source: trunk/doc/src/docbook/userdoc/biomaterials.xml @ 3373

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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 3373 2007-05-24 14:26:41Z martin $
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28<chapter id="biomaterials">
29 <title>Biomaterials</title>
30 <sect1 id="biomaterial.introduction">
31  <title>Introduction</title>
32  <para> The generic term Biomaterial refers to any biological material used in an Experiment.
33   Biomaterials are subdivided in 4 components, BioSource, Sample, Extract and Labeled Extract. The
34   order use in presenting those entities is not inocuous as it represents the sequence of
35   transformation a source material undergoes until it is in a state compatible with the realization
36   of a microarray Hybridization. This progression is actually mimicked in the BASE2 View menu again
37   to insist on this natural progression. </para>
38  <para>BioSources correspond to the native biological entity used in an experiment prior to any
39   treatment. </para>
40  <para>Samples are central to BASE2 to describe the sample processing. So Samples can be created
41   from other Samples if user want to track sample processing event in a finely granular fashion.</para>
42  <para>Extracts correspond to nucleic acid material extracted from a tissue sample or a cell
43   culture sample.</para>
44  <para>LabeledExtracts correspond to nucleic acid materials which have undergone a marking
45   procedure using a fluorescent or radioactive compound for detection in a microarray assay.</para>
46  <para>BASE2 allows users to create any of the these entities fairly freely, however it is expected
47   that users will follow the natural path of the laboratory workflow.</para>
48 </sect1>
49 <sect1 id="biosource.manage">
50  <title>Managing BioSources</title>
51
52  <sect2 id="biosource.manage.create">
53   <title>Creating BioSources</title>
54   <para>Go to <menuchoice>
55     <guimenu>View</guimenu>
56     <guimenuitem>BioSources</guimenuitem>
57    </menuchoice> , Click on <guibutton>New&hellip;</guibutton> button </para>
58   <para> A 'Create' pop-up window opens, it contains 2 tabs: <guilabel>Biosource</guilabel> and
59     <guilabel>Annotations</guilabel>. </para>
60   <itemizedlist>
61    <listitem>
62     <para>
63      <guilabel>BioSource</guilabel>
64     </para>
65     <para> This tab allows users to enter essential information about a BioSource.</para>
66     <variablelist>
67      <varlistentry>
68       <term>
69        <guilabel>Name</guilabel>
70       </term>
71       <listitem>
72        <para> This is only mandatory field. BASE2 by default assigns 'New Biosource' as name but it
73         is advised to provide unique sensible names, as this may impact exporting in tab2mage
74         format.</para>
75        <para>For more information about tab2mage format and export, please refer to section <xref
76          linkend="experiments_analysis.magexport"/> and section <xref
77          linkend="annotations.bestpractices"/></para>
78       </listitem>
79      </varlistentry>
80      <varlistentry>
81       <term>
82        <guilabel>Description</guilabel>
83       </term>
84       <listitem>
85        <para> A free text description can be supplied using this field.</para>
86       </listitem>
87      </varlistentry>
88      <varlistentry>
89       <term>
90        <guilabel>External id</guilabel>
91       </term>
92       <listitem>
93        <para> An external reference identifiers (e.g. a patient identification code) can be
94         supplied using this field.</para>
95       </listitem>
96      </varlistentry>
97     </variablelist>
98
99     <figure id="write_docbook_doc.figures.biosource-tab-1">
100      <title>The Biosource tab in the Biosource Create Window</title>
101      <screenshot>
102      <mediaobject>
103       <imageobject>
104        <imagedata contentwidth="10cm" width="10cm" fileref="figures/biosource-tab-1.png" format="PNG"/>
105       </imageobject>
106      </mediaobject>
107     </screenshot>
108     </figure>
109    </listitem>
110    <listitem>
111     <para>
112      <guilabel>Annotations</guilabel>
113     </para>
114     <para> This tab allows BASE2 users to use Annotation Types to refine BioSource description.</para>
115     <para>A list of Annotation Type will be displayed only if owned by or shared to the user.</para>
116     <important>
117      <para> In order to use this feature, Annotation Type must be declared and made available. To
118       learn more about Annotation Types, please refer to <xref linkend="annotations"/>
119      </para>
120     </important>
121     <para> Annotation Types can be filtered based on their grouping properties using the
122       <guilabel>categories</guilabel> select-list feature. For more information about Annotation
123      Type Categories, refer to section <xref linkend="annotations.manage.create_atcategory"/>. </para>
124     <figure id="write_docbook_doc.figures.biosource-tab-2">
125      <title>The Annotation tab from the Biosource Create Window</title>
126      <screenshot>
127      <mediaobject>
128       <imageobject>
129        <imagedata contentwidth="10cm" width="10cm" fileref="figures/biosource-tab-2.png" format="PNG"/>
130       </imageobject>
131      </mediaobject>
132     </screenshot>
133     </figure>
134     <para>To provide a value to a specific Annotation Type, click on it.</para>
135     <para> Upon selection, the windows is updated to present a drop-down list, an entry box or a
136      radio-button check box, depending on the type of the Annotation Type.</para>
137     <para>Once a value has been supplied, an <inlinemediaobject>
138       <imageobject>
139        <imagedata fileref="figures/annotated.gif" format="GIF"/>
140       </imageobject>
141      </inlinemediaobject> symbol appear in front of the annotation type.</para>
142     <para>The actual type of the Annotation Type will be reminded between bracket, for instance
143      appearing in the interface as <guilabel>(float)</guilabel> or <guilabel>(string)</guilabel>.</para>
144     <para>A validation will be applied upon data entry to match the requirements, i.e. check for
145      integer,boolean, string... values are provided.</para>
146     <figure id="write_docbook_doc.figures.biosource-tab-3">
147      <title>Providing Annotation Type values from the Biosource Create Window</title>
148      <screenshot>
149      <mediaobject>
150       <imageobject>
151        <imagedata contentwidth="10cm" width="10cm" fileref="figures/biosource-tab-3.png" format="PNG"/>
152       </imageobject>
153      </mediaobject>
154     </screenshot>
155     </figure>
156    </listitem>
157   </itemizedlist>
158   <para>Click on the <inlinemediaobject>
159     <imageobject>
160      <imagedata fileref="figures/save.gif" format="GIF"/>
161     </imageobject>
162    </inlinemediaobject> Save button to store the information in BASE2 or on the <inlinemediaobject>
163     <imageobject>
164      <imagedata fileref="figures/cancel.gif" format="GIF"/>
165     </imageobject>
166    </inlinemediaobject> button to abort. </para>
167  </sect2>
168  <sect2 id="biosource.manage.detail_view">
169   <title>Viewing/Editing BioSources</title>
170   <para>From the BioSource List View, clicking on the BioSource <guilabel>Name</guilabel> opens a
171    detailed view for that Biosource, showing a summary of all information available in BASE2 about
172    that particular entity.</para>
173   <para> The default behavior opens the detailed view on the <guilabel>Properties</guilabel> tab,
174    which shows a summary information and displays the list of Samples derived from a BioSource, if
175    any.</para>
176   <figure id="write_docbook_doc.figures.biosource-itemview-prop">
177    <title>BioSource Item View, properties tab</title>
178    <screenshot>
179    <mediaobject>
180     <imageobject>
