schemas/vamsas.xsd

   1 <?xml version="1.0" encoding="UTF-8"?>
   2 <!-- edited with XMLSPY v5 rel. 4 U (http://www.xmlspy.com) by MSD (EMBL OUTSTATION THE EBI WELLCOME TRUST GENOME CAMPUS) -->
   3 <!-- edited with XMLSpy v2005 rel. 3 U (http://www.altova.com) by lj (jl) -->
   4 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="http://www.vamsas.org" targetNamespace="http://www.vamsas.org" elementFormDefault="qualified" attributeFormDefault="unqualified">
   5         <xs:complexType name="rangeType">
   6                 <xs:annotation>
   7                         <xs:documentation>Specify positions and/or regions on the principle dimension of some associated vamsas object
   8                         TODO: this is abstract. should provide context to scope the range of ids for each use</xs:documentation>
   9                 <xs:documentation>Keeping to jaxb-1.0 specification for the moment - this choice should become a substitution group when we use jaxb-2.0 capable bindings
  10                 </xs:documentation></xs:annotation>
  11                 <!--  Do we really need this - a position could be just a seg with start=end and inclusive=true -->
  12                 <xs:choice>
  13                         <xs:element name="pos" maxOccurs="unbounded" minOccurs="1">
  14                                 <xs:annotation><xs:documentation>a position within the associated object's coordinate system</xs:documentation></xs:annotation>
  15                                 <xs:complexType>
  16                                         <xs:attribute name="i" type="xs:int" use="required"/>
  17                                 </xs:complexType>
  18                         </xs:element>
  19                         <xs:element name="seg" maxOccurs="unbounded" minOccurs="1">
  20                                 <xs:annotation><xs:documentation>a region from start to end, with flag for inclusivity of terminii</xs:documentation></xs:annotation>
  21                                 <xs:complexType>
  22                                         <xs:attribute name="start" type="xs:int" use="required"/>
  23                                         <xs:attribute name="end" type="xs:int" use="required"/>
  24                                         <xs:attribute name="inclusive" type="xs:boolean" use="required"><xs:annotation><xs:documentation>when false, a consecutive range like 'start=1, end=2' means the region lying after position 1 and before position 2</xs:documentation></xs:annotation></xs:attribute>
  25                                 </xs:complexType>
  26                         </xs:element>
  27                 </xs:choice>
  28         </xs:complexType>
  29         <xs:element name="VAMSAS">
  30                 <xs:annotation><xs:documentation>contains unassociated trees and a number of analysis sets</xs:documentation></xs:annotation>
  31                 <xs:complexType>
  32                         <xs:sequence>
  33                                 <xs:element ref="vamsas:Tree" minOccurs="0" maxOccurs="unbounded"/>
  34                                 <xs:element ref="vamsas:DataSet" minOccurs="0" maxOccurs="unbounded"/>
  35                         </xs:sequence>
  36                         <xs:attribute name="id" type="xs:ID" use="optional">                    <xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation>
  37                         </xs:attribute>
  38                         <xs:attribute name="modifiable" type="xs:boolean" default="true" use="optional"><xs:annotation><xs:documentation>objects with modifiable=false will not be modified by a vamsas client update</xs:documentation></xs:annotation>
  39                         </xs:attribute>
  40                 </xs:complexType>
  41         </xs:element>
  42         <xs:annotation>
  43                 <xs:documentation> Properties. Generally, these are mutable so an application should check them each time. This may change depending on the context of the property</xs:documentation>
  44         </xs:annotation>
  45         <xs:element name="Tree">
  46                 <xs:complexType>
  47                         <xs:annotation><xs:documentation>Contains a named collection of trees TODO: define way of referencing leaves of global tree for any sequence/alignment object</xs:documentation></xs:annotation>
  48                         <xs:sequence>
  49                                 <xs:element name="title" type="xs:string" minOccurs="0"/>
  50                                 <xs:element name="newick" maxOccurs="unbounded">
  51                                         <xs:complexType>
  52                                                 <xs:simpleContent>
  53                                                         <xs:extension base="xs:string">
  54                                                                 <xs:attribute name="title" type="xs:string" use="optional"/>
  55                                                                 <xs:attribute name="id" type="xs:ID"  use="optional">
  56                                                                         <xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation>
  57                                                                 </xs:attribute>
  58                                                                 <xs:attribute name="modifiable" type="xs:boolean" default="true"  use="optional"><xs:annotation><xs:documentation>objects with modifiable=false will not be modified by a vamsas client update</xs:documentation></xs:annotation>
  59                                                                 </xs:attribute>
  60                                                         </xs:extension>
  61                                                 </xs:simpleContent>
  62                                         </xs:complexType>
  63                                 </xs:element>
