schemas/vamsas.xsd

   1 <?xml version="1.0" encoding="UTF-8"?>
   2 <!-- edited with XMLSPY v5 rel. 4 U (http://www.xmlspy.com) by MSD (EMBL OUTSTATION THE EBI WELLCOME TRUST GENOME CAMPUS) -->
   3 <!-- edited with XMLSpy v2006 sp1 U (http://www.altova.com) by ioh[ (o[ih[oh) -->
   4 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes" targetNamespace="http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes" elementFormDefault="qualified" attributeFormDefault="unqualified">
   5         <xs:annotation>
   6                 <xs:documentation> Vorba ID - Vamsas Object Request Broker Address ID (name needs to be
   7                         worked on): Suggest it could be of the form documentRoot/datasetName/SequenceUID for a
   8                         dataset sequence. Alignment sequence: documentRoot/datasetName/AlignmentId/SequenceUID
   9                         for an aligned form of a dataset sequence </xs:documentation>
  10         </xs:annotation>
  11         <xs:element name="VAMSAS">
  12                 <xs:annotation>
  13                         <xs:documentation> contains unassociated trees and a number of analysis sets
  14                         </xs:documentation>
  15                 </xs:annotation>
  16                 <xs:complexType>
  17                         <xs:sequence>
  18                                 <xs:element ref="vamsas:Tree" minOccurs="0" maxOccurs="unbounded"/>
  19                                 <xs:element ref="vamsas:DataSet" minOccurs="0" maxOccurs="unbounded"/>
  20                         </xs:sequence>
  21                         <xs:attribute name="id" type="xs:ID" use="optional">
  22                                 <xs:annotation>
  23                                         <xs:documentation> Primary Key for vamsas object referencing </xs:documentation>
  24                                 </xs:annotation>
  25                         </xs:attribute>
  26                         <xs:attribute name="modifiable" type="vamsas:locks" use="optional"/>
  27                 </xs:complexType>
  28         </xs:element>
  29         <xs:annotation>
  30                 <xs:documentation> Properties. Generally, these are mutable so an application should check
  31                         them each time. This may change depending on the context of the property
  32                 </xs:documentation>
  33         </xs:annotation>
  34         <xs:element name="Tree">
  35                 <xs:complexType>
  36                         <xs:annotation>
  37                                 <xs:documentation> Contains a named collection of trees </xs:documentation>
  38                                 <xs:documentation> TODO: define way of referencing leaves of global tree for any
  39                                         sequence/alignment object. SUggestion 1: Each named tree leafnode has a unique
  40                                         id (which may be unique in combination with trees own vorba ID). Dataset
  41                                         sequences can be tagged with a property "vamsas:tree_leaf" </xs:documentation>
  42                         </xs:annotation>
  43                         <xs:sequence>
  44                                 <xs:element name="title" type="xs:string" minOccurs="0"/>
  45                                 <xs:element name="newick" maxOccurs="unbounded">
  46                                         <xs:complexType>
  47                                                 <xs:simpleContent>
  48                                                         <xs:extension base="xs:string">
  49                                                                 <xs:attribute name="title" type="xs:string" use="optional"/>
  50                                                                 <xs:attribute name="id" type="xs:ID" use="optional">
  51                                                                         <xs:annotation>
  52                                                                                 <xs:documentation> Primary Key for vamsas object referencing
  53                                                                                 </xs:documentation>
  54                                                                         </xs:annotation>
  55                                                                 </xs:attribute>
  56                                                                 <xs:attribute name="modifiable" type="vamsas:locks" use="optional"/>
  57                                                         </xs:extension>
  58                                                 </xs:simpleContent>
  59                                         </xs:complexType>
  60                                 </xs:element>
  61                                 <xs:element name="treenode" minOccurs="0" maxOccurs="unbounded">
  62                                         <xs:annotation>
  63                                                 <xs:documentation>
  64                                                         node identity and mapping data between tree representations and vamsas document objects
  65                                                 </xs:documentation>
  66                                         </xs:annotation>
  67                                         <xs:complexType>
  68                                                 <xs:complexContent>
  69                                                         <xs:extension base="vamsas:nodeType">
  70                                                                 <xs:attribute name="treeId" type="xs:IDREFS">
  71                                                                         <xs:annotation>
  72                                                                                 <xs:documentation>
  73                                                                                         reference to one or more trees containing the node being described.
  74                                                                                 </xs:documentation>
  75                                                                         </xs:annotation>
  76                                                                 </xs:attribute>
  77                                                                 <xs:attribute name="nodespec" type="xs:string">
  78                                                                         <xs:annotation>
  79                                                                                 <xs:documentation>
  80                                                                                         String uniquely identifying a particular node in the referenced tree according to the format of the tree representation that is referenced.
