forester/resources/phyloxml_schema/0.90/phyloxml.xsd

   1 <?xml version="1.0" encoding="UTF-8"?>
   2 <!--                                                -->
   3 <!-- phyloXML                                       -->
   4 <!--                                                -->
   5 <!-- schema in XMLSchema                            -->
   6 <!-- Version: 0.90                                  -->
   7 <!-- Last modifed: 2008.03.10 by Christian M Zmasek -->
   8 <!--                                                -->
   9 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:phy="http://www.phyloxml.org"
  10    targetNamespace="http://www.phyloxml.org" elementFormDefault="qualified" attributeFormDefault="unqualified">
  11    <!-- phyloxml is the root element:-->
  12    <xs:element name="phyloxml" type="phy:Phyloxml"/>
  13    <!-- phyloXML definition:-->
  14    <xs:complexType name="Phyloxml">
  15       <xs:sequence maxOccurs="unbounded">
  16          <xs:element name="phylogeny" type="phy:Phylogeny" minOccurs="0" maxOccurs="unbounded"/>
  17          <xs:any minOccurs="0" maxOccurs="unbounded" processContents="lax" namespace="##other"/>
  18       </xs:sequence>
  19    </xs:complexType>
  20    <!-- Phylogeny:-->
  21    <xs:complexType name="Phylogeny">
  22       <xs:sequence>
  23          <xs:element name="name" type="xs:token" minOccurs="0"/>
  24          <xs:element name="id" type="phy:Id" minOccurs="0"/>
  25          <xs:element name="description" type="xs:token" minOccurs="0"/>
  26          <xs:element name="date" type="xs:dateTime" minOccurs="0"/>
  27          <xs:element name="confidence" type="phy:Confidence" minOccurs="0" maxOccurs="unbounded"/>
  28          <xs:element name="clade" type="phy:Clade" minOccurs="0"/>
  29          <xs:element name="clade_relation" type="phy:CladeRelation" minOccurs="0" maxOccurs="unbounded"/>
  30          <xs:element name="sequence_relation" type="phy:SequenceRelation" minOccurs="0" maxOccurs="unbounded"/>
  31          <xs:element name="custom" type="phy:Custom" minOccurs="0" maxOccurs="unbounded"/>
  32          <xs:any minOccurs="0" maxOccurs="unbounded" processContents="lax" namespace="##other"/>
  33       </xs:sequence>
  34       <xs:attribute name="rooted" type="xs:boolean" use="required"/>
  35       <xs:attribute name="rerootable" type="xs:boolean"/>
  36       <xs:attribute name="distance_unit" type="xs:token"/>
  37       <xs:attribute name="type" type="xs:token"/>
  38    </xs:complexType>
  39    <!-- Clade:-->
  40    <xs:complexType name="Clade">
  41       <xs:sequence>
  42          <xs:element name="name" type="xs:token" minOccurs="0"/>
  43          <xs:element name="distance" type="xs:double" minOccurs="0"/>
  44          <xs:element name="confidence" type="phy:Confidence" minOccurs="0" maxOccurs="unbounded"/>
  45          <xs:element name="width" type="xs:double" minOccurs="0"/>
  46          <xs:element name="color" type="phy:BranchColor" minOccurs="0"/>
  47          <xs:element name="node_id" type="phy:Id" minOccurs="0"/>
  48          <xs:element name="taxonomy" type="phy:Taxonomy" minOccurs="0" maxOccurs="unbounded"/>
  49          <xs:element name="sequence" type="phy:Sequence" minOccurs="0" maxOccurs="unbounded"/>
  50          <xs:element name="event" type="phy:Event" minOccurs="0"/>
  51          <xs:element name="binary_characters" type="phy:BinaryCharacters" minOccurs="0"/>
  52          <xs:element name="distribution" type="xs:token" minOccurs="0"/>
  53          <xs:element name="date" type="xs:token" minOccurs="0"/>
  54          <xs:element name="clade" type="phy:Clade" minOccurs="0" maxOccurs="unbounded"/>
  55          <xs:element name="custom" type="phy:Custom" minOccurs="0"/>
  56          <xs:any minOccurs="0" maxOccurs="unbounded" processContents="lax" namespace="##other"/>
  57       </xs:sequence>
  58       <xs:attribute name="distance" type="xs:double"/>
