schemas/vamsas.xsd

   1 <?xml version="1.0" encoding="UTF-8"?>
   2 <!-- edited with XMLSPY v5 rel. 4 U (http://www.xmlspy.com) by MSD (EMBL OUTSTATION THE EBI WELLCOME TRUST GENOME CAMPUS) -->
   3 <!-- edited with XMLSpy v2006 sp1 U (http://www.altova.com) by ioh[ (o[ih[oh) -->
   4 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="http://www.vamsas.org" targetNamespace="http://www.vamsas.org" elementFormDefault="qualified" attributeFormDefault="unqualified">
   5         <xs:annotation>
   6                 <xs:documentation>
   7                         Vorba ID - Vamsas Object Request Broker Address ID (name
   8                         needs to be worked on): Suggest it could be of the form
   9                         documentRoot/datasetName/SequenceUID for a dataset sequence.
  10                         Alignment sequence:
  11                         documentRoot/datasetName/AlignmentId/SequenceUID for an
  12                         aligned form of a dataset sequence
  13
  14                 </xs:documentation>
  15         </xs:annotation>
  16         <xs:element name="VAMSAS">
  17                 <xs:annotation>
  18                         <xs:documentation>
  19                                 contains unassociated trees and a number of analysis
  20                                 sets
  21                         </xs:documentation>
  22                 </xs:annotation>
  23                 <xs:complexType>
  24                         <xs:sequence>
  25                                 <xs:element ref="vamsas:Tree" minOccurs="0" maxOccurs="unbounded"/>
  26                                 <xs:element ref="vamsas:DataSet" minOccurs="0" maxOccurs="unbounded"/>
  27                         </xs:sequence>
  28                         <xs:attribute name="id" type="xs:ID" use="optional">
  29                                 <xs:annotation>
  30                                         <xs:documentation>
  31                                                 Primary Key for vamsas object referencing
  32                                         </xs:documentation>
  33                                 </xs:annotation>
  34                         </xs:attribute>
  35                         <xs:attribute name="modifiable" type="xs:boolean" use="optional" default="true">
  36                                 <xs:annotation>
  37                                         <xs:documentation>
  38                                                 objects with modifiable=false will not be
  39                                                 modified by a vamsas client update
  40                                         </xs:documentation>
  41                                 </xs:annotation>
  42                         </xs:attribute>
  43                 </xs:complexType>
  44         </xs:element>
  45         <xs:annotation>
  46                 <xs:documentation>
  47                         Properties. Generally, these are mutable so an application
  48                         should check them each time. This may change depending on
  49                         the context of the property
  50                 </xs:documentation>
  51         </xs:annotation>
  52         <xs:element name="Tree">
  53                 <xs:complexType>
  54                         <xs:annotation>
  55                                 <xs:documentation>
  56                                         Contains a named collection of trees
  57                                 </xs:documentation>
  58                                 <xs:documentation>
  59                                  TODO: define
  60                                         way of referencing leaves of global tree for any
  61                                         sequence/alignment object.
  62                                 SUggestion 1: Each named tree leafnode has a unique id (which may be unique in combination with trees own vorba ID).
  63                                 Dataset sequences can be tagged with a property "vamsas:tree_leaf"
  64                                 </xs:documentation>
  65                         </xs:annotation>
  66                         <xs:sequence>
  67                                 <xs:element name="title" type="xs:string" minOccurs="0"/>
  68                                 <xs:element name="newick" maxOccurs="unbounded">
  69                                         <xs:complexType>
  70                                                 <xs:simpleContent>
  71                                                         <xs:extension base="xs:string">
  72                                                                 <xs:attribute name="title" type="xs:string" use="optional"/>
  73                                                                 <xs:attribute name="id" type="xs:ID" use="optional">
  74                                                                         <xs:annotation>
  75                                                                                 <xs:documentation>
  76                                                                                         Primary Key for vamsas
  77                                                                                         object referencing
  78                                                                                 </xs:documentation>
  79                                                                         </xs:annotation>
  80                                                                 </xs:attribute>
  81                                                                 <xs:attribute name="modifiable" type="xs:boolean" use="optional" default="true">
  82                                                                         <xs:annotation>
  83                                                                                 <xs:documentation>
  84                                                                                         objects with
  85                                                                                         modifiable=false will not be
  86                                                                                         modified by a vamsas client
  87                                                                                         update
  88                                                                                 </xs:documentation>
  89                                                                         </xs:annotation>
  90                                                                 </xs:attribute>
  91                                                         </xs:extension>
  92                                                 </xs:simpleContent>
  93                                         </xs:complexType>
  94                                 </xs:element>
  95                                 <xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded"/>
  96                                 <xs:element ref="vamsas:Provenance"/>
  97                         </xs:sequence>
  98                         <xs:attribute name="id" type="xs:ID" use="optional">
  99                                 <xs:annotation>
 100                                         <xs:documentation>
 101                                                 Primary Key for vamsas object referencing
 102                                         </xs:documentation>
 103                                 </xs:annotation>
 104                         </xs:attribute>
 105                         <xs:attribute name="modifiable" type="xs:boolean" use="optional" default="true">
 106                                 <xs:annotation>
 107                                         <xs:documentation>
 108                                                 objects with modifiable=false will not be
 109                                                 modified by a vamsas client update
 110                                         </xs:documentation>
 111                                 </xs:annotation>
 112                         </xs:attribute>
 113                 </xs:complexType>
 114         </xs:element>
 115         <xs:element name="property">
 116                 <xs:complexType>
 117                         <xs:simpleContent>
 118                                 <xs:annotation>
 119                                         <xs:documentation>
 120                                                 Named and typed property string
 121                                         </xs:documentation>
 122                                 </xs:annotation>
 123                                 <xs:extension base="xs:string">
 124                                         <xs:attribute name="name" type="xs:string" use="required"/>
 125                                         <xs:attribute name="type" type="xs:string" use="required">
 126                                                 <xs:annotation>
 127                                                         <xs:documentation>
 128                                                                 The type specifies how the property will
 129                                                                 be parsed. Empty property strings are
 130                                                                 allowed, and can be used to prototype
 131                                                                 the input to a document. TODO: specify
 132                                                                 allowed types
 133                                                         </xs:documentation>