  81                                                                                 </xs:documentation>
  82                                                                         </xs:annotation>
  83                                                                 </xs:attribute>
  84
  85                                                         </xs:extension>
  86                                                 </xs:complexContent>
  87                                         </xs:complexType>
  88                                 </xs:element>
  89                                 <xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded"/>
  90                                 <xs:element ref="vamsas:Provenance"/>
  91                         </xs:sequence>
  92                         <xs:attribute name="id" type="xs:ID" use="optional">
  93                                 <xs:annotation>
  94                                         <xs:documentation> Primary Key for vamsas object referencing </xs:documentation>
  95                                 </xs:annotation>
  96                         </xs:attribute>
  97                         <xs:attribute name="modifiable" type="vamsas:locks" use="optional"/>
  98                 </xs:complexType>
  99         </xs:element>
 100         <xs:complexType name="referenceType">
 101                 <xs:annotation>
 102                         <xs:documentation>
 103                                 base type for citing arbitrary links between vamsas objects
 104                         </xs:documentation>
 105                 </xs:annotation>
 106                 <xs:simpleContent>
 107                         <xs:extension base="xs:string">
 108                                 <xs:annotation>
 109                                         <xs:documentation>
 110                                                 Optional human readable description of the relationship
 111                                         </xs:documentation>
 112                                 </xs:annotation>
 113                                 <xs:attribute name="id" type="xs:ID" use="optional">
 114                                         <xs:annotation>
 115                                                 <xs:documentation> Primary Key for vamsas object referencing </xs:documentation>
 116                                         </xs:annotation>
 117                                 </xs:attribute>
 118                                 <xs:attribute name="refs" type="xs:IDREFS">
 119                                         <xs:annotation>
 120                                                 <xs:documentation>List of one or more vamsas object references</xs:documentation>
 121                                         </xs:annotation>
 122                                 </xs:attribute>
 123                         </xs:extension>
 124                 </xs:simpleContent>
 125         </xs:complexType>
 126         <xs:complexType name="nodeType">
 127                 <xs:sequence>
 128                         <xs:element name="name" type="xs:string" minOccurs="0" maxOccurs="1">
 129                                 <xs:annotation>
 130                                         <xs:documentation>Short name for this node</xs:documentation>
 131                                 </xs:annotation>
 132                         </xs:element>
 133                         <xs:element name="description" type="xs:string" minOccurs="0" maxOccurs="1">
 134                                 <xs:annotation>
 135                                         <xs:documentation>Descriptive text for this node</xs:documentation>
 136                                 </xs:annotation>
 137                         </xs:element>
 138                         <xs:element name="vref" type="vamsas:referenceType" minOccurs="0" maxOccurs="unbounded">
 139                                 <xs:annotation>
 140                                         <xs:documentation>Direct associations between this node and any vamsas objects</xs:documentation>
 141                                 </xs:annotation>
 142                         </xs:element>
 143                         <xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded"/>
 144                 </xs:sequence>
 145                 <xs:attribute name="id" type="xs:ID" use="optional">
 146                         <xs:annotation>
 147                                 <xs:documentation> Primary Key for vamsas object referencing </xs:documentation>
 148                         </xs:annotation>
 149                 </xs:attribute>
 150                 <xs:attribute name="modifiable" type="vamsas:locks" use="optional"/>
 151         </xs:complexType>
 152         <xs:element name="property">
 153                 <xs:complexType>
 154                         <xs:simpleContent>
 155                                 <xs:annotation>
 156                                         <xs:documentation> Named and typed property string </xs:documentation>
 157                                 </xs:annotation>
 158                                 <xs:extension base="xs:string">
 159                                         <xs:attribute name="name" type="xs:string" use="required"/>
 160                                         <xs:attribute name="type" type="xs:string" use="required">
 161                                                 <xs:annotation>
 162                                                         <xs:documentation> The type specifies how the property will be parsed.
 163                                                                 Empty property strings are allowed, and can be used to prototype the
 164                                                                 input to a document. TODO: specify allowed types </xs:documentation>
 165                                                 </xs:annotation>
 166                                         </xs:attribute>
 167                                 </xs:extension>
 168                         </xs:simpleContent>
 169                 </xs:complexType>
 170         </xs:element>
 171         <xs:element name="link">
 172                 <xs:complexType>
 173                         <xs:annotation>
 174                                 <xs:documentation> Primitive labelled URI object </xs:documentation>
 175                         </xs:annotation>
 176                         <xs:simpleContent>
 177                                 <xs:extension base="xs:string">
 178                                         <xs:attribute name="href" type="xs:anyURI">
 179                                                 <xs:annotation>
 180                                                         <xs:documentation>The URI</xs:documentation>
 181                                                 </xs:annotation>
 182                                         </xs:attribute>
 183                                 </xs:extension>
 184                         </xs:simpleContent>
 185                 </xs:complexType>
 186         </xs:element>
 187         <xs:complexType name="rangeType" abstract="true">
 188                 <xs:annotation>
 189                         <xs:documentation> Specify an ordered set of positions and/or regions on the principle
 190                                 dimension of some associated vamsas object </xs:documentation>
 191                         <xs:documentation> Keeping to jaxb-1.0 specification for the moment - this choice should
 192                                 become a substitution group when we use jaxb-2.0 capable bindings
 193                         </xs:documentation>
 194                 </xs:annotation>
 195                 <xs:choice>
 196                         <xs:element name="pos" maxOccurs="unbounded">
 197                                 <xs:annotation>
 198                                         <xs:documentation> a position within the associated object's coordinate system
 199                                         </xs:documentation>
 200                                 </xs:annotation>
 201                                 <xs:complexType>
 202                                         <xs:attribute name="i" type="xs:int" use="required"/>
 203                                 </xs:complexType>
 204                         </xs:element>
 205                         <xs:element name="seg" maxOccurs="unbounded">
 206                                 <xs:annotation>
 207                                         <xs:documentation> a region from start to end, with flag for inclusivity of
 208                                                 terminii </xs:documentation>
 209                                 </xs:annotation>
 210                                 <xs:complexType>
 211                                         <xs:attribute name="start" type="xs:int" use="required"/>
 212                                         <xs:attribute name="end" type="xs:int" use="required"/>
 213                                         <xs:attribute name="inclusive" type="xs:boolean" use="required">
 214                                                 <xs:annotation>
 215                                                         <xs:documentation> when false, a consecutive range like 'start=1, end=2'
 216                                                                 means the region lying after position 1 and before position 2
 217                                                         </xs:documentation>
 218                                                 </xs:annotation>
 219                                         </xs:attribute>
 220                                 </xs:complexType>
 221                         </xs:element>
 222                 </xs:choice>
 223                 <!--  Do we really need this - a position could be just a seg with start=end and inclusive=true -->
 224         </xs:complexType>
 225         <xs:complexType name="rangeAnnotation">
 226                 <xs:annotation>
 227                         <xs:documentation> Annotation for a rangeSpec - values can be attached for the whole
 228                                 specification, and to each position within the spec. following the orientation
 229                                 specified by the ordered set of rangeSpec (pos, seg) elements. </xs:documentation>
 230                 </xs:annotation>
 231                 <xs:complexContent>
 232                         <xs:extension base="vamsas:rangeType">
 233                                 <xs:sequence>
 234                                         <xs:element name="label" type="xs:string" minOccurs="0">
 235                                                 <xs:annotation>
 236                                                         <xs:documentation> Short, meaningful name for the annotation - if this
 237                                                                 is absent, then the type string should be used in its place.