  59       <xs:attribute name="id_source" type="phy:id_source"/>
  60    </xs:complexType>
  61    <!-- Taxonomy:-->
  62    <xs:complexType name="Taxonomy">
  63       <xs:sequence>
  64          <xs:element name="id" type="phy:Id" minOccurs="0"/>
  65          <xs:element name="code" type="phy:TaxonomyCode" minOccurs="0"/>
  66          <xs:element name="scientific_name" type="xs:token" minOccurs="0"/>
  67          <xs:element name="common_name" type="xs:token" minOccurs="0"/>
  68          <xs:element name="rank" type="phy:Rank" minOccurs="0"/>
  69          <xs:element name="uri" type="phy:Uri" minOccurs="0"/>
  70          <xs:any minOccurs="0" maxOccurs="unbounded" processContents="lax" namespace="##other"/>
  71       </xs:sequence>
  72       <xs:attribute name="type" type="xs:token"/>
  73    </xs:complexType>
  74    <xs:simpleType name="TaxonomyCode">
  75       <xs:restriction base="xs:token">
  76          <xs:pattern value="[a-zA-Z0-9_]{2,20}"/>
  77       </xs:restriction>
  78    </xs:simpleType>
  79    <xs:simpleType name="Rank">
  80       <xs:restriction base="xs:token">
  81          <xs:enumeration value="domain"/>
  82          <xs:enumeration value="kingdom"/>
  83          <xs:enumeration value="branch"/>
  84          <xs:enumeration value="phylum"/>
  85          <xs:enumeration value="subphylum"/>
  86          <xs:enumeration value="division"/>
  87          <xs:enumeration value="superclass"/>
  88          <xs:enumeration value="class"/>
  89          <xs:enumeration value="subclass"/>
  90          <xs:enumeration value="superorder"/>
  91          <xs:enumeration value="order"/>
  92          <xs:enumeration value="suborder"/>
  93          <xs:enumeration value="superfamily"/>
  94          <xs:enumeration value="family"/>
  95          <xs:enumeration value="subfamily"/>
  96          <xs:enumeration value="genus"/>
  97          <xs:enumeration value="subgenus"/>
  98          <xs:enumeration value="species"/>
  99          <xs:enumeration value="subspecies"/>
 100          <xs:enumeration value="variety"/>
 101          <xs:enumeration value="form"/>
 102          <xs:enumeration value="cultivar"/>
 103          <xs:enumeration value="unknown"/>
 104          <xs:enumeration value="other"/>
 105       </xs:restriction>
 106    </xs:simpleType>
 107    <!-- Sequence:-->
 108    <xs:complexType name="Sequence">
 109       <xs:sequence>
 110          <xs:element name="id" type="phy:Id" minOccurs="0"/>
 111          <xs:element name="accession" type="xs:token" minOccurs="0"/>
 112          <xs:element name="gene_name" type="xs:token" minOccurs="0"/>
 113          <xs:element name="location" type="xs:token" minOccurs="0"/>
 114          <xs:element name="mol_seq" type="phy:MolSeq" minOccurs="0"/>
 115          <xs:element name="uri" type="phy:Uri" minOccurs="0"/>
 116          <xs:element name="annotation" type="phy:Annotation" minOccurs="0" maxOccurs="unbounded"/>
 117          <xs:element name="domain_architecture" type="phy:DomainArchitecture" minOccurs="0"/>
 118          <xs:any minOccurs="0" maxOccurs="unbounded" processContents="lax" namespace="##other"/>
 119       </xs:sequence>
 120       <xs:attribute name="id_source" type="phy:id_source"/>
 121       <xs:attribute name="type" type="xs:token"/>
 122    </xs:complexType>
 123    <xs:simpleType name="MolSeq">
 124       <xs:restriction base="xs:token">
 125          <xs:pattern value="[a-zA-Z\.\-\?\*_]+"/>
 126       </xs:restriction>
 127    </xs:simpleType>
 128    <!-- DomainArchitecture: -->
 129    <xs:complexType name="DomainArchitecture">
 130       <xs:sequence>
 131          <xs:element name="domain" type="phy:ProteinDomain" minOccurs="1" maxOccurs="unbounded"/>
 132       </xs:sequence>
 133       <xs:attribute name="length" type="xs:nonNegativeInteger"/>
 134    </xs:complexType>
 135    <xs:complexType name="ProteinDomain">
