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 v2005 rel. 3 U (http://www.altova.com) by lj (jl) -->
   4 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"
   5         xmlns:vamsas="http://www.vamsas.org"
   6         targetNamespace="http://www.vamsas.org" elementFormDefault="qualified"
   7         attributeFormDefault="unqualified">
   8         <xs:annotation>
   9                 <xs:documentation>
  10                         Vorba ID - Vamsas Object Request Broker Address ID (name
  11                         needs to be worked on): Suggest it could be of the form
  12                         documentRoot/datasetName/SequenceUID for a dataset sequence.
  13                         Alignment sequence:
  14                         documentRoot/datasetName/AlignmentId/SequenceUID for an
  15                         aligned form of a dataset sequence
  16
  17                 </xs:documentation>
  18         </xs:annotation>
  19         <xs:element name="VAMSAS">
  20                 <xs:annotation>
  21                         <xs:documentation>
  22                                 contains unassociated trees and a number of analysis
  23                                 sets
  24                         </xs:documentation>
  25                 </xs:annotation>
  26                 <xs:complexType>
  27                         <xs:sequence>
  28                                 <xs:element ref="vamsas:Tree" minOccurs="0"
  29                                         maxOccurs="unbounded" />
  30                                 <xs:element ref="vamsas:DataSet" minOccurs="0"
  31                                         maxOccurs="unbounded" />
  32                         </xs:sequence>
  33                         <xs:attribute name="id" type="xs:ID" use="optional">
  34                                 <xs:annotation>
  35                                         <xs:documentation>
  36                                                 Primary Key for vamsas object referencing
  37                                         </xs:documentation>
  38                                 </xs:annotation>
  39                         </xs:attribute>
  40                         <xs:attribute name="modifiable" type="xs:boolean"
  41                                 default="true" use="optional">
  42                                 <xs:annotation>
  43                                         <xs:documentation>
  44                                                 objects with modifiable=false will not be
  45                                                 modified by a vamsas client update
  46                                         </xs:documentation>
  47                                 </xs:annotation>
  48                         </xs:attribute>
  49                 </xs:complexType>
  50         </xs:element>
  51         <xs:annotation>
  52                 <xs:documentation>
  53                         Properties. Generally, these are mutable so an application
  54                         should check them each time. This may change depending on
  55                         the context of the property
  56                 </xs:documentation>
  57         </xs:annotation>
  58         <xs:element name="Tree">
  59                 <xs:complexType>
  60                         <xs:annotation>
  61                                 <xs:documentation>
  62                                         Contains a named collection of trees
  63                                 </xs:documentation>
  64                                 <xs:documentation>
  65                                  TODO: define
  66                                         way of referencing leaves of global tree for any
  67                                         sequence/alignment object.
  68                                 SUggestion 1: Each named tree leafnode has a unique id (which may be unique in combination with trees own vorba ID).
  69                                 Dataset sequences can be tagged with a property "vamsas:tree_leaf"
  70                                 </xs:documentation>
  71                         </xs:annotation>
  72                         <xs:sequence>
  73                                 <xs:element name="title" type="xs:string" minOccurs="0" />
  74                                 <xs:element name="newick" maxOccurs="unbounded">
  75                                         <xs:complexType>
  76                                                 <xs:simpleContent>
  77                                                         <xs:extension base="xs:string">
  78                                                                 <xs:attribute name="title"
  79                                                                         type="xs:string" use="optional" />
  80                                                                 <xs:attribute name="id" type="xs:ID"
  81                                                                         use="optional">
  82                                                                         <xs:annotation>
  83                                                                                 <xs:documentation>
  84                                                                                         Primary Key for vamsas
  85                                                                                         object referencing
  86                                                                                 </xs:documentation>
  87                                                                         </xs:annotation>
  88                                                                 </xs:attribute>
  89                                                                 <xs:attribute name="modifiable"
  90                                                                         type="xs:boolean" default="true" use="optional">
  91                                                                         <xs:annotation>
  92                                                                                 <xs:documentation>
  93                                                                                         objects with
  94                                                                                         modifiable=false will not be
  95                                                                                         modified by a vamsas client
  96                                                                                         update
  97                                                                                 </xs:documentation>
  98                                                                         </xs:annotation>
  99                                                                 </xs:attribute>
 100                                                         </xs:extension>
 101                                                 </xs:simpleContent>
 102                                         </xs:complexType>
 103                                 </xs:element>
 104                                 <xs:element ref="vamsas:property" maxOccurs="unbounded"
 105                                         minOccurs="0" />
 106                                 <xs:element ref="vamsas:Provenance" />
 107                         </xs:sequence>
 108                         <xs:attribute name="id" type="xs:ID" use="optional">
 109                                 <xs:annotation>
 110                                         <xs:documentation>
 111                                                 Primary Key for vamsas object referencing
 112                                         </xs:documentation>
 113                                 </xs:annotation>
 114                         </xs:attribute>
 115                         <xs:attribute name="modifiable" type="xs:boolean"
 116                                 default="true" use="optional">
 117                                 <xs:annotation>
 118                                         <xs:documentation>
 119                                                 objects with modifiable=false will not be
 120                                                 modified by a vamsas client update
 121                                         </xs:documentation>
 122                                 </xs:annotation>
 123                         </xs:attribute>
 124                 </xs:complexType>
 125         </xs:element>
 126         <xs:element name="property">
 127                 <xs:complexType>
 128                         <xs:simpleContent>
 129                                 <xs:annotation>
 130                                         <xs:documentation>
 131                                                 Named and typed property string
 132                                         </xs:documentation>
 133                                 </xs:annotation>
 134                                 <xs:extension base="xs:string">
 135                                         <xs:attribute name="name" type="xs:string"
 136                                                 use="required" />
 137                                         <xs:attribute name="type" type="xs:string"
 138                                                 use="required">
 139                                                 <xs:annotation>
 140                                                         <xs:documentation>
 141                                                                 The type specifies how the property will
 142                                                                 be parsed. Empty property strings are
 143                                                                 allowed, and can be used to prototype
 144                                                                 the input to a document. TODO: specify