181      <imagedata contentwidth="12cm" width="12cm" fileref="figures/biosource-itemview-prop.png" format="PNG"/>
182     </imageobject>
183    </mediaobject>
184   </screenshot>
185   </figure>
186   <para>By clicking on the <guilabel>Annotations</guilabel> tab, users can display the list of
187    Annotation Types used to annotate a Biosource. </para>
188   <figure id="write_docbook_doc.figures.biosource-itemview-annot">
189    <title>BioSource Item View, annotations tab</title>
190    <screenshot>
191    <mediaobject>
192     <imageobject>
193      <imagedata contentwidth="13cm" width="13cm" fileref="figures/biosource-itemview-annot.png" format="PNG"/>
194     </imageobject>
195    </mediaobject>
196   </screenshot>
197   </figure>
198   <para>Clicking the <inlinemediaobject>
199     <imageobject>
200      <imagedata fileref="figures/edit.gif" format="GIF"/>
201     </imageobject>
202    </inlinemediaobject><guiicon> edit icon</guiicon> in the <interface>value</interface> for any of
203    the annotations (e.g. 'antibiotic' in our example), opens an Annotate window (which is a
204    BioSource Edit window set on the annotation tab) and highlights the selected Annotation Type,
205    prompting for data entry.</para>
206   <figure id="write_docbook_doc.figures.biosource-itemview-annot-edit">
207    <title>BioSource annotations edit</title>
208    <screenshot>
209    <mediaobject>
210     <imageobject>
211      <imagedata contentwidth="12cm" width="12cm" fileref="figures/biosource-itemview-annot-edit.png" format="PNG"/>
212     </imageobject>
213    </mediaobject>
214   </screenshot>
215   </figure>
216   <para> The relevant Annotation Type is highlighted and a list of possible values is displayed. </para>
217   <para>Again, all Annotation types marked with a <inlinemediaobject>
218     <imageobject>
219      <imagedata fileref="figures/annotated.gif" format="GIF"/>
220     </imageobject>
221    </inlinemediaobject> symbol have been used to provided information.</para>
222   <para>Click on the <inlinemediaobject>
223     <imageobject>
224      <imagedata fileref="figures/save.gif" format="GIF"/>
225     </imageobject>
226    </inlinemediaobject> Save button to store the information in BASE2 or on the <inlinemediaobject>
227     <imageobject>
228      <imagedata fileref="figures/cancel.gif" format="GIF"/>
229     </imageobject>
230    </inlinemediaobject> button to abort. </para>
231  </sect2>
232  <sect2 id="biosource.manage.delete_restore">
233   <title>Deleting/Restoring BioSources</title>
234   <para>As for other items in BASE2, BioSources can be removed. For a generic overview on how to
235    delete and restore items, refer to section <xref linkend="webclient.items.delete"/>
236   </para>
237   <para> To delete, do the following</para>
238   <itemizedlist>
239    <listitem>
240     <para> Select one or more BioSources and click <guibutton>Delete</guibutton> button in the menu
241      bar. </para>
242     <para> All the selected BioSources have been marked as deleted and are no longer available from
243      the interface. </para>
244     <para> From the <guilabel>view/preset&hellip;</guilabel> select box, ticking the
245       <guilabel>Removed</guilabel> option allows to display those of the BioSources earmarked for
246      deletion. They will be shown with a symbol <inlinemediaobject>
247       <imageobject>
248        <imagedata fileref="figures/deleted.gif" format="GIF"/>
249       </imageobject>
250      </inlinemediaobject> in front of them. </para>
251    </listitem>
252    <listitem>
253     <para> Alternately, navigating to the BioSource Item View, hitting the
254      <guibutton>Delete</guibutton> will perform the task.</para>
255     <para> As shown in the next picture, the BioSource is then marked with the <inlinemediaobject>
256       <imageobject>
257        <imagedata fileref="figures/deleted.gif" format="GIF"/>
258       </imageobject>
259      </inlinemediaobject><guilabel>This item has been flagged for deletion</guilabel> label.</para>
260     <figure id="write_docbook_doc.figures.biosource-delete">
261      <title>Deleting BioSource from the Item View</title>
262      <screenshot>
263     <mediaobject>
264      <imageobject>
265       <imagedata contentwidth="12cm" width="12cm" fileref="figures/biosource-delete.png" format="PNG"/>
266      </imageobject>
267     </mediaobject>
268    </screenshot>
269     </figure>
270    </listitem>
271    <listitem>
272     <para>Deletion errors can be easily recovered. Select the item to recover from the List View
273      (be sure to check the <guilabel>Removed</guilabel> option in the View/preset.. filter) and hit
274      the <guibutton>Restore</guibutton> to performed the task. </para>
275    </listitem>
276   </itemizedlist>
277   <important>
278    <para>To really delete an item from the database you must use the trashcan. Items deleted from
279     the Trashcan can not be recovered. To learn more about the trashcan function, please refer to
280      <xref linkend="trashcan"/>
281    </para>
282   </important>
283  </sect2>
284 </sect1>
285 <sect1 id="sample.manage">
286  <title>Managing Samples</title>
287  <para>Samples result from processing events applied to <guilabel>BioSource</guilabel> material or
288   other <guilabel>Samples</guilabel> before they are turned into an <guilabel>Extract</guilabel>.</para>
289  <para>In other words, Samples can be created from BioSource items or from one or more Sample
290   items.</para>
291  <para>When a Sample is created from several other Samples, a 'pooling' event is performed. A
292   specific section details how to create pools, refer to <xref
293    linkend="sample.manage.createsample.pool"/></para>
294  <para>For every step of transformation from BioSource to Sample, it is possible to provide
295   information about the protocol used to perform this task. It is not enforced in BASE2 but it
296   should serve as guidance when devising the granularity of the sample processing task. Also, it is
297   good practice to provide protocol information to ensure MIAME compliance.</para>
298  <sect2 id="sample.manage.createsamplefrombiosource">
299   <title>Creating Samples</title>
300   <orderedlist>
301    <listitem>
302     <para>Creating Samples from the BioSource page</para>
303     <para>No matter how complex the sample processing phase is, at least one Sample has to be
304      anchored to a BioSource.</para>
305     <para>Therefore, a natural way to create a Sample is to click on the <inlinemediaobject>
306       <imageobject>
307        <imagedata fileref="figures/add.gif" format="GIF"/>
308       </imageobject>
309      </inlinemediaobject>
310      <guibutton>Create new Sample</guibutton> from the Sample column of the BioSource list view.</para>
311     <figure id="write_docbook_doc.figures.biosource-create-sample">
312      <title>Creating a Sample from the BioSource list view</title>
313      <screenshot>
314       <mediaobject>
315        <imageobject>
316         <imagedata contentwidth="13cm" width="13cm" fileref="figures/biosource-create-sample.png" format="PNG"/>
317        </imageobject>
318       </mediaobject>
319      </screenshot>
320     </figure>
321    </listitem>
322    <listitem>
323     <para>Creating Samples from the Sample List view page</para>
324     <para> This is the alternative for creating Sample from the BioSource. To do so, go to <menuchoice>
325       <guimenu>View</guimenu>
326       <guimenuitem>BioSamples</guimenuitem>
327      </menuchoice> , Click on <guibutton>New&hellip;</guibutton> button </para>
328     <para> A 'Create' pop-up window opens, it contains 4 tabs: <guilabel>Sample</guilabel>,
329       <guilabel>Parents</guilabel>, <guilabel> Annotations &amp; parameters</guilabel> and
330       <guilabel>Inherited Annotations</guilabel>. </para>
331     <itemizedlist>
332      <listitem>
333       <para>The Sample Tab </para>
334       <para>This tab contains 1 mandatory field for providing the Sample <guilabel>Name</guilabel>.
