seq' is used to store molecular sequences. The 'is_aligned' attribute is used
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+ to indicated that this molecular sequence is aligned with all other sequences in the same phylogeny for
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+ which 'is aligned' is true as well (which, in most cases, means that gaps were introduced, and that all
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+ sequences for which 'is aligned' is true must have the same length).</xs:documentation>
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+ </xs:annotation>
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+ <xs:simpleContent>
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+ <xs:extension base="phy:MolSeqChars">
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+ <xs:attribute name="is_aligned" type="xs:boolean"/>
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+ </xs:extension>
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+ </xs:simpleContent>
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+ </xs:complexType>
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+ <xs:simpleType name="MolSeqChars">
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+ <xs:restriction base="xs:token">
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+ <xs:pattern value="[a-zA-Z\.\-\?\*_]+"/>
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+ </xs:restriction>
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+ </xs:simpleType>
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+ <xs:simpleType name="SequenceType">
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+ <xs:restriction base="xs:token">
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+ <xs:enumeration value="rna"/>
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+ <xs:enumeration value="dna"/>
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+ <xs:enumeration value="protein"/>
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+ </xs:restriction>
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+ </xs:simpleType>
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+ <!-- Accession:-->
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+ <xs:complexType name="Accession">
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+ <xs:annotation>
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+ <xs:documentation> Element Accession is used to capture the local part in a sequence identifier (e.g. 'P17304'
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+ in 'UniProtKB:P17304', in which case the 'source' attribute would be 'UniProtKB'). </xs:documentation>
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+ </xs:annotation>
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+ <xs:simpleContent>
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+ <xs:extension base="xs:token">
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+ <xs:attribute name="source" type="xs:token" use="required"/>
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+ </xs:extension>
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+ </xs:simpleContent>
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+ </xs:complexType>
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+ <!-- DomainArchitecture: -->
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+ <xs:complexType name="DomainArchitecture">
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+ <xs:annotation>
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+ <xs:documentation> This is used describe the domain architecture of a protein. Attribute 'length' is the total
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+ length of the protein</xs:documentation>
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+ </xs:annotation>
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+ <xs:sequence>
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+ <xs:element name="domain" type="phy:ProteinDomain" minOccurs="1" maxOccurs="unbounded"/>
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+ </xs:sequence>
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+ <xs:attribute name="length" type="xs:nonNegativeInteger"/>
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+ </xs:complexType>
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+ <xs:complexType name="ProteinDomain">
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+ <xs:annotation>
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+ <xs:documentation> To represent an individual domain in a domain architecture. The name/unique identifier is
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+ described via the 'id' attribute. 'confidence' can be used to store (i.e.) E-values.</xs:documentation>
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+ </xs:annotation>
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+ <xs:simpleContent>
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+ <xs:extension base="xs:token">
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+ <xs:attribute name="from" type="xs:nonNegativeInteger" use="required"/>
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+ <xs:attribute name="to" type="xs:nonNegativeInteger" use="required"/>
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+ <xs:attribute name="confidence" type="xs:double"/>
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+ <xs:attribute name="id" type="xs:token"/>
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+ </xs:extension>
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+ </xs:simpleContent>
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+ </xs:complexType>
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+ <!-- Events:-->
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+ <xs:complexType name="Events">
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+ <xs:annotation>
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+ <xs:documentation> Events at the root node of a clade (e.g. one gene duplication). </xs:documentation>
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+ </xs:annotation>
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+ <xs:sequence>
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+ <xs:element name="type" type="phy:EventType" minOccurs="0"/>
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+ <xs:element name="duplications" type="xs:nonNegativeInteger" minOccurs="0"/>
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+ <xs:element name="speciations" type="xs:nonNegativeInteger" minOccurs="0"/>
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+ <xs:element name="losses" type="xs:nonNegativeInteger" minOccurs="0"/>
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+ <xs:element name="confidence" type="phy:Confidence" minOccurs="0"/>
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+ </xs:sequence>
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+ </xs:complexType>
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+ <xs:simpleType name="EventType">
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+ <xs:restriction base="xs:token">
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+ <xs:enumeration value="transfer"/>
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+ <xs:enumeration value="fusion"/>