 145                                                                 allowed types
 146                                                         </xs:documentation>
 147                                                 </xs:annotation>
 148                                         </xs:attribute>
 149                                 </xs:extension>
 150                         </xs:simpleContent>
 151                 </xs:complexType>
 152         </xs:element>
 153         <xs:element name="link">
 154         <xs:complexType>
 155                 <xs:annotation>
 156                         <xs:documentation>
 157                                 Primitive labelled URI object
 158                         </xs:documentation>
 159                 </xs:annotation>
 160                 <xs:simpleContent>
 161                         <xs:extension base="xs:string">
 162                                 <xs:attribute name="href" type="xs:anyURI">
 163                                         <xs:annotation>
 164                                                 <xs:documentation>The URI</xs:documentation>
 165                                         </xs:annotation>
 166                                 </xs:attribute>
 167                         </xs:extension>
 168                 </xs:simpleContent>
 169         </xs:complexType>
 170         </xs:element>
 171         <xs:complexType name="rangeType" abstract="true">
 172                 <xs:annotation>
 173                         <xs:documentation>
 174                                 Specify an ordered set of positions and/or regions on the principle
 175                                 dimension of some associated vamsas object
 176                         </xs:documentation>
 177                         <xs:documentation>
 178                                 Keeping to jaxb-1.0 specification for the moment - this
 179                                 choice should become a substitution group when we use
 180                                 jaxb-2.0 capable bindings
 181                         </xs:documentation>
 182                 </xs:annotation>
 183                 <!--  Do we really need this - a position could be just a seg with start=end and inclusive=true -->
 184                 <xs:choice>
 185                         <xs:element name="pos" maxOccurs="unbounded"
 186                                 minOccurs="1">
 187                                 <xs:annotation>
 188                                         <xs:documentation>
 189                                                 a position within the associated object's
 190                                                 coordinate system
 191                                         </xs:documentation>
 192                                 </xs:annotation>
 193                                 <xs:complexType>
 194                                         <xs:attribute name="i" type="xs:int" use="required" />
 195                                 </xs:complexType>
 196                         </xs:element>
 197                         <xs:element name="seg" maxOccurs="unbounded"
 198                                 minOccurs="1">
 199                                 <xs:annotation>
 200                                         <xs:documentation>
 201                                                 a region from start to end, with flag for
 202                                                 inclusivity of terminii
 203                                         </xs:documentation>
 204                                 </xs:annotation>
 205                                 <xs:complexType>
 206                                         <xs:attribute name="start" type="xs:int"
 207                                                 use="required" />
 208                                         <xs:attribute name="end" type="xs:int"
 209                                                 use="required" />
 210                                         <xs:attribute name="inclusive" type="xs:boolean"
 211                                                 use="required">
 212                                                 <xs:annotation>
 213                                                         <xs:documentation>
 214                                                                 when false, a consecutive range like
 215                                                                 'start=1, end=2' means the region lying
 216                                                                 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         </xs:complexType>
 224         <xs:complexType name="rangeAnnotation">
 225                 <xs:annotation>
 226                         <xs:documentation>
 227                                 Annotation for a rangeSpec - values can be attached for the whole specification, and to each position within the spec. following the orientation specified by the ordered set of rangeSpec (pos, seg) elements.
 228                         </xs:documentation>
 229                 </xs:annotation>
 230                 <xs:complexContent>
 231                         <xs:extension base="vamsas:rangeType">
 232                                 <xs:sequence>
 233                                         <xs:element name="label" type="xs:string"
 234                                                 minOccurs="0" >
 235                                                 <xs:annotation>
 236                                                 <xs:documentation>
 237                                                         Short, meaningful name for the annotation - if this 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"
 242                                                 minOccurs="0" >
 243                                                 <xs:annotation>
 244                                                 <xs:documentation>
 245                                                         Human readable description of the annotation
 246                                                 </xs:documentation>
 247                                                 </xs:annotation>
 248                                                 </xs:element>
 249                                         <xs:element name="status" type="xs:string"
 250                                                 minOccurs="0" >
 251                                                 <xs:annotation><xs:documentation>
 252                                                         TODO: specify this - we have considered taking the GO evidence codes as a model for assessing a measure of quality to an annotation.
 253                                                 </xs:documentation></xs:annotation>
 254                                                 </xs:element>
 255                                         <xs:element ref="vamsas:annotationElement"
 256                                                 minOccurs="0" maxOccurs="unbounded">
 257                                                 <xs:annotation>
 258                                                         <xs:documentation>
 259                                                                 Annotation Element position maps to
 260                                                                 ordered positions defined by the
 261                                                                 sequence of rangeType pos positions or
 262                                                                 concatenated seg start/end segments.
 263                                                         </xs:documentation>
 264                                                 </xs:annotation>
 265                                         </xs:element>
 266                                         <xs:element name="score" minOccurs="0"
 267                                                 maxOccurs="unbounded">
 268                                                 <xs:annotation>
 269                                                         <xs:documentation>
 270                                                                 Ordered set of optionally named float
 271                                                                 values for the whole annotation
 272                                                         </xs:documentation>
 273                                                 </xs:annotation>
 274                                                 <xs:complexType>
 275                                                         <xs:simpleContent>
 276                                                                 <xs:extension base="xs:float">
 277                                                                         <xs:attribute name="name"
 278                                                                                 type="xs:string" use="optional" default="score">
 279                                                                         </xs:attribute>
 280                                                                 </xs:extension>
 281                                                         </xs:simpleContent>
 282                                                 </xs:complexType>
 283                                         </xs:element>
 284                                         <xs:element ref="vamsas:link" minOccurs="0" maxOccurs="unbounded" />
 285                                         <xs:element ref="vamsas:property" minOccurs="0"
 286                                                 maxOccurs="unbounded">
 287                                                 <xs:annotation>
 288                                                         <xs:documentation>
 289                                                                 Note:These are mutable so an application
 290                                                                 should check them each time.