 136       <xs:simpleContent>
 137          <xs:extension base="xs:token">
 138             <xs:attribute name="from" type="xs:nonNegativeInteger" use="required"/>
 139             <xs:attribute name="to" type="xs:nonNegativeInteger" use="required"/>
 140             <xs:attribute name="confidence" type="xs:double"/>
 141             <xs:attribute name="id" type="xs:token"/>
 142          </xs:extension>
 143       </xs:simpleContent>
 144    </xs:complexType>
 145    <!-- Event:-->
 146    <xs:complexType name="Event">
 147       <xs:sequence>
 148          <xs:element name="type" type="phy:EventType" minOccurs="0"/>
 149          <xs:element name="duplications" type="xs:nonNegativeInteger" minOccurs="0"/>
 150          <xs:element name="speciations" type="xs:nonNegativeInteger" minOccurs="0"/>
 151          <xs:element name="losses" type="xs:nonNegativeInteger" minOccurs="0"/>
 152          <xs:element name="confidence" type="phy:Confidence" minOccurs="0"/>
 153       </xs:sequence>
 154    </xs:complexType>
 155    <xs:simpleType name="EventType">
 156       <xs:restriction base="xs:token">
 157          <xs:enumeration value="transfer"/>
 158          <xs:enumeration value="fusion"/>
 159          <xs:enumeration value="root"/>
 160          <xs:enumeration value="speciation_or_duplication"/>
 161          <xs:enumeration value="other"/>
 162          <xs:enumeration value="mixed"/>
 163          <xs:enumeration value="unassigned"/>
 164       </xs:restriction>
 165    </xs:simpleType>
 166    <!--BinaryCharacters:-->
 167    <xs:complexType name="BinaryCharacters">
 168       <xs:sequence>
 169          <xs:element name="gained" type="phy:BinaryCharacterList" minOccurs="0"/>
 170          <xs:element name="lost" type="phy:BinaryCharacterList" minOccurs="0"/>
 171          <xs:element name="present" type="phy:BinaryCharacterList" minOccurs="0"/>
 172          <xs:element name="absent" type="phy:BinaryCharacterList" minOccurs="0"/>
 173       </xs:sequence>
 174       <xs:attribute name="type" type="xs:token"/>
 175       <xs:attribute name="gained_count" type="xs:nonNegativeInteger"/>
 176       <xs:attribute name="lost_count" type="xs:nonNegativeInteger"/>
 177       <xs:attribute name="present_count" type="xs:nonNegativeInteger"/>
 178       <xs:attribute name="absent_count" type="xs:nonNegativeInteger"/>
 179    </xs:complexType>
 180    <xs:complexType name="BinaryCharacterList">
 181       <xs:sequence>
 182          <xs:element name="bc" type="xs:token" maxOccurs="unbounded"/>
 183       </xs:sequence>
 184    </xs:complexType>
 185    <!-- Annotation:-->
 186    <xs:complexType mixed="true" name="Annotation">
 187       <xs:sequence>
 188          <xs:element name="id" type="phy:Id" minOccurs="0"/>
 189          <xs:element name="confidence" type="phy:Confidence" minOccurs="0"/>
 190          <xs:element name="uri" type="phy:Uri" minOccurs="0"/>
 191       </xs:sequence>
 192       <xs:attribute name="type" type="xs:token"/>
 193    </xs:complexType>
 194    <!-- Custom:-->
 195    <xs:complexType name="Custom">
 196       <xs:sequence>
 197          <xs:element name="name" type="xs:token"/>
 198          <xs:element name="value" type="xs:token"/>
 199       </xs:sequence>
 200       <xs:attribute name="unit" type="xs:token"/>
 201       <xs:attribute name="custom_type" type="phy:CustomType" use="required"/>
 202       <xs:attribute name="custom_property" type="phy:CustomProperty" use="required"/>
 203       <xs:attribute name="id_ref" type="phy:id_ref"/>
 204    </xs:complexType>
 205    <xs:simpleType name="CustomType">
 206       <xs:restriction base="xs:token">
 207          <xs:enumeration value="string"/>
 208          <xs:enumeration value="character"/>
 209          <xs:enumeration value="decimal"/>
 210          <xs:enumeration value="integer"/>
 211          <xs:enumeration value="byte"/>
 212          <xs:enumeration value="boolean"/>
