Changeset 3370 for trunk/doc/src/docbook/userdoc/array_lims.xml
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trunk/doc/src/docbook/userdoc/array_lims.xml
r3246 r3370 30 30 <?dbhtml dir="array_lims"?> 31 31 <title>Array LIMS</title> 32 <sect1> 33 <title></title> 34 <para></para> 35 </sect1> 32 <sect1> 33 <title>Introduction</title> 34 35 <para>Arrays are at the core of the BASE2 business and are essential elements to describe in 36 order to be MIAME compliant. It is also critical to track and manage information about 37 microarray design as accurately as possible since mistakes could prove extremely costly 38 in downstream analysis.</para> 39 <para>Finally, as a good practice, all Array related information should be entered into 40 BASE2 system prior to start describing the sample processing and hybridizations events 41 making up a microarray experiment.</para> 42 43 <para>BASE2 has been engineered to support microarray printing facilities. The system 44 therefore offers objects to describe plates, their geometries and the events (merging, 45 printing) affected them. The first section of the chapter deals with this functionality. 46 as well as plate management.</para> 47 48 <para>For users buying their arrays from commercial sources, the Plate Management component 49 can be ignored and they can go immediatly to the second section <xref 50 linkend="array_lims.arraydesign"/> of the chapter.</para> 51 52 </sect1> 53 54 <sect1 id="array_lims.platemanagement"> 55 <title>Managing Plates</title> 56 <para>TO DO</para> 57 </sect1> 58 59 <sect1 id="array_lims.arraydesign"> 60 <title>Managing ArrayDesigns</title> 61 <para> ArrayDesign should be understood as a plan which can be realized during a printing 62 process producing microarray slides. During the course of the printing process, reagents 63 may run out leading to the interruption of this process. All slides created during this 64 printing process belong to the same printing 'batch'. It is the array slide that will 65 eventually be used in a Hybridization event. BASE2 allows user to track those 3 entities 66 with great details. This is an important functionality for users producing their own 67 arrays and for those caring for quality control and tracking of microarray slides in a 68 printing facility. The following sections detail how to use BASE2 to help in these 69 tasks. </para> 70 <sect2 id="array_lims.arraydesign.create"> 71 <title>Creating ArrayDesigns</title> 72 <para>To create an ArrayDesign, do the following</para> 73 <para>Go To <menuchoice> 74 <guimenu>Array LIMS</guimenu> 75 <guimenuitem>ArrayDesign</guimenuitem> 76 </menuchoice> 77 </para> 78 <para>The ArrayDesign List view now presents all ArrayDesigns available to the user 79 (shared to or owned by).</para> 80 <para>Click on <guibutton>New…</guibutton> button</para> 81 <para>A 'Create' pop-up window opens. It contains 3 tabs</para> 82 83 <variablelist> 84 <varlistentry> 85 <term> 86 <guilabel>Array design</guilabel> 87 </term> 88 <listitem> 89 90 <para>The tab contains four fields, namely:</para> 91 92 <variablelist> 93 94 <varlistentry> 95 <term> 96 <guilabel>Name</guilabel> 97 </term> 98 <listitem> 99 <para> Provide a unique sensible name for the design. Possibly 100 follow the convention [organisation-species-feature 101 number-version] as in EMBL-Hsapiens-wholegenome-45k-v1. For 102 commercial platforms such as Agilent and Affymetrix, it is 103 probably better to use the commercial names, such as Agilent 104 Whole Mouse Genome G4122A or HG_U133A respectively</para> 105 </listitem> 106 </varlistentry> 107 108 <varlistentry> 109 <term> 110 <guilabel>Description</guilabel> 111 </term> 112 <listitem> 113 <para>Provide a short but meaningful of the ArrayDesign</para> 114 </listitem> 115 </varlistentry> 116 117 <varlistentry> 118 <term> 119 <guilabel>Affy Chip</guilabel> 120 </term> 121 <listitem> 122 <para>This is a radio button for providing a boolean entry, 123 essentially telling the system whether the ArrayDesign being 124 created is of Affymetrix technology or not.