schemas/embl.xsd

   1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
   2 <!--
   3     Retrieved for Jalview 14-Sep-2018 from ftp://ftp.sra.ebi.ac.uk/meta/xsd/sra_1_5/ENA.embl.xsd
   4         Modified to match ftp://ftp.sra.ebi.ac.uk/meta/xsd/sra_1_5/ENA.root.xsd with only ENA.embl.xsd included
   5         root element "ROOT" contains a <choice> of "entry" (single accession) or "entrySet" (one or more accessions)
   6         Java binding classes are generated by
   7                 xjc schemas/embl.xsd -b schemas/embl_bindings.xml -d src -p jalview.xml.binding.embl
   8 -->
   9 <xs:schema xmlns:ebi="http://www.ebi.ac.uk/embl/schema"
  10         xmlns:xs="http://www.w3.org/2001/XMLSchema"
  11         attributeFormDefault="unqualified" elementFormDefault="qualified"
  12         version="1.1">
  13         <xs:complexType name="XrefType">
  14                 <xs:annotation>
  15                         <xs:documentation>Database cross-reference.</xs:documentation>
  16                 </xs:annotation>
  17                 <xs:attribute name="db" type="xs:string" use="required" />
  18                 <xs:attribute name="id" type="xs:string" use="required" />
  19                 <xs:attribute name="secondaryId" type="xs:string"
  20                         use="optional" />
  21         </xs:complexType>
  22         <xs:complexType name="EntrySetType">
  23                 <xs:sequence minOccurs="1" maxOccurs="unbounded">
  24                         <xs:element name="entry" type="EntryType" />
  25                 </xs:sequence>
  26         </xs:complexType>
  27         <xs:complexType name="EntryType">
  28                 <xs:sequence>
  29                         <xs:element maxOccurs="unbounded" minOccurs="0"
  30                                 name="secondaryAccession" type="xs:string" />
  31                         <xs:element maxOccurs="unbounded" minOccurs="0"
  32                                 name="projectAccession" type="xs:string" />
  33                         <xs:element maxOccurs="1" minOccurs="1" name="description"
  34                                 type="xs:string" />
  35                         <xs:element maxOccurs="1" minOccurs="0" name="comment"
  36                                 type="xs:string" />
  37                         <xs:element maxOccurs="unbounded" minOccurs="0"
  38                                 name="keyword" type="xs:string" />
  39                         <xs:element maxOccurs="unbounded" minOccurs="0"
  40                                 name="reference">
  41                                 <xs:annotation>
  42                                         <xs:documentation>Not supported for EMBL-CDS.</xs:documentation>
  43                                 </xs:annotation>
  44                                 <xs:complexType>
  45                                         <xs:sequence>
  46                                                 <xs:element maxOccurs="1" minOccurs="0" name="title"
  47                                                         type="xs:string" />
  48                                                 <xs:element maxOccurs="unbounded" minOccurs="0"
  49                                                         name="author" type="xs:string" />
  50                                                 <xs:element maxOccurs="unbounded" minOccurs="0"
  51                                                         name="applicant" type="xs:string">
  52                                                         <xs:annotation>
  53                                                                 <xs:documentation>Patent applicant.</xs:documentation>
  54                                                         </xs:annotation>
  55                                                 </xs:element>
  56                                                 <xs:element maxOccurs="1" minOccurs="0"
  57                                                         name="consortium" type="xs:string" />
  58                                                 <xs:element maxOccurs="1" minOccurs="0"
  59                                                         name="submissionDate" type="xs:date">
  60                                                         <xs:annotation>
  61                                                                 <xs:documentation>The submission date (used only for submission
  62                                                                         references).</xs:documentation>
  63                                                         </xs:annotation>
  64                                                 </xs:element>
  65                                                 <xs:element maxOccurs="1" minOccurs="0" name="journal"
  66                                                         type="xs:string">
  67                                                         <xs:annotation>
  68                                                                 <xs:documentation>The journal name (used only for article
  69                                                                         references).</xs:documentation>
  70                                                         </xs:annotation>
  71                                                 </xs:element>
  72                                                 <xs:element maxOccurs="1" minOccurs="0" name="year"
  73                                                         type="xs:string">
  74                                                         <xs:annotation>
  75                                                                 <xs:documentation>The publication year (used only for article
  76                                                                         references).</xs:documentation>
  77                                                         </xs:annotation>
  78                                                 </xs:element>
  79                                                 <xs:element maxOccurs="1" minOccurs="0" name="volume"
  80                                                         type="xs:string">
  81                                                         <xs:annotation>
  82                                                                 <xs:documentation>The volume number (used only for article
