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1<?xml version="1.0" encoding="UTF-8"?>
2<!DOCTYPE chapter PUBLIC
3    "-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN"
4    "../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd">
5<!--
6  $Id: biomaterials.xml 3399 2007-05-28 15:18:03Z martin $
7 
8  Copyright (C) Authors contributing to this file.
9 
10  This file is part of BASE - BioArray Software Environment.
11  Available at http://base.thep.lu.se/
12 
13  BASE is free software; you can redistribute it and/or
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16  of the License, or (at your option) any later version.
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18  BASE is distributed in the hope that it will be useful,
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23  You should have received a copy of the GNU General Public License
24  along with this program; if not, write to the Free Software
25  Foundation, Inc., 59 Temple Place - Suite 330,
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27-->
28<chapter id="biomaterials">
29  <?dbhtml dir="biomaterials"?>
30  <title>Biomaterials</title>
31  <sect1 id="biomaterial.introduction">
32    <title>Introduction</title>
33    <para>
34      The generic term biomaterial refers to any biological material used in an experiment.
35      biomaterials are subdivided in 4 components, biosource, sample, extract and labeled
36      extract. The order use in presenting those entities is not inocuous as it represents the
37      sequence of transformation a source material undergoes until it is in a state compatible
38      with the realization of a microarray hybridization. This progression is actually
39      mimicked in the BASE2
40      <guimenu>View</guimenu>
41      menu again to insist on this natural progression.
42    </para>
43    <para>
44      Biosources correspond to the native biological entity used in an experiment prior to any
45      treatment.
46    </para>
47    <para>
48      Samples are central to BASE2 to describe the sample processing. So samples can be
49      created from other samples if user want to track sample processing event in a finely
50      granular fashion.
51    </para>
52    <para>
53      Extracts correspond to nucleic acid material extracted from a tissue sample or a cell
54      culture sample.
55    </para>
56    <para>
57      Labeled extracts correspond to nucleic acid materials which have undergone a marking
58      procedure using a fluorescent or radioactive compound for detection in a microarray
59      assay.
60    </para>
61    <para>
62      BASE2 allows users to create any of the these entities fairly freely, however it is
63      expected that users will follow the natural path of the laboratory workflow.
64    </para>
65    <tip>
66      <para>
67        It is highly recommended that you have read
68        <xref linkend="webclient.items" />
69        before continuing with this chapter.
70      </para>
71    </tip>
72  </sect1>
73  <sect1 id="biomaterial.biosources">
74    <title>Biosources</title>
75    <para>
76      Go to
77      <menuchoice>
78        <guimenu>View</guimenu>
79        <guimenuitem>Biosources</guimenuitem>
80      </menuchoice>
81      .
82    </para>
83    <itemizedlist>
84      <listitem>
85        <para>
86          <guilabel>Biosource</guilabel>
87        </para>
88        <helptext external_id="biosources.edit" title="Edit biosources">
89          <para>
90            This tab allows users to enter essential information about a biosource.
91          </para>
92          <variablelist>
93            <varlistentry>
94              <term>
95                <guilabel>Name</guilabel>
96              </term>
97              <listitem>
98                <para>
99                  This is the only mandatory field. BASE2 by default assigns
100                  <replaceable>New Biosource</replaceable>
101                  as name but it is advised to provide unique sensible names.
102                </para>
103              </listitem>
104            </varlistentry>
105            <varlistentry>
106              <term>
107                <guilabel>External id</guilabel>
108              </term>
109              <listitem>
110                <para>
111                  An external reference identifiers (e.g. a patient identification
112                  code) can be supplied using this field.
113                </para>
114              </listitem>
115            </varlistentry>
116            <varlistentry>
117              <term>
118                <guilabel>Description</guilabel>
119              </term>
120              <listitem>
121                <para>
122                  A free text description can be supplied using this field.
123                </para>
124              </listitem>
125            </varlistentry>
126          </variablelist>
127          <para>
128            Change tab to
129            <guilabel>Annotations</guilabel>
130            if you want annotate the biosource, otherwise close the pop-up window by
131            either clicking on the &gbSave; button to store the information in BASE2 or
132            on the &gbCancel; button to abort.
133          </para>
134        </helptext>
135        <nohelp>
136          <figure id="write_docbook_doc.figures.biosource-tab-1">
137            <title>
138              The
139              <guilabel>Biosource</guilabel>
140              tab
141            </title>
142            <screenshot>
143              <mediaobject>
144                <imageobject>
145                  <imagedata contentwidth="10cm" width="10cm"
146                    fileref="figures/biosource-tab-1.png" format="PNG" />
147                </imageobject>
148              </mediaobject>
149            </screenshot>
150          </figure>
151        </nohelp>
152      </listitem>
153      <listitem>
154        <para>
155          <guilabel>Annotations</guilabel>
156        </para>
157        <para>
158          This tab allows BASE2 users to use annotation types to refine biosource
159          description.
160        </para>
161        <para>
162          A list of annotation types that are owned by or shared to you will be displayed.
163        </para>
164        <important>
165          <para>
166            In order to use this feature, annotation type must be declared and made
167            available. To learn more about annotation types, please refer to
168            <xref linkend="annotations" />
169          </para>
170        </important>
171        <para>
172          See
173          <xref linkend="annotations.annotating" />
174          to get more information on how to set annotation types.
175        </para>
176      </listitem>
177    </itemizedlist>
178    <para>
179      Click on the &gbSave; button to store the information in BASE2 or on the &gbCancel;
180      button to abort.
181    </para>
182
183    <sect2 id="biomaterial.biosource.manage.detail_view">
184      <title>Viewing biosources</title>
185      <para>
186        From the biosource list view, clicking on the biosource
187        <guilabel>Name</guilabel>
188        opens a detailed view for that biosource, showing a summary of all information
189        available in BASE2 about that particular entity.
190      </para>
191      <para>
192        The default behavior opens the detailed view on the
193        <guilabel>Properties</guilabel>
194        tab, which shows a summary information and displays the list of samples derived from
195        a biosource, if any.
196      </para>
197      <figure id="write_docbook_doc.figures.biosource-itemview-prop">
198        <title>BioSource Item View, properties tab</title>
199        <screenshot>
200          <mediaobject>
201            <imageobject>
202              <imagedata contentwidth="12cm" width="12cm"
203                fileref="figures/biosource-itemview-prop.png" format="PNG" />
204            </imageobject>
205          </mediaobject>
206        </screenshot>
207      </figure>
208      <para>
209        By clicking on the
210        <guilabel>Annotations</guilabel>
211        tab, users can display the list of Annotation Types used to annotate a Biosource.
212      </para>
213      <figure id="write_docbook_doc.figures.biosource-itemview-annot">
214        <title>BioSource Item View, annotations tab</title>
215        <screenshot>
216          <mediaobject>
217            <imageobject>
218              <imagedata contentwidth="13cm" width="13cm"
219                fileref="figures/biosource-itemview-annot.png" format="PNG" />
220            </imageobject>
221          </mediaobject>
222        </screenshot>
223      </figure>
224      <para>
225        Clicking the
226        <inlinemediaobject>
227          <imageobject>
228            <imagedata fileref="figures/edit.gif" format="GIF" />
229          </imageobject>
230        </inlinemediaobject>
231        <guiicon>edit icon</guiicon>
232        in the
233        <interface>value</interface>
234        for any of the annotations (e.g. 'antibiotic' in our example), opens an Annotate
235        window (which is a BioSource Edit window set on the annotation tab) and highlights
236        the selected Annotation Type, prompting for data entry.
237      </para>
238      <figure id="write_docbook_doc.figures.biosource-itemview-annot-edit">
239        <title>BioSource annotations edit</title>
240        <screenshot>
241          <mediaobject>
242            <imageobject>
243              <imagedata contentwidth="12cm" width="12cm"
244                fileref="figures/biosource-itemview-annot-edit.png" format="PNG" />
245            </imageobject>
246          </mediaobject>
247        </screenshot>
248      </figure>
249      <para>
250        The relevant Annotation Type is highlighted and a list of possible values is
251        displayed.
252      </para>
253      <para>
254        Again, all Annotation types marked with a
255        <inlinemediaobject>
256          <imageobject>
257            <imagedata fileref="figures/annotated.gif" format="GIF" />
258          </imageobject>
259        </inlinemediaobject>
260        symbol have been used to provided information.
261      </para>
262      <para>
263        Click on the &gbSave; button to store the information in BASE2 or on the &gbCancel;
264        button to abort.