 291                                                         </xs:documentation>
 292                                                 </xs:annotation>
 293                                         </xs:element>
 294                                 </xs:sequence>
 295                                 <xs:attribute name="id" type="xs:ID" use="optional">
 296                                         <xs:annotation>
 297                                                 <xs:documentation>
 298                                                         Primary Key for vamsas object referencing
 299                                                 </xs:documentation>
 300                                         </xs:annotation>
 301                                 </xs:attribute>
 302                                 <xs:attribute name="modifiable" type="xs:boolean"
 303                                         default="true" use="optional">
 304                                         <xs:annotation>
 305                                                 <xs:documentation>
 306                                                         objects with modifiable=false will not be
 307                                                         modified by a vamsas client update
 308                                                 </xs:documentation>
 309                                         </xs:annotation>
 310                                 </xs:attribute>
 311                                 <xs:attribute name="group" type="xs:string"
 312                                         use="optional" default="">
 313                                         <xs:annotation>
 314                                                 <xs:documentation>
 315                                                         Annotation with the same non-empty group
 316                                                         name are grouped together
 317                                                 </xs:documentation>
 318                                         </xs:annotation>
 319                                 </xs:attribute>
 320                                 <xs:attribute name="type" type="xs:string"
 321                                         use="required">
 322                                         <xs:annotation>
 323                                                 <xs:documentation>
 324                                                         A Das Feature has both a type and a Type ID.
 325                                                         We go the route of requiring the type string
 326                                                         to be taken from a controlled vocabulary if
 327                                                         an application expects others to make sense
 328                                                         of it.
 329                                                         The type may qualified - so uniprot:CHAIN is a valid type name,
 330                                                         and considered distinct from someotherDB:CHAIN
 331                                                 </xs:documentation>
 332                                         </xs:annotation>
 333                                 </xs:attribute>
 334                         </xs:extension>
 335                 </xs:complexContent>
 336         </xs:complexType>
 337         <xs:element name="param">
 338                 <xs:complexType>
 339                         <xs:annotation>
 340                                 <xs:documentation>
 341                                         Specifies a named and typed value used to perform
 342                                         some data transformation.
 343                                 </xs:documentation>
 344                                 <xs:documentation>
 345                                         LATER: experiment with xml validation of property
 346                                         set prototypes for services
 347                                 </xs:documentation>
 348                         </xs:annotation>
 349                         <xs:simpleContent>
 350                                 <xs:annotation>
 351                                         <xs:documentation>
 352                                                 Named and typed property string
 353                                         </xs:documentation>
 354                                 </xs:annotation>
 355                                 <xs:extension base="xs:string">
 356                                         <xs:attribute name="name" type="xs:string"
 357                                                 use="required" />
 358                                         <xs:attribute name="type" type="xs:string"
 359                                                 use="required">
 360                                                 <xs:annotation>
 361                                                         <xs:documentation>
 362                                                                 The type specifies how the property will
 363                                                                 be parsed. Empty property strings are
 364                                                                 allowed, and can be used to prototype
 365                                                                 the input to a document. TODO: specify
 366                                                                 allowed types
 367                                                         </xs:documentation>
 368                                                 </xs:annotation>
 369                                         </xs:attribute>
 370                                 </xs:extension>
 371                         </xs:simpleContent>
 372                 </xs:complexType>
 373         </xs:element>
 374         <xs:element name="input">
 375                 <xs:complexType>
 376                         <xs:annotation>
 377                                 <xs:documentation>
 378                                         Selects all or part of a collection of vamsas
 379                                         objects as a named input to some transformation
 380                                         process. Many inputs with the same name imply a
 381                                         group input (such as a collection of sequences)
 382                                 </xs:documentation>
 383                         </xs:annotation>
 384                         <xs:complexContent>
 385
 386                                 <xs:extension base="vamsas:rangeType">
 387                                         <xs:attribute name="name" type="xs:string"
 388                                                 use="required">
 389                                         </xs:attribute>
 390                                         <xs:attribute name="objRef" type="xs:IDREF"
 391                                                 use="optional">
 392                                                 <xs:annotation>
 393                                                         <xs:documentation>
 394                                                                 Reference Frame for rangeType
 395                                                                 specfication
 396                                                         </xs:documentation>
 397                                                 </xs:annotation>
 398                                         </xs:attribute>
 399                                 </xs:extension>
 400                         </xs:complexContent>
 401                 </xs:complexType>
 402         </xs:element>
 403
 404         <xs:element name="Provenance">
 405                 <xs:complexType>
 406                         <xs:annotation>
 407                                 <xs:documentation>
 408                                         Defines the origin and series of operations applied
 409                                         directly to the object that references it.
 410                                 </xs:documentation>
 411                         </xs:annotation>
 412                         <xs:sequence>
 413                                 <xs:element name="entry" maxOccurs="unbounded">
 414                                         <xs:complexType>
 415                                                 <xs:sequence>
 416                                                         <xs:element name="User" type="xs:string">
 417                                                                 <xs:annotation>
 418                                                                         <xs:documentation>
 419                                                                                 Who
 420                                                                         </xs:documentation>
 421                                                                 </xs:annotation>
 422                                                         </xs:element>
 423                                                         <xs:element name="App" type="xs:string">
 424                                                                 <xs:annotation>
 425                                                                         <xs:documentation>
 426                                                                                 With which application
 427                                                                         </xs:documentation>
 428                                                                 </xs:annotation>
 429                                                         </xs:element>
 430                                                         <xs:element name="Action"
 431                                                                 type="xs:string">
 432                                                                 <xs:annotation>
 433                                                                         <xs:documentation>
 434                                                                                 Did what
 435                                                                         </xs:documentation>
 436                                                                 </xs:annotation>
 437                                                         </xs:element>
 438                                                         <xs:element name="Date" type="xs:date">
 439                                                                 <xs:annotation>
 440                                                                         <xs:documentation>
 441                                                                                 When
 442                                                                         </xs:documentation>
 443                                                                 </xs:annotation>
 444                                                         </xs:element>
 445                                                         <xs:element ref="vamsas:property"
 446                                                                 minOccurs="0" maxOccurs="unbounded">
 447                                                                 <xs:annotation>
 448                                                                         <xs:documentation>
 449                                                                                 additional information
 450                                                                         </xs:documentation>
 451                                                                 </xs:annotation>
 452                                                         </xs:element>
 453                                                         <xs:element ref="vamsas:param" minOccurs="0"
 454                                                                 maxOccurs="unbounded">
 455                                                                 <xs:annotation>
 456                                                                         <xs:documentation>
 457                                                                                 parameter for the action
 458                                                                         </xs:documentation>
 459                                                                 </xs:annotation>
 460                                                         </xs:element>
 461                                                         <xs:element ref="vamsas:input" minOccurs="0"
 462                                                                 maxOccurs="unbounded">
 463                                                                 <xs:annotation>
 464                                                                         <xs:documentation>
 465                                                                                 bioinformatic objects input to
 466                                                                                 action
 467                                                                         </xs:documentation>
 468                                                                 </xs:annotation>
 469                                                         </xs:element>
 470                                                 </xs:sequence>
 471                                                 <xs:attribute name="id" type="xs:ID"
 472                                                         use="optional">
 473                                                         <xs:annotation>
 474                                                                 <xs:documentation>
 475                                                                         Primary Key for vamsas object
 476                                                                         referencing
 477                                                                 </xs:documentation>
 478                                                         </xs:annotation>
 479                                                 </xs:attribute>
 480                                         </xs:complexType>
 481                                 </xs:element>
 482                         </xs:sequence>
 483                 </xs:complexType>
 484         </xs:element>
 485         <xs:element name="DataSet">
 486                 <xs:complexType>
 487                         <xs:annotation>
 488                                 <xs:documentation>
 489                                         A collection of sequences, alignments, trees and
 490                                         other things.