 134                                                 </xs:annotation>
 135                                         </xs:attribute>
 136                                 </xs:extension>
 137                         </xs:simpleContent>
 138                 </xs:complexType>
 139         </xs:element>
 140         <xs:element name="link">
 141                 <xs:complexType>
 142                         <xs:annotation>
 143                                 <xs:documentation>
 144                                 Primitive labelled URI object
 145                         </xs:documentation>
 146                         </xs:annotation>
 147                         <xs:simpleContent>
 148                                 <xs:extension base="xs:string">
 149                                         <xs:attribute name="href" type="xs:anyURI">
 150                                                 <xs:annotation>
 151                                                         <xs:documentation>The URI</xs:documentation>
 152                                                 </xs:annotation>
 153                                         </xs:attribute>
 154                                 </xs:extension>
 155                         </xs:simpleContent>
 156                 </xs:complexType>
 157         </xs:element>
 158         <xs:complexType name="rangeType" abstract="true">
 159                 <xs:annotation>
 160                         <xs:documentation>
 161                                 Specify an ordered set of positions and/or regions on the principle
 162                                 dimension of some associated vamsas object
 163                         </xs:documentation>
 164                         <xs:documentation>
 165                                 Keeping to jaxb-1.0 specification for the moment - this
 166                                 choice should become a substitution group when we use
 167                                 jaxb-2.0 capable bindings
 168                         </xs:documentation>
 169                 </xs:annotation>
 170                 <xs:choice>
 171                         <xs:element name="pos" maxOccurs="unbounded">
 172                                 <xs:annotation>
 173                                         <xs:documentation>
 174                                                 a position within the associated object's
 175                                                 coordinate system
 176                                         </xs:documentation>
 177                                 </xs:annotation>
 178                                 <xs:complexType>
 179                                         <xs:attribute name="i" type="xs:int" use="required"/>
 180                                 </xs:complexType>
 181                         </xs:element>
 182                         <xs:element name="seg" maxOccurs="unbounded">
 183                                 <xs:annotation>
 184                                         <xs:documentation>
 185                                                 a region from start to end, with flag for
 186                                                 inclusivity of terminii
 187                                         </xs:documentation>
 188                                 </xs:annotation>
 189                                 <xs:complexType>
 190                                         <xs:attribute name="start" type="xs:int" use="required"/>
 191                                         <xs:attribute name="end" type="xs:int" use="required"/>
 192                                         <xs:attribute name="inclusive" type="xs:boolean" use="required">
 193                                                 <xs:annotation>
 194                                                         <xs:documentation>
 195                                                                 when false, a consecutive range like
 196                                                                 'start=1, end=2' means the region lying
 197                                                                 after position 1 and before position 2
 198                                                         </xs:documentation>
 199                                                 </xs:annotation>
 200                                         </xs:attribute>
 201                                 </xs:complexType>
 202                         </xs:element>
 203                 </xs:choice>
 204                 <!--  Do we really need this - a position could be just a seg with start=end and inclusive=true -->
 205         </xs:complexType>
 206         <xs:complexType name="rangeAnnotation">
 207                 <xs:annotation>
 208                         <xs:documentation>
 209                                 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.
 210                         </xs:documentation>
 211                 </xs:annotation>
 212                 <xs:complexContent>
 213                         <xs:extension base="vamsas:rangeType">
 214                                 <xs:sequence>
 215                                         <xs:element name="label" type="xs:string" minOccurs="0">
 216                                                 <xs:annotation>
 217                                                         <xs:documentation>
 218                                                         Short, meaningful name for the annotation - if this is absent, then the type string should be used in its place.
 219                                                 </xs:documentation>
 220                                                 </xs:annotation>
 221                                         </xs:element>
 222                                         <xs:element name="description" type="xs:string" minOccurs="0">
 223                                                 <xs:annotation>
 224                                                         <xs:documentation>
 225                                                         Human readable description of the annotation
 226                                                 </xs:documentation>
 227                                                 </xs:annotation>
 228                                         </xs:element>
 229                                         <xs:element name="status" type="xs:string" minOccurs="0">
 230                                                 <xs:annotation>
 231                                                         <xs:documentation>
 232                                                         TODO: specify this - we have considered taking the GO evidence codes as a model for assessing a measure of quality to an annotation.
 233                                                 </xs:documentation>
 234                                                 </xs:annotation>
 235                                         </xs:element>
 236                                         <xs:element ref="vamsas:annotationElement" minOccurs="0" maxOccurs="unbounded">
 237                                                 <xs:annotation>
 238                                                         <xs:documentation>
 239                                                                 Annotation Element position maps to
 240                                                                 ordered positions defined by the
 241                                                                 sequence of rangeType pos positions or
 242                                                                 concatenated seg start/end segments.
 243                                                         </xs:documentation>
 244                                                 </xs:annotation>
 245                                         </xs:element>
 246                                         <xs:element name="score" minOccurs="0" maxOccurs="unbounded">
 247                                                 <xs:annotation>
 248                                                         <xs:documentation>
 249                                                                 Ordered set of optionally named float
 250                                                                 values for the whole annotation
 251                                                         </xs:documentation>
 252                                                 </xs:annotation>
 253                                                 <xs:complexType>
 254                                                         <xs:simpleContent>
 255                                                                 <xs:extension base="xs:float">
 256                                                                         <xs:attribute name="name" type="xs:string" use="optional" default="score"/>
 257                                                                 </xs:extension>
 258                                                         </xs:simpleContent>
 259                                                 </xs:complexType>
 260                                         </xs:element>
 261                                         <xs:element ref="vamsas:link" minOccurs="0" maxOccurs="unbounded"/>
 262                                         <xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded">
 263                                                 <xs:annotation>
 264                                                         <xs:documentation>
 265                                                                 Note:These are mutable so an application
 266                                                                 should check them each time.