265      </para>
266    </sect2>
267  </sect1>
268  <sect1 id="sample.manage">
269    <title>Managing Samples</title>
270    <para>
271      Samples result from processing events applied to
272      <guilabel>BioSource</guilabel>
273      material or other
274      <guilabel>Samples</guilabel>
275      before they are turned into an
276      <guilabel>Extract</guilabel>
277      .
278    </para>
279    <para>
280      In other words, Samples can be created from BioSource items or from one or more Sample
281      items.
282    </para>
283    <para>
284      When a Sample is created from several other Samples, a 'pooling' event is performed. A
285      specific section details how to create pools, refer to
286      <xref linkend="sample.manage.createsample.pool" />
287    </para>
288    <para>
289      For every step of transformation from BioSource to Sample, it is possible to provide
290      information about the protocol used to perform this task. It is not enforced in BASE2
291      but it should serve as guidance when devising the granularity of the sample processing
292      task. Also, it is good practice to provide protocol information to ensure MIAME
293      compliance.
294    </para>
295    <sect2 id="sample.manage.createsamplefrombiosource">
296      <title>Creating Samples</title>
297      <orderedlist>
298        <listitem>
299          <para>Creating Samples from the BioSource page</para>
300          <para>
301            No matter how complex the sample processing phase is, at least one Sample
302            has to be anchored to a BioSource.
303          </para>
304          <para>
305            Therefore, a natural way to create a Sample is to click on the
306            <inlinemediaobject>
307              <imageobject>
308                <imagedata fileref="figures/add.gif" format="GIF" />
309              </imageobject>
310            </inlinemediaobject>
311            <guibutton>Create new Sample</guibutton>
312            from the Sample column of the BioSource list view.
313          </para>
314          <figure id="write_docbook_doc.figures.biosource-create-sample">
315            <title>Creating a Sample from the BioSource list view</title>
316            <screenshot>
317              <mediaobject>
318                <imageobject>
319                  <imagedata contentwidth="13cm" width="13cm"
320                    fileref="figures/biosource-create-sample.png" format="PNG" />
321                </imageobject>
322              </mediaobject>
323            </screenshot>
324          </figure>
325        </listitem>
326        <listitem>
327          <para>Creating Samples from the Sample List view page</para>
328          <para>
329            This is the alternative for creating Sample from the BioSource. To do so, go
330            to
331            <menuchoice>
332              <guimenu>View</guimenu>
333              <guimenuitem>BioSamples</guimenuitem>
334            </menuchoice>
335            , Click on &gbNew; button
336          </para>
337          <para>
338            A 'Create' pop-up window opens, it contains 4 tabs:
339            <guilabel>Sample</guilabel>
340            ,
341            <guilabel>Parents</guilabel>
342            ,
343            <guilabel>Annotations &amp; parameters</guilabel>
344            and
345            <guilabel>Inherited Annotations</guilabel>
346            .
347          </para>
348          <itemizedlist>
349            <listitem>
350              <para>The Sample Tab</para>
351              <para>
352                This tab contains 1 mandatory field for providing the Sample
353                <guilabel>Name</guilabel>
354                . BASE2 by default assigns names to Samples (by suffixing 's#' when
355                creating a Sample from an existing Biosource or 'New Sample'
356                otherwise) but it is possible to edit at will.
357              </para>
358              <para>
359                There are 5 optional fields to provide more detailed information
360              </para>
361              <itemizedlist>
362                <listitem>
363                  <para>
364                    <guilabel>External ID</guilabel>
365                    : for instance to report a barcode attached to a Sample
366                  </para>
367                </listitem>
368                <listitem>
369                  <para>
370                    <guilabel>Original Quantity (ug)</guilabel>
371                    : this is meant to report information about the actual mass
372                    of biomaterial created
373                  </para>
374                </listitem>
375                <listitem>
376                  <para>
377                    <guilabel>Created</guilabel>
378                    : a date should be provided. The information can be
379                    important when running quality controls on data and account
380                    for potential confounding factor (e.g. day effect)
381                  </para>
382                </listitem>
383                <listitem>
384                  <para>
385                    <guilabel>Protocol</guilabel>
386                    : this a controled field. A select-list displays protocols
387                    whose type is
388                    <guilabel>sampling</guilabel>
389                    and which are shared to or owned by the logged-in user.
390                  </para>
391                  <important>
392                    <para>
393                      It is not mandatory to supply protocol in BASE2
394                      Reporting protocols is a MIAME requirement
395                    </para>
396                  </important>
397                </listitem>
398                <listitem>
399                  <para>
400                    <guilabel>Description</guilabel>
401                    : a free text field to report any information that not can
402                    be captured otherwise
403                  </para>
404                </listitem>
405              </itemizedlist>
406              <para>
407                Finally, a 7th field,
408                <guilabel>Registered</guilabel>
409                is automatically populated with a date at which the Sample was
410                entered in BASE2 system.
411              </para>
412              <figure id="write_docbook_doc.figures.biosample-tab-1">
413                <title>Sample tab</title>
414                <screenshot>
415                  <mediaobject>
416                    <imageobject>
417                      <imagedata contentwidth="10cm" width="10cm"
418                        fileref="figures/biosample-tab-1.png" format="PNG" />
419                    </imageobject>
420                  </mediaobject>
421                </screenshot>
422              </figure>
423            </listitem>
424            <listitem>
425              <para>The Parents Tab</para>
426              <para>
427                This important tab does what it says on the tin: It is meant to keep
428                track of the Sample origin. BASE2 distinguished between 2 cases
429                which are controled by the
430                <guibutton>pooled</guibutton>
431                radio-button
432              </para>
433              <orderedlist>
434                <listitem>
435                  <para>The Parent is a BioSource</para>
436                  <para>
437                    The
438                    <guibutton>Pooled</guibutton>
439                    radio-button is set to
440                    <guilabel>No</guilabel>
441                  </para>
442                  <para>
443                    The BioSource select button is active and allows users to
444                    point to one and only one BioSource from which the Sample
445                    originates from.
446                  </para>
447                  <figure
448                    id="write_docbook_doc.figures.biosample-tab-2-select-biosource">
449                    <title>
450                      Parent tab and interaction when pooled button is set to
451                      No
452                    </title>
453                    <screenshot>
454                      <mediaobject>
455                        <imageobject>
456                          <imagedata contentwidth="12cm" width="12cm"
457                            fileref="figures/biosample-tab-2-select-biosource.png" format="PNG" />
458                        </imageobject>
459                      </mediaobject>
460                    </screenshot>
461                  </figure>
462                </listitem>
463                <listitem>
464                  <para>The Parent is another Sample</para>
465                  <para>
466                    The
467                    <guibutton>Pooled</guibutton>
468                    radio-button has to be set to
469                    <guilabel>Yes</guilabel>
470                  </para>
471                  <para>
472                    Upon selection, the BioSource select button is deactivated
473                    and the Samples box and button are activated.
474                  </para>
475                  <para>
476                    This allows users to specify one or more Samples to be
477                    selected from the Sample List View page.
478                  </para>
479                  <figure
480                    id="write_docbook_doc.figures.biosample-tab-2-select-sample">
481                    <title>
482                      Parent tab and interaction when pooled button is set to
483                      Yes
484                    </title>
485                    <screenshot>
486                      <mediaobject>
487                        <imageobject>
488                          <imagedata contentwidth="12cm" width="12cm"
489                            fileref="figures/biosample-tab-2-select-sample.png" format="PNG" />
490                        </imageobject>
491                      </mediaobject>
492                    </screenshot>
493                  </figure>
494                </listitem>
495              </orderedlist>
496            </listitem>
497            <listitem>
498              <para>Annotations &amp; parameters</para>
499              <para>
500                As seen in the BioSource section, this tab allows users to further
501                supply information about the Sample provided they have defined or
502                shared annotation types to annotate Sample items.
503              </para>
504              <para>
505                The display of Annotation Type can be filtered based on the
506                Annotation Type Category they belong to.
507              </para>
508              <important>
509                <para>
510                  In order to use this feature, Annotation Type must be declared
511                  and made available. To learn more about Annotation Types, please
512                  refer to
513                  <xref linkend="annotations" />
514                </para>
515              </important>
516              <para>
517                To provide a value for a given annotation type, simply click on it
518                an use the input field or select a value from the drop-down lists or
519                radio buttons.