 491                                 </xs:documentation>
 492                         </xs:annotation>
 493                         <xs:sequence>
 494                                 <xs:element name="Sequence" maxOccurs="unbounded">
 495                                         <xs:complexType>
 496                                                 <xs:annotation>
 497                                                         <xs:documentation>
 498                                                                 a primary or secondary sequence record
 499                                                                 from which all other sequences may be
 500                                                                 derived
 501                                                         </xs:documentation>
 502                                                 </xs:annotation>
 503                                                 <xs:complexContent>
 504                                                         <xs:extension base="vamsas:SequenceType">
 505                                                                 <xs:sequence>
 506                                                                         <xs:element name="dbRef"
 507                                                                                 minOccurs="0" maxOccurs="unbounded">
 508                                                                                 <xs:annotation>
 509                                                                                         <xs:documentation>
 510                                                                                                 Store a list of database
 511                                                                                                 references for this
 512                                                                                                 sequence record - with
 513                                                                                                 optional mapping from
 514                                                                                                 database sequence to the
 515                                                                                                 given sequence record
 516                                                                                         </xs:documentation>
 517                                                                                         <xs:documentation></xs:documentation>
 518                                                                                         <xs:documentation></xs:documentation>
 519                                                                                 </xs:annotation>
 520                                                                                 <xs:complexType>
 521                                                                                         <xs:sequence>
 522                                                                                                 <xs:element name="map"
 523                                                                                                         minOccurs="0" maxOccurs="unbounded">
 524                                                                                                         <xs:complexType>
 525                                                                                                                 <xs:attribute
 526                                                                                                                         name="from" type="xs:integer" default="0"
 527                                                                                                                         use="optional">
 528                                                                                                                         <xs:annotation>
 529                                                                                                                                 <xs:documentation>
 530                                                                                                                                         Offset
 531                                                                                                                                         to
 532                                                                                                                                         first
 533                                                                                                                                         position
 534                                                                                                                                         in
 535                                                                                                                                         dataset
 536                                                                                                                                         sequence
 537                                                                                                                                         record
 538                                                                                                                                         that
 539                                                                                                                                         this
 540                                                                                                                                         database
 541                                                                                                                                         entry
 542                                                                                                                                         maps
 543                                                                                                                                         to
 544                                                                                                                                 </xs:documentation>
 545                                                                                                                         </xs:annotation>
 546                                                                                                                 </xs:attribute>
 547                                                                                                                 <xs:attribute
 548                                                                                                                         name="to" type="xs:integer" default="0" use="optional">
 549                                                                                                                         <xs:annotation>
 550                                                                                                                                 <xs:documentation>
 551                                                                                                                                         Offset
 552                                                                                                                                         to
 553                                                                                                                                         last
 554                                                                                                                                         position
 555                                                                                                                                         in
 556                                                                                                                                         dataset
 557                                                                                                                                         sequence
 558                                                                                                                                         record
 559                                                                                                                                         that
 560                                                                                                                                         this
 561                                                                                                                                         database
 562                                                                                                                                         entry
 563                                                                                                                                         maps
 564                                                                                                                                         to
 565                                                                                                                                 </xs:documentation>
 566                                                                                                                         </xs:annotation>
 567                                                                                                                 </xs:attribute>
 568                                                                                                                 <xs:attribute
 569                                                                                                                         name="start" type="xs:integer" use="required">
 570                                                                                                                 <xs:annotation>
 571                                                                                                                         <xs:documentation>
 572                                                                                                                                 Offset
 573                                                                                                                                 to first
 574                                                                                                                                 last
 575                                                                                                                                 position
 576                                                                                                                                 in
 577                                                                                                                                 database
 578                                                                                                                                 entry
 579                                                                                                                                 that
 580                                                                                                                                 first
 581                                                                                                                                 (or
 582                                                                                                                                 offset)
 583                                                                                                                                 position
 584                                                                                                                                 in
 585                                                                                                                                 sequence
 586                                                                                                                                 maps to
 587                                                                                                                         </xs:documentation>
 588                                                                                                                 </xs:annotation>
 589                                                                                                                 </xs:attribute>
 590                                                                                                                 <xs:attribute
 591                                                                                                                         name="end" type="xs:integer" use="required">
 592                                                                                                                 <xs:annotation>
 593                                                                                                                         <xs:documentation>
 594                                                                                                                                 Offset
 595                                                                                                                                 to last
 596                                                                                                                                 position
 597                                                                                                                                 in
 598                                                                                                                                 database
 599                                                                                                                                 entry
 600                                                                                                                                 that
 601                                                                                                                                 last