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+ <xs:enumeration value="speciation_or_duplication"/>
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+ <xs:enumeration value="other"/>
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+ <xs:enumeration value="mixed"/>
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+ <xs:enumeration value="unassigned"/>
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+ </xs:restriction>
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+ </xs:simpleType>
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+ <!--BinaryCharacters:-->
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+ <xs:complexType name="BinaryCharacters">
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+ <xs:annotation>
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+ <xs:documentation> The names and/or counts of binary characters present, gained, and lost at the root of a
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+ clade. </xs:documentation>
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+ </xs:annotation>
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+ <xs:sequence>
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+ <xs:element name="gained" type="phy:BinaryCharacterList" minOccurs="0"/>
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+ <xs:element name="lost" type="phy:BinaryCharacterList" minOccurs="0"/>
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+ <xs:element name="present" type="phy:BinaryCharacterList" minOccurs="0"/>
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+ <xs:element name="absent" type="phy:BinaryCharacterList" minOccurs="0"/>
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+ </xs:sequence>
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+ <xs:attribute name="type" type="xs:token"/>
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+ <xs:attribute name="gained_count" type="xs:nonNegativeInteger"/>
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+ <xs:attribute name="lost_count" type="xs:nonNegativeInteger"/>
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+ <xs:attribute name="present_count" type="xs:nonNegativeInteger"/>
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+ <xs:attribute name="absent_count" type="xs:nonNegativeInteger"/>
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+ </xs:complexType>
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+ <xs:complexType name="BinaryCharacterList">
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+ <xs:sequence>
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+ <xs:element name="bc" type="xs:token" maxOccurs="unbounded"/>
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+ </xs:sequence>
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+ </xs:complexType>
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+ <!-- Reference:-->
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+ <xs:complexType name="Reference">
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+ <xs:annotation>
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+ <xs:documentation> A literature reference for a clade. It is recommended to use the 'doi' attribute instead of
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+ the free text 'desc' element whenever possible. </xs:documentation>
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+ </xs:annotation>
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+ <xs:sequence>
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+ <xs:element name="desc" type="xs:token" minOccurs="0"/>
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+ </xs:sequence>
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+ <xs:attribute name="doi" type="phy:Doi"/>
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+ </xs:complexType>
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+ <xs:simpleType name="Doi">
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+ <xs:restriction base="xs:token">
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+ <xs:pattern value="[a-zA-Z0-9_\.]+/\S+"/>
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+ </xs:restriction>
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+ </xs:simpleType>
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+ <!-- Annotation:-->
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+ <xs:complexType name="Annotation">
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+ <xs:annotation>
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+ <xs:documentation> The annotation of a molecular sequence. It is recommended to annotate by using the optional
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+ 'ref' attribute (some examples of acceptable values for the ref attribute: 'GO:0008270',
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+ 'KEGG:Tetrachloroethene degradation', 'EC:1.1.1.1'). Optional element 'desc' allows for a free text
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+ description. Optional element 'confidence' is used to state the type and value of support for a annotation.
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+ Similarly, optional attribute 'evidence' is used to describe the evidence for a annotation as free text
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+ (e.g. 'experimental'). Optional element 'property' allows for further, typed and referenced annotations from
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+ external resources.</xs:documentation>
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+ </xs:annotation>
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+ <xs:sequence>
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+ <xs:element name="desc" type="xs:token" minOccurs="0"/>
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+ <xs:element name="confidence" type="phy:Confidence" minOccurs="0"/>
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+ <xs:element name="property" type="phy:Property" minOccurs="0" maxOccurs="unbounded"/>
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+ <xs:element name="uri" type="phy:Uri" minOccurs="0"/>
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+ </xs:sequence>
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+ <xs:attribute name="ref" type="phy:ref"/>
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+ <xs:attribute name="source" type="xs:token"/>
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+ <xs:attribute name="evidence" type="xs:token"/>
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+ <xs:attribute name="type" type="xs:token"/>
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+ </xs:complexType>
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+ <!-- Property:-->
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+ <xs:complexType name="Property" mixed="true">
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+ <xs:annotation>
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+ <xs:documentation> Property allows for typed and referenced properties from external resources to be attached
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+ to 'Phylogeny', 'Clade', and 'Annotation'. The value of a property is its mixed (free text) content.