520              </para>
521              <figure id="write_docbook_doc.figures.biosample-tab-3">
522                <title>Annotations &amp; parameters</title>
523                <screenshot>
524                  <mediaobject>
525                    <imageobject>
526                      <imagedata contentwidth="12cm" width="12cm"
527                        fileref="figures/biosample-tab-3.png" format="PNG" />
528                    </imageobject>
529                  </mediaobject>
530                </screenshot>
531              </figure>
532            </listitem>
533            <listitem>
534              <para>Inherited Annotations case1</para>
535              <para>The next picture shows</para>
536              <figure id="write_docbook_doc.figures.biosample-tab-4">
537                <title>Inherited Annotations</title>
538                <screenshot>
539                  <mediaobject>
540                    <imageobject>
541                      <imagedata contentwidth="12cm" width="12cm"
542                        fileref="figures/biosample-tab-4.png" format="PNG" />
543                    </imageobject>
544                  </mediaobject>
545                </screenshot>
546              </figure>
547              <para>Inherited Annotations case2</para>
548              <figure id="write_docbook_doc.figures.biosample-tab-4bis">
549                <title>Inherited Annotations</title>
550                <screenshot>
551                  <mediaobject>
552                    <imageobject>
553                      <imagedata contentwidth="12cm" width="12cm"
554                        fileref="figures/biosample-tab-4bis.png" format="PNG" />
555                    </imageobject>
556                  </mediaobject>
557                </screenshot>
558              </figure>
559            </listitem>
560          </itemizedlist>
561        </listitem>
562      </orderedlist>
563    </sect2>
564    <sect2 id="sample.manage.createsample.pool">
565      <title>Creating Pooled Samples</title>
566      <para>
567        It is common practice when biological material is scarce to pool Samples from
568        equivalent sources. BASE2 provides mechanisms to report on such practice.
569      </para>
570      <para>This section details how.</para>
571      <para>There are 2 ways to create Pooled Samples in BASE2</para>
572      <orderedlist>
573        <listitem>
574          <para>
575            Using the Pooled radio button option from the Sample Create page, and this
576            has been shown already
577          </para>
578        </listitem>
579        <listitem>
580          <para>Using the Pool button in the Menu bar</para>
581          <para>
582            The Sample List View page menu bar contains an additionnal button the usage
583            of which is detailed now.
584          </para>
585          <para>
586            The &gbPool; button
587            <inlinemediaobject>
588              <imageobject>
589                <imagedata fileref="figures/new_pooled.gif" format="GIF" />
590              </imageobject>
591            </inlinemediaobject>
592            allows users to create Pooled Samples by selecting the list of Samples used
593            to produce that new Sample.
594          </para>
595          <para>
596            Users simply need to tick the select-boxes in front of each relevant Sample
597            and click the
598            <inlinemediaobject>
599              <imageobject>
600                <imagedata fileref="figures/new_pooled.gif" format="GIF" />
601              </imageobject>
602            </inlinemediaobject>
603            button.
604          </para>
605          <para>
606            This provides an easy and simple way to create Pooled Samples. The result of
607            such process is the creation of a New Sample, which Parent Samples are
608            listing and preset in the Parent tab
609          </para>
610          <figure id="write_docbook_doc.figures.biosample-tab-2-pool-sample">
611            <title>Pooling of Samples</title>
612            <screenshot>
613              <mediaobject>
614                <imageobject>
615                  <imagedata contentwidth="12cm" width="12cm"
616                    fileref="figures/biosample-tab-2-pool-sample.png" format="PNG" />
617                </imageobject>
618              </mediaobject>
619            </screenshot>
620          </figure>
621        </listitem>
622      </orderedlist>
623    </sect2>
624    <sect2 id="sample.manage.delete">
625      <title>Deleting/Restoring Samples</title>
626      <para>
627        As for other items in BASE2, Samples can be removed. For a generic overview on how
628        to delete and restore items, refer to section
629        <xref linkend="webclient.items.delete" />
630      </para>
631      <para>To delete, do the following</para>
632      <itemizedlist>
633        <listitem>
634          <para>
635            Select one or more Samples and click &gbDelete; button in the menu bar.
636          </para>
637          <para>
638            All the selected Samples have been marked as deleted and are no longer
639            available from the interface.
640          </para>
641          <para>
642            From the
643            <guilabel>view/preset&hellip;</guilabel>
644            select box, ticking the
645            <guilabel>Removed</guilabel>
646            option allows to display those Samples earmarked for deletion. They will be
647            shown with a symbol
648            <guiicon>D</guiicon>
649            in front of them.
650          </para>
651        </listitem>
652        <listitem>
653          <para>
654            Alternately, navigating to the Sample Item View, one can hit the &gbDelete;
655            to performed the task. As showen in the next picture, the Sample is then
656            flagged with the
657            <guiicon>This item has been flagged for deletion</guiicon>
658          </para>
659          <figure id="write_docbook_doc.figures.sample-delete">
660            <title>Deleting Samples from the Item View</title>
661            <screenshot>
662              <mediaobject>
663                <imageobject>
664                  <imagedata contentwidth="12cm" width="12cm"
665                    fileref="figures/sample-delete.png" format="PNG" />
666                </imageobject>
667              </mediaobject>
668            </screenshot>
669          </figure>
670        </listitem>
671        <listitem>
672          <para>
673            Deletion errors can be easily recovered. Select the item to recover from the
674            List View (be sure to check the
675            <guilabel>removed</guilabel>
676            option in the View/preset.. filter) and hit the &gbRestore; to performed the
677            task.
678          </para>
679        </listitem>
680      </itemizedlist>
681      <important>
682        <para>
683          To really delete an item from the database you must use the trashcan. Items
684          deleted from the Trashcan can not be recovered. To learn more about the trashcan
685          function, please refer to
686          <xref linkend="trashcan" />
687        </para>
688      </important>
689    </sect2>
690  </sect1>
691
692  <sect1 id="extract.manage">
693    <title>Managing Extracts</title>
694    <para>
695      Extract items should be used to describe the events that transform a Sample material in
696      an Extract material.
697    </para>
698    <para>Extracts can be created from Sample items or from one or more Extract items.</para>
699    <para>
700      When an Extract is created from several other Extracts, a Pooling event is performed. A
701      specific section details how to create pooled Extracts
702    </para>
703    <para>
704      During the transformation from Samples to Extracts, it is possible to provide
705      information about the protocol used to perform this task.
706    </para>
707    <para>
708      It is not enforced in BASE2 but it should serve as guidance when devising the
709      granularity of the sample processing task. Also, it is good practice to provide protocol
710      information.
711    </para>
712    <sect2 id="extract.manage.createextractfromsample">
713      <title>Creating Extracts</title>
714      <orderedlist>
715        <listitem>
716          <para>Creating Extracts from the Sample page</para>
717          <para>
718            Following the laboratory workflow, a natural way to create a new Extract is
719            to click on the
720            <guibutton>New extract</guibutton>
721            from the Extract column of the Sample List View.
722          </para>
723          <figure id="write_docbook_doc.figures.sample-create-extract">
724            <title>Creating an Extract from the Sample list view</title>
725            <screenshot>
726              <mediaobject>
727                <imageobject>
728                  <imagedata contentwidth="12cm" width="12cm"
729                    fileref="figures/sample-create-extract.png" format="PNG" />
730                </imageobject>
731              </mediaobject>
732            </screenshot>
733          </figure>
734        </listitem>
735        <listitem>
736          <para>Creating Extracts from the Sample List view page</para>
737          <para>
738            Alternately, Extracts can be created directly ysing the Extract create page.
739            To do so, go to
740            <menuchoice>
741              <guimenu>View</guimenu>
742              <guimenuitem>Extracts</guimenuitem>
743            </menuchoice>
744            , Click on &gbNew; button
745          </para>
746          <para>
747            A 'Create' pop-up window opens, it contains 4 tabs:
748            <guilabel>Extract</guilabel>
749            ,
750            <guilabel>Parents</guilabel>
751            ,
752            <guilabel>Annotations &amp; parameters</guilabel>
753            and
754            <guilabel>Inherited Annotations</guilabel>
755            .