 238                                                         </xs:documentation>
 239                                                 </xs:annotation>
 240                                         </xs:element>
 241                                         <xs:element name="description" type="xs:string" minOccurs="0">
 242                                                 <xs:annotation>
 243                                                         <xs:documentation> Human readable description of the annotation
 244                                                         </xs:documentation>
 245                                                 </xs:annotation>
 246                                         </xs:element>
 247                                         <xs:element name="status" type="xs:string" minOccurs="0">
 248                                                 <xs:annotation>
 249                                                         <xs:documentation> TODO: specify this - we have considered taking the GO
 250                                                                 evidence codes as a model for assessing a measure of quality to an
 251                                                                 annotation. </xs:documentation>
 252                                                 </xs:annotation>
 253                                         </xs:element>
 254                                         <xs:element ref="vamsas:annotationElement" minOccurs="0" maxOccurs="unbounded">
 255                                                 <xs:annotation>
 256                                                         <xs:documentation> Annotation Element position maps to ordered positions
 257                                                                 defined by the sequence of rangeType pos positions or concatenated
 258                                                                 seg start/end segments. </xs:documentation>
 259                                                 </xs:annotation>
 260                                         </xs:element>
 261                                         <xs:element name="score" minOccurs="0" maxOccurs="unbounded">
 262                                                 <xs:annotation>
 263                                                         <xs:documentation> Ordered set of optionally named float values for the
 264                                                                 whole annotation </xs:documentation>
 265                                                 </xs:annotation>
 266                                                 <xs:complexType>
 267                                                         <xs:simpleContent>
 268                                                                 <xs:extension base="xs:float">
 269                                                                         <xs:attribute name="name" type="xs:string" use="optional" default="score"/>
 270                                                                 </xs:extension>
 271                                                         </xs:simpleContent>
 272                                                 </xs:complexType>
 273                                         </xs:element>
 274                                         <xs:element ref="vamsas:link" minOccurs="0" maxOccurs="unbounded"/>
 275                                         <xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded">
 276                                                 <xs:annotation>
 277                                                         <xs:documentation> Note:These are mutable so an application should check
 278                                                                 them each time. </xs:documentation>
 279                                                 </xs:annotation>
 280                                         </xs:element>
 281                                 </xs:sequence>
 282                                 <xs:attribute name="id" type="xs:ID" use="optional">
 283                                         <xs:annotation>
 284                                                 <xs:documentation> Primary Key for vamsas object referencing
 285                                                 </xs:documentation>
 286                                         </xs:annotation>
 287                                 </xs:attribute>
 288                                 <xs:attribute name="modifiable" type="vamsas:locks" use="optional"/>
 289                                 <xs:attribute name="group" type="xs:string" use="optional" default="">
 290                                         <xs:annotation>
 291                                                 <xs:documentation> Annotation with the same non-empty group name are grouped
 292                                                         together </xs:documentation>
 293                                         </xs:annotation>
 294                                 </xs:attribute>
 295                                 <xs:attribute name="type" type="xs:string" use="required">
 296                                         <xs:annotation>
 297                                                 <xs:documentation> A Das Feature has both a type and a Type ID. We go the
 298                                                         route of requiring the type string to be taken from a controlled
 299                                                         vocabulary if an application expects others to make sense of it. The
 300                                                         type may qualified - so uniprot:CHAIN is a valid type name, and
 301                                                         considered distinct from someotherDB:CHAIN </xs:documentation>
 302                                         </xs:annotation>
 303                                 </xs:attribute>
 304                         </xs:extension>
 305                 </xs:complexContent>
 306         </xs:complexType>
 307         <xs:element name="param">
 308                 <xs:complexType>
 309                         <xs:annotation>
 310                                 <xs:documentation> Specifies a named and typed value used to perform some data
 311                                         transformation. </xs:documentation>
 312                                 <xs:documentation> LATER: experiment with xml validation of property set prototypes
 313                                         for services </xs:documentation>
 314                         </xs:annotation>
 315                         <xs:simpleContent>
 316                                 <xs:annotation>
 317                                         <xs:documentation> Named and typed property string </xs:documentation>
 318                                 </xs:annotation>
 319                                 <xs:extension base="xs:string">
 320                                         <xs:attribute name="name" type="xs:string" use="required"/>
 321                                         <xs:attribute name="type" type="xs:string" use="required">
 322                                                 <xs:annotation>
 323                                                         <xs:documentation> The type specifies how the property will be parsed.