335        BASE2 by default assigns names to Samples (by suffixing 's#' when creating a Sample from an
336        existing Biosource or 'New Sample' otherwise) but it is possible to edit at will.</para>
337       <para>There are 5 optional fields to provide more detailed information</para>
338       <itemizedlist>
339        <listitem>
340         <para><guilabel>External ID</guilabel>: for instance to report a barcode attached to a
341          Sample</para>
342        </listitem>
343        <listitem>
344         <para><guilabel>Original Quantity (ug)</guilabel>: this is meant to report information
345          about the actual mass of biomaterial created</para>
346        </listitem>
347        <listitem>
348         <para><guilabel>Created</guilabel>: a date should be provided. The information can be
349          important when running quality controls on data and account for potential confounding
350          factor (e.g. day effect)</para>
351        </listitem>
352        <listitem>
353         <para><guilabel>Protocol</guilabel>: this a controled field. A select-list displays
354          protocols whose type is <guilabel>sampling</guilabel> and which are shared to or owned by
355          the logged-in user. </para>
356         <important>
357          <para>It is not mandatory to supply protocol in BASE2 Reporting protocols is a MIAME
358           requirement</para>
359         </important>
360        </listitem>
361        <listitem>
362         <para><guilabel>Description</guilabel>: a free text field to report any information that
363          not can be captured otherwise</para>
364        </listitem>
365       </itemizedlist>
366       <para>Finally, a 7th field, <guilabel>Registered</guilabel> is automatically populated with a
367        date at which the Sample was entered in BASE2 system.</para>
368       <figure id="write_docbook_doc.figures.biosample-tab-1">
369        <title>Sample tab</title>
370        <screenshot>
371         <mediaobject>
372          <imageobject>
373           <imagedata contentwidth="10cm" width="10cm" fileref="figures/biosample-tab-1.png" format="PNG"/>
374          </imageobject>
375         </mediaobject>
376        </screenshot>
377       </figure>
378      </listitem>
379      <listitem>
380       <para>The Parents Tab </para>
381       <para>This important tab does what it says on the tin: It is meant to keep track of the
382        Sample origin. BASE2 distinguished between 2 cases which are controled by the
383         <guibutton>pooled</guibutton> radio-button</para>
384       <orderedlist>
385        <listitem>
386         <para>The Parent is a BioSource</para>
387         <para> The <guibutton>Pooled</guibutton> radio-button is set to <guilabel>No</guilabel></para>
388         <para> The BioSource select button is active and allows users to point to one and only one
389          BioSource from which the Sample originates from.</para>
390         <figure id="write_docbook_doc.figures.biosample-tab-2-select-biosource">
391          <title>Parent tab and interaction when pooled button is set to No</title>
392          <screenshot>
393           <mediaobject>
394            <imageobject>
395             <imagedata contentwidth="12cm" width="12cm" fileref="figures/biosample-tab-2-select-biosource.png" format="PNG"/>
396            </imageobject>
397           </mediaobject>
398          </screenshot>
399         </figure>
400        </listitem>
401        <listitem>
402         <para>The Parent is another Sample</para>
403         <para> The <guibutton>Pooled</guibutton> radio-button has to be set to
404          <guilabel>Yes</guilabel></para>
405         <para>Upon selection, the BioSource select button is deactivated and the Samples box and
406          button are activated.</para>
407         <para>This allows users to specify one or more Samples to be selected from the Sample List
408          View page. </para>
409         <figure id="write_docbook_doc.figures.biosample-tab-2-select-sample">
410          <title>Parent tab and interaction when pooled button is set to Yes</title>
411          <screenshot>
412           <mediaobject>
413            <imageobject>
414             <imagedata contentwidth="12cm" width="12cm" fileref="figures/biosample-tab-2-select-sample.png" format="PNG"/>
415            </imageobject>
416           </mediaobject>
417          </screenshot>
418         </figure>
419        </listitem>
420       </orderedlist>
421      </listitem>
422      <listitem>
423       <para>Annotations &amp; parameters </para>
424       <para>As seen in the BioSource section, this tab allows users to further supply information
425        about the Sample provided they have defined or shared annotation types to annotate Sample
426        items.</para>
427       <para>The display of Annotation Type can be filtered based on the Annotation Type Category
428        they belong to. </para>
429       <important>
430        <para> In order to use this feature, Annotation Type must be declared and made available. To
431         learn more about Annotation Types, please refer to <xref linkend="annotations"/>
432        </para>
433       </important>
434       <para>To provide a value for a given annotation type, simply click on it an use the input
435        field or select a value from the drop-down lists or radio buttons.</para>
436       <figure id="write_docbook_doc.figures.biosample-tab-3">
437        <title>Annotations &amp; parameters</title>
438        <screenshot>
439         <mediaobject>
440          <imageobject>
441           <imagedata contentwidth="12cm" width="12cm" fileref="figures/biosample-tab-3.png" format="PNG"/>
442          </imageobject>
443         </mediaobject>
444        </screenshot>
445       </figure>
446      </listitem>
447      <listitem>
448       <para>Inherited Annotations case1 </para>
449       <para>The next picture shows </para>
450       <figure id="write_docbook_doc.figures.biosample-tab-4">
451        <title>Inherited Annotations</title>
452        <screenshot>
453         <mediaobject>
454          <imageobject>
455           <imagedata contentwidth="12cm" width="12cm" fileref="figures/biosample-tab-4.png" format="PNG"/>
456          </imageobject>
457         </mediaobject>
458        </screenshot>
459       </figure>
460       <para>Inherited Annotations case2</para>
461       <figure id="write_docbook_doc.figures.biosample-tab-4bis">
462        <title>Inherited Annotations</title>
463        <screenshot>
464         <mediaobject>
465          <imageobject>
466           <imagedata contentwidth="12cm" width="12cm" fileref="figures/biosample-tab-4bis.png" format="PNG"/>
467          </imageobject>
468         </mediaobject>
469        </screenshot>
470       </figure>
471      </listitem>
472     </itemizedlist>
473    </listitem>
474   </orderedlist>
475  </sect2>
476  <sect2 id="sample.manage.createsample.pool">
477   <title>Creating Pooled Samples</title>
478   <para>It is common practice when biological material is scarce to pool Samples from equivalent
479    sources. BASE2 provides mechanisms to report on such practice.</para>
480   <para>This section details how.</para>
481   <para>There are 2 ways to create Pooled Samples in BASE2</para>
482   <orderedlist>
483    <listitem>
484     <para>Using the Pooled radio button option from the Sample Create page, and this has been shown
485      already </para>
486    </listitem>
487    <listitem>
488     <para>Using the Pool button in the Menu bar</para>
489     <para>The Sample List View page menu bar contains an additionnal button the usage of which is
490      detailed now.</para>
491     <para>The <guibutton>Pool&hellip;</guibutton> button <inlinemediaobject>
492       <imageobject>
493        <imagedata fileref="figures/new_pooled.gif" format="GIF"/>
494       </imageobject>
495      </inlinemediaobject> allows users to create Pooled Samples by selecting the list of Samples
496      used to produce that new Sample.</para>
497     <para> Users simply need to tick the select-boxes in front of each relevant Sample and click
498      the <inlinemediaobject>
499       <imageobject>
500        <imagedata fileref="figures/new_pooled.gif" format="GIF"/>
501       </imageobject>
502      </inlinemediaobject> button. </para>
503     <para>This provides an easy and simple way to create Pooled Samples. The result of such process
504      is the creation of a New Sample, which Parent Samples are listing and preset in the Parent tab</para>
505     <figure id="write_docbook_doc.figures.biosample-tab-2-pool-sample">
506      <title>Pooling of Samples</title>
507      <screenshot>
508       <mediaobject>
509        <imageobject>
510         <imagedata contentwidth="12cm" width="12cm" fileref="figures/biosample-tab-2-pool-sample.png" format="PNG"/>
511        </imageobject>
512       </mediaobject>
513      </screenshot>
514     </figure>
515    </listitem>
516   </orderedlist>
517  </sect2>
518  <sect2 id="sample.manage.delete">
519   <title>Deleting/Restoring Samples</title>
520   <para>As for other items in BASE2, Samples can be removed. For a generic overview on how to
521    delete and restore items, refer to section <xref linkend="webclient.items.delete"/></para>
522   <para>To delete, do the following</para>
523   <itemizedlist>
524    <listitem>
525     <para> Select one or more Samples and click <guibutton>Delete</guibutton> button in the menu
526      bar. </para>
527     <para> All the selected Samples have been marked as deleted and are no longer available from
528      the interface. </para>
529     <para> From the <guilabel>view/preset&hellip;</guilabel> select box, ticking the
530       <guilabel>Removed</guilabel> option allows to display those Samples earmarked for deletion.