756          </para>
757          <itemizedlist>
758            <listitem>
759              <para>The Extract Tab</para>
760              <para>
761                This tab contains 1 mandatory field for providing the extract name.
762              </para>
763              <para>
764                BASE2 by default assigns names to Extract (by suffixing 'e#' when
765                creating an Extract from an existing Sample or 'New Extract'
766                otherwise) but it is possible to edit it at will
767              </para>
768              <para>
769                There 5 optional fields to provide more detailed information
770              </para>
771              <itemizedlist>
772                <listitem>
773                  <para>
774                    <guilabel>External ID</guilabel>
775                    : for instance to report a barcode attached to an extract
776                  </para>
777                </listitem>
778                <listitem>
779                  <para>
780                    <guilabel>Original Quantity (ug)</guilabel>
781                    : this is meant to report information about the actual mass
782                    of biomaterial created
783                  </para>
784                </listitem>
785                <listitem>
786                  <para>
787                    <guilabel>Created</guilabel>
788                    : a date should be provided. The information can be
789                    important when running quality controls on data and account
790                    for potential confounding factor (e.g. day effect)
791                  </para>
792                </listitem>
793                <listitem>
794                  <para>
795                    <guilabel>Protocol</guilabel>
796                    : this a controled field. A select-list displays protocol
797                    whose type is '
798                    <guilabel>extraction</guilabel>
799                    ' and which are shared to or owned by the logged-in user.
800                    Reporting Protocol should be viewed as a MIAME requirement
801                  </para>
802                </listitem>
803                <listitem>
804                  <para>
805                    <guilabel>Description</guilabel>
806                    : a free text field to report any information that not can
807                    be captured otherwise
808                  </para>
809                </listitem>
810              </itemizedlist>
811              <para>
812                Finally, a 7th field
813                <guilabel>Registered</guilabel>
814                is automatically populated with a date at which the sample was
815                entered in BASE2 system.
816              </para>
817              <figure id="write_docbook_doc.figures.extract-tab-1">
818                <title>Extract tab</title>
819                <screenshot>
820                  <mediaobject>
821                    <imageobject>
822                      <imagedata contentwidth="12cm" width="12cm"
823                        fileref="figures/extract-tab-1.png" format="PNG" />
824                    </imageobject>
825                  </mediaobject>
826                </screenshot>
827              </figure>
828            </listitem>
829            <listitem>
830              <para>The Parents Tab</para>
831              <para>
832                This important tab allows users to select the Extract origin. BASE2
833                distinguished between 2 cases which are controled by the
834                <guibutton>'pooled'</guibutton>
835                radio-button
836              </para>
837              <orderedlist>
838                <listitem>
839                  <para>The Parent is a Sample</para>
840                  <para>
841                    The
842                    <guibutton>pooled</guibutton>
843                    radio-button is set to
844                    <guilabel>No</guilabel>
845                  </para>
846                  <para>
847                    The Sample select button is active and allows users to point
848                    to one and only one Sample from which the sample originates
849                    from.
850                  </para>
851                  <figure
852                    id="write_docbook_doc.figures.extract-tab-2-select-sample">
853                    <title>
854                      Parent tab and interaction when pooled button is set to
855                      No
856                    </title>
857                    <screenshot>
858                      <mediaobject>
859                        <imageobject>
860                          <imagedata contentwidth="12cm" width="12cm"
861                            fileref="figures/extract-tab-2-select-sample.png" format="PNG" />
862                        </imageobject>
863                      </mediaobject>
864                    </screenshot>
865                  </figure>
866                </listitem>
867                <listitem>
868                  <para>The Parent is another Extract</para>
869                  <para>
870                    The
871                    <guibutton>pooled</guibutton>
872                    radio-button has to be set to
873                    <guilabel>Yes</guilabel>
874                  </para>
875                  <para>
876                    Upon selection, the Samples select button is deactivated and
877                    the Extracts box and button are activated.
878                  </para>
879                  <para>
880                    This allows users to specify one or more extracts to be
881                    selected from the Extract list View page.
882                  </para>
883                  <figure
884                    id="write_docbook_doc.figures.extract-tab-2-select-extract">
885                    <title>
886                      Parent tab and interaction when pooled button is set to
887                      Yes
888                    </title>
889                    <screenshot>
890                      <mediaobject>
891                        <imageobject>
892                          <imagedata contentwidth="12cm" width="12cm"
893                            fileref="figures/extract-tab-2-select-extract.png" format="PNG" />
894                        </imageobject>
895                      </mediaobject>
896                    </screenshot>
897                  </figure>
898                </listitem>
899              </orderedlist>
900            </listitem>
901            <listitem>
902              <para>Annotations &amp; parameters</para>
903              <para>
904                As seen in the BioSource and Sample sections, this tab allows users
905                to supply further information about the Extract, provided they have
906                defined Annotation Types to annotation Extract items or have such
907                elements shared to them.
908              </para>
909              <para>
910                The display of Annotation Type can be filtered based on the
911                Annotation Type Category they belong to.
912              </para>
913              <important>
914                <para>
915                  In order to use this feature, Annotation Type must be declared
916                  and made available. To learn more about Annotation Types, please
917                  refer to
918                  <xref linkend="annotations" />
919                </para>
920              </important>
921              <para>
922                To provide a value for a given annotation type, simply click on it
923                an use the input field or select a value from the drop-down lists or
924                radio buttons.
925              </para>
926              <figure id="write_docbook_doc.figures.extract-tab-3">
927                <title>Annotations &amp; parameters</title>
928                <screenshot>
929                  <mediaobject>
930                    <imageobject>
931                      <imagedata contentwidth="12cm" width="12cm"
932                        fileref="figures/extract-tab-3.png" format="PNG" />
933                    </imageobject>
934                  </mediaobject>
935                </screenshot>
936              </figure>
937            </listitem>
938            <listitem>
939              <para>Inherited Annotations case1</para>
940              <para>The next picture shows</para>
941              <figure id="write_docbook_doc.figures.extract-tab-4">
942                <title>Inherited Annotations</title>
943                <screenshot>
944                  <mediaobject>
945                    <imageobject>
946                      <imagedata contentwidth="12cm" width="12cm"
947                        fileref="figures/extract-tab-4.png" format="PNG" />
948                    </imageobject>
949                  </mediaobject>
950                </screenshot>
951              </figure>
952            </listitem>
953          </itemizedlist>
954        </listitem>
955      </orderedlist>
956    </sect2>
957    <sect2 id="extract.manage.createextractpool">
958      <title>Creating Pooled Extracts</title>
959      <para>
960        It is common practice when biological material is scarce to pool extracts from
961        equivalent sources. BASE2 provides mechanisms to report on such practice. This
962        section details how.
963      </para>
964      <para>There are 2 ways to create pooled samples in BASE2:</para>
965      <orderedlist>
966        <listitem>
967          <para>
968            Using the Pooled radio button option from the Extract Create page, and this
969            has been shown already.
970          </para>
971        </listitem>
972        <listitem>
973          <para>Using the Pool button in the Menu bar</para>
974          <para>
975            The Sample List View page menu bar contains an addition &gbPool;
976            <inlinemediaobject>
977              <imageobject>
978                <imagedata fileref="figures/new_pooled.gif" format="GIF" />
979              </imageobject>
980            </inlinemediaobject>
981            button, the usage of which is detailed now.
982          </para>
983          <para>
984            The &gbPool;
985            <inlinemediaobject>
986              <imageobject>
987                <imagedata fileref="figures/new_pooled.gif" format="GIF" />
988              </imageobject>
989            </inlinemediaobject>
990            button allows users to create Pooled Extracts by selecting the list of
991            Extracts used to derived a new Extract. Users simply to tick to boxes in
992            front of each relevant Extract and click the
993            <guibutton>Pool...</guibutton>
994          </para>
995          <para>
996            This provides an easy and simple way to create pooled Extracts. The result
997            of such process is the creation of a New Extract, in which, when navigating
998            to the Parent tab, shows that all the Extracts involved are already set and
999            listed in the Extract box of the tab.
1000          </para>
1001          <figure id="write_docbook_doc.figures.biosample-tab-2-pool-extract">
1002            <title>Pooling of Extracts</title>
1003            <screenshot>
1004              <mediaobject>
1005                <imageobject>
1006                  <imagedata contentwidth="12cm" width="12cm"
1007                    fileref="figures/extract-tab-2-pool-extract.png" format="PNG" />
1008                </imageobject>
1009              </mediaobject>
1010            </screenshot>
1011          </figure>
1012        </listitem>
1013      </orderedlist>
1014    </sect2>
1015    <sect2 id="extract.manage.delete">
1016      <title>Deleting/Restoring Extracts</title>
1017      <para>
1018        As for other items in BASE2, Extracts can be removed. For a generic overview on how
1019        to delete and restore items, refer to section
1020        <xref linkend="webclient.items.delete" />
1021      </para>
1022      <para>To delete, do the following</para>
1023      <itemizedlist>
1024        <listitem>
1025          <para>
1026            Select one or more Extract and click &gbDelete; button in the menu bar.
1027          </para>
1028          <para>
1029            All the selected Extracts have been marked as deleted and are no longer
1030            available from the interface.