</para> 125 <warning> 126 <para>As indicated on the interface, once saved, this 127 information cannot be modified, so if a mistake is made, 128 the entry will have to be deleted.</para> 129 </warning> 130 </listitem> 131 </varlistentry> 132 133 <varlistentry> 134 <term> 135 <guilabel>CDF file</guilabel> 136 </term> 137 <listitem> 138 <para>This field allows to upload an Affymetrix CDF file. A CDF 139 file is a binary file describing Affymetrix chip layout. 140 This file is necessary for performing analysis using BASE2 141 plugins (e.g RMAExpress plugin).</para> 142 <note> 143 <para>Affymetrix users, you can also upload CLF or BPMAP 144 files defined for exon and tiling arrays 145 respectively.</para> 146 </note> 147 </listitem> 148 </varlistentry> 149 150 </variablelist> 151 </listitem> 152 </varlistentry> 153 154 <varlistentry> 155 <term> 156 <guilabel>Annotations</guilabel> 157 </term> 158 <listitem> 159 <para>This tab allows to input values associated to Annotation Types devised 160 to refine ArrayDesign description.</para> 161 <para>The windows will be empty if no Annotation Types have been declared to 162 annotation ArrayDesign item or if none are shared to the user</para> 163 </listitem> 164 </varlistentry> 165 166 <varlistentry> 167 <term> 168 <guilabel>Inherited Annotations</guilabel> 169 </term> 170 <listitem> 171 <para>TO DO</para> 172 </listitem> 173 </varlistentry> 174 175 </variablelist> 176 <para>Click on the <inlinemediaobject> 177 <imageobject> 178 <imagedata fileref="figures/save.gif" format="GIF"/> 179 </imageobject> 180 </inlinemediaobject> Save button to store the information in BASE2 or on the <inlinemediaobject> 181 <imageobject> 182 <imagedata fileref="figures/cancel.gif" format="GIF"/> 183 </imageobject> 184 </inlinemediaobject> button to abort. </para> 185 <para>Upon saving, the Array Design List View page is displayed. Users should pay 186 attention to the column <guilabel>Has features</guilabel>. Unless an Affymetrix 187 ArrayDesign was created, the value will be by default set to 188 <guilabel>no</guilabel>. For all other cases, this value will only be updated 189 following <guilabel>Importing the Features</guilabel>, a process which is detailed 190 in the next section.</para> 191 192 </sect2> 193 194 <sect2 id="array_lims.arraydesign.importfeature"> 195 <title>Importing Features associated to an ArrayDesign</title> 196 <important> 197 <para>For non-Affymetrix ArrayDesigns, Importing Features is an important step in 198 order to fully define an ArrayDesign. It should be noted that BASE2 does not 199 enforce the immediate Feature import upon creation of ArrayDesign. However, It 200 is STRONGLY advised to do so when creating an ArrayDesign. Doing so enables to 201 use the Array Design for downstream analysis with no further trouble. It also 202 matters when importing rawBioassay data and matching those to the corresponding 203 ArrayDesign. It is interesting to note that the processes of importing features 204 associated to Array Design and importing Data associated to Raw BioAssay are in 205 essence very similar.</para> Please see section <xref 206 linkend="experiments_analysis.rawbioassay.rawdata"/> for more information. </important> 207 <para>This section applies only to non-affymetrix ArrayDesign since Affymetrix designs 208 are handled differently. For Affymetrix platform, features are considered imported 209 when the Affymetrix CDF file is actually uploaded.</para> 210 <para>From the ArrayDesign Item View, click on the <guibutton>Import</guibutton> 211 button</para>. <note> 212 <para>The button only shows up if the logged in user has enough permissions.</para> 213 </note> 214 <para>A plugin interface is launched. One can either run the import using the autodetect 215 settings or for more control, select a <guilabel>'Reporter Map Importer'</guilabel> 216 plugin and then choose a <guilabel>plugin configuration</guilabel> available from 217 the drop-down list populated from configurations shared to or owned by the user.</para> 218 <para>BASE2 ships with Reporter Map Importer plugin configurations allowing to import 219 features from Axon gal files and also gpr files (2 configurations_Block/Column/Row 220 and Block/Row/Column for each file formats) and for Agilent FeatureExtraction files 221 (to be confirmed). </para> 222 <para>For more about the plugin configuration, refer to section <xref 223 linkend="plugins.installation"/>.