 324                                                                 Empty property strings are allowed, and can be used to prototype the
 325                                                                 input to a document. TODO: specify allowed types </xs:documentation>
 326                                                 </xs:annotation>
 327                                         </xs:attribute>
 328                                 </xs:extension>
 329                         </xs:simpleContent>
 330                 </xs:complexType>
 331         </xs:element>
 332         <xs:element name="input">
 333                 <xs:complexType>
 334                         <xs:annotation>
 335                                 <xs:documentation> Selects all or part of a collection of vamsas objects as a named
 336                                         input to some transformation process. Many inputs with the same name imply a
 337                                         group input (such as a collection of sequences) </xs:documentation>
 338                         </xs:annotation>
 339                         <xs:complexContent>
 340                                 <xs:extension base="vamsas:rangeType">
 341                                         <xs:attribute name="name" type="xs:string" use="required"/>
 342                                         <xs:attribute name="objRef" type="xs:IDREFS" use="optional">
 343                                                 <xs:annotation>
 344                                                         <xs:documentation> Reference Frame for rangeType specfication
 345                                                         </xs:documentation>
 346                                                 </xs:annotation>
 347                                         </xs:attribute>
 348                                 </xs:extension>
 349                         </xs:complexContent>
 350                 </xs:complexType>
 351         </xs:element>
 352         <xs:element name="Provenance">
 353                 <xs:complexType>
 354                         <xs:annotation>
 355                                 <xs:documentation> Defines the origin and series of operations applied directly to
 356                                         the object that references it. </xs:documentation>
 357                         </xs:annotation>
 358                         <xs:sequence>
 359                                 <xs:element name="entry" maxOccurs="unbounded">
 360                                         <xs:complexType>
 361                                                 <xs:sequence>
 362                                                         <xs:element name="User" type="xs:string">
 363                                                                 <xs:annotation>
 364                                                                         <xs:documentation> Who </xs:documentation>
 365                                                                 </xs:annotation>
 366                                                         </xs:element>
 367                                                         <xs:element name="App" type="xs:string">
 368                                                                 <xs:annotation>
 369                                                                         <xs:documentation> With which application </xs:documentation>
 370                                                                 </xs:annotation>
 371                                                         </xs:element>
 372                                                         <xs:element name="Action" type="xs:string">
 373                                                                 <xs:annotation>
 374                                                                         <xs:documentation> Did what </xs:documentation>
 375                                                                 </xs:annotation>
 376                                                         </xs:element>
 377                                                         <xs:element name="Date" type="xs:dateTime">
 378                                                                 <xs:annotation>
 379                                                                         <xs:documentation> When</xs:documentation>
 380                                                                 </xs:annotation>
 381                                                         </xs:element>
 382                                                         <xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded">
 383                                                                 <xs:annotation>
 384                                                                         <xs:documentation> additional information </xs:documentation>
 385                                                                 </xs:annotation>
 386                                                         </xs:element>
 387                                                         <xs:element ref="vamsas:param" minOccurs="0" maxOccurs="unbounded">
 388                                                                 <xs:annotation>
 389                                                                         <xs:documentation> parameter for the action </xs:documentation>
 390                                                                 </xs:annotation>
 391                                                         </xs:element>
 392                                                         <xs:element ref="vamsas:input" minOccurs="0" maxOccurs="unbounded">
 393                                                                 <xs:annotation>
 394                                                                         <xs:documentation> bioinformatic objects input to action
 395                                                                         </xs:documentation>
 396                                                                 </xs:annotation>
 397                                                         </xs:element>
 398                                                 </xs:sequence>
 399                                                 <xs:attribute name="id" type="xs:ID" use="optional">
 400                                                         <xs:annotation>
 401                                                                 <xs:documentation> Primary Key for vamsas object referencing
 402                                                                 </xs:documentation>
 403                                                         </xs:annotation>
 404                                                 </xs:attribute>
 405                                         </xs:complexType>
 406                                 </xs:element>
 407                         </xs:sequence>
 408                 </xs:complexType>
 409         </xs:element>
 410         <xs:element name="DataSet">
 411                 <xs:complexType>
 412                         <xs:annotation>
 413                                 <xs:documentation> A collection of sequences, alignments, trees and other things.
 414                                 </xs:documentation>
 415                         </xs:annotation>
 416                         <xs:sequence>
 417                                 <xs:element name="Sequence" maxOccurs="unbounded">
 418                                         <xs:complexType>
 419                                                 <xs:annotation>
 420                                                         <xs:documentation> a primary or secondary sequence record from which all
 421                                                                 other sequences may be derived </xs:documentation>
 422                                                 </xs:annotation>
 423                                                 <xs:complexContent>
 424                                                         <xs:extension base="vamsas:SequenceType">
 425                                                                 <xs:sequence>
 426                                                                         <xs:element name="dbRef" minOccurs="0" maxOccurs="unbounded">
 427                                                                                 <xs:annotation>
 428                                                                                         <xs:documentation> Store a list of database references
 429                                                                                                 for this sequence record - with optional mapping
 430                                                                                                 from database sequence to the given sequence record </xs:documentation>
 431                                                                                         <xs:documentation/>
 432                                                                                         <xs:documentation/>
 433                                                                                 </xs:annotation>
 434                                                                                 <xs:complexType>
 435                                                                                         <xs:sequence>
 436                                                                                                 <xs:element name="map" minOccurs="0" maxOccurs="unbounded">
 437                                                                                                         <xs:annotation>
 438                                                                                                                 <xs:documentation> From: Offset to first
 439                                                                                                                 position in dataset sequence record that
 440                                                                                                                 this database entry maps to To: Offset
 441                                                                                                                 to last position in dataset sequence
 442                                                                                                                 record that this database entry maps to
 443                                                                                                                 Start: Offset to first last position in
 444                                                                                                                 database entry that first (or offset)
 445                                                                                                                 position in sequence maps to End: Offset
 446                                                                                                                 to last position in database entry that
 447                                                                                                                 last (offset) position in sequence maps
 448                                                                                                                 to </xs:documentation>
 449                                                                                                         </xs:annotation>
 450                                                                                                         <xs:complexType>
 451                                                                                                                 <xs:complexContent>
 452                                                                                                                         <xs:extension base="vamsas:mapList"/>
 453                                                                                                                 </xs:complexContent>
 454                                                                                                         </xs:complexType>
 455                                                                                                 </xs:element>
 456                                                                                                 <xs:element ref="vamsas:link" minOccurs="0" maxOccurs="unbounded"/>
 457                                                                                                 <xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded"/>
 458                                                                                         </xs:sequence>
 459                                                                                         <xs:attribute name="source" type="xs:string" use="required">
 460                                                                                                 <xs:annotation>
 461                                                                                                         <xs:documentation> TODO Database Naming
 462                                                                                                 Convention: either start using LSID (so
 463                                                                                                 change type to URI) or leave this as an
 464                                                                                                 uncontrolled/unspecified string ID
 465                                                                                                 </xs:documentation>
 466                                                                                                 </xs:annotation>
 467                                                                                         </xs:attribute>
 468                                                                                         <xs:attribute name="version" type="xs:string" use="required">
 469                                                                                                 <xs:annotation>
 470                                                                                                         <xs:documentation> Version must be specified -
 471                                                                                                 </xs:documentation>
 472                                                                                                 </xs:annotation>
 473                                                                                         </xs:attribute>
 474                                                                                         <xs:attribute name="accessionId" type="xs:string" use="required">
 475                                                                                                 <xs:annotation>
 476                                                                                                         <xs:documentation> TODO: make some specification
 477                                                                                                 of the database field from which this
 478                                                                                                 accessionId is taken from - should that be a
 479                                                                                                 special property of the dbRef object ?