1031          </para>
1032          <para>
1033            Only by selecting from the
1034            <guilabel>view/preset&hellip;</guilabel>
1035            select box the
1036            <guilabel>Removed</guilabel>
1037            option, one can see those of the Extracts earmarked for deletion. They will
1038            be shown with a symbol in front of them.
1039          </para>
1040        </listitem>
1041        <listitem>
1042          <para>
1043            Alternately, navigating to the Extract Item View, one can hit the &gbDelete;
1044            to performed the task.
1045          </para>
1046          <para>
1047            As shown in the next picture, the Extract is then marked with the
1048            <guilabel>This item has been flagged for deletion</guilabel>
1049          </para>
1050          <figure id="write_docbook_doc.figures.extract-delete">
1051            <title>Deleting Extracts from the Item View</title>
1052            <screenshot>
1053              <mediaobject>
1054                <imageobject>
1055                  <imagedata contentwidth="12cm" width="12cm"
1056                    fileref="figures/extract-delete.png" format="PNG" />
1057                </imageobject>
1058              </mediaobject>
1059            </screenshot>
1060          </figure>
1061        </listitem>
1062        <listitem>
1063          <para>
1064            Deletion errors at this stage can be easily recovered. Select the item to
1065            recover from the List View (be sure to check the
1066            <guilabel>removed</guilabel>
1067            option in the View/preset.. filter) and hit the &gbRestore; to performed the
1068            task.
1069          </para>
1070        </listitem>
1071      </itemizedlist>
1072      <important>
1073        <para>
1074          To really delete an item from the database you must use the trashcan. Items
1075          deleted from the Trashcan can not be recovered. To learn more about the trashcan
1076          function, please refer to
1077          <xref linkend="trashcan" />
1078        </para>
1079      </important>
1080    </sect2>
1081  </sect1>
1082
1083
1084
1085  <sect1 id="label">
1086    <title>Managing Labels</title>
1087
1088    <sect2 id="label.browse">
1089      <title>Browsing Labels</title>
1090      <para>
1091        Before attempting to create Labeled Extracts, users should make sure that the
1092        appropriate Label object is present in BASE2
1093      </para>
1094      <para>
1095        To browse the list of Labels, go to
1096        <menuchoice>
1097          <guimenu>View</guimenu>
1098          <guimenuitem>Labels</guimenuitem>
1099        </menuchoice>
1100        It is wise to select the clear filter option or select the
1101        <guilabel>shared to me</guilabel>
1102        option from the view/preset select box in order to view all different dyes.
1103      </para>
1104      <para>Clicking on any of item opens an item view page</para>
1105      <figure id="write_docbook_doc.figures.label-itemview">
1106        <title>The Label Item View Page</title>
1107        <screenshot>
1108          <mediaobject>
1109            <imageobject>
1110              <imagedata contentwidth="12cm" width="12cm"
1111                fileref="figures/label-itemview.png" format="PNG" />
1112            </imageobject>
1113          </mediaobject>
1114        </screenshot>
1115      </figure>
1116      <para>
1117        Note the
1118        <guibutton>New labeled extract&hellip;</guibutton>
1119        button available from this page. For more detailed about creating Labeled extracts,
1120        see
1121        <xref linkend="labeledextract.manage" />
1122      </para>
1123
1124    </sect2>
1125    <sect2 id="label.create">
1126      <title>Creating Labels</title>
1127      <para>
1128        Click on &gbNew; button, a pop-up window opens. Fill in Name and description if
1129        required. Label item are very simple object and do not bear association to
1130        Annotation Type.
1131      </para>
1132    </sect2>
1133  </sect1>
1134  <sect1 id="labeledextract.manage">
1135    <title>Managing Labeled Extracts</title>
1136    <para>
1137      Labeled Extract items should be used to describe the event that transformed a Extract
1138      material in a Labeled Extract material.
1139    </para>
1140    <para>
1141      Labeled extracts can be created from Extract items or from one or more Labeled extract
1142      items.
1143    </para>
1144    <para>
1145      When a Labeled Extract is created from several other Labeled Extracts, a Pooling event
1146      is performed. A specific section details how to create pooled Labeled Extracts
1147    </para>
1148    <para>
1149      During the transformation from Extracts to Labeled Extracts, it is possible to provide
1150      information about the protocol used to perform this task.
1151    </para>
1152    <para>
1153      It is not enforced in BASE2 but it should serve as guidance when devising the
1154      granularity of the extract processing task. Also, it is good practice to provide
1155      protocol information.
1156    </para>
1157    <sect2 id="labeledextract.manage.createlabeledextractfromextract">
1158      <title>Creating Labeled Extracts</title>
1159      <orderedlist>
1160        <listitem>
1161          <para>Creating Labeled Extracts from the Extract page</para>
1162          <para>
1163            Following the laboratory workflow, a natural way to create a Labeled Extract
1164            is to click on the
1165            <guibutton>New labeled extract</guibutton>
1166            from the Labeled Extract column of the Extract List View.
1167          </para>
1168          <figure id="write_docbook_doc.figures.sample-create-labeledextract">
1169            <title>Creating a Labeled Extract from the Extract List View</title>
1170            <screenshot>
1171              <mediaobject>
1172                <imageobject>
1173                  <imagedata contentwidth="12cm" width="12cm"
1174                    fileref="figures/sample-create-labeledextract.png" format="PNG" />
1175                </imageobject>
1176              </mediaobject>
1177            </screenshot>
1178          </figure>
1179        </listitem>
1180        <listitem>
1181          <para>Creating Labeled Extracts from the Extract Item View page</para>
1182          <para>
1183            Alternately, Labeled Extracts can be created directly using the Labeled
1184            Extract create page. To do so, go to
1185            <menuchoice>
1186              <guimenu>View</guimenu>
1187              <guimenuitem>Labeled Extracts</guimenuitem>
1188            </menuchoice>
1189            , Click on &gbNew; button
1190          </para>
1191          <para>
1192            A 'Create' pop-up window opens, it contains 4 tabs:
1193            <guilabel>Labeled Extract</guilabel>
1194            ,
1195            <guilabel>Parents</guilabel>
1196            ,
1197            <guilabel>Annotations &amp; parameters</guilabel>
1198            and
1199            <guilabel>Inherited Annotations</guilabel>
1200            .
1201          </para>
1202          <itemizedlist>
1203            <listitem>
1204              <para>The Labeled Extract Tab</para>
1205              <para>
1206                This tab contains 2 mandatory fields, one for providing the Labeled
1207                Extract
1208                <guilabel>Name</guilabel>
1209                , the other one
1210                <guilabel>Label</guilabel>
1211                to specify which dye or marker was used in the labeling reaction.
1212              </para>
1213              <para>
1214                BASE2 by default assigns names to Labeled Extract(by suffixing
1215                'lbe#' when creating a Labeled Extract from an existing Extract or
1216                'New labeled extract' otherwise) but it is possible to edit it at
1217                will
1218              </para>
1219              <para>
1220                There 5 optional fields to provide more detailed information
1221              </para>
1222              <itemizedlist>
1223                <listitem>
1224                  <para>
1225                    <guilabel>External ID</guilabel>
1226                    : for instance to report a barcode attached to an extract
1227                  </para>
1228                </listitem>
1229                <listitem>
1230                  <para>
1231                    <guilabel>Original Quantity (ug)</guilabel>
1232                    : this is meant to report information about the actual mass
1233                    of biomaterial created
1234                  </para>
1235                </listitem>
1236                <listitem>
1237                  <para>
1238                    <guilabel>Created</guilabel>
1239                    : a date should be provided. The information can be
1240                    important when running quality controls on data and account
1241                    for potential confounding factor (e.g. day effect)
1242                  </para>
1243                </listitem>
1244                <listitem>
1245                  <para>
1246                    <guilabel>Protocol</guilabel>
1247                    : this a controled field. A select-list displays protocol
1248                    whose type is '
1249                    <guilabel>labeling</guilabel>
1250                    ' and which are shared to or owned by the logged-in user.