</para> 224 <para>If the import run is successful, go to the ArrayDesign List view. The 225 <guilabel>Has features</guilabel> column will show <guilabel>Yes (n)</guilabel> 226 where n is the number of features actually present on the microarray and now 227 associated to the newly created ArrayDesign.</para> 228 <tip> 229 <para>A list of Reporter Map Importer plugin configurations is maintained at BASE2 230 site and each can be downloaded as xml file from <ulink url="tbd"/>.</para> 231 </tip> 232 </sect2> 233 <para>If both actions have been successfully completed, the ArrayDesign is now fully defined 234 and ArrayBatches and Array slides items can be created. This process is described in the 235 following sections.</para> 236 237 238 <sect2 id="array_lims.arraydesign.detail_view"> 239 <title>Viewing/Editing ArrayDesigns</title> 240 <itemizedlist> 241 <listitem> 242 <para> Press and hold one of the <keycap>CTRL</keycap>, <keycap>ALT</keycap> or 243 <keycap>SHIFT</keycap> keys while clicking on the name of an ArrayDesign 244 Item, which is a live link. </para> 245 </listitem> 246 <listitem> 247 <para> Alternately, navigating to the ArrayDesign Item View, one can hit the 248 <guibutton>Edit…</guibutton> to performed the task.</para> 249 <para>In both cases, an Edit pop-up windows opens. It is essentially identical 250 to a Create window and allows updating information about a particular 251 ArrayDesign item stored in BASE2.</para> 252 <figure id="write_docbook_doc.figures.arraydesign-itemview"> 253 <title>ArrayDesign Item View</title> 254 <screenshot> 255 <mediaobject> 256 <imageobject> 257 <imagedata contentwidth="10cm" width="10cm" fileref="figures/arraydesign-itemview.png" format="PNG"/> 258 </imageobject> 259 </mediaobject> 260 </screenshot> 261 </figure> 262 </listitem> 263 <listitem> 264 <para>From the ArrayDesign item View, all associated 265 <guilabel>ArrayBatches</guilabel> are indicated as navigable links. Also 266 present on the ArrayDesign Item View are the links back to 267 <guilabel>Plates</guilabel> possibly used to define the ArrayDesign (none 268 used in the screenshot).</para> 269 </listitem> 270 </itemizedlist> 271 </sect2> 272 <sect2 id="array_lims.arraydesign.delete"> 273 <title>Deleting/Restoring ArrayDesigns</title> 274 <para>As for other items in BASE2, ArrayDesigns can be removed and restored. To do so, 275 do the following:</para> 276 <itemizedlist> 277 <listitem> 278 <para>Select one or more ArrayDesigns and click <guibutton>Delete</guibutton> 279 button in the menu bar. </para> 280 <para>All the selected ArrayDesigns have been marked as deleted and are no 281 longer available from the interface. </para> 282 <para>Only by selecting from the <guilabel>view/preset…</guilabel> 283 select box the <guilabel>Removed</guilabel> option, one can see those of the 284 ArrayDesigns earmarked for deletion. They will be shown with a symbol <inlinemediaobject> 285 <imageobject> 286 <imagedata fileref="figures/deleted.gif" format="GIF"/> 287 </imageobject> 288 </inlinemediaobject> in front of them. </para> 289 </listitem> 290 <listitem> 291 <para>Alternately, navigating to the ArrayDesign Item View, one can hit the 292 <guibutton>Delete</guibutton> to performed the task. </para> 293 </listitem> 294 <listitem> 295 <para>Deletion errors at this stage can be easily recovered. Select the item to 296 recover from the List View (be sure to check the 297 <guilabel>Removed</guilabel> option in the 298 <guilabel>view/preset…</guilabel> filter) and hit the 299 <guibutton>Restore</guibutton> button to performed the task. </para> 300 </listitem> 301 </itemizedlist> 302 <important> 303 <para>To really delete an item from the database you must use the trashcan. Items 304 deleted from the Trashcan can not be recovered. To learn more about the trashcan 305 function, please refer to <xref linkend="trashcan"/> 306 </para> 307 </important> 308 </sect2> 309 310 </sect1> 311 <sect1 