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+ Attribute 'datatype' indicates the type of a property and is limited to xsd-datatypes (e.g. 'xsd:string',
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+ 'xsd:boolean', 'xsd:integer', 'xsd:decimal', 'xsd:float', 'xsd:double', 'xsd:date', 'xsd:anyURI'). Attribute
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+ 'applies_to' indicates the item to which a property applies to (e.g. 'node' for the parent node of a clade,
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+ 'parent_branch' for the parent branch of a clade). Attribute 'id_ref' allows to attached a property
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+ specifically to one element (on the xml-level). Optional attribute 'unit' is used to indicate the unit of
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+ the property. An example: &lt;property datatype="xsd:integer" ref="NOAA:depth" applies_to="clade"
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+ unit="METRIC:m"&gt; 200 &lt;/property&gt; </xs:documentation>
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+ </xs:annotation>
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+ <xs:attribute name="ref" type="phy:ref" use="required"/>
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+ <xs:attribute name="unit" type="phy:ref"/>
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+ <xs:attribute name="datatype" type="phy:PropertyDataType" use="required"/>
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+ <xs:attribute name="applies_to" type="phy:AppliesTo" use="required"/>
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+ <xs:attribute name="id_ref" type="phy:id_ref"/>
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+ </xs:complexType>
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+ <xs:simpleType name="ref">
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+ <xs:restriction base="xs:token">
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+ <xs:pattern value="[a-zA-Z0-9_]+:[a-zA-Z0-9_\.\-\s]+"/>
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+ </xs:restriction>
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+ </xs:simpleType>
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+ <xs:simpleType name="AppliesTo">
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+ <xs:restriction base="xs:token">
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+ <xs:enumeration value="phylogeny"/>
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+ <xs:enumeration value="clade"/>
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+ <xs:enumeration value="node"/>
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+ <xs:enumeration value="annotation"/>
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+ <xs:enumeration value="parent_branch"/>
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+ <xs:enumeration value="other"/>
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+ </xs:restriction>
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+ </xs:simpleType>
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+ <xs:simpleType name="PropertyDataType">
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+ <xs:restriction base="xs:token">
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+ <xs:enumeration value="xsd:string"/>
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+ <xs:enumeration value="xsd:boolean"/>
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+ <xs:enumeration value="xsd:decimal"/>
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+ <xs:enumeration value="xsd:float"/>
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+ <xs:enumeration value="xsd:double"/>
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+ <xs:enumeration value="xsd:duration"/>
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+ <xs:enumeration value="xsd:dateTime"/>
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+ <xs:enumeration value="xsd:time"/>
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+ <xs:enumeration value="xsd:date"/>
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+ <xs:enumeration value="xsd:gYearMonth"/>
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+ <xs:enumeration value="xsd:gYear"/>
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+ <xs:enumeration value="xsd:gMonthDay"/>