 602                                                                                                                                 (offset)
 603                                                                                                                                 position
 604                                                                                                                                 in
 605                                                                                                                                 sequence
 606                                                                                                                                 maps to
 607                                                                                                                         </xs:documentation>
 608                                                                                                                 </xs:annotation>
 609                                                                                                                 </xs:attribute>
 610                                                                                                         </xs:complexType>
 611                                                                                                 </xs:element>
 612                                                                                                 <xs:element ref="vamsas:link" minOccurs="0" maxOccurs="unbounded"/>
 613                                                                                                 <xs:element
 614                                                                                                         ref="vamsas:property" minOccurs="0" maxOccurs="unbounded" />
 615                                                                                         </xs:sequence>
 616                                                                                         <xs:attribute name="source"
 617                                                                                                 type="xs:string" use="required">
 618                                                                                                 <xs:annotation>
 619                                                                                                         <xs:documentation>
 620                                                                                                                 TODO Database
 621                                                                                                                 Naming
 622                                                                                                                 Convention:
 623                                                                                                                 either start
 624                                                                                                                 using LSID (so
 625                                                                                                                 change type to
 626                                                                                                                 URI) or leave
 627                                                                                                                 this as an
 628                                                                                                                 uncontrolled/unspecified
 629                                                                                                                 string ID
 630                                                                                                         </xs:documentation>
 631                                                                                                 </xs:annotation>
 632                                                                                         </xs:attribute>
 633                                                                                         <xs:attribute name="version"
 634                                                                                                 type="xs:string" use="required">
 635                                                                                                 <xs:annotation>
 636                                                                                                         <xs:documentation>
 637                                                                                                                 Version must be
 638                                                                                                                 specified -
 639                                                                                                         </xs:documentation>
 640                                                                                                 </xs:annotation>
 641                                                                                         </xs:attribute>
 642                                                                                         <xs:attribute
 643                                                                                                 name="accessionId" type="xs:string" use="required">
 644                                                                                                 <xs:annotation>
 645                                                                                                         <xs:documentation>
 646                                                                                                                 TODO: make some
 647                                                                                                                 specification of
 648                                                                                                                 the database
 649                                                                                                                 field from which
 650                                                                                                                 this accessionId
 651                                                                                                                 is taken from -
 652                                                                                                                 should that be a
 653                                                                                                                 special property
 654                                                                                                                 of the dbRef
 655                                                                                                                 object ?
 656                                                                                                         </xs:documentation>
 657                                                                                                 </xs:annotation>
 658                                                                                         </xs:attribute>
 659                                                                                         <xs:attribute name="id"
 660                                                                                                 type="xs:ID" use="optional">
 661                                                                                                 <xs:annotation>
 662                                                                                                         <xs:documentation>
 663                                                                                                                 Primary Key for
 664                                                                                                                 vamsas object
 665                                                                                                                 referencing
 666                                                                                                         </xs:documentation>
 667                                                                                                 </xs:annotation>
 668                                                                                         </xs:attribute>
 669                                                                                 </xs:complexType>
 670                                                                         </xs:element>
 671                                                                 </xs:sequence>
 672                                                                 <xs:attribute name="id" type="xs:ID"
 673                                                                         use="optional">
 674                                                                         <xs:annotation>
 675                                                                                 <xs:documentation>
 676                                                                                         Primary Key for vamsas
 677                                                                                         object referencing
 678                                                                                 </xs:documentation>
 679                                                                         </xs:annotation>
 680                                                                 </xs:attribute>
 681                                                                 <xs:attribute name="dictionary"
 682                                                                         type="xs:string" use="required">
 683                                                                         <xs:annotation>
 684                                                                                 <xs:documentation>
 685                                                                                         symbol class for sequence
 686                                                                                 </xs:documentation>
 687                                                                         </xs:annotation>
 688                                                                 </xs:attribute>
 689                                                         </xs:extension>
 690                                                 </xs:complexContent>
 691                                         </xs:complexType>
 692                                 </xs:element>
 693                                 <xs:element name="DataSetAnnotations" minOccurs="0"
 694                                         maxOccurs="unbounded">
 695                                         <xs:complexType>
 696                                                 <xs:annotation>
 697                                                         <xs:documentation>
 698                                                                 Annotate over positions and regions of a
 699                                                                 dataset sequence
 700                                                         </xs:documentation>
 701                                                 </xs:annotation>
 702                                                 <xs:complexContent>
 703                                                         <xs:extension
 704                                                                 base="vamsas:rangeAnnotation">
 705                                                                 <xs:sequence>
 706                                                                         <xs:element ref="vamsas:Provenance"
 707                                                                                 maxOccurs="1" minOccurs="1" />
 708                                                                 </xs:sequence>
 709                                                                 <xs:attribute name="seqRef"
 710                                                                         type="xs:IDREF" use="required">
 711                                                                         <xs:annotation>
 712                                                                                 <xs:documentation>
 713                                                                                         annotation is associated
 714                                                                                         with a particular dataset
 715                                                                                         sequence
 716                                                                                 </xs:documentation>
 717                                                                         </xs:annotation>
 718                                                                 </xs:attribute>
 719                                                         </xs:extension>
 720                                                 </xs:complexContent>
 721                                         </xs:complexType>
 722                                 </xs:element>
 723                                 <xs:element name="Alignment" minOccurs="0"
 724                                         maxOccurs="unbounded">
 725                                         <xs:complexType>
 726                                                 <xs:sequence>
 727                                                         <xs:element name="AlignmentAnnotation"
 728                                                                 minOccurs="0" maxOccurs="unbounded">
 729                                                                 <xs:annotation>
 730                                                                         <xs:documentation>
 731                                                                                 This is annotation over the
 732                                                                                 coordinate frame defined by all
 733                                                                                 the columns in the alignment.