  64                                 <xs:element ref="vamsas:property" maxOccurs="unbounded" minOccurs="0"/>
  65                                 <xs:element ref="vamsas:Provenance"/>
  66                         </xs:sequence>
  67                         <xs:attribute name="id" type="xs:ID"  use="optional">                   <xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation>
  68                         </xs:attribute>
  69                         <xs:attribute name="modifiable" type="xs:boolean" default="true" use="optional"><xs:annotation><xs:documentation>objects with modifiable=false will not be modified by a vamsas client update</xs:documentation></xs:annotation>
  70                         </xs:attribute>
  71                         </xs:complexType>
  72         </xs:element>
  73         <xs:element name="property">
  74                 <xs:complexType><xs:simpleContent>
  75                         <xs:annotation><xs:documentation>Named and typed property string</xs:documentation></xs:annotation>
  76                         <xs:extension base="xs:string">
  77                                 <xs:attribute name="name" type="xs:string" use="required"/>
  78                                         <xs:attribute name="type" type="xs:string" use="required"><xs:annotation><xs:documentation>The type specifies how the property will be parsed. Empty property strings are allowed, and can be used to prototype the input to a document. TODO: specify allowed types</xs:documentation></xs:annotation></xs:attribute>
  79                         </xs:extension>
  80                 </xs:simpleContent></xs:complexType>
  81         </xs:element>
  82         <xs:complexType name="rangeAnnotation">
  83                 <xs:annotation>
  84                         <xs:documentation>provenance contains source of annotation</xs:documentation>
  85                         <xs:documentation>polymorphism for having collection of single points,
  86                                 or ordered set of regions with polarity (start.lt.end or end.lt.start)</xs:documentation>
  87                 </xs:annotation>
  88                 <xs:complexContent>
  89                         <xs:extension base="vamsas:rangeType">
  90                                 <xs:sequence>
  91                                         <xs:element name="description" type="xs:string" minOccurs="0"/>
  92                                         <xs:element name="status" type="xs:string" minOccurs="0"/>
  93                                         <xs:element ref="vamsas:annotationElement" minOccurs="0" maxOccurs="unbounded"/>
  94                                         <xs:element ref="vamsas:Provenance" maxOccurs="1" minOccurs="1"/>
  95                                         <xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded"><xs:annotation>
  96                                                 <xs:documentation>Note:These are mutable so an application should check them each time.</xs:documentation>
  97                                         </xs:annotation></xs:element>
  98                                 </xs:sequence>
  99                                 <xs:attribute name="id" type="xs:ID" use="optional">
 100                                                         <xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation>
 101                                 </xs:attribute>
 102                                 <xs:attribute name="modifiable" type="xs:boolean" default="true" use="optional">
 103                                 <xs:annotation><xs:documentation>objects with modifiable=false will not be modified by a vamsas client update</xs:documentation></xs:annotation>
 104                                 </xs:attribute>
 105                                 <xs:attribute name="group" type="xs:string" use="optional">
 106                                 <xs:annotation><xs:documentation>Annotation with the same non-empty group name are grouped together</xs:documentation></xs:annotation></xs:attribute>
 107                                 <xs:attribute name="type" type="xs:string" use="required"/>
 108
 109                         </xs:extension>
 110                 </xs:complexContent>
 111         </xs:complexType>
 112         <xs:element name="param"><xs:complexType>
 113                         <xs:annotation>
 114                                 <xs:documentation>
 115                                         Specifies a named and typed value used to perform some data transformation.
 116                                 </xs:documentation>
 117                                 <xs:documentation>
 118                                         LATER: experiment with xml validation of property set prototypes for services</xs:documentation></xs:annotation>
 119                         <xs:simpleContent>
 120                                 <xs:annotation><xs:documentation>Named and typed property string</xs:documentation></xs:annotation>
 121                                 <xs:extension base="xs:string">
 122                                         <xs:attribute name="name" type="xs:string" use="required"/>
 123                                         <xs:attribute name="type" type="xs:string" use="required"><xs:annotation><xs:documentation>The type specifies how the property will be parsed. Empty property strings are allowed, and can be used to prototype the input to a document. TODO: specify allowed types</xs:documentation></xs:annotation></xs:attribute>
 124                                 </xs:extension>
 125                         </xs:simpleContent>
 126         </xs:complexType></xs:element>
 127         <xs:element name="input"><xs:complexType>
 128                         <xs:annotation>
 129                                 <xs:documentation>
 130                                         Selects all or part of a collection of vamsas objects as a named input to some transformation process.