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+ <xs:enumeration value="xsd:gDay"/>
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+ <xs:enumeration value="xsd:gMonth"/>
410
+ <xs:enumeration value="xsd:hexBinary"/>
411
+ <xs:enumeration value="xsd:base64Binary"/>
412
+ <xs:enumeration value="xsd:anyURI"/>
413
+ <xs:enumeration value="xsd:normalizedString"/>
414
+ <xs:enumeration value="xsd:token"/>
415
+ <xs:enumeration value="xsd:integer"/>
416
+ <xs:enumeration value="xsd:nonPositiveInteger"/>
417
+ <xs:enumeration value="xsd:negativeInteger"/>
418
+ <xs:enumeration value="xsd:long"/>
419
+ <xs:enumeration value="xsd:int"/>
420
+ <xs:enumeration value="xsd:short"/>
421
+ <xs:enumeration value="xsd:byte"/>
422
+ <xs:enumeration value="xsd:nonNegativeInteger"/>
423
+ <xs:enumeration value="xsd:unsignedLong"/>
424
+ <xs:enumeration value="xsd:unsignedInt"/>
425
+ <xs:enumeration value="xsd:unsignedShort"/>
426
+ <xs:enumeration value="xsd:unsignedByte"/>
427
+ <xs:enumeration value="xsd:positiveInteger"/>
428
+ </xs:restriction>
429
+ </xs:simpleType>
430
+ <!--Uri-->
431
+ <xs:complexType name="Uri">
432
+ <xs:annotation>
433
+ <xs:documentation> A uniform resource identifier. In general, this is expected to be an URL (for example, to
434
+ link to an image on a website, in which case the 'type' attribute might be 'image' and 'desc' might be
435
+ 'image of a California sea hare'). </xs:documentation>
436
+ </xs:annotation>
437
+ <xs:simpleContent>
438
+ <xs:extension base="xs:anyURI">
439
+ <xs:attribute name="desc" type="xs:token"/>
440
+ <xs:attribute name="type" type="xs:token"/>
441
+ </xs:extension>
442
+ </xs:simpleContent>
443
+ </xs:complexType>
444
+ <!-- Confidence:-->
445
+ <xs:complexType name="Confidence">
446
+ <xs:annotation>
447
+ <xs:documentation> A general purpose confidence element. For example this can be used to express the bootstrap
448
+ support value of a clade (in which case the 'type' attribute is 'bootstrap').</xs:documentation>
449
+ </xs:annotation>
450
+ <xs:simpleContent>
451
+ <xs:extension base="xs:double">
452
+ <xs:attribute name="type" type="xs:token" use="required"/>
453
+ </xs:extension>
454
+ </xs:simpleContent>
455
+ </xs:complexType>
456
+ <!-- Identifier:-->
457
+ <xs:complexType name="Id">
458
+ <xs:annotation>
459
+ <xs:documentation> A general purpose identifier element. Allows to indicate the provider (or authority) of an
460
+ identifier. </xs:documentation>
461
+ </xs:annotation>
462
+ <xs:simpleContent>
463
+ <xs:extension base="xs:token">
464
+ <xs:attribute name="provider" type="xs:token"/>
465
+ </xs:extension>
466
+ </xs:simpleContent>
467
+ </xs:complexType>
468
+ <!-- Distribution:-->
469
+ <xs:complexType name="Distribution">
470
+ <xs:annotation>
471
+ <xs:documentation> The geographic distribution of the items of a clade (species, sequences), intended for
472
+ phylogeographic applications. The location can be described either by free text in the 'desc' element and/or
473
+ by the coordinates of one or more 'Points' (similar to the 'Point' element in Google's KML format) or by
474
+ 'Polygons'. </xs:documentation>
475
+ </xs:annotation>
476
+ <xs:sequence>
477
+ <xs:element name="desc" type="xs:token" minOccurs="0"/>
478
+ <xs:element name="point" type="phy:Point" minOccurs="0" maxOccurs="unbounded"/>
479
+ <xs:element name="polygon" type="phy:Polygon" minOccurs="0" maxOccurs="unbounded"/>
480
+ </xs:sequence>
481
+ </xs:complexType>
482
+ <xs:complexType name="Point">
483
+ <xs:annotation>
484
+ <xs:documentation> The coordinates of a point with an optional altitude (used by element 'Distribution').
485
+ Required attributes are the 'geodetic_datum' used to indicate the geodetic datum (also called 'map datum',
486
+ for example Google's KML uses 'WGS84'). Attribute 'alt_unit' is the unit for the altitude (e.g. 'meter').
487
+ </xs:documentation>
488
+ </xs:annotation>
489
+ <xs:sequence>
490
+ <xs:element name="lat" type="xs:decimal"/>
491
+ <xs:element name="long" type="xs:decimal"/>
492
+ <xs:element name="alt" type="xs:decimal" minOccurs="0"/>
493
+ </xs:sequence>
494
+ <xs:attribute name="geodetic_datum" type="xs:token" use="required"/>
495
+ <xs:attribute name="alt_unit" type="xs:token"/>
496
+ </xs:complexType>
497
+ <xs:complexType name="Polygon">
498
+ <xs:annotation>
499
+ <xs:documentation> A polygon defined by a list of 'Points' (used by element 'Distribution').