531      They will be shown with a symbol <guiicon>D</guiicon> in front of them. </para>
532    </listitem>
533    <listitem>
534     <para> Alternately, navigating to the Sample Item View, one can hit the
535      <guibutton>Delete</guibutton> to performed the task. As showen in the next picture, the Sample
536      is then flagged with the <guiicon>This item has been flagged for deletion</guiicon>
537     </para>
538     <figure id="write_docbook_doc.figures.sample-delete">
539      <title>Deleting Samples from the Item View</title>
540      <screenshot>
541     <mediaobject>
542      <imageobject>
543       <imagedata contentwidth="12cm" width="12cm" fileref="figures/sample-delete.png" format="PNG"/>
544      </imageobject>
545     </mediaobject>
546    </screenshot>
547     </figure>
548    </listitem>
549    <listitem>
550     <para>Deletion errors can be easily recovered. Select the item to recover from the List View
551      (be sure to check the <guilabel>removed</guilabel> option in the View/preset.. filter) and hit
552      the <guibutton>Restore</guibutton> to performed the task. </para>
553    </listitem>
554   </itemizedlist>
555   <important>
556    <para>To really delete an item from the database you must use the trashcan. Items deleted from
557     the Trashcan can not be recovered. To learn more about the trashcan function, please refer to
558      <xref linkend="trashcan"/>
559    </para>
560   </important>
561  </sect2>
562 </sect1>
563
564 <sect1 id="extract.manage">
565  <title>Managing Extracts</title>
566  <para>Extract items should be used to describe the events that transform a Sample material in an
567   Extract material.</para>
568  <para>Extracts can be created from Sample items or from one or more Extract items.</para>
569  <para>When an Extract is created from several other Extracts, a Pooling event is performed. A
570   specific section details how to create pooled Extracts</para>
571  <para>During the transformation from Samples to Extracts, it is possible to provide information
572   about the protocol used to perform this task.</para>
573  <para>It is not enforced in BASE2 but it should serve as guidance when devising the granularity of
574   the sample processing task. Also, it is good practice to provide protocol information.</para>
575  <sect2 id="extract.manage.createextractfromsample">
576   <title>Creating Extracts</title>
577   <orderedlist>
578    <listitem>
579     <para>Creating Extracts from the Sample page</para>
580     <para>Following the laboratory workflow, a natural way to create a new Extract is to click on
581      the <guibutton>New extract</guibutton> from the Extract column of the Sample List View.</para>
582     <figure id="write_docbook_doc.figures.sample-create-extract">
583      <title>Creating an Extract from the Sample list view</title>
584      <screenshot>
585       <mediaobject>
586        <imageobject>
587         <imagedata contentwidth="12cm" width="12cm" fileref="figures/sample-create-extract.png" format="PNG"/>
588        </imageobject>
589       </mediaobject>
590      </screenshot>
591     </figure>
592    </listitem>
593    <listitem>
594     <para>Creating Extracts from the Sample List view page</para>
595     <para> Alternately, Extracts can be created directly ysing the Extract create page. To do so,
596      go to <menuchoice>
597       <guimenu>View</guimenu>
598       <guimenuitem>Extracts</guimenuitem>
599      </menuchoice> , Click on <guibutton>New&hellip;</guibutton> button </para>
600     <para> A 'Create' pop-up window opens, it contains 4 tabs: <guilabel>Extract</guilabel>,
601       <guilabel>Parents</guilabel>, <guilabel> Annotations &amp; parameters</guilabel> and
602       <guilabel>Inherited Annotations</guilabel>. </para>
603     <itemizedlist>
604      <listitem>
605       <para>The Extract Tab </para>
606       <para>This tab contains 1 mandatory field for providing the extract name. </para>
607       <para>BASE2 by default assigns names to Extract (by suffixing 'e#' when creating an Extract
608        from an existing Sample or 'New Extract' otherwise) but it is possible to edit it at will</para>
609       <para>There 5 optional fields to provide more detailed information</para>
610       <itemizedlist>
611        <listitem>
612         <para><guilabel>External ID</guilabel>: for instance to report a barcode attached to an
613          extract</para>
614        </listitem>
615        <listitem>
616         <para><guilabel>Original Quantity (ug)</guilabel>: this is meant to report information
617          about the actual mass of biomaterial created</para>
618        </listitem>
619        <listitem>
620         <para><guilabel>Created</guilabel>: a date should be provided. The information can be
621          important when running quality controls on data and account for potential confounding
622          factor (e.g. day effect)</para>
623        </listitem>
624        <listitem>
625         <para><guilabel>Protocol</guilabel>: this a controled field. A select-list displays
626          protocol whose type is '<guilabel>extraction</guilabel>' and which are shared to or owned
627          by the logged-in user. Reporting Protocol should be viewed as a MIAME requirement</para>
628        </listitem>
629        <listitem>
630         <para><guilabel>Description</guilabel>: a free text field to report any information that
631          not can be captured otherwise</para>
632        </listitem>
633       </itemizedlist>
634       <para>Finally, a 7th field <guilabel>Registered</guilabel> is automatically populated with a
635        date at which the sample was entered in BASE2 system.</para>
636       <figure id="write_docbook_doc.figures.extract-tab-1">
637        <title>Extract tab</title>
638        <screenshot>
639         <mediaobject>
640          <imageobject>
641           <imagedata contentwidth="12cm" width="12cm" fileref="figures/extract-tab-1.png" format="PNG"/>
642          </imageobject>
643         </mediaobject>
644        </screenshot>
645       </figure>
646      </listitem>
647      <listitem>
648       <para>The Parents Tab </para>
649       <para>This important tab allows users to select the Extract origin. BASE2 distinguished
650        between 2 cases which are controled by the <guibutton>'pooled'</guibutton> radio-button</para>
651       <orderedlist>
652        <listitem>
653         <para>The Parent is a Sample</para>
654         <para> The <guibutton>pooled</guibutton> radio-button is set to <guilabel>No</guilabel></para>
655         <para> The Sample select button is active and allows users to point to one and only one
656          Sample from which the sample originates from.</para>
657         <figure id="write_docbook_doc.figures.extract-tab-2-select-sample">
658          <title>Parent tab and interaction when pooled button is set to No</title>
659          <screenshot>
660           <mediaobject>
661            <imageobject>
662             <imagedata contentwidth="12cm" width="12cm" fileref="figures/extract-tab-2-select-sample.png" format="PNG"/>
663            </imageobject>
664           </mediaobject>
665          </screenshot>
666         </figure>
667        </listitem>
668        <listitem>
669         <para>The Parent is another Extract</para>
670         <para> The <guibutton>pooled</guibutton> radio-button has to be set to
671          <guilabel>Yes</guilabel></para>
672         <para>Upon selection, the Samples select button is deactivated and the Extracts box and
673          button are activated.</para>
674         <para>This allows users to specify one or more extracts to be selected from the Extract
675          list View page.</para>
676         <figure id="write_docbook_doc.figures.extract-tab-2-select-extract">
677          <title>Parent tab and interaction when pooled button is set to Yes</title>
678          <screenshot>
679           <mediaobject>
680            <imageobject>
681              <imagedata contentwidth="12cm" width="12cm" fileref="figures/extract-tab-2-select-extract.png" format="PNG"/>
682            </imageobject>
683           </mediaobject>
684          </screenshot>
685         </figure>
686        </listitem>
687       </orderedlist>
688      </listitem>
689      <listitem>
690       <para>Annotations &amp; parameters </para>
691       <para>As seen in the BioSource and Sample sections, this tab allows users to supply further
692        information about the Extract, provided they have defined Annotation Types to annotation
693        Extract items or have such elements shared to them.</para>
694       <para>The display of Annotation Type can be filtered based on the Annotation Type Category
695        they belong to.</para>
696       <important>
697        <para> In order to use this feature, Annotation Type must be declared and made available. To
698         learn more about Annotation Types, please refer to <xref linkend="annotations"/>
699        </para>
700       </important>
701       <para>To provide a value for a given annotation type, simply click on it an use the input
702        field or select a value from the drop-down lists or radio buttons.</para>
703       <figure id="write_docbook_doc.figures.extract-tab-3">
704        <title>Annotations &amp; parameters</title>
705        <screenshot>
706         <mediaobject>
707          <imageobject>
708           <imagedata contentwidth="12cm" width="12cm" fileref="figures/extract-tab-3.png" format="PNG"/>
709          </imageobject>
710         </mediaobject>
711        </screenshot>
712       </figure>
713      </listitem>
714      <listitem>
715       <para>Inherited Annotations case1 </para>
716       <para>The next picture shows </para>
717       <figure id="write_docbook_doc.figures.extract-tab-4">
718        <title>Inherited Annotations</title>
719        <screenshot>
720         <mediaobject>
721          <imageobject>
722           <imagedata contentwidth="12cm" width="12cm" fileref="figures/extract-tab-4.png" format="PNG"/>
723          </imageobject>
