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