 267                                                         </xs:documentation>
 268                                                 </xs:annotation>
 269                                         </xs:element>
 270                                 </xs:sequence>
 271                                 <xs:attribute name="id" type="xs:ID" use="optional">
 272                                         <xs:annotation>
 273                                                 <xs:documentation>
 274                                                         Primary Key for vamsas object referencing
 275                                                 </xs:documentation>
 276                                         </xs:annotation>
 277                                 </xs:attribute>
 278                                 <xs:attribute name="modifiable" type="xs:boolean" use="optional" default="true">
 279                                         <xs:annotation>
 280                                                 <xs:documentation>
 281                                                         objects with modifiable=false will not be
 282                                                         modified by a vamsas client update
 283                                                 </xs:documentation>
 284                                         </xs:annotation>
 285                                 </xs:attribute>
 286                                 <xs:attribute name="group" type="xs:string" use="optional" default="">
 287                                         <xs:annotation>
 288                                                 <xs:documentation>
 289                                                         Annotation with the same non-empty group
 290                                                         name are grouped together
 291                                                 </xs:documentation>
 292                                         </xs:annotation>
 293                                 </xs:attribute>
 294                                 <xs:attribute name="type" type="xs:string" use="required">
 295                                         <xs:annotation>
 296                                                 <xs:documentation>
 297                                                         A Das Feature has both a type and a Type ID.
 298                                                         We go the route of requiring the type string
 299                                                         to be taken from a controlled vocabulary if
 300                                                         an application expects others to make sense
 301                                                         of it.
 302                                                         The type may qualified - so uniprot:CHAIN is a valid type name,
 303                                                         and considered distinct from someotherDB:CHAIN
 304                                                 </xs:documentation>
 305                                         </xs:annotation>
 306                                 </xs:attribute>
 307                         </xs:extension>
 308                 </xs:complexContent>
 309         </xs:complexType>
 310         <xs:element name="param">
 311                 <xs:complexType>
 312                         <xs:annotation>
 313                                 <xs:documentation>
 314                                         Specifies a named and typed value used to perform
 315                                         some data transformation.
 316                                 </xs:documentation>
 317                                 <xs:documentation>
 318                                         LATER: experiment with xml validation of property
 319                                         set prototypes for services
 320                                 </xs:documentation>
 321                         </xs:annotation>
 322                         <xs:simpleContent>
 323                                 <xs:annotation>
 324                                         <xs:documentation>
 325                                                 Named and typed property string
 326                                         </xs:documentation>
 327                                 </xs:annotation>
 328                                 <xs:extension base="xs:string">
 329                                         <xs:attribute name="name" type="xs:string" use="required"/>
 330                                         <xs:attribute name="type" type="xs:string" use="required">
 331                                                 <xs:annotation>
 332                                                         <xs:documentation>
 333                                                                 The type specifies how the property will
 334                                                                 be parsed. Empty property strings are
 335                                                                 allowed, and can be used to prototype
 336                                                                 the input to a document. TODO: specify
 337                                                                 allowed types
 338                                                         </xs:documentation>
 339                                                 </xs:annotation>
 340                                         </xs:attribute>
 341                                 </xs:extension>
 342                         </xs:simpleContent>
 343                 </xs:complexType>
 344         </xs:element>
 345         <xs:element name="input">
 346                 <xs:complexType>
 347                         <xs:annotation>
 348                                 <xs:documentation>
 349                                         Selects all or part of a collection of vamsas
 350                                         objects as a named input to some transformation
 351                                         process. Many inputs with the same name imply a
 352                                         group input (such as a collection of sequences)
 353                                 </xs:documentation>
 354                         </xs:annotation>
 355                         <xs:complexContent>
 356                                 <xs:extension base="vamsas:rangeType">
 357                                         <xs:attribute name="name" type="xs:string" use="required"/>
 358                                         <xs:attribute name="objRef" type="xs:IDREF" use="optional">
 359                                                 <xs:annotation>
 360                                                         <xs:documentation>
 361                                                                 Reference Frame for rangeType
 362                                                                 specfication
 363                                                         </xs:documentation>
 364                                                 </xs:annotation>
 365                                         </xs:attribute>
 366                                 </xs:extension>
 367                         </xs:complexContent>
 368                 </xs:complexType>
 369         </xs:element>
 370         <xs:element name="Provenance">
 371                 <xs:complexType>
 372                         <xs:annotation>
 373                                 <xs:documentation>
 374                                         Defines the origin and series of operations applied
 375                                         directly to the object that references it.
 376                                 </xs:documentation>
 377                         </xs:annotation>
 378                         <xs:sequence>
 379                                 <xs:element name="entry" maxOccurs="unbounded">
 380                                         <xs:complexType>
 381                                                 <xs:sequence>
 382                                                         <xs:element name="User" type="xs:string">
 383                                                                 <xs:annotation>
 384                                                                         <xs:documentation>
 385                                                                                 Who
 386                                                                         </xs:documentation>
 387                                                                 </xs:annotation>
 388                                                         </xs:element>
 389                                                         <xs:element name="App" type="xs:string">
 390                                                                 <xs:annotation>
 391                                                                         <xs:documentation>
 392                                                                                 With which application
 393                                                                         </xs:documentation>
 394                                                                 </xs:annotation>
 395                                                         </xs:element>
 396                                                         <xs:element name="Action" type="xs:string">
 397                                                                 <xs:annotation>
 398                                                                         <xs:documentation>
 399                                                                                 Did what
 400                                                                         </xs:documentation>
 401                                                                 </xs:annotation>
 402                                                         </xs:element>
 403                                                         <xs:element name="Date" type="xs:date">
 404                                                                 <xs:annotation>
 405                                                                         <xs:documentation>
 406                                                                                 When
 407                                                                         </xs:documentation>
 408                                                                 </xs:annotation>
 409                                                         </xs:element>
 410                                                         <xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded">
 411                                                                 <xs:annotation>
 412                                                                         <xs:documentation>
 413                                                                                 additional information
 414                                                                         </xs:documentation>
 415                                                                 </xs:annotation>
 416                                                         </xs:element>
 417                                                         <xs:element ref="vamsas:param" minOccurs="0" maxOccurs="unbounded">
 418                                                                 <xs:annotation>
 419                                                                         <xs:documentation>
 420                                                                                 parameter for the action
 421                                                                         </xs:documentation>
 422                                                                 </xs:annotation>
 423                                                         </xs:element>
 424                                                         <xs:element ref="vamsas:input" minOccurs="0" maxOccurs="unbounded">
 425                                                                 <xs:annotation>
 426                                                                         <xs:documentation>
 427                                                                                 bioinformatic objects input to
 428                                                                                 action
 429                                                                         </xs:documentation>
 430                                                                 </xs:annotation>
 431                                                         </xs:element>
 432                                                 </xs:sequence>
 433                                                 <xs:attribute name="id" type="xs:ID" use="optional">
 434                                                         <xs:annotation>
 435                                                                 <xs:documentation>
 436                                                                         Primary Key for vamsas object
 437                                                                         referencing
 438                                                                 </xs:documentation>
 439                                                         </xs:annotation>
 440                                                 </xs:attribute>
 441                                         </xs:complexType>
 442                                 </xs:element>
 443                         </xs:sequence>
 444                 </xs:complexType>
 445         </xs:element>
 446         <xs:element name="DataSet">
 447                 <xs:complexType>
 448                         <xs:annotation>
 449                                 <xs:documentation>
 450                                         A collection of sequences, alignments, trees and
 451                                         other things.