  83                                                                         references).</xs:documentation>
  84                                                         </xs:annotation>
  85                                                 </xs:element>
  86                                                 <xs:element maxOccurs="1" minOccurs="0" name="issue"
  87                                                         type="xs:string">
  88                                                         <xs:annotation>
  89                                                                 <xs:documentation>The issue number (used only for article
  90                                                                         references).</xs:documentation>
  91                                                         </xs:annotation>
  92                                                 </xs:element>
  93                                                 <xs:element maxOccurs="1" minOccurs="0"
  94                                                         name="firstPage" type="xs:string">
  95                                                         <xs:annotation>
  96                                                                 <xs:documentation>The first page (used only for article
  97                                                                         references).</xs:documentation>
  98                                                         </xs:annotation>
  99                                                 </xs:element>
 100                                                 <xs:element maxOccurs="1" minOccurs="0" name="lastPage"
 101                                                         type="xs:string">
 102                                                         <xs:annotation>
 103                                                                 <xs:documentation>The last page (used only for article
 104                                                                         references).</xs:documentation>
 105                                                         </xs:annotation>
 106                                                 </xs:element>
 107                                                 <xs:element maxOccurs="1" minOccurs="0" name="comment"
 108                                                         type="xs:string" />
 109                                                 <xs:element maxOccurs="1" minOccurs="0"
 110                                                         name="referenceLocation" type="xs:string" />
 111                                                 <xs:element maxOccurs="unbounded" minOccurs="0"
 112                                                         name="xref" type="XrefType" />
 113                                         </xs:sequence>
 114                                         <xs:attribute name="type" use="required">
 115                                                 <xs:simpleType>
 116                                                         <xs:restriction base="xs:string">
 117                                                                 <xs:enumeration value="submission" />
 118                                                                 <xs:enumeration value="book" />
 119                                                                 <xs:enumeration value="article" />
 120                                                                 <xs:enumeration value="patent" />
 121                                                                 <xs:enumeration value="thesis" />
 122                                                                 <xs:enumeration value="unpublished" />
 123                                                         </xs:restriction>
 124                                                 </xs:simpleType>
 125                                         </xs:attribute>
 126                                         <xs:attribute name="number" type="xs:integer"
 127                                                 use="required" />
 128                                         <xs:attribute name="location" type="xs:string" />
 129                                 </xs:complexType>
 130                         </xs:element>
 131                         <xs:element maxOccurs="unbounded" minOccurs="0"
 132                                 name="xref" type="XrefType" />
 133                         <xs:element maxOccurs="unbounded" minOccurs="0"
 134                                 name="feature">
 135                                 <xs:annotation>
 136                                         <xs:documentation>Sequence feature.</xs:documentation>
 137                                 </xs:annotation>
 138                                 <xs:complexType>
 139                                         <xs:sequence>
 140                                                 <xs:element maxOccurs="1" minOccurs="0" name="taxon">
 141                                                         <xs:complexType>
 142                                                                 <xs:sequence>
 143                                                                         <xs:element maxOccurs="1" minOccurs="0"
 144                                                                                 name="lineage">
 145                                                                                 <xs:complexType>
 146                                                                                         <xs:sequence>
 147                                                                                                 <xs:element maxOccurs="unbounded" minOccurs="1"
 148                                                                                                         name="taxon">
 149                                                                                                         <xs:complexType>
 150                                                                                                                 <xs:attribute name="scientificName"
 151                                                                                                                         type="xs:string" use="required" />
 152                                                                                                         </xs:complexType>
