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