 213          <xs:enumeration value="uri"/>
 214          <xs:enumeration value="other"/>
 215       </xs:restriction>
 216    </xs:simpleType>
 217    <xs:simpleType name="CustomProperty">
 218       <xs:restriction base="xs:token">
 219          <xs:enumeration value="phylogeny"/>
 220          <xs:enumeration value="clade"/>
 221          <xs:enumeration value="node"/>
 222          <xs:enumeration value="sequence"/>
 223          <xs:enumeration value="taxonomy"/>
 224          <xs:enumeration value="other"/>
 225       </xs:restriction>
 226    </xs:simpleType>
 227    <!--Uri-->
 228    <xs:complexType name="Uri">
 229       <xs:simpleContent>
 230          <xs:extension base="xs:anyURI">
 231             <xs:attribute name="desc" type="xs:token"/>
 232             <xs:attribute name="type" type="xs:token"/>
 233          </xs:extension>
 234       </xs:simpleContent>
 235    </xs:complexType>
 236    <!-- Confidence:-->
 237    <xs:complexType name="Confidence">
 238       <xs:simpleContent>
 239          <xs:extension base="xs:double">
 240             <xs:attribute name="type" type="xs:token" use="required"/>
 241          </xs:extension>
 242       </xs:simpleContent>
 243    </xs:complexType>
 244    <!-- Identifier:-->
 245    <xs:complexType name="Id">
 246       <xs:simpleContent>
 247          <xs:extension base="xs:token">
 248             <xs:attribute name="type" type="xs:token"/>
 249          </xs:extension>
 250       </xs:simpleContent>
 251    </xs:complexType>
 252    <!-- Distribution:-->
 253    <xs:simpleType name="Distribution">
 254       <xs:restriction base="xs:token"/>
 255    </xs:simpleType>
 256    <!-- BranchColor:-->
 257    <xs:complexType name="BranchColor">
 258       <xs:sequence>
 259          <xs:element name="red" type="xs:unsignedByte"/>
 260          <xs:element name="green" type="xs:unsignedByte"/>
 261          <xs:element name="blue" type="xs:unsignedByte"/>
 262       </xs:sequence>
 263    </xs:complexType>
 264    <!-- SequenceRelation:-->
 265    <xs:complexType name="SequenceRelation">
 266       <xs:sequence>
 267          <xs:element name="confidence" type="phy:Confidence" minOccurs="0"/>
 268       </xs:sequence>
 269       <xs:attribute name="id_ref_0" type="phy:id_ref" use="required"/>
 270       <xs:attribute name="id_ref_1" type="phy:id_ref" use="required"/>
 271       <xs:attribute name="distance" type="xs:double"/>
 272       <xs:attribute name="type" type="phy:SequenceRelationType" use="required"/>
 273    </xs:complexType>
 274    <xs:simpleType name="SequenceRelationType">
 275       <xs:restriction base="xs:token">
 276          <xs:enumeration value="orthology"/>
 277          <xs:enumeration value="one_to_one_orthology"/>
 278          <xs:enumeration value="super_orthology"/>
 279          <xs:enumeration value="paralogy"/>
 280          <xs:enumeration value="ultra_paralogy"/>
 281          <xs:enumeration value="xenology"/>
 282          <xs:enumeration value="unknown"/>
 283          <xs:enumeration value="other"/>
 284       </xs:restriction>
 285    </xs:simpleType>
 286    <!-- CladeRelation:-->
 287    <xs:complexType name="CladeRelation">
 288       <xs:sequence>
 289          <xs:element name="confidence" type="phy:Confidence" minOccurs="0"/>
 290       </xs:sequence>
 291       <xs:attribute name="id_ref_0" type="phy:id_ref" use="required"/>
 292       <xs:attribute name="id_ref_1" type="phy:id_ref" use="required"/>
 293       <xs:attribute name="distance" type="xs:double"/>
 294       <xs:attribute name="type" type="xs:token" use="required"/>
 295    </xs:complexType>
 296    <!-- Used to link elements together on the xml level:-->
 297    <xs:simpleType name="id_source">
 298       <xs:restriction base="xs:ID"/>
 299    </xs:simpleType>
 300    <xs:simpleType name="id_ref">
 301       <xs:restriction base="xs:IDREF"/>
 302    </xs:simpleType>
 303 </xs:schema>