id="array_lims.arraybatch"> 312 <title>Managing Array Batches</title> 313 314 <sect2 id="array_lims.arraybatch.create"> 315 <title>Creating Array Batches </title> 316 <para>In BASE2, Array Batches can be created by 2 routes:</para> 317 <orderedlist> 318 <listitem> 319 <para>Creating Array Batch from the ArrayDesign List View page</para> 320 <para>Clicking on the <inlinemediaobject> 321 <imageobject> 322 <imagedata fileref="figures/add.gif" format="GIF"/> 323 </imageobject> 324 </inlinemediaobject> add Array batch button available from the 325 <guilabel>Batches</guilabel> column of the ArrayDesign list view page. 326 </para> 327 </listitem> 328 <listitem> 329 <para>Creating ArrayBatch from the ArrayBatch List View page</para> 330 <para>Go to <menuchoice> 331 <guimenu>View</guimenu> 332 <guimenuitem>ArrayBatch</guimenuitem> 333 </menuchoice></para> 334 <para>Click on <guibutton>New…</guibutton> button </para> 335 </listitem> 336 </orderedlist> 337 338 <para>In both cases, an ArrayBatch Create pop-up window opens. The window contains 2 339 mandatory fields:</para> 340 <figure id="write_docbook_doc.figures.arraybatch-create"> 341 <title>Create New Array batch from the ArrayDesign List View</title> 342 <screenshot> 343 <mediaobject> 344 <imageobject> 345 <imagedata contentwidth="10cm" width="10cm" fileref="figures/arraybatch-create.png" format="PNG"/> 346 </imageobject> 347 </mediaobject> 348 </screenshot> 349 </figure> 350 <itemizedlist> 351 <listitem> 352 <para> 353 <guilabel>Name</guilabel> and <guilabel>ArrayDesign</guilabel>.</para> 354 <para>The later is a select-list population from ArrayDesigns owned by or shared 355 to the user.</para> 356 </listitem> 357 <listitem> 358 <para><guilabel>Print robot</guilabel> and <guilabel>Protocol</guilabel>, the 359 other 2 fields, are optional and self explanatory.</para> 360 </listitem> 361 </itemizedlist> 362 <para>Click on the <inlinemediaobject> 363 <imageobject> 364 <imagedata fileref="figures/save.gif" format="GIF"/> 365 </imageobject> 366 </inlinemediaobject> Save button to store the information in BASE2 or on the <inlinemediaobject> 367 <imageobject> 368 <imagedata fileref="figures/cancel.gif" format="GIF"/> 369 </imageobject> 370 </inlinemediaobject> button to abort.</para> 371 </sect2> 372 373 <sect2 id="array_lims.arraybatch.detail_view"> 374 <title>Viewing/Editing ArrayBatches</title> 375 <itemizedlist> 376 <listitem> 377 <para> Press and hold one of the <keycap>CTRL</keycap>, <keycap>ALT</keycap> or 378 <keycap>SHIFT</keycap> keys while clicking on the name of an ArrayBatch 379 Item, which is a live link. </para> 380 </listitem> 381 <listitem> 382 <para> Alternately, navigating to the ArrayBatch Item View, one can hit the 383 <guibutton>Edit…</guibutton> to performed the task.</para> 384 <para>In both cases, an Edit pop-up windows opens. It is essentially identical 385 to a Create window and allows updating information about a particular 386 ArrayBatch item stored in BASE2</para> 387 <figure id="write_docbook_doc.figures.arraybatch-itemview"> 388 <title>ArrayBatch Item View</title> 389 <screenshot> 390 <mediaobject> 391 <imageobject> 392 <imagedata contentwidth="10cm" width="10cm" fileref="figures/arraybatch-itemview.png" format="PNG"/> 393 </imageobject> 394 </mediaobject> 395 </screenshot> 396 </figure> 397 </listitem> 398 <listitem> 399 <para>From the ArrayBatch item View, all associated <guilabel/>ArraySlides are 400 indicated as their use in Hybridization events. Both ArraySlides and 401 Hybridations are clickable items, enabling easy navigation.