 153                                                                                                 </xs:element>
 154                                                                                         </xs:sequence>
 155                                                                                 </xs:complexType>
 156                                                                         </xs:element>
 157                                                                 </xs:sequence>
 158                                                                 <xs:attribute name="scientificName"
 159                                                                         type="xs:string" use="required" />
 160                                                                 <xs:attribute name="commonName" type="xs:string"
 161                                                                         use="optional" />
 162                                                                 <xs:attribute name="taxId" type="xs:integer"
 163                                                                         use="optional" />
 164                                                         </xs:complexType>
 165                                                 </xs:element>
 166                                                 <xs:element maxOccurs="unbounded" minOccurs="0"
 167                                                         name="xref" type="XrefType" />
 168                                                 <xs:element maxOccurs="unbounded" minOccurs="0"
 169                                                         name="qualifier">
 170                                                         <xs:annotation>
 171                                                                 <xs:documentation>Sequence feature qualifier.</xs:documentation>
 172                                                         </xs:annotation>
 173                                                         <xs:complexType>
 174                                                                 <xs:sequence>
 175                                                                         <xs:element maxOccurs="1" minOccurs="0" name="value"
 176                                                                                 type="xs:string" />
 177                                                                 </xs:sequence>
 178                                                                 <xs:attribute name="name" type="xs:string"
 179                                                                         use="required" />
 180                                                         </xs:complexType>
 181                                                 </xs:element>
 182                                         </xs:sequence>
 183                                         <xs:attribute name="name" type="xs:string"
 184                                                 use="required" />
 185                                         <xs:attribute name="location" type="xs:string"
 186                                                 use="required" />
 187                                 </xs:complexType>
 188                         </xs:element>
 189                         <xs:element maxOccurs="1" minOccurs="0" name="assembly">
 190                                 <xs:complexType>
 191                                         <xs:sequence>
 192                                                 <xs:element maxOccurs="unbounded" minOccurs="1"
 193                                                         name="range">
 194                                                         <xs:complexType>
 195                                                                 <xs:attribute name="begin" type="xs:integer"
 196                                                                         use="required" />
 197                                                                 <xs:attribute name="end" type="xs:integer"
 198                                                                         use="required" />
 199                                                                 <xs:attribute name="primaryBegin" type="xs:integer"
 200                                                                         use="optional" />
 201                                                                 <xs:attribute name="primaryEnd" type="xs:integer"
 202                                                                         use="optional" />
 203                                                                 <xs:attribute name="accession" type="xs:string"
 204                                                                         use="required" />
 205                                                                 <xs:attribute name="version" type="xs:integer"
 206                                                                         use="required" />
 207                                                                 <xs:attribute default="false" name="complement"
 208                                                                         type="xs:boolean" use="optional" />
 209                                                         </xs:complexType>
 210                                                 </xs:element>
 211                                         </xs:sequence>
 212                                 </xs:complexType>
 213                         </xs:element>
 214                         <xs:element maxOccurs="1" minOccurs="0" name="contig">
 215                                 <xs:complexType>
 216                                         <xs:sequence>
 217                                                 <xs:choice maxOccurs="unbounded" minOccurs="0">
 218                                                         <xs:element maxOccurs="1" minOccurs="1" name="range">
 219                                                                 <xs:complexType>
 220                                                                         <xs:attribute name="begin" type="xs:integer"
 221                                                                                 use="required" />