724         </mediaobject>
725        </screenshot>
726       </figure>
727      </listitem>
728     </itemizedlist>
729    </listitem>
730   </orderedlist>
731  </sect2>
732  <sect2 id="extract.manage.createextractpool">
733   <title>Creating Pooled Extracts</title>
734   <para>It is common practice when biological material is scarce to pool extracts from equivalent
735    sources. BASE2 provides mechanisms to report on such practice. This section details how.</para>
736   <para>There are 2 ways to create pooled samples in BASE2:</para>
737   <orderedlist>
738    <listitem>
739     <para>Using the Pooled radio button option from the Extract Create page, and this has been
740      shown already.</para>
741    </listitem>
742    <listitem>
743     <para>Using the Pool button in the Menu bar</para>
744     <para>The Sample List View page menu bar contains an addition <guibutton>Pool&hellip;</guibutton>
745      <inlinemediaobject>
746       <imageobject>
747        <imagedata fileref="figures/new_pooled.gif" format="GIF"/>
748       </imageobject>
749      </inlinemediaobject> button, the usage of which is detailed now.</para>
750     <para>The <guibutton>Pool&hellip;</guibutton>
751      <inlinemediaobject>
752       <imageobject>
753        <imagedata fileref="figures/new_pooled.gif" format="GIF"/>
754       </imageobject>
755      </inlinemediaobject> button allows users to create Pooled Extracts by selecting the list of
756      Extracts used to derived a new Extract. Users simply to tick to boxes in front of each
757      relevant Extract and click the <guibutton>Pool...</guibutton></para>
758     <para>This provides an easy and simple way to create pooled Extracts. The result of such
759      process is the creation of a New Extract, in which, when navigating to the Parent tab, shows
760      that all the Extracts involved are already set and listed in the Extract box of the tab.</para>
761     <figure id="write_docbook_doc.figures.biosample-tab-2-pool-extract">
762      <title>Pooling of Extracts</title>
763      <screenshot>
764       <mediaobject>
765        <imageobject>
766         <imagedata contentwidth="12cm" width="12cm" fileref="figures/extract-tab-2-pool-extract.png" format="PNG"/>
767        </imageobject>
768       </mediaobject>
769      </screenshot>
770     </figure>
771    </listitem>
772   </orderedlist>
773  </sect2>
774  <sect2 id="extract.manage.delete">
775   <title>Deleting/Restoring Extracts</title>
776   <para>As for other items in BASE2, Extracts can be removed. For a generic overview on how to
777    delete and restore items, refer to section <xref linkend="webclient.items.delete"/>
778   </para>
779   <para>To delete, do the following</para>
780   <itemizedlist>
781    <listitem>
782     <para> Select one or more Extract and click <guibutton>Delete</guibutton> button in the menu
783      bar.</para>
784     <para> All the selected Extracts have been marked as deleted and are no longer available from
785      the interface.</para>
786     <para> Only by selecting from the <guilabel>view/preset&hellip;</guilabel> select box the
787       <guilabel>Removed</guilabel> option, one can see those of the Extracts earmarked for
788      deletion. They will be shown with a symbol in front of them.</para>
789    </listitem>
790    <listitem>
791     <para> Alternately, navigating to the Extract Item View, one can hit the
792      <guibutton>Delete</guibutton> to performed the task.</para>
793     <para> As shown in the next picture, the Extract is then marked with the <guilabel>This item
794       has been flagged for deletion</guilabel>
795     </para>
796     <figure id="write_docbook_doc.figures.extract-delete">
797      <title>Deleting Extracts from the Item View</title>
798      <screenshot>
799       <mediaobject>
800        <imageobject>
801         <imagedata contentwidth="12cm" width="12cm" fileref="figures/extract-delete.png" format="PNG"/>
802        </imageobject>
803       </mediaobject>
804      </screenshot>
805     </figure>
806    </listitem>
807    <listitem>
808     <para>Deletion errors at this stage can be easily recovered. Select the item to recover from
809      the List View (be sure to check the <guilabel>removed</guilabel> option in the View/preset..
810      filter) and hit the <guibutton>Restore</guibutton> to performed the task. </para>
811    </listitem>
812   </itemizedlist>
813   <important>
814    <para>To really delete an item from the database you must use the trashcan. Items deleted from
815     the Trashcan can not be recovered. To learn more about the trashcan function, please refer to
816      <xref linkend="trashcan"/>
817    </para>
818   </important>
819  </sect2>
820 </sect1>
821
822
823
824 <sect1 id="label">
825  <title>Managing Labels</title>
826
827  <sect2 id="label.browse">
828   <title>Browsing Labels</title>
829   <para>Before attempting to create Labeled Extracts, users should make sure that the appropriate
830    Label object is present in BASE2</para>
831   <para>To browse the list of Labels, go to <menuchoice>
832     <guimenu>View</guimenu>
833     <guimenuitem>Labels</guimenuitem>
834    </menuchoice> It is wise to select the clear filter option or select the <guilabel>shared to
835    me</guilabel> option from the view/preset select box in order to view all different dyes.</para>
836   <para>Clicking on any of item opens an item view page</para>
837   <figure id="write_docbook_doc.figures.label-itemview">
838    <title>The Label Item View Page</title>
839    <screenshot>
840     <mediaobject>
841      <imageobject>
842       <imagedata contentwidth="12cm" width="12cm" fileref="figures/label-itemview.png" format="PNG"/>
843      </imageobject>
844     </mediaobject>
845    </screenshot>
846   </figure>
847   <para>Note the <guibutton>New labeled extract</guibutton> button available from this page. For
848    more detailed about creating Labeled extracts, see <xref linkend="labeledextract.manage"/></para>
849
850  </sect2>
851  <sect2 id="label.create">
852   <title>Creating Labels</title>
853   <para> Click on <guibutton>New&hellip;</guibutton> button, a pop-up window opens. Fill in
854    Name and description if required. Label item are very simple object and do not bear association
855    to Annotation Type. </para>
856  </sect2>
857 </sect1>
858 <sect1 id="labeledextract.manage">
859  <title>Managing Labeled Extracts</title>
860  <para>Labeled Extract items should be used to describe the event that transformed a Extract
861   material in a Labeled Extract material.</para>
862  <para>Labeled extracts can be created from Extract items or from one or more Labeled extract
863   items.</para>
864  <para>When a Labeled Extract is created from several other Labeled Extracts, a Pooling event is
865   performed. A specific section details how to create pooled Labeled Extracts</para>
866  <para>During the transformation from Extracts to Labeled Extracts, it is possible to provide
867   information about the protocol used to perform this task.</para>
868  <para>It is not enforced in BASE2 but it should serve as guidance when devising the granularity of
869   the extract processing task. Also, it is good practice to provide protocol information.</para>
870  <sect2 id="labeledextract.manage.createlabeledextractfromextract">
871   <title>Creating Labeled Extracts</title>
872   <orderedlist>
873    <listitem>
874     <para>Creating Labeled Extracts from the Extract page</para>
875     <para>Following the laboratory workflow, a natural way to create a Labeled Extract is to click
876      on the <guibutton>New labeled extract</guibutton> from the Labeled Extract column of the
877      Extract List View.</para>
878     <figure id="write_docbook_doc.figures.sample-create-labeledextract">
879      <title>Creating a Labeled Extract from the Extract List View</title>
880      <screenshot>
881       <mediaobject>
882        <imageobject>
883         <imagedata contentwidth="12cm" width="12cm" fileref="figures/sample-create-labeledextract.png" format="PNG"/>
884        </imageobject>
885       </mediaobject>
886      </screenshot>
887     </figure>
888    </listitem>
889    <listitem>
890     <para>Creating Labeled Extracts from the Extract Item View page</para>
891     <para> Alternately, Labeled Extracts can be created directly using the Labeled Extract create
892      page. To do so, go to <menuchoice>
893       <guimenu>View</guimenu>
894       <guimenuitem>Labeled Extracts</guimenuitem>
895      </menuchoice> , Click on <guibutton>New&hellip;</guibutton> button </para>
896     <para> A 'Create' pop-up window opens, it contains 4 tabs: <guilabel>Labeled
897      Extract</guilabel>, <guilabel>Parents</guilabel>, <guilabel> Annotations &amp;
898      parameters</guilabel> and <guilabel>Inherited Annotations</guilabel>. </para>
899     <itemizedlist>
900      <listitem>
901       <para>The Labeled Extract Tab </para>
902       <para>This tab contains 2 mandatory fields, one for providing the Labeled Extract
903         <guilabel>Name</guilabel>, the other one <guilabel>Label</guilabel> to specify which dye or
904        marker was used in the labeling reaction.</para>
905       <para> BASE2 by default assigns names to Labeled Extract(by suffixing 'lbe#' when creating a
906        Labeled Extract from an existing Extract or 'New labeled extract' otherwise) but it is
907        possible to edit it at will</para>
908       <para>There 5 optional fields to provide more detailed information</para>
909       <itemizedlist>
910        <listitem>
911         <para><guilabel>External ID</guilabel>: for instance to report a barcode attached to an
912          extract</para>
913        </listitem>
914        <listitem>
915         <para><guilabel>Original Quantity (ug)</guilabel>: this is meant to report information
916          about the actual mass of biomaterial created</para>
917        </listitem>
918        <listitem>
919         <para><guilabel>Created</guilabel>: a date should be provided. The information can be