 452                                 </xs:documentation>
 453                         </xs:annotation>
 454                         <xs:sequence>
 455                                 <xs:element name="Sequence" maxOccurs="unbounded">
 456                                         <xs:complexType>
 457                                                 <xs:annotation>
 458                                                         <xs:documentation>
 459                                                                 a primary or secondary sequence record
 460                                                                 from which all other sequences may be
 461                                                                 derived
 462                                                         </xs:documentation>
 463                                                 </xs:annotation>
 464                                                 <xs:complexContent>
 465                                                         <xs:extension base="vamsas:SequenceType">
 466                                                                 <xs:sequence>
 467                                                                         <xs:element name="dbRef" minOccurs="0" maxOccurs="unbounded">
 468                                                                                 <xs:annotation>
 469                                                                                         <xs:documentation>
 470                                                                                                 Store a list of database
 471                                                                                                 references for this
 472                                                                                                 sequence record - with
 473                                                                                                 optional mapping from
 474                                                                                                 database sequence to the
 475                                                                                                 given sequence record
 476                                                                                         </xs:documentation>
 477                                                                                         <xs:documentation/>
 478                                                                                         <xs:documentation/>
 479                                                                                 </xs:annotation>
 480                                                                                 <xs:complexType>
 481                                                                                         <xs:sequence>
 482                                                                                                 <xs:element name="map" minOccurs="0" maxOccurs="unbounded">
 483                                                                                                         <xs:complexType>
 484                                                                                                                 <xs:attribute name="from" type="xs:integer" use="optional" default="0">
 485                                                                                                                         <xs:annotation>
 486                                                                                                                                 <xs:documentation>
 487                                                                                                                                         Offset
 488                                                                                                                                         to
 489                                                                                                                                         first
 490                                                                                                                                         position
 491                                                                                                                                         in
 492                                                                                                                                         dataset
 493                                                                                                                                         sequence
 494                                                                                                                                         record
 495                                                                                                                                         that
 496                                                                                                                                         this
 497                                                                                                                                         database
 498                                                                                                                                         entry
 499                                                                                                                                         maps
 500                                                                                                                                         to
 501                                                                                                                                 </xs:documentation>
 502                                                                                                                         </xs:annotation>
 503                                                                                                                 </xs:attribute>
 504                                                                                                                 <xs:attribute name="to" type="xs:integer" use="optional" default="0">
 505                                                                                                                         <xs:annotation>
 506                                                                                                                                 <xs:documentation>
 507                                                                                                                                         Offset
 508                                                                                                                                         to
 509                                                                                                                                         last
 510                                                                                                                                         position
 511                                                                                                                                         in
 512                                                                                                                                         dataset
 513                                                                                                                                         sequence
 514                                                                                                                                         record
 515                                                                                                                                         that
 516                                                                                                                                         this
 517                                                                                                                                         database
 518                                                                                                                                         entry
 519                                                                                                                                         maps
 520                                                                                                                                         to
 521                                                                                                                                 </xs:documentation>
 522                                                                                                                         </xs:annotation>
 523                                                                                                                 </xs:attribute>
 524                                                                                                                 <xs:attribute name="start" type="xs:integer" use="required">
 525                                                                                                                         <xs:annotation>
 526                                                                                                                                 <xs:documentation>
 527                                                                                                                                 Offset
 528                                                                                                                                 to first
 529                                                                                                                                 last
 530                                                                                                                                 position
 531                                                                                                                                 in
 532                                                                                                                                 database
 533                                                                                                                                 entry
 534                                                                                                                                 that
 535                                                                                                                                 first
 536                                                                                                                                 (or
 537                                                                                                                                 offset)
 538                                                                                                                                 position
 539                                                                                                                                 in
 540                                                                                                                                 sequence
 541                                                                                                                                 maps to
 542                                                                                                                         </xs:documentation>
 543                                                                                                                         </xs:annotation>
 544                                                                                                                 </xs:attribute>
 545                                                                                                                 <xs:attribute name="end" type="xs:integer" use="required">
 546                                                                                                                         <xs:annotation>
 547                                                                                                                                 <xs:documentation>
 548                                                                                                                                 Offset
 549                                                                                                                                 to last
 550                                                                                                                                 position
 551                                                                                                                                 in
 552                                                                                                                                 database
 553                                                                                                                                 entry
 554                                                                                                                                 that
 555                                                                                                                                 last
 556                                                                                                                                 (offset)
 557                                                                                                                                 position
 558                                                                                                                                 in
 559                                                                                                                                 sequence
 560                                                                                                                                 maps to
 561                                                                                                                         </xs:documentation>
 562                                                                                                                         </xs:annotation>
 563                                                                                                                 </xs:attribute>
 564                                                                                                         </xs:complexType>
 565                                                                                                 </xs:element>
 566                                                                                                 <xs:element ref="vamsas:link" minOccurs="0" maxOccurs="unbounded"/>
 567                                                                                                 <xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded"/>
 568                                                                                         </xs:sequence>
 569                                                                                         <xs:attribute name="source" type="xs:string" use="required">
 570                                                                                                 <xs:annotation>
 571                                                                                                         <xs:documentation>
 572                                                                                                                 TODO Database
 573                                                                                                                 Naming
 574                                                                                                                 Convention:
 575                                                                                                                 either start
 576                                                                                                                 using LSID (so
 577                                                                                                                 change type to
 578                                                                                                                 URI) or leave
 579                                                                                                                 this as an
 580                                                                                                                 uncontrolled/unspecified
 581                                                                                                                 string ID
 582                                                                                                         </xs:documentation>
 583                                                                                                 </xs:annotation>
 584                                                                                         </xs:attribute>
 585                                                                                         <xs:attribute name="version" type="xs:string" use="required">
 586                                                                                                 <xs:annotation>
 587                                                                                                         <xs:documentation>
 588                                                                                                                 Version must be
 589                                                                                                                 specified -
 590                                                                                                         </xs:documentation>
 591                                                                                                 </xs:annotation>
 592                                                                                         </xs:attribute>
 593                                                                                         <xs:attribute name="accessionId" type="xs:string" use="required">
 594                                                                                                 <xs:annotation>
 595                                                                                                         <xs:documentation>
 596                                                                                                                 TODO: make some
 597                                                                                                                 specification of
 598                                                                                                                 the database
 599                                                                                                                 field from which
 600                                                                                                                 this accessionId
 601                                                                                                                 is taken from -
 602                                                                                                                 should that be a
 603                                                                                                                 special property
 604                                                                                                                 of the dbRef
 605                                                                                                                 object ?