1251                    Reporting Protocol should be viewed as a MIAME requirement
1252                  </para>
1253                </listitem>
1254                <listitem>
1255                  <para>
1256                    <guilabel>Description</guilabel>
1257                    : a free text field to report any information that can not
1258                    be captured otherwise
1259                  </para>
1260                </listitem>
1261              </itemizedlist>
1262              <para>
1263                Finally, a 7th field
1264                <guilabel>Created</guilabel>
1265                is automatically populated with a date at which the Labeled Extract
1266                was actually entered in BASE2 system.
1267              </para>
1268              <figure id="write_docbook_doc.figures.labeledextract-tab-1">
1269                <title>Labeled Extract tab</title>
1270                <screenshot>
1271                  <mediaobject>
1272                    <imageobject>
1273                      <imagedata contentwidth="12cm" width="12cm"
1274                        fileref="figures/labeledextract-tab-1.png" format="PNG" />
1275                    </imageobject>
1276                  </mediaobject>
1277                </screenshot>
1278              </figure>
1279            </listitem>
1280            <listitem>
1281              <para>The Parents Tab</para>
1282              <para>
1283                This important tab allows users to select the Labeled Extract
1284                origin. BASE2 distinguished between 2 cases which are controled by
1285                the
1286                <guibutton>'pooled'</guibutton>
1287                radio-button
1288              </para>
1289              <orderedlist>
1290                <listitem>
1291                  <para>The Parent is an Extract</para>
1292                  <para>
1293                    The
1294                    <guibutton>pooled</guibutton>
1295                    radio-button is set to
1296                    <guilabel>No</guilabel>
1297                  </para>
1298                  <para>
1299                    The Extract select button is active and allows users to
1300                    point to one and only one Extract from which the Labeled
1301                    Extract originates from.
1302                  </para>
1303                  <figure
1304                    id="write_docbook_doc.figures.labeledextract-tab-2-select-extract">
1305                    <title>
1306                      Parent tab and interaction when pooled button is set to
1307                      No
1308                    </title>
1309                    <screenshot>
1310                      <mediaobject>
1311                        <imageobject>
1312                          <imagedata contentwidth="12cm" width="12cm"
1313                            fileref="figures/labeledextract-tab-2-select-extract.png" format="PNG" />
1314                        </imageobject>
1315                      </mediaobject>
1316                    </screenshot>
1317                  </figure>
1318                </listitem>
1319                <listitem>
1320                  <para>The Parent is another Labeled Extract</para>
1321                  <para>
1322                    The
1323                    <guibutton>pooled</guibutton>
1324                    radio-button has to be set to
1325                    <guilabel>Yes</guilabel>
1326                  </para>
1327                  <para>
1328                    Upon selection, the Extract select button is deactivated and
1329                    the Labeled Extracts box and button are activated.
1330                  </para>
1331                  <para>
1332                    This allows users to specify one or more extracts to be
1333                    selected from the Labeled Extract list View page.
1334                  </para>
1335                  <figure
1336                    id="write_docbook_doc.figures.labeledextract-tab-2-select-labeledextract">
1337                    <title>
1338                      Parent tab and interaction when pooled button is set to
1339                      Yes
1340                    </title>
1341                    <screenshot>
1342                      <mediaobject>
1343                        <imageobject>
1344                          <imagedata contentwidth="12cm" width="12cm"
1345                            fileref="figures/labeledextract-tab-2-select-labeledextract.png" format="PNG" />
1346                        </imageobject>
1347                      </mediaobject>
1348                    </screenshot>
1349                  </figure>
1350                </listitem>
1351              </orderedlist>
1352            </listitem>
1353            <listitem>
1354              <para>Annotations &amp; parameters</para>
1355              <para>
1356                As seen in the BioSource and Sample sections, this tab allows users
1357                to further supply information about the labeled extract provided
1358                they have defined annotation types to annotate Labeled Extract items
1359                or have such elements shared to them.
1360              </para>
1361              <para>
1362                The display of Annotation Types can be filtered based on the
1363                Annotation Type Categories they belong to.
1364              </para>
1365              <important>
1366                <para>
1367                  In order to use this feature, Annotation Type must be declared
1368                  and made available. To learn more about Annotation Types, please
1369                  refer to
1370                  <xref linkend="annotations" />
1371                </para>
1372              </important>
1373              <para>
1374                To provide a value for a given annotation type, simply click on it
1375                an use the input field or select a value from the drop-down lists or
1376                radio buttons.
1377              </para>
1378              <figure id="write_docbook_doc.figures.labeledextract-tab-3">
1379                <title>Annotations &amp; parameters</title>
1380                <screenshot>
1381                  <mediaobject>
1382                    <imageobject>
1383                      <imagedata contentwidth="12cm" width="12cm"
1384                        fileref="figures/labeledextract-tab-3.png" format="PNG" />
1385                    </imageobject>
1386                  </mediaobject>
1387                </screenshot>
1388              </figure>
1389            </listitem>
1390            <listitem>
1391              <para>Inherited Annotations case1</para>
1392              <para>The next picture shows</para>
1393              <figure id="write_docbook_doc.figures.labeledextract-tab-4">
1394                <title>Inherited Annotations</title>
1395                <screenshot>
1396                  <mediaobject>
1397                    <imageobject>
1398                      <imagedata contentwidth="12cm" width="12cm"
1399                        fileref="figures/labeledextract-tab-4.png" format="PNG" />
1400                    </imageobject>
1401                  </mediaobject>
1402                </screenshot>
1403              </figure>
1404            </listitem>
1405          </itemizedlist>
1406        </listitem>
1407      </orderedlist>
1408    </sect2>
1409    <sect2 id="labeledextract.manage.createelabeledxtract.pool">
1410      <title>Creating Pooled Labeled Extracts</title>
1411      <para>
1412        It is common practice when biological material is scarce to pool extracts from
1413        equivalent sources. BASE2 provides mechanisms to report on such practice.
1414      </para>
1415      <para>This section details how.</para>
1416      <para>There are 2 ways to create pooled Labeled Extracts in BASE2</para>
1417      <orderedlist>
1418        <listitem>
1419          <para>
1420            Using the Pooled radio button option from the Labeled Extract Create page,
1421            and this has been shown already
1422          </para>
1423        </listitem>
1424        <listitem>
1425          <para>Using the Pool button in the Menu bar</para>
1426          <para>
1427            The Labeled Extracts List View page menu bar contains an addition &gbPool;
1428            button, the usage of which is detailed now.
1429          </para>
1430          <para>
1431            The &gbPool; button
1432            <inlinemediaobject>
1433              <imageobject>
1434                <imagedata fileref="figures/new_pooled.gif" format="GIF" />
1435              </imageobject>
1436            </inlinemediaobject>
1437            allows users to create Pooled Labeled Extracts by selecting the list of
1438            Labeled Extracts used to derived a new Labeled Extract. Users simply have to
1439            tick to boxes in front of each relevant Labeled Extract and click the
1440            <guibutton>Pool...</guibutton>
1441          </para>
1442          <para>
1443            This provides an easy and simple way to create pooled Labeled Extracts. The
1444            result of such process is the creation of a New Labeled Extract, in which,
1445            when navigating to the Parent tab, shows that all the Labeled Extracts
1446            involved are already set and listed in the Labeled Extract box of the tab.
1447          </para>
1448          <figure
1449            id="write_docbook_doc.figures.labeledextract-tab-2-pool-labeledextract">
1450            <title>Pooling of Labeled Extracts:</title>
1451            <screenshot>
1452              <mediaobject>
1453                <imageobject>
1454                  <imagedata contentwidth="12cm" width="12cm"
1455                    fileref="figures/labeledextract-tab-2-pool-labeledextract.png" format="PNG" />
1456                </imageobject>
1457              </mediaobject>
1458            </screenshot>
1459          </figure>
1460        </listitem>
1461      </orderedlist>
1462    </sect2>
1463    <sect2 id="labeledextract.manage.delete">
1464      <title>Deleting/Restoring Labeled Extracts</title>
1465      <para>
1466        As for other items in BASE2, Labeled Extracts can be deleted. For a generic overview
1467        on how to delete and restore items, refer to section
1468        <xref linkend="webclient.items.delete" />
1469      </para>
1470      <para>To delete, do the following</para>
1471      <itemizedlist>
1472        <listitem>
1473          <para>
1474            Select one or more Labeled Extract and click &gbDelete; button in the menu
1475            bar.
1476          </para>
1477          <para>
1478            All the selected Labeled Extracts have been marked as deleted and are no
1479            longer available from the interface.
1480          </para>
1481          <para>
1482            Only by selecting from the
1483            <guilabel>view/preset&hellip;</guilabel>
1484            select box the
1485            <guilabel>Removed</guilabel>
1486            option, one can see those of the Labeled Extracts earmarked for deletion.