 480                                                                                                 </xs:documentation>
 481                                                                                                 </xs:annotation>
 482                                                                                         </xs:attribute>
 483                                                                                         <xs:attribute name="id" type="xs:ID" use="optional">
 484                                                                                                 <xs:annotation>
 485                                                                                                         <xs:documentation> Primary Key for vamsas object
 486                                                                                                 referencing </xs:documentation>
 487                                                                                                 </xs:annotation>
 488                                                                                         </xs:attribute>
 489                                                                                 </xs:complexType>
 490                                                                         </xs:element>
 491                                                                         <xs:element name="vxref" type="vamsas:referenceType" minOccurs="0" maxOccurs="unbounded">
 492                                                                                 <xs:annotation>
 493                                                                                         <xs:documentation>
 494                                                                                                 explicitly named cross reference to other objects in the document.
 495                                                                                         </xs:documentation>
 496                                                                                 </xs:annotation>
 497                                                                         </xs:element>
 498                                                                 </xs:sequence>
 499                                                                 <xs:attribute name="id" type="xs:ID" use="optional">
 500                                                                         <xs:annotation>
 501                                                                                 <xs:documentation> Primary Key for vamsas object referencing
 502                                                                                 </xs:documentation>
 503                                                                         </xs:annotation>
 504                                                                 </xs:attribute>
 505                                                                 <xs:attribute name="dictionary" type="xs:string" use="required">
 506                                                                         <xs:annotation>
 507                                                                                 <xs:documentation> symbol class for sequence
 508                                                                                 </xs:documentation>
 509                                                                         </xs:annotation>
 510                                                                 </xs:attribute>
 511                                                         </xs:extension>
 512                                                 </xs:complexContent>
 513                                         </xs:complexType>
 514                                 </xs:element>
 515                                 <xs:element name="sequenceMapping" minOccurs="0" maxOccurs="unbounded">
 516                                         <xs:complexType>
 517                                                 <xs:sequence>
 518                                                         <xs:element name="range" maxOccurs="unbounded">
 519                                                                 <xs:complexType>
 520                                                                         <xs:attribute name="seqAStart" type="xs:int"/>
 521                                                                         <xs:attribute name="seqAEnd" type="xs:int"/>
 522                                                                         <xs:attribute name="seqBStart" type="xs:int"/>
 523                                                                         <xs:attribute name="seqBEnd" type="xs:int"/>
 524                                                                 </xs:complexType>
 525                                                         </xs:element>
 526                                                         <xs:element ref="vamsas:Provenance"/>
 527                                                 </xs:sequence>
 528                                                 <xs:attribute name="sequenceA" type="xs:IDREF" use="required"/>
 529                                                 <xs:attribute name="sequenceB" type="xs:IDREF" use="required"/>
 530                                                 <xs:attribute name="id" type="xs:ID" use="optional"/>
 531                                         </xs:complexType>
 532                                 </xs:element>
 533                                 <xs:element name="DataSetAnnotations" minOccurs="0" maxOccurs="unbounded">
 534                                         <xs:complexType>
 535                                                 <xs:annotation>
 536                                                         <xs:documentation> Annotate over positions and regions of a dataset
 537                                                                 sequence </xs:documentation>
 538                                                 </xs:annotation>
 539                                                 <xs:complexContent>
 540                                                         <xs:extension base="vamsas:rangeAnnotation">
 541                                                                 <xs:sequence>
 542                                                                         <xs:element ref="vamsas:Provenance"/>
 543                                                                 </xs:sequence>
 544                                                                 <xs:attribute name="seqRef" type="xs:IDREFS" use="required">
 545                                                                         <xs:annotation>
 546                                                                                 <xs:documentation> annotation is associated with a
 547                                                                                         particular dataset sequence </xs:documentation>
 548                                                                         </xs:annotation>
 549                                                                 </xs:attribute>
 550                                                         </xs:extension>
 551                                                 </xs:complexContent>
 552                                         </xs:complexType>
 553                                 </xs:element>
 554                                 <xs:element name="Alignment" minOccurs="0" maxOccurs="unbounded">
 555                                         <xs:complexType>
 556                                                 <xs:sequence>
 557                                                         <xs:element name="AlignmentAnnotation" minOccurs="0" maxOccurs="unbounded">
 558                                                                 <xs:annotation>
 559                                                                         <xs:documentation> This is annotation over the coordinate frame
 560                                                                                 defined by all the columns in the alignment.