 606                                                                                                         </xs:documentation>
 607                                                                                                 </xs:annotation>
 608                                                                                         </xs:attribute>
 609                                                                                         <xs:attribute name="id" type="xs:ID" use="optional">
 610                                                                                                 <xs:annotation>
 611                                                                                                         <xs:documentation>
 612                                                                                                                 Primary Key for
 613                                                                                                                 vamsas object
 614                                                                                                                 referencing
 615                                                                                                         </xs:documentation>
 616                                                                                                 </xs:annotation>
 617                                                                                         </xs:attribute>
 618                                                                                 </xs:complexType>
 619                                                                         </xs:element>
 620                                                                 </xs:sequence>
 621                                                                 <xs:attribute name="id" type="xs:ID" use="optional">
 622                                                                         <xs:annotation>
 623                                                                                 <xs:documentation>
 624                                                                                         Primary Key for vamsas
 625                                                                                         object referencing
 626                                                                                 </xs:documentation>
 627                                                                         </xs:annotation>
 628                                                                 </xs:attribute>
 629                                                                 <xs:attribute name="dictionary" type="xs:string" use="required">
 630                                                                         <xs:annotation>
 631                                                                                 <xs:documentation>
 632                                                                                         symbol class for sequence
 633                                                                                 </xs:documentation>
 634                                                                         </xs:annotation>
 635                                                                 </xs:attribute>
 636                                                         </xs:extension>
 637                                                 </xs:complexContent>
 638                                         </xs:complexType>
 639                                 </xs:element>
 640                                 <xs:element name="DataSetAnnotations" minOccurs="0" maxOccurs="unbounded">
 641                                         <xs:complexType>
 642                                                 <xs:annotation>
 643                                                         <xs:documentation>
 644                                                                 Annotate over positions and regions of a
 645                                                                 dataset sequence
 646                                                         </xs:documentation>
 647                                                 </xs:annotation>
 648                                                 <xs:complexContent>
 649                                                         <xs:extension base="vamsas:rangeAnnotation">
 650                                                                 <xs:sequence>
 651                                                                         <xs:element ref="vamsas:Provenance"/>
 652                                                                 </xs:sequence>
 653                                                                 <xs:attribute name="seqRef" type="xs:IDREF" use="required">
 654                                                                         <xs:annotation>
 655                                                                                 <xs:documentation>
 656                                                                                         annotation is associated
 657                                                                                         with a particular dataset
 658                                                                                         sequence
 659                                                                                 </xs:documentation>
 660                                                                         </xs:annotation>
 661                                                                 </xs:attribute>
 662                                                         </xs:extension>
 663                                                 </xs:complexContent>
 664                                         </xs:complexType>
 665                                 </xs:element>
 666                                 <xs:element name="Alignment" minOccurs="0" maxOccurs="unbounded">
 667                                         <xs:complexType>
 668                                                 <xs:sequence>
 669                                                         <xs:element name="AlignmentAnnotation" minOccurs="0" maxOccurs="unbounded">
 670                                                                 <xs:annotation>
 671                                                                         <xs:documentation>
 672                                                                                 This is annotation over the
 673                                                                                 coordinate frame defined by all
 674                                                                                 the columns in the alignment.