1487            They will be shown with a symbol in front of them.
1488          </para>
1489        </listitem>
1490        <listitem>
1491          <para>
1492            Alternately, navigating to the Labeled Extract Item View, one can hit the
1493            &gbDelete; to performed the task. As showed in the next picture, the Labeled
1494            Extract is then marked with the
1495            <inlinemediaobject>
1496              <imageobject>
1497                <imagedata fileref="figures/deleted.gif" format="GIF" />
1498              </imageobject>
1499            </inlinemediaobject>
1500            <guiicon>This item has been flagged for deletion</guiicon>
1501          </para>
1502          <figure id="write_docbook_doc.figures.labeledextract-delete">
1503            <title>Deleting Labeled Extracts from the Item View</title>
1504            <screenshot>
1505              <mediaobject>
1506                <imageobject>
1507                  <imagedata contentwidth="12cm" width="12cm"
1508                    fileref="figures/labeledextract-delete.png" format="PNG" />
1509                </imageobject>
1510              </mediaobject>
1511            </screenshot>
1512          </figure>
1513        </listitem>
1514        <listitem>
1515          <para>
1516            Deletion errors at this stage can be easily recovered. Select the item to
1517            recover from the List View (be sure to check the
1518            <guilabel>Removed</guilabel>
1519            option in the View/preset.. filter) and hit the &gbRestore; to performed the
1520            task.
1521          </para>
1522        </listitem>
1523      </itemizedlist>
1524      <important>
1525        <para>
1526          To really delete an item from the database you must use the trashcan. Items
1527          deleted from the Trashcan can not be recovered. To learn more about the trashcan
1528          function, please refer to
1529          <xref linkend="trashcan" />
1530        </para>
1531      </important>
1532    </sect2>
1533  </sect1>
1534  <sect1 id="hybridization.manage">
1535    <title>Managing Hybridizations</title>
1536    <para>
1537      An hybridization event corresponds to the application of one or more labeled extracts
1538      materials to a microarray slide under conditions detailed in hybridization protocols.
1539    </para>
1540    <para>In BASE2, there are 3 possible routes to create an hybridization object.</para>
1541    <sect2 id="hybridization.manage.create">
1542      <title>Creating Hybridizations</title>
1543      <orderedlist>
1544        <listitem>
1545          <para>Creating Hybridization from the Labeled Extract List View page</para>
1546          <para>
1547            Select at least one Labeled Extract by ticking to selection boxes before the
1548            name field.
1549          </para>
1550          <para>
1551            Click on the
1552            <guibutton>New hybridzation (to be changed)</guibutton>
1553            from the menu bar of Labeled Extract list view.
1554          </para>
1555          <figure id="write_docbook_doc.figures.hyb-create-labeledlistview">
1556            <title>Creating a Hybridization from the Labeled Extract List View</title>
1557            <screenshot>
1558              <mediaobject>
1559                <imageobject>
1560                  <imagedata contentwidth="12cm" width="12cm"
1561                    fileref="figures/hyb-create-labeledlistview.png" format="PNG" />
1562                </imageobject>
1563              </mediaobject>
1564            </screenshot>
1565          </figure>
1566        </listitem>
1567        <listitem>
1568          <para>Creating Hybridization from the Labeled Extract Item View page</para>
1569          <para>
1570            After having selected a Labeled Extract and displayed it in the Item View,
1571            Click on the
1572            <guibutton>New hybridization</guibutton>
1573            button from the Menu bar of the Labeled Extract Item View.
1574          </para>
1575          <figure id="write_docbook_doc.figures.hyb-create-labeleditemview">
1576            <title>Creating a Hybridization from the Labeled Extract Item View</title>
1577            <screenshot>
1578              <mediaobject>
1579                <imageobject>
1580                  <imagedata contentwidth="12cm" width="12cm"
1581                    fileref="figures/hyb-create-labeleditemview.png" format="PNG" />
1582                </imageobject>
1583              </mediaobject>
1584            </screenshot>
1585          </figure>
1586        </listitem>
1587        <listitem>
1588          <para>Creating Hybridizations from the Hybridization List View page</para>
1589          <para>
1590            Hybridizations can be created directly using the Hybridization create page.
1591            To do so, go to
1592            <menuchoice>
1593              <guimenu>View</guimenu>
1594              <guimenuitem>Hybridizations</guimenuitem>
1595            </menuchoice>
1596            , Click on &gbNew;
1597          </para>
1598          <figure id="write_docbook_doc.figures.hyb-create">
1599            <title>Creating Hybridizations from the Hybridization List View</title>
1600            <screenshot>
1601              <mediaobject>
1602                <imageobject>
1603                  <imagedata contentwidth="12cm" width="12cm"
1604                    fileref="figures/hyb-create.png" format="PNG" />
1605                </imageobject>
1606              </mediaobject>
1607            </screenshot>
1608          </figure>
1609          <para>
1610            Irrespective of the methods chosen to create the Hybridization item, A
1611            'Create' pop-up window will open. It contains 4 distinct tabs:
1612            <guilabel>Hybridization</guilabel>
1613            ,
1614            <guilabel>Parents</guilabel>
1615            ,
1616            <guilabel>Annotations &amp; parameters</guilabel>
1617            and
1618            <guilabel>Inherited Annotations</guilabel>
1619            .
1620          </para>
1621          <itemizedlist>
1622            <listitem>
1623              <para>The Hybridization Tab</para>
1624
1625              <variablelist>
1626                <varlistentry>
1627                  <term>
1628                    <interface>Name</interface>
1629                  </term>
1630                  <listitem>
1631                    <para>
1632                      New Hybridization is BASE2 default name but it is
1633                      strongly advise to provide a meaningful and unique name
1634                      as it matters for tab2mage export to function properly.
1635                    </para>
1636                    <para>
1637                      There are 5 optional fields to provide more detailed
1638                      information
1639                    </para>
1640
1641                  </listitem>
1642                </varlistentry>
1643
1644                <varlistentry>
1645                  <term>
1646                    <guilabel>Created</guilabel>
1647                  </term>
1648                  <listitem>
1649                    <para>
1650                      A date should be provided. The information can be
1651                      important when running quality controls on data and
1652                      account for potential confounding factor (e.g. to
1653                      account for a day effect)
1654                    </para>
1655                  </listitem>
1656                </varlistentry>
1657
1658                <varlistentry>
1659                  <term>
1660                    <guilabel>Protocol</guilabel>
1661                  </term>
1662                  <listitem>
1663                    <para>
1664                      This is a controled field. A select-list displays
1665                      protocol whose type is '
1666                      <guilabel>hybridization</guilabel>
1667                      ' and which are shared to or owned by the logged-in
1668                      user.
1669                    </para>
1670                    <important>
1671                      <para>
1672                        Reporting Protocols should be viewed as a MIAME
1673                        requirement
1674                      </para>
1675                    </important>
1676                  </listitem>
1677                </varlistentry>
1678
1679                <varlistentry>
1680                  <term>
1681                    <guilabel>Hardware</guilabel>
1682                  </term>
1683                  <listitem>
1684                    <para>
1685                      This is a controled field. A select-list displays
1686                      Hardware whose type is '
1687                      <guilabel>Hybridization station</guilabel>
1688                      ' and which are shared to or owned by the logged-in
1689                      user.
1690                    </para>
1691                  </listitem>
1692                </varlistentry>
1693
1694                <varlistentry>
1695                  <term>
1696                    <guilabel>Array Slide</guilabel>
1697                  </term>
1698                  <listitem>
1699                    <para>
1700                      This is meant to specify the actual microarray slide.
1701                    </para>
1702                    <note>
1703                      <para>
1704                        Ideally, The Array Slides should have been created
1705                        but for those users with permission to do, Array
1706                        Slides could be generated at that point.
1707                      </para>
1708                    </note>
1709                  </listitem>
1710                </varlistentry>
1711
1712                <varlistentry>
1713                  <term>
1714                    <guilabel>Description</guilabel>
1715                  </term>
1716                  <listitem>
1717                    <para>
1718                      A free text field to report any information that can not
1719                      be captured otherwise
1720                    </para>
1721                  </listitem>
1722                </varlistentry>
1723
1724                <varlistentry>
1725                  <term>
1726                    <guilabel>Registered</guilabel>
1727                  </term>
1728                  <listitem>
1729                    <para>
1730                      This 7th field is automatically populated with a date at
1731                      which the sample was entered in BASE2 system.