 131                                 </xs:documentation>
 132                         </xs:annotation>
 133                         <xs:complexContent>
 134                                 <xs:extension base="vamsas:rangeType">
 135                                         <xs:attribute name="name" type="xs:string" use="required"></xs:attribute>
 136                                         <xs:attribute name="objRef" type="xs:IDREF" use="optional"><xs:annotation><xs:documentation>Reference Frame for rangeType specfication</xs:documentation></xs:annotation></xs:attribute>
 137                                 </xs:extension>
 138                         </xs:complexContent>
 139                 </xs:complexType>
 140         </xs:element>
 141
 142         <xs:element name="Provenance">
 143                 <xs:complexType>
 144                         <xs:annotation>
 145                                 <xs:documentation>
 146                                         Defines the origin and series of operations applied directly to the object that references it.
 147                                 </xs:documentation>
 148                         </xs:annotation>
 149                         <xs:sequence>
 150                                 <xs:element name="entry" maxOccurs="unbounded">
 151                                         <xs:complexType>
 152                                                 <xs:sequence>
 153                                                         <xs:element name="User" type="xs:string"><xs:annotation><xs:documentation>Who</xs:documentation></xs:annotation></xs:element>
 154                                                         <xs:element name="App" type="xs:string"><xs:annotation><xs:documentation>With which application</xs:documentation></xs:annotation></xs:element>
 155                                                         <xs:element name="Action" type="xs:string"><xs:annotation><xs:documentation>Did what</xs:documentation></xs:annotation></xs:element>
 156                                                         <xs:element name="Date" type="xs:date"><xs:annotation><xs:documentation>When</xs:documentation></xs:annotation></xs:element>
 157                                                         <xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded"><xs:annotation><xs:documentation>additional information</xs:documentation></xs:annotation></xs:element>
 158                                                         <xs:element ref="vamsas:param" minOccurs="0" maxOccurs="unbounded"><xs:annotation><xs:documentation>parameter for the action</xs:documentation></xs:annotation></xs:element>
 159                                                         <xs:element ref="vamsas:input" minOccurs="0" maxOccurs="unbounded"><xs:annotation><xs:documentation>bioinformatic objects input to action</xs:documentation></xs:annotation></xs:element>
 160                                                 </xs:sequence>
 161                                                 <xs:attribute name="id" type="xs:ID" use="optional">                    <xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation>
 162                                                 </xs:attribute>
 163                                         </xs:complexType>
 164                                 </xs:element>
 165                         </xs:sequence>
 166                 </xs:complexType>
 167         </xs:element>
 168         <xs:element name="DataSet">
 169                 <xs:complexType>
 170                         <xs:annotation><xs:documentation>A collection of sequences, alignments, trees and other things.</xs:documentation></xs:annotation>
 171                         <xs:sequence>
 172                                 <xs:element name="Sequence" maxOccurs="unbounded">
 173                                         <xs:complexType>
 174                                                 <xs:annotation><xs:documentation>a primary or secondary sequence record from which all other sequences may be derived</xs:documentation></xs:annotation>
 175                                                 <xs:complexContent>
 176                                                         <xs:extension base="vamsas:SequenceType">
 177                                                                 <xs:sequence>
 178                                                                         <xs:element name="dbRef" minOccurs="0" maxOccurs="unbounded">
 179                                                                                 <xs:complexType>
 180                                                                                         <xs:sequence>
 181                                                                                                 <xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded"/>
 182                                                                                         </xs:sequence>
 183                                                                                         <xs:attribute name="source" type="xs:string"/>
 184                                                                                         <xs:attribute name="version" type="xs:string"/>
 185                                                                                         <xs:attribute name="accessionId" type="xs:string"/>
 186                                                                                         <xs:attribute name="id" type="xs:ID" use="optional">                    <xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation>
 187                                                                                         </xs:attribute>
 188                                                                                 </xs:complexType>
 189                                                                         </xs:element>
 190                                                                 </xs:sequence>
 191                                                                 <xs:attribute name="id" type="xs:ID" use="optional">                    <xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation>
 192                                                                 </xs:attribute>
 193                                                                 <xs:attribute name="dictionary" type="xs:string" use="required"><xs:annotation><xs:documentation>symbol class for sequence</xs:documentation></xs:annotation></xs:attribute>
 194                                                         </xs:extension>
 195                                                 </xs:complexContent>