 675                                                                         </xs:documentation>
 676                                                                 </xs:annotation>
 677                                                                 <xs:complexType>
 678                                                                         <xs:complexContent>
 679                                                                                 <xs:extension base="vamsas:rangeAnnotation">
 680                                                                                         <xs:sequence>
 681                                                                                                 <xs:element ref="vamsas:Provenance"/>
 682                                                                                         </xs:sequence>
 683                                                                                         <xs:attribute name="graph" type="xs:boolean" use="required">
 684                                                                                                 <xs:annotation>
 685                                                                                                         <xs:documentation>
 686                                                                                                                 TODO: decide if
 687                                                                                                                 this flag is
 688                                                                                                                 redundant - when
 689                                                                                                                 true it would
 690                                                                                                                 suggest that the
 691                                                                                                                 annotationElement
 692                                                                                                                 values together
 693                                                                                                                 form a graph
 694                                                                                                         </xs:documentation>
 695                                                                                                 </xs:annotation>
 696                                                                                         </xs:attribute>
 697                                                                                 </xs:extension>
 698                                                                         </xs:complexContent>
 699                                                                 </xs:complexType>
 700                                                         </xs:element>
 701                                                         <xs:element ref="vamsas:Tree" minOccurs="0" maxOccurs="unbounded"/>
 702                                                         <xs:element name="alignmentSequence" maxOccurs="unbounded">
 703                                                                 <xs:complexType>
 704                                                                         <xs:complexContent>
 705                                                                                 <xs:extension base="vamsas:SequenceType">
 706                                                                                         <xs:sequence>
 707                                                                                                 <xs:element name="AlignmentSequenceAnnotation" minOccurs="0" maxOccurs="unbounded">
 708                                                                                                         <xs:complexType>
 709                                                                                                                 <xs:annotation>
 710                                                                                                                         <xs:documentation>
 711                                                                                                                                 Annotate
 712                                                                                                                                 over
 713                                                                                                                                 positions
 714                                                                                                                                 and
 715                                                                                                                                 regions
 716                                                                                                                                 of the
 717                                                                                                                                 ungapped
 718                                                                                                                                 sequence
 719                                                                                                                                 in the
 720                                                                                                                                 context
 721                                                                                                                                 of the
 722                                                                                                                                 alignment
 723                                                                                                                         </xs:documentation>
 724                                                                                                                         <xs:documentation/>
 725                                                                                                                 </xs:annotation>
 726                                                                                                                 <xs:complexContent>
 727                                                                                                                         <xs:extension base="vamsas:rangeAnnotation">
 728                                                                                                                                 <xs:sequence>
 729                                                                                                                                         <xs:element ref="vamsas:Provenance"/>
 730                                                                                                                                 </xs:sequence>
 731                                                                                                                                 <xs:attribute name="graph" type="xs:boolean" use="required">
 732                                                                                                                                         <xs:annotation>
 733                                                                                                                                                 <xs:documentation>
 734                                                                                                                                                         TODO:
 735                                                                                                                                                         decide
 736                                                                                                                                                         if
 737                                                                                                                                                         this
 738                                                                                                                                                         flag
 739                                                                                                                                                         is
 740                                                                                                                                                         redundant
 741                                                                                                                                                         -
 742                                                                                                                                                         when
 743                                                                                                                                                         true
 744                                                                                                                                                         it
 745                                                                                                                                                         would
 746                                                                                                                                                         suggest
 747                                                                                                                                                         that
 748                                                                                                                                                         the
 749                                                                                                                                                         annotationElement
 750                                                                                                                                                         values
 751                                                                                                                                                         together
 752                                                                                                                                                         form
 753                                                                                                                                                         a
 754                                                                                                                                                         graph
 755                                                                                                                                                 </xs:documentation>
 756                                                                                                                                         </xs:annotation>
 757                                                                                                                                 </xs:attribute>
 758                                                                                                                         </xs:extension>
 759                                                                                                                 </xs:complexContent>
 760                                                                                                                 <!--
 761                                                                                                                         This replaces the flat list of sequenceFeatures.
 762                                                                                                                         <xs:element name="AlignmentFeatures" minOccurs="0" maxOccurs="unbounded"><xs:complexType><xs:annotation>
 763                                                                                                                         <xs:documentation>Annotate over positions and regions of the alignment</xs:documentation>
 764                                                                                                                         </xs:annotation><xs:complexContent>
 765                                                                                                                         <xs:extension base="vamsas:rangeFeature">
 766                                                                                                                         <xs:attribute name="seqRef" type="xs:IDREF" use="optional">
 767                                                                                                                         <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>
 768                                                                                                                         </xs:attribute>
 769                                                                                                                         </xs:extension>
 770                                                                                                                         </xs:complexContent></xs:complexType></xs:element> -->
 771                                                                                                         </xs:complexType>
 772                                                                                                 </xs:element>
 773                                                                                         </xs:sequence>
 774                                                                                         <xs:attribute name="id" type="xs:ID" use="optional">
 775                                                                                                 <xs:annotation>
 776                                                                                                         <xs:documentation>
 777                                                                                                                 Primary Key for
 778                                                                                                                 vamsas object
 779                                                                                                                 referencing
 780                                                                                                         </xs:documentation>
 781                                                                                                 </xs:annotation>
 782                                                                                         </xs:attribute>
 783                                                                                         <xs:attribute name="refid" type="xs:IDREF" use="required">
 784                                                                                                 <xs:annotation>
 785                                                                                                         <xs:documentation>
 786                                                                                                                 Dataset Sequence
 787                                                                                                                 from which this
 788                                                                                                                 alignment
 789                                                                                                                 sequence is
 790                                                                                                                 taken from
 791                                                                                                         </xs:documentation>
 792                                                                                                 </xs:annotation>
 793                                                                                         </xs:attribute>
 794                                                                                 </xs:extension>
 795                                                                         </xs:complexContent>
 796                                                                 </xs:complexType>