</para> 402 </listitem> 403 </itemizedlist> 404 </sect2> 405 <sect2 id="array_lims.arraybatch.delete"> 406 <title>Deleting/Restoring ArrayBatches</title> 407 <para>As for other items in BASE2, ArrayBatches can be removed and restored. To do so, 408 do the following</para> 409 <itemizedlist> 410 <listitem> 411 <para>Select one or more ArrayBatches and click <guibutton>Delete</guibutton> 412 button in the menu bar. </para> 413 <para>All the selected ArrayBatches have been marked as deleted and are no 414 longer available from the interface. </para> 415 <para>Only by selecting from the <guilabel>view/preset…</guilabel> 416 select box the <guilabel>Removed</guilabel> option, one can see those of the 417 ArrayBatches earmarked for deletion. They will be shown with a symbol <inlinemediaobject> 418 <imageobject> 419 <imagedata fileref="figures/deleted.gif" format="GIF"/> 420 </imageobject> 421 </inlinemediaobject> in front of them. </para> 422 </listitem> 423 <listitem> 424 <para>Alternately, navigating to the ArrayBatch Item View, one can hit the 425 <guibutton>Delete</guibutton> to performed the task. </para> 426 </listitem> 427 <listitem> 428 <para>Deletion errors at this stage can be easily recovered. Select the item to 429 recover from the List View (be sure to check the 430 <guilabel>Removed</guilabel> option in the 431 <guilabel>view/preset…</guilabel> filter) and hit the 432 <guibutton>Restore</guibutton> button to performed the task. </para> 433 </listitem> 434 </itemizedlist> 435 <important> 436 <para>To really delete an item from the database you must use the trashcan. Items 437 deleted from the Trashcan can not be recovered. To learn more about the trashcan 438 function, please refer to <xref linkend="trashcan"/> 439 </para> 440 </important> 441 </sect2> 442 </sect1> 443 <sect1 id="array_lims.arrayslide"> 444 <title>Managing Array Slides</title> 445 <sect2 id="array_lims.arrayslide.create"> 446 <title>Creating Array Slides </title> 447 <para>In BASE2, Array Slides can be created by 2 routes:</para> 448 <orderedlist> 449 <listitem> 450 <para>Creating Array Slides from the ArrayBatch View page</para> 451 <para>Clicking on the <inlinemediaobject> 452 <imageobject> 453 <imagedata fileref="figures/add.gif" format="GIF"/> 454 </imageobject> 455 </inlinemediaobject> add Array slides button. </para> 456 <figure id="write_docbook_doc.figures.arrayslide-single-create"> 457 <title>Create New Array Slide from the ArrayBatch List View</title> 458 <screenshot> 459 <mediaobject> 460 <imageobject> 461 <imagedata contentwidth="10cm" width="10cm" fileref="figures/arrayslide-single-create.png" format="PNG"/> 462 </imageobject> 463 </mediaobject> 464 </screenshot> 465 </figure> 466 </listitem> 467 <listitem> 468 <para>Creating ArraySlides from the ArrayBatch List View page</para> 469 <para>Go to <menuchoice> 470 <guimenu>View</guimenu> 471 <guimenuitem>ArraySlides</guimenuitem> 472 </menuchoice></para> 473 <para>Click on <guibutton>New…</guibutton> button </para> 474 </listitem> 475 </orderedlist> 476 477 <para>In both cases, an ArraySlide Create pop-up window opens. The window contains 2 478 mandatory fields:</para> 479 <itemizedlist> 480 <listitem> 481 <para> 482 <guilabel>Name</guilabel> and <guilabel>ArrayBatch</guilabel>.</para> 483 <para>The later is a select-list populated with ArrayBatches owned by or shared 484 to the user.</para> 485 </listitem> 486 <listitem> 487 <para><guilabel>Barcode</guilabel>, <guilabel>Index</guilabel> and 488 <guilabel>Destroyed</guilabel>, a tick box enabling to record microarray 489 slides lost by accident.</para> 490 </listitem> 491 </itemizedlist> 492 <para>Click on the <inlinemediaobject> 493 <imageobject> 494 <imagedata fileref="figures/save.gif" format="GIF"/> 495 </imageobject> 496 </inlinemediaobject> Save button to store the information in BASE2 or on the <inlinemediaobject> 497 <imageobject> 498 <imagedata fileref="figures/cancel.gif" format="GIF"/> 499 </imageobject> 500 </inlinemediaobject> button to abort. </para> 501 502 <para> In addition to this classic way of creating BASE items, Arrays Slides can be 503 created with a wizard available from both the ArraySlide Item view or from the 504 ArrayBatch List View page. To call the wizard:</para> 505 <para>Click on the <inlinemediaobject> 506 <imageobject> 507 <imagedata fileref="figures/new_wizard.gif" format="GIF"/> 508 </imageobject> 509 </inlinemediaobject> add multiple Array slides button in the 510 <guilabel>Slides</guilabel> column of the ArrayBatch List view page.