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