 734                                                                         </xs:documentation>
 735                                                                 </xs:annotation>
 736                                                                 <xs:complexType>
 737                                                                         <xs:complexContent>
 738                                                                                 <xs:extension
 739                                                                                         base="vamsas:rangeAnnotation">
 740                                                                                         <xs:sequence>
 741                                                                                                 <xs:element
 742                                                                                                         ref="vamsas:Provenance" minOccurs="1" maxOccurs="1" />
 743                                                                                         </xs:sequence>
 744                                                                                         <xs:attribute name="graph"
 745                                                                                                 type="xs:boolean" use="required">
 746                                                                                                 <xs:annotation>
 747                                                                                                         <xs:documentation>
 748                                                                                                                 TODO: decide if
 749                                                                                                                 this flag is
 750                                                                                                                 redundant - when
 751                                                                                                                 true it would
 752                                                                                                                 suggest that the
 753                                                                                                                 annotationElement
 754                                                                                                                 values together
 755                                                                                                                 form a graph
 756                                                                                                         </xs:documentation>
 757                                                                                                 </xs:annotation>
 758                                                                                         </xs:attribute>
 759                                                                                 </xs:extension>
 760                                                                         </xs:complexContent>
 761                                                                 </xs:complexType>
 762                                                         </xs:element>
 763                                                         <xs:element ref="vamsas:Tree" minOccurs="0"
 764                                                                 maxOccurs="unbounded" />
 765                                                         <xs:element name="alignmentSequence"
 766                                                                 maxOccurs="unbounded">
 767                                                                 <xs:complexType>
 768                                                                         <xs:complexContent>
 769                                                                                 <xs:extension
 770                                                                                         base="vamsas:SequenceType">
 771                                                                                         <xs:sequence>
 772                                                                                                 <xs:element
 773                                                                                                         name="AlignmentSequenceAnnotation" minOccurs="0"
 774                                                                                                         maxOccurs="unbounded">
 775                                                                                                         <xs:complexType>
 776                                                                                                                 <xs:annotation>
 777                                                                                                                         <xs:documentation>
 778                                                                                                                                 Annotate
 779                                                                                                                                 over
 780                                                                                                                                 positions
 781                                                                                                                                 and
 782                                                                                                                                 regions
 783                                                                                                                                 of the
 784                                                                                                                                 ungapped
 785                                                                                                                                 sequence
 786                                                                                                                                 in the
 787                                                                                                                                 context
 788                                                                                                                                 of the
 789                                                                                                                                 alignment
 790                                                                                                                         </xs:documentation>
 791                                                                                                                         <xs:documentation></xs:documentation>
 792                                                                                                                 </xs:annotation>
 793                                                                                                                 <xs:complexContent>
 794                                                                                                                         <xs:extension
 795                                                                                                                                 base="vamsas:rangeAnnotation">
 796                                                                                                                                 <xs:sequence>
 797                                                                                                                                         <xs:element
 798                                                                                                                                                 ref="vamsas:Provenance" minOccurs="1" maxOccurs="1" />
 799                                                                                                                                 </xs:sequence>
 800                                                                                                                                 <xs:attribute
 801                                                                                                                                         name="graph" type="xs:boolean" use="required">
 802                                                                                                                                         <xs:annotation>
 803                                                                                                                                                 <xs:documentation>
 804                                                                                                                                                         TODO:
 805                                                                                                                                                         decide
 806                                                                                                                                                         if
 807                                                                                                                                                         this
 808                                                                                                                                                         flag
 809                                                                                                                                                         is
 810                                                                                                                                                         redundant
 811                                                                                                                                                         -
 812                                                                                                                                                         when
 813                                                                                                                                                         true
 814                                                                                                                                                         it
 815                                                                                                                                                         would
 816                                                                                                                                                         suggest
 817                                                                                                                                                         that
 818                                                                                                                                                         the
 819                                                                                                                                                         annotationElement
 820                                                                                                                                                         values
 821                                                                                                                                                         together
 822                                                                                                                                                         form
 823                                                                                                                                                         a
 824                                                                                                                                                         graph
 825                                                                                                                                                 </xs:documentation>
 826                                                                                                                                         </xs:annotation>
 827                                                                                                                                 </xs:attribute>
 828                                                                                                                         </xs:extension>
 829                                                                                                                 </xs:complexContent>
 830
 831                                                                                                                 <!--
 832                                                                                                                         This replaces the flat list of sequenceFeatures.
 833                                                                                                                         <xs:element name="AlignmentFeatures" minOccurs="0" maxOccurs="unbounded"><xs:complexType><xs:annotation>
 834                                                                                                                         <xs:documentation>Annotate over positions and regions of the alignment</xs:documentation>
 835                                                                                                                         </xs:annotation><xs:complexContent>
 836                                                                                                                         <xs:extension base="vamsas:rangeFeature">
 837                                                                                                                         <xs:attribute name="seqRef" type="xs:IDREF" use="optional">
 838                                                                                                                         <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>