500
+ </xs:documentation>
501
+ </xs:annotation>
502
+ <xs:sequence>
503
+ <xs:element name="point" type="phy:Point" minOccurs="3" maxOccurs="unbounded"/>
504
+ </xs:sequence>
505
+ </xs:complexType>
506
+ <!-- Date:-->
507
+ <xs:complexType name="Date">
508
+ <xs:annotation>
509
+ <xs:documentation> A date associated with a clade/node. Its value can be numerical by using the 'value' element
510
+ and/or free text with the 'desc' element' (e.g. 'Silurian'). If a numerical value is used, it is recommended
511
+ to employ the 'unit' attribute to indicate the type of the numerical value (e.g. 'mya' for 'million years
512
+ ago'). The elements 'minimum' and 'maximum' are used the indicate a range/confidence
513
+ interval</xs:documentation>
514
+ </xs:annotation>
515
+ <xs:sequence>
516
+ <xs:element name="desc" type="xs:token" minOccurs="0"/>
517
+ <xs:element name="value" type="xs:decimal" minOccurs="0"/>
518
+ <xs:element name="minimum" type="xs:decimal" minOccurs="0"/>
519
+ <xs:element name="maximum" type="xs:decimal" minOccurs="0"/>
520
+ </xs:sequence>
521
+ <xs:attribute name="unit" type="xs:token"/>
522
+ </xs:complexType>
523
+ <!-- BranchColor:-->
524
+ <xs:complexType name="BranchColor">
525
+ <xs:annotation>
526
+ <xs:documentation> This indicates the color of a clade when rendered (the color applies to the whole clade
527
+ unless overwritten by the color(s) of sub clades).</xs:documentation>
528
+ </xs:annotation>
529
+ <xs:sequence>
530
+ <xs:element name="red" type="xs:unsignedByte"/>
531
+ <xs:element name="green" type="xs:unsignedByte"/>
532
+ <xs:element name="blue" type="xs:unsignedByte"/>
533
+ </xs:sequence>
534
+ </xs:complexType>
535
+ <!-- SequenceRelation:-->
536
+ <xs:complexType name="SequenceRelation">
537
+ <xs:annotation>
538
+ <xs:documentation> This is used to express a typed relationship between two sequences. For example it could be
539
+ used to describe an orthology (in which case attribute 'type' is 'orthology'). </xs:documentation>
540
+ </xs:annotation>
541
+ <xs:sequence>
542
+ <xs:element name="confidence" type="phy:Confidence" minOccurs="0"/>
543
+ </xs:sequence>
544
+ <xs:attribute name="id_ref_0" type="phy:id_ref" use="required"/>
545
+ <xs:attribute name="id_ref_1" type="phy:id_ref" use="required"/>
546
+ <xs:attribute name="distance" type="xs:double"/>
547
+ <xs:attribute name="type" type="phy:SequenceRelationType" use="required"/>
548
+ </xs:complexType>
549
+ <xs:simpleType name="SequenceRelationType">
550
+ <xs:restriction base="xs:token">
551
+ <xs:enumeration value="orthology"/>
552
+ <xs:enumeration value="one_to_one_orthology"/>
553
+ <xs:enumeration value="super_orthology"/>
554
+ <xs:enumeration value="paralogy"/>
555
+ <xs:enumeration value="ultra_paralogy"/>
556
+ <xs:enumeration value="xenology"/>
557
+ <xs:enumeration value="unknown"/>
558
+ <xs:enumeration value="other"/>
559
+ </xs:restriction>
560
+ </xs:simpleType>
561
+ <!-- CladeRelation:-->
562
+ <xs:complexType name="CladeRelation">
563
+ <xs:annotation>
564
+ <xs:documentation> This is used to express a typed relationship between two clades. For example it could be
565
+ used to describe multiple parents of a clade.</xs:documentation>
566
+ </xs:annotation>
567
+ <xs:sequence>
568
+ <xs:element name="confidence" type="phy:Confidence" minOccurs="0"/>
569
+ </xs:sequence>
570
+ <xs:attribute name="id_ref_0" type="phy:id_ref" use="required"/>
571
+ <xs:attribute name="id_ref_1" type="phy:id_ref" use="required"/>
572
+ <xs:attribute name="distance" type="xs:double"/>
573
+ <xs:attribute name="type" type="xs:token" use="required"/>
574
+ </xs:complexType>
575
+ <!-- Used to link elements together on the xml level:-->
576
+ <xs:simpleType name="id_source">
577
+ <xs:restriction base="xs:ID"/>
578
+ </xs:simpleType>
579
+ <xs:simpleType name="id_ref">
580
+ <xs:restriction base="xs:IDREF"/>
581
+ </xs:simpleType>
582
+ </xs:schema>