 196                                         </xs:complexType>
 197                                 </xs:element>
 198                                 <xs:element name="DataSetAnnotations" minOccurs="0" maxOccurs="unbounded">
 199                                         <xs:complexType>
 200                                                 <xs:annotation><xs:documentation>Annotate over positions and regions of dataset sequences</xs:documentation>
 201                                                 </xs:annotation>
 202                                                 <xs:complexContent>
 203                                                         <xs:extension base="vamsas:rangeAnnotation">
 204                                                                 <xs:attribute name="seqRef" type="xs:IDREF" use="optional">
 205                                                                         <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>
 206                                                                 </xs:attribute>
 207                                                         </xs:extension>
 208                                                 </xs:complexContent>
 209                                         </xs:complexType>
 210                                 </xs:element>
 211                                 <xs:element name="Alignment" minOccurs="0" maxOccurs="unbounded">
 212                                         <xs:complexType>
 213                                                 <xs:sequence>
 214                                                         <xs:element name="AlignmentFeatures" minOccurs="0" maxOccurs="unbounded"><xs:complexType><xs:annotation>
 215                                                                 <xs:documentation>Annotate over positions and regions of the alignment</xs:documentation>
 216                                                         </xs:annotation><xs:complexContent>
 217                                                                 <xs:extension base="vamsas:rangeAnnotation">
 218                                                                         <xs:attribute name="seqRef" type="xs:IDREF" use="optional">
 219                                                                         <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>
 220                                                                 </xs:attribute>
 221                                                                 </xs:extension>
 222                                                         </xs:complexContent></xs:complexType></xs:element>
 223                                                         <xs:element name="AlignmentAnnotations" minOccurs="0" maxOccurs="unbounded">
 224                                                                 <xs:annotation>
 225                                                                         <xs:documentation>
 226                                                                                 TODO: hard to distinguish this from the alignment features element. Do we merge them and leave the applications
 227                                                                         </xs:documentation>
 228                                                                 </xs:annotation>
 229                                                                 <xs:complexType>
 230                                                                         <xs:sequence>
 231                                                                                 <xs:element ref="vamsas:annotationElement" maxOccurs="unbounded"/>
 232                                                                                 <xs:element name="label" type="xs:string"/>
 233                                                                                 <xs:element name="description" type="xs:string"/>
 234                                                                                 <xs:element ref="vamsas:Provenance"/>
 235                                                                         </xs:sequence>
 236                                                                         <xs:attribute name="graph" type="xs:boolean" use="required"/>
 237                                                                         <xs:attribute name="id" type="xs:ID" use="optional">                    <xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation>
 238                                                                         </xs:attribute>
 239                                                                 </xs:complexType>
 240                                                         </xs:element>
 241                                                         <xs:element ref="vamsas:Tree" minOccurs="0" maxOccurs="unbounded"/>
 242                                                         <xs:element name="alignmentSequence" maxOccurs="unbounded">
 243                                                                 <xs:complexType>
 244                                                                         <xs:complexContent>
 245                                                                                 <xs:extension base="vamsas:SequenceType">
 246                                                                                         <xs:sequence>
 247                                                                                                 <xs:element name="AlignmentSequenceFeature" type="vamsas:rangeAnnotation" minOccurs="0" maxOccurs="unbounded">
 248                                                                                                         <xs:annotation>
 249                                                                                                         <xs:documentation>Annotate over positions and regions of the ungapped sequences in the alignment</xs:documentation>
 250                                                                                                                 <xs:documentation>TODO: have to remove id rangeSpec or require it to be the same as dataset sequence reference</xs:documentation>
 251                                                                                                 </xs:annotation>
 252                                                                                                 </xs:element>
 253                                                                                         </xs:sequence>
 254                                                                                         <xs:attribute name="id" type="xs:ID" use="optional">