 797                                                         </xs:element>
 798                                                         <xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded">
 799                                                                 <xs:annotation>
 800                                                                         <xs:documentation>
 801                                                                                 typical properties may be
 802                                                                                 additional alignment score
 803                                                                                 objects
 804                                                                         </xs:documentation>
 805                                                                 </xs:annotation>
 806                                                         </xs:element>
 807                                                         <xs:element ref="vamsas:Provenance"/>
 808                                                 </xs:sequence>
 809                                                 <xs:attribute name="gapChar" type="xs:string" use="required"/>
 810                                                 <xs:attribute name="aligned" type="xs:boolean" use="optional"/>
 811                                                 <xs:attribute name="id" type="xs:ID" use="optional">
 812                                                         <xs:annotation>
 813                                                                 <xs:documentation>
 814                                                                         Primary Key for vamsas object
 815                                                                         referencing
 816                                                                 </xs:documentation>
 817                                                         </xs:annotation>
 818                                                 </xs:attribute>
 819                                                 <xs:attribute name="modifiable" type="xs:boolean" use="optional" default="true">
 820                                                         <xs:annotation>
 821                                                                 <xs:documentation>
 822                                                                         objects with modifiable=false will
 823                                                                         not be modified by a vamsas client
 824                                                                         update
 825                                                                 </xs:documentation>
 826                                                         </xs:annotation>
 827                                                 </xs:attribute>
 828                                         </xs:complexType>
 829                                 </xs:element>
 830                                 <xs:element ref="vamsas:Tree" minOccurs="0" maxOccurs="unbounded"/>
 831                                 <xs:element ref="vamsas:Provenance"/>
 832                         </xs:sequence>
 833                         <xs:attribute name="id" type="xs:ID" use="optional">
 834                                 <xs:annotation>
 835                                         <xs:documentation>
 836                                                 Primary Key for vamsas object referencing
 837                                         </xs:documentation>
 838                                 </xs:annotation>
 839                         </xs:attribute>
 840                 </xs:complexType>
 841         </xs:element>
 842         <xs:element name="annotationElement">
 843                 <xs:complexType>
 844                         <xs:annotation>
 845                                 <xs:documentation>
 846                                         per-site symbolic and/or quantitative annotation
 847                                 </xs:documentation>
 848                                 <xs:documentation>
 849                                         SecondaryStructure and display character (from
 850                                         Jalview) have been subsumed into the glyph element
 851                                 </xs:documentation>
 852                         </xs:annotation>
 853                         <xs:sequence>
 854                                 <xs:element name="description" type="xs:string" minOccurs="0">
 855                                         <xs:annotation>
 856                                                 <xs:documentation>
 857                                                         Free text at this position
 858                                                 </xs:documentation>
 859                                         </xs:annotation>
 860                                 </xs:element>
 861                                 <xs:element name="glyph" minOccurs="0" maxOccurs="unbounded">
 862                                         <xs:annotation>
 863                                                 <xs:documentation>
 864                                                         Discrete symbol - possibly graphically
 865                                                         represented
 866                                                 </xs:documentation>
 867                                         </xs:annotation>
 868                                         <xs:complexType>
 869                                                 <xs:simpleContent>
 870                                                         <xs:extension base="xs:string">
 871                                                                 <xs:attribute name="dict" type="xs:string" use="optional" default="utf8">
 872                                                                         <xs:annotation>
 873                                                                                 <xs:documentation>
 874                                                                                         specifies the symbol
 875                                                                                         dictionary for this glyph -
 876                                                                                         eg utf8 (the default),
 877                                                                                         aasecstr_3 or
 878                                                                                         kd_hydrophobicity - the
 879                                                                                         content is not validated so
 880                                                                                         applications must ensure
 881                                                                                         they gracefully deal with
 882                                                                                         invalid entries here
 883                                                                                 </xs:documentation>
 884                                                                                 <xs:documentation>
 885                                                                                         TODO: specify a minimum list
 886                                                                                         of glyph dictionaries to get
 887                                                                                         us started and provide a way
 888                                                                                         for the vamsasClient to
 889                                                                                         validate their content if
 890                                                                                         regexes are specified
 891                                                                                 </xs:documentation>
 892                                                                         </xs:annotation>
 893                                                                 </xs:attribute>
 894                                                         </xs:extension>
 895                                                 </xs:simpleContent>
 896                                         </xs:complexType>
 897                                 </xs:element>
 898                                 <xs:element name="value" type="xs:float" minOccurs="0" maxOccurs="unbounded">
 899                                         <xs:annotation>
 900                                                 <xs:documentation>
 901                                                         Ordered set of float values - an application
 902                                                         may treat the values together as a vector
 903                                                         with common support for a set of annotation
 904                                                         elements - but this is, again, not validated
 905                                                         so applications should deal gracefully with
 906                                                         varying numbers of dimensions
 907                                                 </xs:documentation>
 908                                         </xs:annotation>
 909                                 </xs:element>
 910                         </xs:sequence>
 911                         <xs:attribute name="position" type="xs:integer" use="required">
 912                                 <xs:annotation>
 913                                         <xs:documentation>
 914                                                 position with respect to the coordinate frame
 915                                                 defined by a rangeType specification
 916                                         </xs:documentation>
 917                                 </xs:annotation>
 918                         </xs:attribute>
 919                         <xs:attribute name="after" type="xs:boolean" use="optional" default="false">
 920                                 <xs:annotation>
 921                                         <xs:documentation>
 922                                                 true means the annotation element appears
 923                                                 between the specified position and the next
 924                                         </xs:documentation>
 925                                 </xs:annotation>
 926                         </xs:attribute>
 927                         <xs:attribute name="id" type="xs:ID" use="optional">
 928                                 <xs:annotation>
 929                                         <xs:documentation>
 930                                                 Primary Key for vamsas object referencing
 931                                         </xs:documentation>
 932                                 </xs:annotation>
 933                         </xs:attribute>
 934                 </xs:complexType>
 935         </xs:element>
 936         <xs:complexType name="SequenceType">
 937                 <xs:sequence>
 938                         <xs:element name="sequence" type="xs:string"/>
 939                         <xs:element name="name" type="xs:string"/>
 940                         <xs:element name="description" type="xs:string" minOccurs="0"/>
 941                         <xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded">
 942                                 <xs:annotation>
 943                                         <xs:documentation>
 944                                                 additional typed properties
 945                                         </xs:documentation>
 946                                 </xs:annotation>
 947                         </xs:element>
 948                         <xs:element ref="vamsas:mapping" minOccurs="0" maxOccurs="unbounded"/>
 949                 </xs:sequence>
 950                 <xs:attribute name="start" type="xs:integer" use="required"/>
 951                 <xs:attribute name="end" type="xs:integer" use="required"/>
 952         </xs:complexType>
 953         <xs:element name="ApplicationData">
 954                 <xs:complexType>
 955                         <xs:annotation>
 956                                 <xs:documentation>
 957                                         Data specific to a particular type and version of
 958                                         vamsas application
 959                                 </xs:documentation>
 960                         </xs:annotation>
 961                         <xs:complexContent>
 962                                 <xs:extension base="vamsas:appData">
 963                                         <xs:sequence>
 964                                                 <xs:element name="User" minOccurs="0" maxOccurs="unbounded">
 965                                                         <xs:complexType>
 966                                                                 <xs:complexContent>
 967                                                                         <xs:extension base="vamsas:appData">
 968                                                                                 <xs:annotation>
 969                                                                                         <xs:documentation>
 970                                                                                                 Data available to just a
 971                                                                                                 particular user
 972                                                                                         </xs:documentation>
 973                                                                                 </xs:annotation>
 974                                                                                 <xs:attribute name="fullname" type="xs:string" use="required"/>
 975                                                                                 <xs:attribute name="organization" type="xs:string" use="required"/>
 976                                                                         </xs:extension>
 977                                                                 </xs:complexContent>
 978                                                         </xs:complexType>
 979                                                 </xs:element>
 980                                                 <xs:element name="Common" minOccurs="0">
 981                                                         <xs:complexType>
 982                                                                 <xs:complexContent>
 983                                                                         <xs:extension base="vamsas:appData"/>
 984                                                                 </xs:complexContent>
 985                                                         </xs:complexType>
 986                                                 </xs:element>
 987                                                 <xs:element name="Instance" minOccurs="0" maxOccurs="unbounded">
 988                                                         <xs:complexType>
 989                                                                 <xs:complexContent>
 990                                                                         <xs:extension base="vamsas:appData">
 991                                                                                 <xs:annotation>
 992                                                                                         <xs:documentation>
 993                                                                                                 Data available to just a
 994                                                                                                 specific instance of the
 995                                                                                                 application
 996                                                                                         </xs:documentation>
 997                                                                                         <xs:documentation>
 998                                                                                                 VAMSAS/Pierre: Is this
 999                                                                                                 data volatile ?