 222                                                                         <xs:attribute name="end" type="xs:integer"
 223                                                                                 use="required" />
 224                                                                         <xs:attribute name="primaryBegin"
 225                                                                                 type="xs:integer" use="optional" />
 226                                                                         <xs:attribute name="primaryEnd" type="xs:integer"
 227                                                                                 use="optional" />
 228                                                                         <xs:attribute name="accession" type="xs:string"
 229                                                                                 use="required" />
 230                                                                         <xs:attribute name="version" type="xs:integer"
 231                                                                                 use="required" />
 232                                                                         <xs:attribute default="false" name="complement"
 233                                                                                 type="xs:boolean" use="optional" />
 234                                                                 </xs:complexType>
 235                                                         </xs:element>
 236                                                         <xs:element maxOccurs="1" minOccurs="1" name="gap">
 237                                                                 <xs:complexType>
 238                                                                         <xs:attribute name="begin" type="xs:integer"
 239                                                                                 use="required" />
 240                                                                         <xs:attribute name="end" type="xs:integer"
 241                                                                                 use="required" />
 242                                                                         <xs:attribute name="length" type="xs:integer"
 243                                                                                 use="required" />
 244                                                                         <xs:attribute default="false" name="unknownLength"
 245                                                                                 type="xs:boolean" use="optional" />
 246                                                                 </xs:complexType>
 247                                                         </xs:element>
 248                                                 </xs:choice>
 249                                         </xs:sequence>
 250                                 </xs:complexType>
 251                         </xs:element>
 252                         <xs:element maxOccurs="1" minOccurs="0" name="sequence"
 253                                 type="xs:string" />
 254                 </xs:sequence>
 255                 <xs:attribute name="accession" type="xs:string"
 256                         use="required" />
 257                 <xs:attribute name="version" type="xs:integer"
 258                         use="required" />
 259                 <xs:attribute name="entryVersion" type="xs:integer">
 260                         <xs:annotation>
 261                                 <xs:documentation>Not supported for EMBL-CDS.</xs:documentation>
 262                         </xs:annotation>
 263                 </xs:attribute>
 264                 <xs:attribute name="dataClass" type="xs:string"
 265                         use="required" />
 266                 <xs:attribute name="taxonomicDivision" type="xs:string"
 267                         use="required" />
 268                 <xs:attribute name="moleculeType" type="xs:string"
 269                         use="required" />
 270                 <xs:attribute name="sequenceLength" type="xs:integer"
 271                         use="required" />
 272                 <xs:attribute name="topology" use="required">
 273                         <xs:simpleType>
 274                                 <xs:restriction base="xs:string">
 275                                         <xs:enumeration value="circular" />
 276                                         <xs:enumeration value="linear" />
 277                                 </xs:restriction>
 278                         </xs:simpleType>
 279                 </xs:attribute>
 280                 <xs:attribute name="firstPublic" type="xs:date">
 281                         <xs:annotation>
 282                                 <xs:documentation>Not supported for EMBL-CDS.</xs:documentation>
 283                         </xs:annotation>
 284                 </xs:attribute>
 285                 <xs:attribute name="firstPublicRelease" type="xs:integer">
 286                         <xs:annotation>
 287                                 <xs:documentation>Not supported for EMBL-CDS.</xs:documentation>
 288                         </xs:annotation>
 289                 </xs:attribute>
 290                 <xs:attribute name="lastUpdated" type="xs:date">
 291                         <xs:annotation>
 292                                 <xs:documentation>Not supported for EMBL-CDS.</xs:documentation>
 293                         </xs:annotation>
 294                 </xs:attribute>
 295                 <xs:attribute name="lastUpdatedRelease" type="xs:integer">
 296                         <xs:annotation>
 297                                 <xs:documentation>Not supported for EMBL-CDS.</xs:documentation>
 298                         </xs:annotation>
 299                 </xs:attribute>
 300         </xs:complexType>
 301         <xs:element name="ROOT">
 302                 <xs:complexType>
 303                         <xs:choice>
 304                                 <xs:element name="entrySet" type="EntrySetType" />
 305                                 <xs:element name="entry" type="EntryType" />
 306                         </xs:choice>
 307                 </xs:complexType>
 308         </xs:element>
 309 </xs:schema>