</para> 511 512 <para> or </para> 513 <para>Click on the <inlinemediaobject> 514 <imageobject> 515 <imagedata fileref="figures/new_wizard.gif" format="GIF"/> 516 </imageobject> 517 </inlinemediaobject> 518 <guibutton>Create multiple…</guibutton> button from the menu bar of the 519 ArraySlides List View page </para> 520 521 <para>Either way ill open the a wizzard window as shown below</para> 522 <figure id="write_docbook_doc.figures.arrayslide-multiple-create"> 523 <title>Create Muliple Array Slide from the ArrayBatch List View wizzard</title> 524 <screenshot> 525 <mediaobject> 526 <imageobject> 527 <imagedata contentwidth="10cm" width="10cm" fileref="figures/arrayslide-multiple-create.png" format="PNG"/> 528 </imageobject> 529 </mediaobject> 530 </screenshot> 531 </figure> 532 <para>Fill in the necessary information as exhaustively as possible.</para> 533 <para>Click on the <inlinemediaobject> 534 <imageobject> 535 <imagedata fileref="figures/save.gif" format="GIF"/> 536 </imageobject> 537 </inlinemediaobject> Save button to store the information in BASE2 or on the <inlinemediaobject> 538 <imageobject> 539 <imagedata fileref="figures/cancel.gif" format="GIF"/> 540 </imageobject> 541 </inlinemediaobject> button to abort. </para> 542 </sect2> 543 544 <sect2 id="array_lims.arrayslide.detail_view"> 545 <title>Viewing/Editing ArraySlides</title> 546 <itemizedlist> 547 <listitem> 548 <para> Press and hold one of the <keycap>CTRL</keycap>, <keycap>ALT</keycap> or 549 <keycap>SHIFT</keycap> keys while clicking on the name of an ArraySlide 550 Item, which is a live link. </para> 551 </listitem> 552 <listitem> 553 <para> Alternately, navigating to the ArraySlide Item View, one can hit the 554 <guibutton>Edit…</guibutton> to performed the task.</para> 555 <para>In both cases, an Edit pop-up windows opens. It is essentially identical 556 to a Create window and allows updating information about a particular 557 ArraySlide item stored in BASE2</para> 558 <figure id="write_docbook_doc.figures.arrayslide-itemview"> 559 <title>ArraySlide Item View</title> 560 <screenshot> 561 <mediaobject> 562 <imageobject> 563 <imagedata contentwidth="10cm" width="10cm" fileref="figures/arrayslide-itemview.png" format="PNG"/> 564 </imageobject> 565 </mediaobject> 566 </screenshot> 567 </figure> 568 </listitem> 569 570 <listitem> 571 <para>From the ArraySlide item View, the associated 572 <guilabel>Hybridization</guilabel> can be indicated as navigable 573 links</para> 574 </listitem> 575 </itemizedlist> 576 </sect2> 577 <sect2 id="array_lims.arrayslide.delete"> 578 <title>Deleting/Restoring ArraySlides</title> 579 <para>As for other items in BASE2, ArraySlides can be removed and restored. To do so, do 580 the following</para> 581 <itemizedlist> 582 <listitem> 583 <para>Select one or more ArraySlides and click <guibutton>Delete</guibutton> 584 button in the menu bar. </para> 585 <para>All the selected ArraySlides have been marked as deleted and are no longer 586 available from the interface. </para> 587 <para>Only by selecting from the <guilabel>view/preset…</guilabel> 588 select box the <guilabel>Removed</guilabel> option, one can see those of the 589 ArraySlides earmarked for deletion. They will be shown with a symbol <inlinemediaobject> 590 <imageobject> 591 <imagedata fileref="figures/deleted.gif" format="GIF"/> 592 </imageobject> 593 </inlinemediaobject> in front of them. </para> 594 </listitem> 595 <listitem> 596 <para>Alternately, navigating to the ArraySlide Item View, one can hit the 597 <guibutton>Delete</guibutton> to performed the task. </para> 598 </listitem> 599 <listitem> 600 <para>Deletion errors at this stage can be easily recovered. Select the item to 601 recover from the List View (be sure to check the 602 <guilabel>Removed</guilabel> option in the 603 <guilabel>view/preset…</guilabel> filter) and hit the 604 <guibutton>Restore</guibutton> button to performed the task. </para> 605 </listitem> 606 </itemizedlist> 607 <important> 608 <para>To really delete an item from the database you must use the trashcan. Items 609 deleted from the Trashcan can not be recovered. To learn more about the trashcan 610 function, please refer to <xref linkend="trashcan"/> 611 </para> 612 </important> 613 </sect2> 614 615 616 </sect1> 617 36 618 </chapter>
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