1732                    </para>
1733                  </listitem>
1734                </varlistentry>
1735              </variablelist>
1736
1737              <figure id="write_docbook_doc.figures.hybridization-tab-1">
1738                <title>Hybridization tab</title>
1739                <screenshot>
1740                  <mediaobject>
1741                    <imageobject>
1742                      <imagedata contentwidth="12cm" width="12cm"
1743                        fileref="figures/hybridization-tab-1.png" format="PNG" />
1744                    </imageobject>
1745                  </mediaobject>
1746                </screenshot>
1747              </figure>
1748            </listitem>
1749            <listitem>
1750              <para>The Labeled Extract Tab</para>
1751              <para>
1752                This important tab allows users to select the Labeled Extracts
1753                applied to an Array Slide, and specify the amount of material used,
1754                expressed in microgram.
1755              </para>
1756              <figure id="write_docbook_doc.figures.hybridization-tab-2">
1757                <title>Labeled Extract tab</title>
1758                <screenshot>
1759                  <mediaobject>
1760                    <imageobject>
1761                      <imagedata contentwidth="12cm" width="12cm"
1762                        fileref="figures/hybridization-tab-2.png" format="PNG" />
1763                    </imageobject>
1764                  </mediaobject>
1765                </screenshot>
1766              </figure>
1767            </listitem>
1768            <listitem>
1769              <para>Annotations &amp; parameters</para>
1770              <para>
1771                As seen in the BioSource and Sample sections, this tab allows users
1772                to supply further information about the hybridization provided
1773                annotation types have been defined or shared to annotate
1774                Hybridization items. The display of Annotation Types can be filtered
1775                based on the Annotation Type Category they belong to.
1776              </para>
1777              <important>
1778                <para>
1779                  In order to use this feature, Annotation Type must be declared
1780                  and made available. To learn more about Annotation Types, please
1781                  refer to
1782                  <xref linkend="annotations" />
1783                </para>
1784              </important>
1785              <para>
1786                To provide a value for a given annotation type, simply click on it
1787                and use the input field or select a value from the drop-down lists
1788                or radio buttons.
1789              </para>
1790              <para>
1791                A caption also reminds users if Annotation Types are parameters
1792                <inlinemediaobject>
1793                  <imageobject>
1794                    <imagedata fileref="figures/parameter.gif" format="GIF" />
1795                  </imageobject>
1796                </inlinemediaobject>
1797                and if annotation values have already been supplied, marked by the
1798                <inlinemediaobject>
1799                  <imageobject>
1800                    <imagedata fileref="figures/annotated.gif" format="GIF" />
1801                  </imageobject>
1802                </inlinemediaobject>
1803                logo.
1804              </para>
1805              <figure id="write_docbook_doc.figures.hybridization-tab-3">
1806                <title>Annotations &amp; parameters</title>
1807                <screenshot>
1808                  <mediaobject>
1809                    <imageobject>
1810                      <imagedata contentwidth="12cm" width="12cm"
1811                        fileref="figures/hybridization-tab-3.png" format="PNG" />
1812                    </imageobject>
1813                  </mediaobject>
1814                </screenshot>
1815              </figure>
1816            </listitem>
1817            <listitem>
1818              <para>Inherited Annotations</para>
1819              <para>
1820                The next screenshot shows a typical view of the functionality.
1821              </para>
1822              <figure id="write_docbook_doc.figures.hybridization-tab-4">
1823                <title>Inherited Annotations</title>
1824                <screenshot>
1825                  <mediaobject>
1826                    <imageobject>
1827                      <imagedata contentwidth="12cm" width="12cm"
1828                        fileref="figures/hybridization-tab-4.png" format="PNG" />
1829                    </imageobject>
1830                  </mediaobject>
1831                </screenshot>
1832              </figure>
1833              <para>
1834                Note the tags used to distinguish between Annotation Types which are
1835                parameters noted
1836                <inlinemediaobject>
1837                  <imageobject>
1838                    <imagedata fileref="figures/parameter.gif" format="GIF" />
1839                  </imageobject>
1840                </inlinemediaobject>
1841                and those which are Biomaterial Characteristics,noted
1842                <inlinemediaobject>
1843                  <imageobject>
1844                    <imagedata fileref="figures/annotation.gif" format="GIF" />
1845                  </imageobject>
1846                </inlinemediaobject>
1847              </para>
1848            </listitem>
1849          </itemizedlist>
1850        </listitem>
1851      </orderedlist>
1852    </sect2>
1853    <sect2 id="hybridization.manage.viewedit">
1854      <title>Viewing/Editing Hybridizations</title>
1855      <para>
1856        As for other items in BASE2, Hybridizations can be edited. To do so, do the
1857        following
1858      </para>
1859      <itemizedlist>
1860        <listitem>
1861          <para>
1862            Press and hold one of the
1863            <keycap>CTRL</keycap>
1864            ,
1865            <keycap>ALT</keycap>
1866            or
1867            <keycap>SHIFT</keycap>
1868            keys while clicking on the name of an Hybridization Item, which is a live
1869            link.
1870          </para>
1871        </listitem>
1872        <listitem>
1873          <para>
1874            Alternately, navigating to the Hybridization Item View, one can hit the
1875            <guibutton>Edit</guibutton>
1876            to performed the task.
1877          </para>
1878        </listitem>
1879
1880        <listitem>
1881          <para>
1882            The Hybridization item View summarizes key information such as the list of
1883            <guilabel>Labeled Extracts</guilabel>
1884            , and the list of associated
1885            <guilabel>Scans</guilabel>
1886            . Both are available as hyperlinks to allow quick and easy navigation.
1887          </para>
1888          <figure id="write_docbook_doc.figures.hybridization-itemview">
1889            <title>Hardware Item View</title>
1890            <screenshot>
1891              <mediaobject>
1892                <imageobject>
1893                  <imagedata contentwidth="10cm" width="10cm"
1894                    fileref="figures/hybridization-itemview.png" format="PNG" />
1895                </imageobject>
1896              </mediaobject>
1897            </screenshot>
1898          </figure>
1899        </listitem>
1900      </itemizedlist>
1901
1902    </sect2>
1903
1904    <sect2 id="hybridization.manage.delete">
1905      <title>Deleting/Restoring Hybridizations</title>
1906      <para>
1907        As for other items in BASE2, Hybridizations can be deleted. For a generic overview
1908        on how to delete and restore items, refer to section
1909        <xref linkend="webclient.items.delete" />
1910      </para>
1911
1912      <para>To delete, do the following</para>
1913      <itemizedlist>
1914        <listitem>
1915          <para>
1916            Select one or more Hybridization Items and click on the &gbDelete; button in
1917            the menu bar.
1918          </para>
1919          <para>
1920            All the selected Hybridizations have been marked as deleted and are no
1921            longer available from the interface.
1922          </para>
1923          <para>
1924            Only by selecting from the
1925            <guilabel>view/preset&hellip;</guilabel>
1926            select box the
1927            <guilabel>Removed</guilabel>
1928            option, one can see those of the Hybridizations earmarked for deletion. They
1929            will be shown with a symbol in front of them.
1930          </para>
1931        </listitem>
1932        <listitem>
1933          <para>
1934            Alternately, navigating to the Hybridization Item View, one can hit the
1935            &gbDelete; to performed the task. As shown in the next picture, the
1936            Hybridization is then marked with the
1937            <inlinemediaobject>
1938              <imageobject>
1939                <imagedata fileref="figures/deleted.gif" format="GIF" />
1940              </imageobject>
1941            </inlinemediaobject>
1942            <guilabel>This item has been flagged for deletion</guilabel>
1943          </para>
1944          <figure id="write_docbook_doc.figures.hybridization-delete">
1945            <title>Deleting Hybridizations from the Hybridization Item View</title>
1946            <screenshot>
1947              <mediaobject>
1948                <imageobject>
1949                  <imagedata contentwidth="10cm" width="10cm"
1950                    fileref="figures/hybridization-delete.png" format="PNG" />
1951                </imageobject>
1952              </mediaobject>
1953            </screenshot>
1954          </figure>
1955        </listitem>
1956      </itemizedlist>
1957      <important>
1958        <para>
1959          To really delete an item from the database you must use the trashcan. Items
1960          deleted from the Trashcan can not be recovered. To learn more about the trashcan
1961          function, please refer to
1962          <xref linkend="trashcan" />
1963        </para>
1964      </important>
1965    </sect2>
1966  </sect1>
1967</chapter>
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