920          important when running quality controls on data and account for potential confounding
921          factor (e.g. day effect)</para>
922        </listitem>
923        <listitem>
924         <para><guilabel>Protocol</guilabel>: this a controled field. A select-list displays
925          protocol whose type is '<guilabel>labeling</guilabel>' and which are shared to or owned by
926          the logged-in user. Reporting Protocol should be viewed as a MIAME requirement</para>
927        </listitem>
928        <listitem>
929         <para><guilabel>Description</guilabel>: a free text field to report any information that
930          can not be captured otherwise</para>
931        </listitem>
932       </itemizedlist>
933       <para>Finally, a 7th field <guilabel>Created</guilabel> is automatically populated with a
934        date at which the Labeled Extract was actually entered in BASE2 system.</para>
935       <figure id="write_docbook_doc.figures.labeledextract-tab-1">
936        <title>Labeled Extract tab</title>
937        <screenshot>
938         <mediaobject>
939          <imageobject>
940           <imagedata contentwidth="12cm" width="12cm" fileref="figures/labeledextract-tab-1.png" format="PNG"/>
941          </imageobject>
942         </mediaobject>
943        </screenshot>
944       </figure>
945      </listitem>
946      <listitem>
947       <para>The Parents Tab </para>
948       <para>This important tab allows users to select the Labeled Extract origin. BASE2
949        distinguished between 2 cases which are controled by the <guibutton>'pooled'</guibutton>
950        radio-button</para>
951       <orderedlist>
952        <listitem>
953         <para>The Parent is an Extract</para>
954         <para> The <guibutton>pooled</guibutton> radio-button is set to <guilabel>No</guilabel></para>
955         <para> The Extract select button is active and allows users to point to one and only one
956          Extract from which the Labeled Extract originates from.</para>
957         <figure id="write_docbook_doc.figures.labeledextract-tab-2-select-extract">
958          <title>Parent tab and interaction when pooled button is set to No</title>
959          <screenshot>
960           <mediaobject>
961            <imageobject>
962             <imagedata contentwidth="12cm" width="12cm" fileref="figures/labeledextract-tab-2-select-extract.png" format="PNG"/>
963            </imageobject>
964           </mediaobject>
965          </screenshot>
966         </figure>
967        </listitem>
968        <listitem>
969         <para>The Parent is another Labeled Extract</para>
970         <para> The <guibutton>pooled</guibutton> radio-button has to be set to
971          <guilabel>Yes</guilabel></para>
972         <para>Upon selection, the Extract select button is deactivated and the Labeled Extracts box
973          and button are activated. </para>
974         <para>This allows users to specify one or more extracts to be selected from the Labeled
975          Extract list View page. </para>
976         <figure id="write_docbook_doc.figures.labeledextract-tab-2-select-labeledextract">
977          <title>Parent tab and interaction when pooled button is set to Yes</title>
978          <screenshot>
979           <mediaobject>
980            <imageobject>
981             <imagedata contentwidth="12cm" width="12cm" fileref="figures/labeledextract-tab-2-select-labeledextract.png" format="PNG"/>
982            </imageobject>
983           </mediaobject>
984          </screenshot>
985         </figure>
986        </listitem>
987       </orderedlist>
988      </listitem>
989      <listitem>
990       <para>Annotations &amp; parameters </para>
991       <para>As seen in the BioSource and Sample sections, this tab allows users to further supply
992        information about the labeled extract provided they have defined annotation types to
993        annotate Labeled Extract items or have such elements shared to them.</para>
994       <para>The display of Annotation Types can be filtered based on the Annotation Type Categories
995        they belong to.</para>
996       <important>
997        <para> In order to use this feature, Annotation Type must be declared and made available. To
998         learn more about Annotation Types, please refer to <xref linkend="annotations"/>
999        </para>
1000       </important>
1001       <para>To provide a value for a given annotation type, simply click on it an use the input
1002        field or select a value from the drop-down lists or radio buttons.</para>
1003       <figure id="write_docbook_doc.figures.labeledextract-tab-3">
1004        <title>Annotations &amp; parameters</title>
1005        <screenshot>
1006         <mediaobject>
1007          <imageobject>
1008           <imagedata contentwidth="12cm" width="12cm" fileref="figures/labeledextract-tab-3.png" format="PNG"/>
1009          </imageobject>
1010         </mediaobject>
1011        </screenshot>
1012       </figure>
1013      </listitem>
1014      <listitem>
1015       <para>Inherited Annotations case1 </para>
1016       <para>The next picture shows </para>
1017       <figure id="write_docbook_doc.figures.labeledextract-tab-4">
1018        <title>Inherited Annotations</title>
1019        <screenshot>
1020         <mediaobject>
1021          <imageobject>
1022           <imagedata contentwidth="12cm" width="12cm" fileref="figures/labeledextract-tab-4.png" format="PNG"/>
1023          </imageobject>
1024         </mediaobject>
1025        </screenshot>
1026       </figure>
1027      </listitem>
1028     </itemizedlist>
1029    </listitem>
1030   </orderedlist>
1031  </sect2>
1032  <sect2 id="labeledextract.manage.createelabeledxtract.pool">
1033   <title>Creating Pooled Labeled Extracts</title>
1034   <para>It is common practice when biological material is scarce to pool extracts from equivalent
1035    sources. BASE2 provides mechanisms to report on such practice.</para>
1036   <para>This section details how.</para>
1037   <para>There are 2 ways to create pooled Labeled Extracts in BASE2</para>
1038   <orderedlist>
1039    <listitem>
1040     <para>Using the Pooled radio button option from the Labeled Extract Create page, and this has
1041      been shown already </para>
1042    </listitem>
1043    <listitem>
1044     <para>Using the Pool button in the Menu bar</para>
1045     <para>The Labeled Extracts List View page menu bar contains an addition
1046       <guibutton>Pool&hellip;</guibutton> button, the usage of which is detailed now.</para>
1047     <para>The <guibutton>Pool&hellip;</guibutton> button <inlinemediaobject>
1048       <imageobject>
1049        <imagedata fileref="figures/new_pooled.gif" format="GIF"/>
1050       </imageobject>
1051      </inlinemediaobject> allows users to create Pooled Labeled Extracts by selecting the list of
1052      Labeled Extracts used to derived a new Labeled Extract. Users simply have to tick to boxes in
1053      front of each relevant Labeled Extract and click the <guibutton>Pool...</guibutton></para>
1054     <para>This provides an easy and simple way to create pooled Labeled Extracts. The result of
1055      such process is the creation of a New Labeled Extract, in which, when navigating to the Parent
1056      tab, shows that all the Labeled Extracts involved are already set and listed in the Labeled
1057      Extract box of the tab.</para>
1058     <figure id="write_docbook_doc.figures.labeledextract-tab-2-pool-labeledextract">
1059      <title>Pooling of Labeled Extracts:</title>
1060      <screenshot>
1061       <mediaobject>
1062        <imageobject>
1063         <imagedata contentwidth="12cm" width="12cm" fileref="figures/labeledextract-tab-2-pool-labeledextract.png" format="PNG"/>
1064        </imageobject>
1065       </mediaobject>
1066      </screenshot>
1067     </figure>
1068    </listitem>
1069   </orderedlist>
1070  </sect2>
1071  <sect2 id="labeledextract.manage.delete">
1072   <title>Deleting/Restoring Labeled Extracts</title>
1073   <para>As for other items in BASE2, Labeled Extracts can be deleted. For a generic overview on how
1074    to delete and restore items, refer to section <xref linkend="webclient.items.delete"/></para>
1075   <para>To delete, do the following</para>
1076   <itemizedlist>
1077    <listitem>
1078     <para> Select one or more Labeled Extract and click <guibutton>Delete</guibutton> button in the
1079      menu bar. </para>
1080     <para> All the selected Labeled Extracts have been marked as deleted and are no longer
1081      available from the interface. </para>
1082     <para> Only by selecting from the <guilabel>view/preset&hellip;</guilabel> select box the
1083       <guilabel>Removed</guilabel> option, one can see those of the Labeled Extracts earmarked for
1084      deletion. They will be shown with a symbol in front of them. </para>
1085    </listitem>
1086    <listitem>
1087     <para> Alternately, navigating to the Labeled Extract Item View, one can hit the
1088       <guibutton>Delete</guibutton> to performed the task. As showed in the next picture, the
1089      Labeled Extract is then marked with the <inlinemediaobject>
1090       <imageobject>
1091        <imagedata fileref="figures/deleted.gif" format="GIF"/>
1092       </imageobject>
1093      </inlinemediaobject>
1094      <guiicon>This item has been flagged for deletion</guiicon>
1095     </para>
1096     <figure id="write_docbook_doc.figures.labeledextract-delete">
1097      <title>Deleting Labeled Extracts from the Item View</title>
1098      <screenshot>
1099       <mediaobject>
1100        <imageobject>
1101         <imagedata contentwidth="12cm" width="12cm" fileref="figures/labeledextract-delete.png" format="PNG"/>
1102        </imageobject>
1103       </mediaobject>
1104      </screenshot>
1105     </figure>
1106    </listitem>
1107    <listitem>
1108     <para>Deletion errors at this stage can be easily recovered. Select the item to recover from
1109      the List View (be sure to check the <guilabel>Removed</guilabel> option in the View/preset..