 839                                                                                                                         </xs:attribute>
 840                                                                                                                         </xs:extension>
 841                                                                                                                         </xs:complexContent></xs:complexType></xs:element> -->
 842                                                                                                         </xs:complexType>
 843                                                                                                 </xs:element>
 844                                                                                         </xs:sequence>
 845                                                                                         <xs:attribute name="id"
 846                                                                                                 type="xs:ID" use="optional">
 847                                                                                                 <xs:annotation>
 848                                                                                                         <xs:documentation>
 849                                                                                                                 Primary Key for
 850                                                                                                                 vamsas object
 851                                                                                                                 referencing
 852                                                                                                         </xs:documentation>
 853                                                                                                 </xs:annotation>
 854                                                                                         </xs:attribute>
 855                                                                                         <xs:attribute name="refid"
 856                                                                                                 type="xs:IDREF" use="required">
 857                                                                                                 <xs:annotation>
 858                                                                                                         <xs:documentation>
 859                                                                                                                 Dataset Sequence
 860                                                                                                                 from which this
 861                                                                                                                 alignment
 862                                                                                                                 sequence is
 863                                                                                                                 taken from
 864                                                                                                         </xs:documentation>
 865                                                                                                 </xs:annotation>
 866                                                                                         </xs:attribute>
 867                                                                                 </xs:extension>
 868                                                                         </xs:complexContent>
 869                                                                 </xs:complexType>
 870                                                         </xs:element>
 871                                                         <xs:element ref="vamsas:property"
 872                                                                 minOccurs="0" maxOccurs="unbounded">
 873                                                                 <xs:annotation>
 874                                                                         <xs:documentation>
 875                                                                                 typical properties may be
 876                                                                                 additional alignment score
 877                                                                                 objects
 878                                                                         </xs:documentation>
 879                                                                 </xs:annotation>
 880                                                         </xs:element>
 881                                                         <xs:element ref="vamsas:Provenance" />
 882                                                 </xs:sequence>
 883                                                 <xs:attribute name="gapChar" type="xs:string"
 884                                                         use="required" />
 885                                                 <xs:attribute name="aligned" type="xs:boolean"
 886                                                         use="optional" />
 887                                                 <xs:attribute name="id" type="xs:ID"
 888                                                         use="optional">
 889                                                         <xs:annotation>
 890                                                                 <xs:documentation>
 891                                                                         Primary Key for vamsas object
 892                                                                         referencing
 893                                                                 </xs:documentation>
 894                                                         </xs:annotation>
 895                                                 </xs:attribute>
 896                                                 <xs:attribute name="modifiable"
 897                                                         type="xs:boolean" default="true" use="optional">
 898                                                         <xs:annotation>
 899                                                                 <xs:documentation>
 900                                                                         objects with modifiable=false will
 901                                                                         not be modified by a vamsas client
 902                                                                         update
 903                                                                 </xs:documentation>
 904                                                         </xs:annotation>
 905                                                 </xs:attribute>
 906                                         </xs:complexType>
 907                                 </xs:element>
 908                                 <xs:element ref="vamsas:Tree" minOccurs="0"
 909                                         maxOccurs="unbounded" />
 910                                 <xs:element ref="vamsas:Provenance" />
 911                         </xs:sequence>
 912                         <xs:attribute name="id" type="xs:ID" use="optional">
 913                                 <xs:annotation>
 914                                         <xs:documentation>
 915                                                 Primary Key for vamsas object referencing
 916                                         </xs:documentation>
 917                                 </xs:annotation>
 918                         </xs:attribute>
 919                 </xs:complexType>
 920         </xs:element>
 921         <xs:element name="annotationElement">
 922                 <xs:complexType>
 923                         <xs:annotation>
 924                                 <xs:documentation>
 925                                         per-site symbolic and/or quantitative annotation
 926                                 </xs:documentation>
 927                                 <xs:documentation>
 928                                         SecondaryStructure and display character (from
 929                                         Jalview) have been subsumed into the glyph element
 930                                 </xs:documentation>
 931                         </xs:annotation>
 932                         <xs:sequence>
 933
 934                                 <xs:element name="description" type="xs:string"
 935                                         minOccurs="0">
 936                                         <xs:annotation>
 937                                                 <xs:documentation>
 938                                                         Free text at this position
 939                                                 </xs:documentation>
 940                                         </xs:annotation>
 941                                 </xs:element>
 942                                 <xs:element name="glyph" minOccurs="0"
 943                                         maxOccurs="unbounded">
 944                                         <xs:annotation>
 945                                                 <xs:documentation>
 946                                                         Discrete symbol - possibly graphically
 947                                                         represented
 948                                                 </xs:documentation>
 949                                         </xs:annotation>
 950                                         <xs:complexType>
 951                                                 <xs:simpleContent>
 952                                                         <xs:extension base="xs:string">
 953                                                                 <xs:attribute name="dict"
 954                                                                         type="xs:string" default="utf8" use="optional">
 955                                                                         <xs:annotation>
 956                                                                                 <xs:documentation>
 957                                                                                         specifies the symbol
 958                                                                                         dictionary for this glyph -
 959                                                                                         eg utf8 (the default),
 960                                                                                         aasecstr_3 or
 961                                                                                         kd_hydrophobicity - the
 962                                                                                         content is not validated so
 963                                                                                         applications must ensure
 964                                                                                         they gracefully deal with
 965                                                                                         invalid entries here
 966                                                                                 </xs:documentation>
 967                                                                                 <xs:documentation>
 968                                                                                         TODO: specify a minimum list
 969                                                                                         of glyph dictionaries to get
 970                                                                                         us started and provide a way
 971                                                                                         for the vamsasClient to
 972                                                                                         validate their content if
 973                                                                                         regexes are specified
 974                                                                                 </xs:documentation>
 975                                                                         </xs:annotation>
 976                                                                 </xs:attribute>
 977                                                         </xs:extension>
 978                                                 </xs:simpleContent>
 979                                         </xs:complexType>
 980                                 </xs:element>
 981                                 <xs:element name="value" type="xs:float" minOccurs="0"
 982                                         maxOccurs="unbounded">
 983                                         <xs:annotation>
 984                                                 <xs:documentation>
 985                                                         Ordered set of float values - an application
 986                                                         may treat the values together as a vector
 987                                                         with common support for a set of annotation
 988                                                         elements - but this is, again, not validated
 989                                                         so applications should deal gracefully with
 990                                                         varying numbers of dimensions
 991                                                 </xs:documentation>
 992                                         </xs:annotation>
 993                                 </xs:element>
 994                         </xs:sequence>
 995                         <xs:attribute name="position" type="xs:integer"
 996                                 use="required">
 997                                 <xs:annotation>
 998                                         <xs:documentation>
 999                                                 position with respect to the coordinate frame
1000                                                 defined by a rangeType specification
1001                                         </xs:documentation>