 561                                                                         </xs:documentation>
 562                                                                 </xs:annotation>
 563                                                                 <xs:complexType>
 564                                                                         <xs:complexContent>
 565                                                                                 <xs:extension base="vamsas:rangeAnnotation">
 566                                                                                         <xs:sequence>
 567                                                                                                 <xs:element ref="vamsas:Provenance"/>
 568                                                                                         </xs:sequence>
 569                                                                                         <xs:attribute name="graph" type="xs:boolean" use="required">
 570                                                                                                 <xs:annotation>
 571                                                                                                         <xs:documentation> TODO: decide if this flag is
 572                                                                                                 redundant - when true it would suggest that
 573                                                                                                 the annotationElement values together form a
 574                                                                                                 graph </xs:documentation>
 575                                                                                                 </xs:annotation>
 576                                                                                         </xs:attribute>
 577                                                                                         <xs:attribute name="seqrefs" type="xs:IDREFS" use="optional">
 578                                                                                                 <xs:annotation>
 579                                                                                                         <xs:documentation> annotation is associated with a
 580                                                                                                                 range on a particular group of alignment sequences</xs:documentation>
 581                                                                                                 </xs:annotation>
 582                                                                                         </xs:attribute>
 583
 584                                                                                 </xs:extension>
 585                                                                         </xs:complexContent>
 586                                                                 </xs:complexType>
 587                                                         </xs:element>
 588                                                         <xs:element ref="vamsas:Tree" minOccurs="0" maxOccurs="unbounded"/>
 589                                                         <xs:element name="alignmentSequence" maxOccurs="unbounded">
 590                                                                 <xs:complexType>
 591                                                                         <xs:complexContent>
 592                                                                                 <xs:extension base="vamsas:SequenceType">
 593                                                                                         <xs:sequence>
 594                                                                                                 <xs:element name="AlignmentSequenceAnnotation" minOccurs="0" maxOccurs="unbounded">
 595                                                                                                         <xs:complexType>
 596                                                                                                                 <xs:annotation>
 597                                                                                                                         <xs:documentation> Annotate over
 598                                                                                                 positions and regions of the
 599                                                                                                 ungapped sequence in the context of
 600                                                                                                 the alignment </xs:documentation>
 601                                                                                                                         <xs:documentation/>
 602                                                                                                                 </xs:annotation>
 603                                                                                                                 <xs:complexContent>
 604                                                                                                                         <xs:extension base="vamsas:rangeAnnotation">
 605                                                                                                                                 <xs:sequence>
 606                                                                                                                                         <xs:element ref="vamsas:Provenance"/>
 607                                                                                                                                 </xs:sequence>
 608                                                                                                                                 <xs:attribute name="graph" type="xs:boolean" use="required">
 609                                                                                                                                         <xs:annotation>
 610                                                                                                                                                 <xs:documentation> TODO:
 611                                                                                                 decide if this flag is
 612                                                                                                 redundant - when true it
 613                                                                                                 would suggest that the
 614                                                                                                 annotationElement values
 615                                                                                                 together form a graph
 616                                                                                                 </xs:documentation>
 617                                                                                                                                         </xs:annotation>
 618                                                                                                                                 </xs:attribute>
 619                                                                                                                         </xs:extension>
 620                                                                                                                 </xs:complexContent>
 621                                                                                                                 <!--
 622                                                                                                                         This replaces the flat list of sequenceFeatures.
 623                                                                                                                         <xs:element name="AlignmentFeatures" minOccurs="0" maxOccurs="unbounded"><xs:complexType><xs:annotation>
 624                                                                                                                         <xs:documentation>Annotate over positions and regions of the alignment</xs:documentation>
 625                                                                                                                         </xs:annotation><xs:complexContent>
 626                                                                                                                         <xs:extension base="vamsas:rangeFeature">
 627                                                                                                                         <xs:attribute name="seqRef" type="xs:IDREF" use="optional">
 628                                                                                                                         <xs:annotation><xs:documentation>annotation may be associated with a particular sequence lying within the same reference frame as the rangeType's objRef</xs:documentation></xs:annotation>
 629                                                                                                                         </xs:attribute>
 630                                                                                                                         </xs:extension>
 631                                                                                                                         </xs:complexContent></xs:complexType></xs:element> -->
 632                                                                                                         </xs:complexType>
 633                                                                                                 </xs:element>
 634                                                                                         </xs:sequence>
 635                                                                                         <xs:attribute name="id" type="xs:ID" use="optional">
 636                                                                                                 <xs:annotation>
 637                                                                                                         <xs:documentation> Primary Key for vamsas object
 638                                                                                                 referencing </xs:documentation>
 639                                                                                                 </xs:annotation>
 640                                                                                         </xs:attribute>
 641                                                                                         <xs:attribute name="refid" type="xs:IDREF" use="required">