1110      filter) and hit the <guibutton>Restore</guibutton> to performed the task. </para>
1111    </listitem>
1112   </itemizedlist>
1113   <important>
1114    <para>To really delete an item from the database you must use the trashcan. Items deleted from
1115     the Trashcan can not be recovered. To learn more about the trashcan function, please refer to
1116      <xref linkend="trashcan"/>
1117    </para>
1118   </important>
1119  </sect2>
1120 </sect1>
1121 <sect1 id="hybridization.manage">
1122  <title>Managing Hybridizations</title>
1123  <para> An hybridization event corresponds to the application of one or more labeled extracts
1124   materials to a microarray slide under conditions detailed in hybridization protocols. </para>
1125  <para>In BASE2, there are 3 possible routes to create an hybridization object.</para>
1126  <sect2 id="hybridization.manage.create">
1127   <title>Creating Hybridizations</title>
1128   <orderedlist>
1129    <listitem>
1130     <para>Creating Hybridization from the Labeled Extract List View page</para>
1131     <para>Select at least one Labeled Extract by ticking to selection boxes before the name field.</para>
1132     <para>Click on the <guibutton>New hybridzation (to be changed)</guibutton> from the menu bar of
1133      Labeled Extract list view.</para>
1134     <figure id="write_docbook_doc.figures.hyb-create-labeledlistview">
1135      <title>Creating a Hybridization from the Labeled Extract List View</title>
1136      <screenshot>
1137       <mediaobject>
1138        <imageobject>
1139         <imagedata contentwidth="12cm" width="12cm" fileref="figures/hyb-create-labeledlistview.png" format="PNG"/>
1140        </imageobject>
1141       </mediaobject>
1142      </screenshot>
1143     </figure>
1144    </listitem>
1145    <listitem>
1146     <para>Creating Hybridization from the Labeled Extract Item View page</para>
1147     <para>After having selected a Labeled Extract and displayed it in the Item View, Click on the
1148       <guibutton>New hybridization</guibutton> button from the Menu bar of the Labeled Extract Item
1149      View.</para>
1150     <figure id="write_docbook_doc.figures.hyb-create-labeleditemview">
1151      <title>Creating a Hybridization from the Labeled Extract Item View</title>
1152      <screenshot>
1153       <mediaobject>
1154        <imageobject>
1155         <imagedata contentwidth="12cm" width="12cm" fileref="figures/hyb-create-labeleditemview.png" format="PNG"/>
1156        </imageobject>
1157       </mediaobject>
1158      </screenshot>
1159     </figure>
1160    </listitem>
1161    <listitem>
1162     <para>Creating Hybridizations from the Hybridization List View page</para>
1163     <para> Hybridizations can be created directly using the Hybridization create page. To do so, go
1164      to <menuchoice>
1165       <guimenu>View</guimenu>
1166       <guimenuitem>Hybridizations</guimenuitem>
1167      </menuchoice> , Click on <guibutton>New&hellip;</guibutton>
1168     </para>
1169     <figure id="write_docbook_doc.figures.hyb-create">
1170      <title>Creating Hybridizations from the Hybridization List View</title>
1171      <screenshot>
1172       <mediaobject>
1173        <imageobject>
1174         <imagedata contentwidth="12cm" width="12cm" fileref="figures/hyb-create.png" format="PNG"/>
1175        </imageobject>
1176       </mediaobject>
1177      </screenshot>
1178     </figure>
1179     <para> Irrespective of the methods chosen to create the Hybridization item, A 'Create' pop-up
1180      window will open. It contains 4 distinct tabs: <guilabel>Hybridization</guilabel>,
1181       <guilabel>Parents</guilabel>, <guilabel> Annotations &amp; parameters</guilabel> and
1182       <guilabel>Inherited Annotations</guilabel>. </para>
1183     <itemizedlist>
1184      <listitem>
1185       <para>The Hybridization Tab </para>
1186
1187       <variablelist>
1188        <varlistentry>
1189         <term>
1190          <interface>Name</interface>
1191         </term>
1192         <listitem>
1193          <para> New Hybridization is BASE2 default name but it is strongly advise to provide a
1194           meaningful and unique name as it matters for tab2mage export to function properly. </para>
1195          <para>There are 5 optional fields to provide more detailed information</para>
1196
1197         </listitem>
1198        </varlistentry>
1199
1200        <varlistentry>
1201         <term>
1202          <guilabel>Created</guilabel>
1203         </term>
1204         <listitem>
1205          <para>A date should be provided. The information can be important when running quality
1206           controls on data and account for potential confounding factor (e.g. to account for a day
1207           effect)</para>
1208         </listitem>
1209        </varlistentry>
1210
1211        <varlistentry>
1212         <term>
1213          <guilabel>Protocol</guilabel>
1214         </term>
1215         <listitem>
1216          <para>This is a controled field. A select-list displays protocol whose type is
1217            '<guilabel>hybridization</guilabel>' and which are shared to or owned by the logged-in
1218           user.</para>
1219          <important>
1220           <para> Reporting Protocols should be viewed as a MIAME requirement </para>
1221          </important>
1222         </listitem>
1223        </varlistentry>
1224
1225        <varlistentry>
1226         <term>
1227          <guilabel>Hardware</guilabel>
1228         </term>
1229         <listitem>
1230          <para>This is a controled field. A select-list displays Hardware whose type is
1231            '<guilabel>Hybridization station</guilabel>' and which are shared to or owned by the
1232           logged-in user.</para>
1233         </listitem>
1234        </varlistentry>
1235
1236        <varlistentry>
1237         <term>
1238          <guilabel>Array Slide</guilabel>
1239         </term>
1240         <listitem>
1241          <para>This is meant to specify the actual microarray slide.</para>
1242          <note>
1243           <para>Ideally, The Array Slides should have been created but for those users with
1244            permission to do, Array Slides could be generated at that point.</para>
1245          </note>
1246         </listitem>
1247        </varlistentry>
1248
1249        <varlistentry>
1250         <term>
1251          <guilabel>Description</guilabel>
1252         </term>
1253         <listitem>
1254          <para>A free text field to report any information that can not be captured
1255          otherwise</para>
1256         </listitem>
1257        </varlistentry>
1258
1259        <varlistentry>
1260         <term>
1261          <guilabel>Registered</guilabel>
1262         </term>
1263         <listitem>
1264          <para>This 7th field is automatically populated with a date at which the sample was
1265           entered in BASE2 system.</para>
1266         </listitem>
1267        </varlistentry>
1268       </variablelist>
1269
1270       <figure id="write_docbook_doc.figures.hybridization-tab-1">
1271        <title>Hybridization tab</title>
1272        <screenshot>
1273         <mediaobject>
1274          <imageobject>
1275           <imagedata contentwidth="12cm" width="12cm" fileref="figures/hybridization-tab-1.png" format="PNG"/>
1276          </imageobject>
1277         </mediaobject>
1278        </screenshot>
1279       </figure>
1280      </listitem>
1281      <listitem>
1282       <para>The Labeled Extract Tab </para>