1000                                                                                                 Application instances
1001                                                                                                 may not be accessible
1002                                                                                                 after the session has
1003                                                                                                 closed - the user may
1004                                                                                                 have to be presented
1005                                                                                                 with the option of
1006                                                                                                 picking up the data in
1007                                                                                                 that instance
1008                                                                                         </xs:documentation>
1009                                                                                 </xs:annotation>
1010                                                                                 <xs:attribute name="urn" type="xs:string" use="required"/>
1011                                                                         </xs:extension>
1012                                                                 </xs:complexContent>
1013                                                         </xs:complexType>
1014                                                 </xs:element>
1015                                         </xs:sequence>
1016                                         <xs:attribute name="version" type="xs:string" use="required">
1017                                                 <xs:annotation>
1018                                                         <xs:documentation>
1019                                                         Version string describing the application specific data storage version used</xs:documentation>
1020                                                 </xs:annotation>
1021                                         </xs:attribute>
1022                                         <xs:attribute name="name" type="xs:string" use="required">
1023                                                 <xs:annotation>
1024                                                         <xs:documentation>
1025                                                         Canonical name of application
1026                                                 </xs:documentation>
1027                                                 </xs:annotation>
1028                                         </xs:attribute>
1029                                 </xs:extension>
1030                         </xs:complexContent>
1031                 </xs:complexType>
1032         </xs:element>
1033         <xs:element name="Attachment">
1034                 <xs:complexType>
1035                         <xs:complexContent>
1036                                 <xs:extension base="vamsas:appData">
1037                                         <xs:annotation>
1038                                                 <xs:documentation>
1039                                                         General data container to attach a typed
1040                                                         data object to any vamsas object
1041                                                 </xs:documentation>
1042                                         </xs:annotation>
1043                                         <xs:attribute name="compressed" type="xs:boolean" use="optional" default="false">
1044                                                 <xs:annotation>
1045                                                         <xs:documentation>
1046                                                                 true implies data will be decompresses
1047                                                                 with Zip before presenting to
1048                                                                 application
1049                                                         </xs:documentation>
1050                                                 </xs:annotation>
1051                                         </xs:attribute>
1052                                         <xs:attribute name="type" type="xs:string" use="required">
1053                                                 <xs:annotation>
1054                                                         <xs:documentation>
1055                                                                 Type of arbitrary data - TODO: decide
1056                                                                 format - use (extended) MIME types ?
1057                                                         </xs:documentation>
1058                                                 </xs:annotation>
1059                                         </xs:attribute>
1060                                         <xs:attribute name="objectref" type="xs:IDREF" use="required">
1061                                                 <xs:annotation>
1062                                                         <xs:documentation>
1063                                                                 Object the arbitrary data is associated
1064                                                                 with
1065                                                         </xs:documentation>
1066                                                 </xs:annotation>
1067                                         </xs:attribute>
1068                                         <xs:attribute name="id" type="xs:ID" use="optional">
1069                                                 <xs:annotation>
1070                                                         <xs:documentation>
1071                                                                 Primary Key for vamsas object
1072                                                                 referencing
1073                                                         </xs:documentation>
1074                                                 </xs:annotation>
1075                                         </xs:attribute>
1076                                 </xs:extension>
1077                         </xs:complexContent>
1078                 </xs:complexType>
1079         </xs:element>
1080         <xs:complexType name="appData">
1081                 <xs:choice>
1082                         <xs:element name="data" type="xs:base64Binary"/>
1083                         <xs:element name="dataReference" type="xs:string"/>
1084                 </xs:choice>
1085         </xs:complexType>
1086         <xs:element name="mapping">
1087                 <xs:complexType>
1088                         <xs:sequence>
1089                                 <xs:element name="objectA">
1090                                         <xs:complexType>
1091                                                 <xs:complexContent>
1092                                                         <xs:extension base="vamsas:rangeType">
1093                                                                 <xs:attribute name="objRefA" type="xs:IDREF" use="required"/>
1094                                                         </xs:extension>
1095                                                 </xs:complexContent>
1096                                         </xs:complexType>
1097                                 </xs:element>
1098                                 <xs:element name="objectB">
1099                                         <xs:complexType>
1100                                                 <xs:complexContent>
1101                                                         <xs:extension base="vamsas:rangeType">
1102                                                                 <xs:attribute name="objRefB" type="xs:IDREF" use="required"/>
1103                                                         </xs:extension>
1104                                                 </xs:complexContent>
1105                                         </xs:complexType>
1106                                 </xs:element>
1107                         </xs:sequence>
1108                 </xs:complexType>
1109         </xs:element>
1110 </xs:schema>