 642                                                                                                 <xs:annotation>
 643                                                                                                         <xs:documentation> Dataset Sequence from which
 644                                                                                                 this alignment sequence is taken from
 645                                                                                                 </xs:documentation>
 646                                                                                                 </xs:annotation>
 647                                                                                         </xs:attribute>
 648                                                                                 </xs:extension>
 649                                                                         </xs:complexContent>
 650                                                                 </xs:complexType>
 651                                                         </xs:element>
 652                                                         <xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded">
 653                                                                 <xs:annotation>
 654                                                                         <xs:documentation> typical properties may be additional
 655                                                                                 alignment score objects </xs:documentation>
 656                                                                 </xs:annotation>
 657                                                         </xs:element>
 658                                                         <xs:element ref="vamsas:Provenance"/>
 659                                                 </xs:sequence>
 660                                                 <xs:attribute name="gapChar" type="xs:string" use="required"/>
 661                                                 <xs:attribute name="aligned" type="xs:boolean" use="optional"/>
 662                                                 <xs:attribute name="id" type="xs:ID" use="optional">
 663                                                         <xs:annotation>
 664                                                                 <xs:documentation> Primary Key for vamsas object referencing
 665                                                                 </xs:documentation>
 666                                                         </xs:annotation>
 667                                                 </xs:attribute>
 668                                                 <xs:attribute name="modifiable" type="vamsas:locks" use="optional"/>
 669                                         </xs:complexType>
 670                                 </xs:element>
 671                                 <xs:element ref="vamsas:Tree" minOccurs="0" maxOccurs="unbounded"/>
 672                                 <xs:element ref="vamsas:Provenance"/>
 673                         </xs:sequence>
 674                         <xs:attribute name="id" type="xs:ID" use="optional">
 675                                 <xs:annotation>
 676                                         <xs:documentation> Primary Key for vamsas object referencing </xs:documentation>
 677                                 </xs:annotation>
 678                         </xs:attribute>
 679                 </xs:complexType>
 680         </xs:element>
 681         <xs:element name="annotationElement">
 682                 <xs:complexType>
 683                         <xs:annotation>
 684                                 <xs:documentation> per-site symbolic and/or quantitative annotation </xs:documentation>
 685                                 <xs:documentation> SecondaryStructure and display character (from Jalview) have been
 686                                         subsumed into the glyph element </xs:documentation>
 687                         </xs:annotation>
 688                         <xs:sequence>
 689                                 <xs:element name="description" type="xs:string" minOccurs="0">
 690                                         <xs:annotation>
 691                                                 <xs:documentation> Free text at this position </xs:documentation>
 692                                         </xs:annotation>
 693                                 </xs:element>
 694                                 <xs:element name="glyph" minOccurs="0" maxOccurs="unbounded">
 695                                         <xs:annotation>
 696                                                 <xs:documentation> Discrete symbol - possibly graphically represented
 697                                                 </xs:documentation>
 698                                         </xs:annotation>
 699                                         <xs:complexType>
 700                                                 <xs:simpleContent>
 701                                                         <xs:extension base="xs:string">
 702                                                                 <xs:attribute name="dict" type="xs:string" use="optional" default="utf8">
 703                                                                         <xs:annotation>
 704                                                                                 <xs:documentation> specifies the symbol dictionary for this
 705                                                                                         glyph - eg utf8 (the default), aasecstr_3 or
 706                                                                                         kd_hydrophobicity - the content is not validated so
 707                                                                                         applications must ensure they gracefully deal with
 708                                                                                         invalid entries here </xs:documentation>
 709                                                                                 <xs:documentation> TODO: specify a minimum list of glyph
 710                                                                                         dictionaries to get us started and provide a way for the
 711                                                                                         vamsasClient to validate their content if regexes are
 712                                                                                         specified </xs:documentation>
 713                                                                         </xs:annotation>
 714                                                                 </xs:attribute>
 715                                                         </xs:extension>
 716                                                 </xs:simpleContent>
 717                                         </xs:complexType>
 718                                 </xs:element>
 719                                 <xs:element name="value" type="xs:float" minOccurs="0" maxOccurs="unbounded">
 720                                         <xs:annotation>
 721                                                 <xs:documentation> Ordered set of float values - an application may treat
 722                                                         the values together as a vector with common support for a set of
 723                                                         annotation elements - but this is, again, not validated so applications
 724                                                         should deal gracefully with varying numbers of dimensions
 725                                                 </xs:documentation>
 726                                         </xs:annotation>
 727                                 </xs:element>
 728                         </xs:sequence>
 729                         <xs:attribute name="position" type="xs:integer" use="required">
 730                                 <xs:annotation>
 731                                         <xs:documentation> position with respect to the coordinate frame defined by a
 732                                                 rangeType specification </xs:documentation>
 733                                 </xs:annotation>
 734                         </xs:attribute>
 735                         <xs:attribute name="after" type="xs:boolean" use="optional" default="false">
 736                                 <xs:annotation>
 737                                         <xs:documentation> true means the annotation element appears between the
 738                                                 specified position and the next </xs:documentation>
 739                                 </xs:annotation>
 740                         </xs:attribute>
 741                         <xs:attribute name="id" type="xs:ID" use="optional">
 742                                 <xs:annotation>
 743                                         <xs:documentation> Primary Key for vamsas object referencing </xs:documentation>
 744                                 </xs:annotation>
 745                         </xs:attribute>
 746                 </xs:complexType>
 747         </xs:element>
 748         <xs:complexType name="SequenceType">
 749                 <xs:sequence>
 750                         <xs:element name="sequence" type="xs:string"/>
 751                         <xs:element name="name" type="xs:string"/>
 752                         <xs:element name="description" type="xs:string" minOccurs="0"/>
 753                         <xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded">
 754                                 <xs:annotation>
 755                                         <xs:documentation> additional typed properties </xs:documentation>
 756                                 </xs:annotation>
 757                         </xs:element>
 758                 </xs:sequence>
 759                 <xs:attribute name="start" type="xs:integer" use="required"/>
 760                 <xs:attribute name="end" type="xs:integer" use="required"/>
 761         </xs:complexType>
 762         <xs:element name="ApplicationData">
 763                 <xs:complexType>
 764                         <xs:annotation>
 765                                 <xs:documentation> Data specific to a particular type and version of vamsas
 766                                         application </xs:documentation>
 767                         </xs:annotation>
 768                         <xs:complexContent>
 769                                 <xs:extension base="vamsas:appData">
 770                                         <xs:sequence>
 771                                                 <xs:element name="User" minOccurs="0" maxOccurs="unbounded">
 772                                                         <xs:complexType>
 773                                                                 <xs:complexContent>