1283       <para>This important tab allows users to select the Labeled Extracts applied to an Array
1284        Slide, and specify the amount of material used, expressed in microgram.</para>
1285       <figure id="write_docbook_doc.figures.hybridization-tab-2">
1286        <title>Labeled Extract tab</title>
1287        <screenshot>
1288         <mediaobject>
1289          <imageobject>
1290           <imagedata contentwidth="12cm" width="12cm" fileref="figures/hybridization-tab-2.png" format="PNG"/>
1291          </imageobject>
1292         </mediaobject>
1293        </screenshot>
1294       </figure>
1295      </listitem>
1296      <listitem>
1297       <para>Annotations &amp; parameters </para>
1298       <para>As seen in the BioSource and Sample sections, this tab allows users to supply further
1299        information about the hybridization provided annotation types have been defined or shared to
1300        annotate Hybridization items. The display of Annotation Types can be filtered based on the
1301        Annotation Type Category they belong to.</para>
1302       <important>
1303        <para> In order to use this feature, Annotation Type must be declared and made available. To
1304         learn more about Annotation Types, please refer to <xref linkend="annotations"/>
1305        </para>
1306       </important>
1307       <para>To provide a value for a given annotation type, simply click on it and use the input
1308        field or select a value from the drop-down lists or radio buttons.</para>
1309       <para>A caption also reminds users if Annotation Types are parameters <inlinemediaobject>
1310         <imageobject>
1311          <imagedata fileref="figures/parameter.gif" format="GIF"/>
1312         </imageobject>
1313        </inlinemediaobject>and if annotation values have already been supplied, marked by the <inlinemediaobject>
1314         <imageobject>
1315          <imagedata fileref="figures/annotated.gif" format="GIF"/>
1316         </imageobject>
1317        </inlinemediaobject> logo.</para>
1318       <figure id="write_docbook_doc.figures.hybridization-tab-3">
1319        <title>Annotations &amp; parameters</title>
1320        <screenshot>
1321         <mediaobject>
1322          <imageobject>
1323           <imagedata contentwidth="12cm" width="12cm" fileref="figures/hybridization-tab-3.png" format="PNG"/>
1324          </imageobject>
1325         </mediaobject>
1326        </screenshot>
1327       </figure>
1328      </listitem>
1329      <listitem>
1330       <para>Inherited Annotations </para>
1331       <para>The next screenshot shows a typical view of the functionality.</para>
1332       <figure id="write_docbook_doc.figures.hybridization-tab-4">
1333        <title>Inherited Annotations</title>
1334        <screenshot>
1335         <mediaobject>
1336          <imageobject>
1337           <imagedata contentwidth="12cm" width="12cm" fileref="figures/hybridization-tab-4.png" format="PNG"/>
1338          </imageobject>
1339         </mediaobject>
1340        </screenshot>
1341       </figure>
1342       <para> Note the tags used to distinguish between Annotation Types which are parameters noted <inlinemediaobject>
1343         <imageobject>
1344          <imagedata fileref="figures/parameter.gif" format="GIF"/>
1345         </imageobject>
1346        </inlinemediaobject> and those which are Biomaterial Characteristics,noted <inlinemediaobject>
1347         <imageobject>
1348          <imagedata fileref="figures/annotation.gif" format="GIF"/>
1349         </imageobject>
1350        </inlinemediaobject></para>
1351      </listitem>
1352     </itemizedlist>
1353    </listitem>
1354   </orderedlist>
1355  </sect2>
1356  <sect2 id="hybridization.manage.viewedit">
1357   <title>Viewing/Editing Hybridizations</title>
1358   <para>As for other items in BASE2, Hybridizations can be edited. To do so, do the following</para>
1359   <itemizedlist>
1360    <listitem>
1361     <para> Press and hold one of the <keycap>CTRL</keycap>, <keycap>ALT</keycap> or
1362      <keycap>SHIFT</keycap> keys while clicking on the name of an Hybridization Item, which is a
1363      live link. </para>
1364    </listitem>
1365    <listitem>
1366     <para> Alternately, navigating to the Hybridization Item View, one can hit the
1367      <guibutton>Edit</guibutton> to performed the task.</para>
1368    </listitem>
1369
1370    <listitem>
1371     <para>The Hybridization item View summarizes key information such as the list of
1372       <guilabel>Labeled Extracts</guilabel>, and the list of associated <guilabel>Scans</guilabel>.
1373      Both are available as hyperlinks to allow quick and easy navigation.</para>
1374     <figure id="write_docbook_doc.figures.hybridization-itemview">
1375      <title>Hardware Item View</title>
1376      <screenshot>
1377       <mediaobject>
1378        <imageobject>
1379         <imagedata contentwidth="10cm" width="10cm" fileref="figures/hybridization-itemview.png" format="PNG"/>
1380        </imageobject>
1381       </mediaobject>
1382      </screenshot>
1383     </figure>
1384    </listitem>
1385   </itemizedlist>
1386
1387  </sect2>
1388
1389  <sect2 id="hybridization.manage.delete">
1390   <title>Deleting/Restoring Hybridizations</title>
1391   <para>As for other items in BASE2, Hybridizations can be deleted. For a generic overview on how
1392    to delete and restore items, refer to section <xref linkend="webclient.items.delete"/>
1393   </para>
1394
1395   <para>To delete, do the following</para>
1396   <itemizedlist>
1397    <listitem>
1398     <para> Select one or more Hybridization Items and click on the <guibutton>Delete</guibutton>
1399      button in the menu bar. </para>
1400     <para> All the selected Hybridizations have been marked as deleted and are no longer available
1401      from the interface. </para>
1402     <para> Only by selecting from the <guilabel>view/preset&hellip;</guilabel> select box the
1403       <guilabel>Removed</guilabel> option, one can see those of the Hybridizations earmarked for
1404      deletion. They will be shown with a symbol in front of them. </para>
1405    </listitem>
1406    <listitem>
1407     <para> Alternately, navigating to the Hybridization Item View, one can hit the
1408       <guibutton>Delete</guibutton> to performed the task. As shown in the next picture, the
1409      Hybridization is then marked with the <inlinemediaobject>
1410       <imageobject>
1411        <imagedata fileref="figures/deleted.gif" format="GIF"/>
1412       </imageobject>
1413      </inlinemediaobject><guilabel>This item has been flagged for deletion</guilabel>
1414     </para>
1415     <figure id="write_docbook_doc.figures.hybridization-delete">
1416      <title>Deleting Hybridizations from the Hybridization Item View</title>
1417      <screenshot>
1418       <mediaobject>
1419        <imageobject>
1420         <imagedata contentwidth="10cm" width="10cm" fileref="figures/hybridization-delete.png" format="PNG"/>
1421        </imageobject>
1422       </mediaobject>
1423      </screenshot>
1424     </figure>
1425    </listitem>
1426   </itemizedlist>
1427   <important>
1428    <para>To really delete an item from the database you must use the trashcan. Items deleted from
1429     the Trashcan can not be recovered. To learn more about the trashcan function, please refer to
1430      <xref linkend="trashcan"/>
1431    </para>
1432   </important>
1433  </sect2>
1434 </sect1>
1435</chapter>
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