 255                                                                                                 <xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation>
 256                                                                                         </xs:attribute>
 257                                                                                         <xs:attribute name="refid" type="xs:IDREF" use="required"><xs:annotation><xs:documentation>Dataset Sequence from which this alignment sequence is taken from</xs:documentation></xs:annotation></xs:attribute>
 258                                                                                 </xs:extension>
 259                                                                         </xs:complexContent>
 260                                                                 </xs:complexType>
 261                                                         </xs:element>
 262                                                         <xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded"><xs:annotation>
 263                                                                 <xs:documentation>typical properties may be alignment score objects </xs:documentation>
 264                                                         </xs:annotation></xs:element>
 265                                                         <xs:element ref="vamsas:Provenance"/>
 266                                                 </xs:sequence>
 267                                                 <xs:attribute name="gapChar" type="xs:string" use="required"/>
 268                                                 <xs:attribute name="aligned" type="xs:boolean" use="optional"/>
 269                                                 <xs:attribute name="id" type="xs:ID" use="optional">                    <xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation>
 270                                                 </xs:attribute>
 271                                                 <xs:attribute name="modifiable" type="xs:boolean" default="true" use="optional"><xs:annotation><xs:documentation>objects with modifiable=false will not be modified by a vamsas client update</xs:documentation></xs:annotation>
 272                                                 </xs:attribute>
 273                                         </xs:complexType>
 274                                 </xs:element>
 275                                 <xs:element ref="vamsas:Tree" minOccurs="0" maxOccurs="unbounded"/>
 276                                 <xs:element ref="vamsas:Provenance"/>
 277                         </xs:sequence>
 278                         <xs:attribute name="id" type="xs:ID" use="optional">                    <xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation>
 279                         </xs:attribute>
 280                 </xs:complexType>
 281         </xs:element>
 282         <xs:element name="annotationElement">
 283                 <xs:complexType>
 284                         <xs:annotation><xs:documentation>per-site symbolic and/or quantitative annotation</xs:documentation>
 285                         <xs:documentation>SecondaryStructure and display character (from Jalview) have been subsumed into the glyph element</xs:documentation></xs:annotation>
 286                         <xs:sequence>
 287
 288                                 <xs:element name="description" type="xs:string" minOccurs="0">
 289                                 <xs:annotation><xs:documentation>Free text at this position</xs:documentation></xs:annotation>
 290                                 </xs:element>
 291                                 <xs:element name="glyph" minOccurs="0" maxOccurs="unbounded">
 292                                         <xs:annotation><xs:documentation>Discrete symbol - possibly graphically represented</xs:documentation></xs:annotation>
 293                                         <xs:complexType>
 294                                         <xs:simpleContent>
 295                                         <xs:extension base="xs:string">
 296                                                 <xs:attribute name="dict" type="xs:string" default="utf8" use="optional">
 297                                                 <xs:annotation><xs:documentation>specifies the symbol dictionary for this glyph - eg utf8 (the default), aasecstr_3 or kd_hydrophobicity - the content is not validated so applications must ensure they gracefully deal with invalid entries here</xs:documentation>
 298                                                 <xs:documentation>TODO: specify a minimum list of glyph dictionaries to get us started and provide a way for the vamsasClient to validate their content if regexes are specified</xs:documentation></xs:annotation></xs:attribute>
 299                                 </xs:extension>
 300                                 </xs:simpleContent>
 301                                 </xs:complexType>
 302                                 </xs:element>
 303                                 <xs:element name="value" type="xs:float" minOccurs="0" maxOccurs="unbounded">
 304                                 <xs:annotation><xs:documentation>Ordered set of float values - an application may treat the values together as a vector with common support for a set of annotation elements - but this is, again, not validated so applications should deal gracefully with varying numbers of dimensions
 305                                 </xs:documentation></xs:annotation></xs:element>
 306                         </xs:sequence>
 307                         <xs:attribute name="position" type="xs:integer" use="required"><xs:annotation><xs:documentation>position with respect to the coordinate frame defined by a rangeType specification</xs:documentation></xs:annotation></xs:attribute>
 308                         <xs:attribute name="after" type="xs:boolean" use="optional" default="false"><xs:annotation><xs:documentation>true means the annotation element appears between the specified position and the next</xs:documentation></xs:annotation></xs:attribute>
 309                         <xs:attribute name="id" type="xs:ID" use="optional">                    <xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation>
 310                         </xs:attribute>
 311                 </xs:complexType>
 312         </xs:element>
 313         <xs:complexType name="SequenceType">
 314                 <xs:sequence>
 315                         <xs:element name="sequence" type="xs:string" minOccurs="1" maxOccurs="1"/>
 316                         <xs:element name="name" type="xs:string" minOccurs="1" maxOccurs="1"/>