 774                                                                         <xs:extension base="vamsas:appData">
 775                                                                                 <xs:annotation>
 776                                                                                         <xs:documentation> Data available to just a particular
 777                                                                                                 user </xs:documentation>
 778                                                                                 </xs:annotation>
 779                                                                                 <xs:attribute name="fullname" type="xs:string" use="required"/>
 780                                                                                 <xs:attribute name="organization" type="xs:string" use="required"/>
 781                                                                         </xs:extension>
 782                                                                 </xs:complexContent>
 783                                                         </xs:complexType>
 784                                                 </xs:element>
 785                                                 <xs:element name="Common" minOccurs="0">
 786                                                         <xs:complexType>
 787                                                                 <xs:complexContent>
 788                                                                         <xs:extension base="vamsas:appData"/>
 789                                                                 </xs:complexContent>
 790                                                         </xs:complexType>
 791                                                 </xs:element>
 792                                                 <xs:element name="Instance" minOccurs="0" maxOccurs="unbounded">
 793                                                         <xs:complexType>
 794                                                                 <xs:complexContent>
 795                                                                         <xs:extension base="vamsas:appData">
 796                                                                                 <xs:annotation>
 797                                                                                         <xs:documentation> Data available to just a specific
 798                                                                                                 instance of the application </xs:documentation>
 799                                                                                         <xs:documentation> VAMSAS/Pierre: Is this data volatile
 800                                                                                                 ? Application instances may not be accessible after
 801                                                                                                 the session has closed - the user may have to be
 802                                                                                                 presented with the option of picking up the data in
 803                                                                                                 that instance </xs:documentation>
 804                                                                                 </xs:annotation>
 805                                                                                 <xs:attribute name="urn" type="xs:string" use="required"/>
 806                                                                         </xs:extension>
 807                                                                 </xs:complexContent>
 808                                                         </xs:complexType>
 809                                                 </xs:element>
 810                                         </xs:sequence>
 811                                         <xs:attribute name="version" type="xs:string" use="required">
 812                                                 <xs:annotation>
 813                                                         <xs:documentation> Version string describing the application specific
 814                                                                 data storage version used</xs:documentation>
 815                                                 </xs:annotation>
 816                                         </xs:attribute>
 817                                         <xs:attribute name="name" type="xs:string" use="required">
 818                                                 <xs:annotation>
 819                                                         <xs:documentation> Canonical name of application </xs:documentation>
 820                                                 </xs:annotation>
 821                                         </xs:attribute>
 822                                 </xs:extension>
 823                         </xs:complexContent>
 824                 </xs:complexType>
 825         </xs:element>
 826         <xs:element name="Attachment">
 827                 <xs:complexType>
 828                         <xs:complexContent>
 829                                 <xs:extension base="vamsas:appData">
 830                                         <xs:annotation>
 831                                                 <xs:documentation> General data container to attach a typed data object to
 832                                                         any vamsas object </xs:documentation>
 833                                         </xs:annotation>
 834                                         <xs:attribute name="compressed" type="xs:boolean" use="optional" default="false">
 835                                                 <xs:annotation>
 836                                                         <xs:documentation> true implies data will be decompresses with Zip
 837                                                                 before presenting to application </xs:documentation>
 838                                                 </xs:annotation>
 839                                         </xs:attribute>
 840                                         <xs:attribute name="type" type="xs:string" use="required">
 841                                                 <xs:annotation>
 842                                                         <xs:documentation> Type of arbitrary data - TODO: decide format - use
 843                                                                 (extended) MIME types ? </xs:documentation>
 844                                                 </xs:annotation>
 845                                         </xs:attribute>
 846                                         <xs:attribute name="objectref" type="xs:IDREF" use="required">
 847                                                 <xs:annotation>
 848                                                         <xs:documentation> Object the arbitrary data is associated with
 849                                                         </xs:documentation>
 850                                                 </xs:annotation>
 851                                         </xs:attribute>
 852                                         <xs:attribute name="id" type="xs:ID" use="optional">
 853                                                 <xs:annotation>
 854                                                         <xs:documentation> Primary Key for vamsas object referencing
 855                                                         </xs:documentation>
 856                                                 </xs:annotation>
 857                                         </xs:attribute>
 858                                 </xs:extension>
 859                         </xs:complexContent>
 860                 </xs:complexType>
 861         </xs:element>
 862         <xs:complexType name="appData">
 863                 <xs:choice>
 864                         <xs:element name="data" type="xs:base64Binary"/>
 865                         <xs:element name="dataReference" type="xs:string"/>
 866                 </xs:choice>
 867         </xs:complexType>
 868         <xs:complexType name="mapList">
 869                 <xs:attribute name="from" type="xs:integer" use="optional" default="0">
 870                         <xs:annotation>
 871                                 <xs:documentation> Offset to first position in dataset sequence record that start
 872                                         position on 'onto' maps to </xs:documentation>
 873                         </xs:annotation>
 874                 </xs:attribute>
 875                 <xs:attribute name="to" type="xs:integer" use="optional" default="0">
 876                         <xs:annotation>
 877                                 <xs:documentation> Offset to last position in dataset sequence record that end
 878                                         position on 'onto' maps to </xs:documentation>
 879                         </xs:annotation>
 880                 </xs:attribute>
 881                 <xs:attribute name="start" type="xs:integer" use="required">
 882                         <xs:annotation>
 883                                 <xs:documentation> Offset to first position in database entry that first (or offset)
 884                                         position in sequence maps to </xs:documentation>
 885                         </xs:annotation>
 886                 </xs:attribute>
 887                 <xs:attribute name="end" type="xs:integer" use="required">
 888                         <xs:annotation>
 889                                 <xs:documentation> Offset to last position in database entry that last (offset)
 890                                         position in sequence maps to </xs:documentation>
 891                         </xs:annotation>
 892                 </xs:attribute>
 893         </xs:complexType>
 894         <xs:simpleType name="locks">
 895                 <xs:annotation>
 896                         <xs:documentation>
 897                                 Contains lock information:
 898                                 locktype:ApplicationHandle
 899                                 locktype is 'local' or 'full'
 900                                 A lock is only valid if the ApplicationHandle resolves to a living application in the vamsas session.
 901                                 A local lock means that the application has locked changes to all local properties on the object.
 902                                 A full lock means that the application has locked changes to all properties on the object, and any objects that it holds references to.
 903                         </xs:documentation>
 904                 </xs:annotation>
 905                 <xs:restriction base="xs:string"/>
 906         </xs:simpleType>
 907 </xs:schema>