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