 317                         <xs:element name="description" type="xs:string" minOccurs="0" maxOccurs="1"/>
 318                         <xs:element ref="vamsas:property" minOccurs="0" maxOccurs="unbounded"><xs:annotation><xs:documentation>additional typed properties</xs:documentation></xs:annotation></xs:element>
 319                 </xs:sequence>
 320                 <xs:attribute name="start" type="xs:integer" use="required"/>
 321                 <xs:attribute name="end" type="xs:integer" use="required"/>
 322         </xs:complexType>
 323         <xs:element name="ApplicationData">
 324                 <xs:complexType>
 325                         <xs:annotation>
 326                                 <xs:documentation>Data specific to a particular type and version of vamsas application</xs:documentation>
 327                         </xs:annotation>
 328                         <xs:complexContent>
 329                                 <xs:extension base="vamsas:appData">
 330                                         <xs:sequence>
 331                                                 <xs:element name="User" maxOccurs="unbounded" minOccurs="0">
 332                                                         <xs:complexType>
 333                                                                 <xs:complexContent>
 334                                                                         <xs:extension base="vamsas:appData">
 335                                                                                 <xs:annotation><xs:documentation>Data available to just a particular user</xs:documentation></xs:annotation>
 336                                                                                 <xs:attribute name="fullname" type="xs:string" use="required"/>
 337                                                                                 <xs:attribute name="organization" type="xs:string" use="required"/>
 338                                                                         </xs:extension>
 339                                                                 </xs:complexContent>
 340                                                         </xs:complexType>
 341                                                 </xs:element>
 342                                                 <xs:element name="Common" maxOccurs="1" minOccurs="0">
 343                                                         <xs:complexType>
 344                                                                 <xs:complexContent>
 345                                                                         <xs:extension base="vamsas:appData">                                                                    </xs:extension>
 346                                                                 </xs:complexContent>
 347                                                         </xs:complexType>
 348                                                 </xs:element>
 349                                                 <xs:element name="Instance" maxOccurs="unbounded" minOccurs="0">
 350                                                         <xs:complexType>
 351                                                                 <xs:complexContent>
 352                                                                         <xs:extension base="vamsas:appData">
 353                                                                                 <xs:annotation>
 354                                                                                         <xs:documentation>Data available to just a specific instance of the application</xs:documentation>
 355                                                                                         <xs:documentation>VAMSAS/Pierre: Is this data volatile ?  Application instances may not be accessible after the session has closed - the user may have to be presented with the option of picking up the data in that instance</xs:documentation>
 356                                                                                 </xs:annotation>
 357                                                                                 <xs:attribute name="urn" type="xs:string" use="required"/>
 358                                                                         </xs:extension>
 359                                                                 </xs:complexContent>
 360                                                         </xs:complexType>
 361                                                 </xs:element>
 362                                         </xs:sequence>
 363                                         <xs:attribute name="version" type="xs:string" use="required"/>
 364                                         <xs:attribute name="name" type="xs:string" use="required"/>
 365                                 </xs:extension>
 366                         </xs:complexContent>
 367                 </xs:complexType>
 368         </xs:element>
 369         <xs:element name="Attachment">
 370         <xs:complexType>
 371         <xs:complexContent>
 372           <xs:extension base="vamsas:appData">
 373           <xs:annotation>
 374           <xs:documentation>General data container to attach a typed data object to any vamsas object</xs:documentation>
 375           </xs:annotation>
 376           <xs:attribute name="compressed" type="xs:boolean" use="optional" default="false"><xs:annotation><xs:documentation>true implies data will be decompresses with Zip before presenting to application</xs:documentation></xs:annotation></xs:attribute>
 377           <xs:attribute name="type" type="xs:string" use="required"><xs:annotation><xs:documentation>Type of arbitrary data - TODO: decide format - use (extended) MIME types ?</xs:documentation></xs:annotation></xs:attribute>
 378           <xs:attribute name="objectref" type="xs:IDREF" use="required"><xs:annotation><xs:documentation>Object the arbitrary data is associated with</xs:documentation></xs:annotation></xs:attribute>
 379           <xs:attribute name="id" type="xs:ID" use="optional">                  <xs:annotation><xs:documentation>Primary Key for vamsas object referencing</xs:documentation></xs:annotation>
 380                         </xs:attribute>
 381           </xs:extension>
 382         </xs:complexContent>
 383         </xs:complexType>
 384         </xs:element>
 385         <xs:complexType name="appData">
 386                 <xs:choice>
 387                         <xs:element name="data" type="xs:base64Binary"/>
 388                         <xs:element name="dataReference" type="xs:string"/>
 389                 </xs:choice>
 390         </xs:complexType>
 391 </xs:schema>