1002                                 </xs:annotation>
1003                         </xs:attribute>
1004                         <xs:attribute name="after" type="xs:boolean" use="optional"
1005                                 default="false">
1006                                 <xs:annotation>
1007                                         <xs:documentation>
1008                                                 true means the annotation element appears
1009                                                 between the specified position and the next
1010                                         </xs:documentation>
1011                                 </xs:annotation>
1012                         </xs:attribute>
1013                         <xs:attribute name="id" type="xs:ID" use="optional">
1014                                 <xs:annotation>
1015                                         <xs:documentation>
1016                                                 Primary Key for vamsas object referencing
1017                                         </xs:documentation>
1018                                 </xs:annotation>
1019                         </xs:attribute>
1020                 </xs:complexType>
1021         </xs:element>
1022         <xs:complexType name="SequenceType">
1023                 <xs:sequence>
1024                         <xs:element name="sequence" type="xs:string" minOccurs="1"
1025                                 maxOccurs="1" />
1026                         <xs:element name="name" type="xs:string" minOccurs="1"
1027                                 maxOccurs="1" />
1028                         <xs:element name="description" type="xs:string"
1029                                 minOccurs="0" maxOccurs="1" />
1030                         <xs:element ref="vamsas:property" minOccurs="0"
1031                                 maxOccurs="unbounded">
1032                                 <xs:annotation>
1033                                         <xs:documentation>
1034                                                 additional typed properties
1035                                         </xs:documentation>
1036                                 </xs:annotation>
1037                         </xs:element>
1038                 </xs:sequence>
1039                 <xs:attribute name="start" type="xs:integer" use="required" />
1040                 <xs:attribute name="end" type="xs:integer" use="required" />
1041         </xs:complexType>
1042         <xs:element name="ApplicationData">
1043                 <xs:complexType>
1044                         <xs:annotation>
1045                                 <xs:documentation>
1046                                         Data specific to a particular type and version of
1047                                         vamsas application
1048                                 </xs:documentation>
1049                         </xs:annotation>
1050                         <xs:complexContent>
1051                                 <xs:extension base="vamsas:appData">
1052                                         <xs:sequence>
1053                                                 <xs:element name="User" maxOccurs="unbounded"
1054                                                         minOccurs="0">
1055                                                         <xs:complexType>
1056                                                                 <xs:complexContent>
1057                                                                         <xs:extension
1058                                                                                 base="vamsas:appData">
1059                                                                                 <xs:annotation>
1060                                                                                         <xs:documentation>
1061                                                                                                 Data available to just a
1062                                                                                                 particular user
1063                                                                                         </xs:documentation>
1064                                                                                 </xs:annotation>
1065                                                                                 <xs:attribute name="fullname"
1066                                                                                         type="xs:string" use="required" />
1067                                                                                 <xs:attribute
1068                                                                                         name="organization" type="xs:string" use="required" />
1069                                                                         </xs:extension>
1070                                                                 </xs:complexContent>
1071                                                         </xs:complexType>
1072                                                 </xs:element>
1073                                                 <xs:element name="Common" maxOccurs="1"
1074                                                         minOccurs="0">
1075                                                         <xs:complexType>
1076                                                                 <xs:complexContent>
1077                                                                         <xs:extension
1078                                                                                 base="vamsas:appData">
1079                                                                         </xs:extension>
1080                                                                 </xs:complexContent>
1081                                                         </xs:complexType>
1082                                                 </xs:element>
1083                                                 <xs:element name="Instance"
1084                                                         maxOccurs="unbounded" minOccurs="0">
1085                                                         <xs:complexType>
1086                                                                 <xs:complexContent>
1087                                                                         <xs:extension
1088                                                                                 base="vamsas:appData">
1089                                                                                 <xs:annotation>
1090                                                                                         <xs:documentation>
1091                                                                                                 Data available to just a
1092                                                                                                 specific instance of the
1093                                                                                                 application
1094                                                                                         </xs:documentation>
1095                                                                                         <xs:documentation>
1096                                                                                                 VAMSAS/Pierre: Is this
1097                                                                                                 data volatile ?
1098                                                                                                 Application instances
1099                                                                                                 may not be accessible
1100                                                                                                 after the session has
1101                                                                                                 closed - the user may
1102                                                                                                 have to be presented
1103                                                                                                 with the option of
1104                                                                                                 picking up the data in
1105                                                                                                 that instance
1106                                                                                         </xs:documentation>
1107                                                                                 </xs:annotation>
1108                                                                                 <xs:attribute name="urn"
1109                                                                                         type="xs:string" use="required" />
1110                                                                         </xs:extension>
1111                                                                 </xs:complexContent>
1112                                                         </xs:complexType>
1113                                                 </xs:element>
1114                                         </xs:sequence>
1115                                         <xs:attribute name="version" type="xs:string"
1116                                                 use="required" ><xs:annotation><xs:documentation>
1117                                                         Version string describing the application specific data storage version used</xs:documentation></xs:annotation></xs:attribute>
1118                                         <xs:attribute name="name" type="xs:string"
1119                                                 use="required" >
1120                                                 <xs:annotation><xs:documentation>
1121                                                         Canonical name of application
1122                                                 </xs:documentation>
1123                                                 </xs:annotation>
1124                                                 </xs:attribute>
1125                                 </xs:extension>
1126                         </xs:complexContent>
1127                 </xs:complexType>
1128         </xs:element>
1129         <xs:element name="Attachment">
1130                 <xs:complexType>
1131                         <xs:complexContent>
1132                                 <xs:extension base="vamsas:appData">
1133                                         <xs:annotation>
1134                                                 <xs:documentation>
1135                                                         General data container to attach a typed
1136                                                         data object to any vamsas object
1137                                                 </xs:documentation>
1138                                         </xs:annotation>
1139                                         <xs:attribute name="compressed" type="xs:boolean"
1140                                                 use="optional" default="false">
1141                                                 <xs:annotation>
1142                                                         <xs:documentation>
1143                                                                 true implies data will be decompresses
1144                                                                 with Zip before presenting to
1145                                                                 application
1146                                                         </xs:documentation>
1147                                                 </xs:annotation>
1148                                         </xs:attribute>
1149                                         <xs:attribute name="type" type="xs:string"
1150                                                 use="required">
1151                                                 <xs:annotation>
1152                                                         <xs:documentation>
1153                                                                 Type of arbitrary data - TODO: decide
1154                                                                 format - use (extended) MIME types ?
1155                                                         </xs:documentation>
1156                                                 </xs:annotation>
1157                                         </xs:attribute>
1158                                         <xs:attribute name="objectref" type="xs:IDREF"
1159                                                 use="required">
1160                                                 <xs:annotation>
1161                                                         <xs:documentation>
1162                                                                 Object the arbitrary data is associated
1163                                                                 with
1164                                                         </xs:documentation>
1165                                                 </xs:annotation>
1166                                         </xs:attribute>
1167                                         <xs:attribute name="id" type="xs:ID"
1168                                                 use="optional">
1169                                                 <xs:annotation>
1170                                                         <xs:documentation>
1171                                                                 Primary Key for vamsas object
1172                                                                 referencing
1173                                                         </xs:documentation>
1174                                                 </xs:annotation>
1175                                         </xs:attribute>
1176                                 </xs:extension>
1177                         </xs:complexContent>
1178                 </xs:complexType>
1179         </xs:element>
1180         <xs:complexType name="appData">
1181                 <xs:choice>
1182                         <xs:element name="data" type="xs:base64Binary" />
1183                         <xs:element name="dataReference" type="xs:string" />
1184                 </xs:choice>
1185         </xs:complexType>
1186 </xs:schema>