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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 4477 2008-09-05 15:15:25Z jari $
7 
8  Copyright (C) 2007 Peter Johansson, Nicklas Nordborg, Philippe Rocca-Serra, Martin Svensson
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
14  modify it under the terms of the GNU General Public License
15  as published by the Free Software Foundation; either version 3
16  of the License, or (at your option) any later version.
17 
18  BASE is distributed in the hope that it will be useful,
19  but WITHOUT ANY WARRANTY; without even the implied warranty of
20  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
21  GNU General Public License for more details.
22 
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,
26  Boston, MA  02111-1307, USA.
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    <itemizedlist>
44      <listitem>
45        <simpara>
46          Biosources correspond to the native biological entity used in an experiment
47          prior to any treatment.
48        </simpara>
49      </listitem>
50      <listitem>
51        <simpara>
52          Samples are central to BASE2 to describe the sample processing. So samples can
53          be created from other samples if user want to track sample processing event in a
54          finely granular fashion.
55        </simpara>
56      </listitem>
57      <listitem>
58        <simpara>
59          Extracts correspond to nucleic acid material extracted from a tissue sample or a
60          cell culture sample.
61        </simpara>
62      </listitem>
63      <listitem>
64        <simpara>
65          Labeled extracts correspond to nucleic acid materials which have undergone a
66          marking procedure using a fluorescent or radioactive compound for detection in a
67          microarray assay.
68        </simpara>
69      </listitem>
70    </itemizedlist>
71    <para>
72      BASE2 allows users to create any of the these entities fairly freely, however it is
73      expected that users will follow the natural path of the laboratory workflow.
74    </para>
75    <tip>
76      <para>
77        It is highly recommended that you have read
78        <xref linkend="webclient.items" />
79        before continuing with this chapter.
80      </para>
81    </tip>
82  </sect1>
83  <sect1 id="biomaterials.biosources">
84    <title>Biosources</title>
85
86
87    <sect2 id="biomaterials.biosources.properties">
88      <title>Properties</title>
89      <sect3 id="biomaterials.biosources.properties.biosource">
90        <title>Biosource</title>
91        <para>This tab allows users to enter essential information about a biosource.</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>A free text description can be supplied using this field.</para>
122            </listitem>
123          </varlistentry>
124        </variablelist>
125        <figure id="write_docbook_doc.figures.biosource-tab-1">
126          <title>Biosource properties</title>
127          <screenshot>
128            <mediaobject>
129              <imageobject>
130                <imagedata 
131                  fileref="figures/biosource-tab-1.png" format="PNG" />
132              </imageobject>
133            </mediaobject>
134          </screenshot>
135        </figure>
136      </sect3>
137      <sect3 id="biomaterials.biosource.properties.annotations">
138        <title>Annotations</title>
139        <para>
140          This allows BASE2 users to use annotation types to refine biosource description.
141          More about annotating items can be read in
142          <xref linkend="annotations.annotating" />
143          .
144        </para>
145      </sect3>
146    </sect2>
147  </sect1>
148  <sect1 id="biomaterial.samples">
149    <title>Samples</title>
150    <para>
151      Samples result from processing events applied to biosource material or other samples
152      before they are turned into an extract. In other words, samples can be created from
153      biosource items or from one or more sample items.When a sample is created from several
154      other samples, a pooling event is performed.
155    </para>
156    <para>
157      For every step of transformation from biosource to sample, it is possible to provide
158      information about the protocol used to perform this task. It is not enforced in BASE2
159      but it should serve as guidance when devising the granularity of the sample processing
160      task. Also, it is good practice to provide protocol information to ensure MIAME
161      compliance.
162    </para>
163    <para>
164      Use
165      <menuchoice>
166        <guimenu>View</guimenu>
167        <guimenuitem>Biosource</guimenuitem>
168      </menuchoice>
169      to get to the list of biosources.
170    </para>
171    <sect2 id="biomaterials.samples.create">
172      <title>Create sample</title>
173      <para>
174        Beside the common way, using the &gbNew; button, a sample can be created in one of
175        the following ways:
176        <variablelist>
177          <varlistentry>
178            <term>from either biosource list- or single view- page.</term>
179            <listitem>
180              <para>
181                No matter how complex the sample processing phase is, at least one
182                sample has to be anchored to a biosource. Therefore, a natural way
183                to create an sample is to click on
184                <guiicon>
185                  <inlinemediaobject>
186                    <imageobject>
187                      <imagedata fileref="figures/add.png" format="PNG" />
188                    </imageobject>
189                  </inlinemediaobject>
190                </guiicon>
191                in the sample column of the biosource list view. There is also a
192                corresponding button,
193                <guibutton>Create sample&hellip;</guibutton>
194                in the toolbar when viewing a single biosource.
195              </para>
196            </listitem>
197          </varlistentry>
198          <varlistentry>
199            <term>from the sample list page</term>
200            <listitem>
201              <para>
202                Pooled samples can also be created by first selecting the parents
203                from the list of samples and then press
204                <guibutton>Pool&hellip;</guibutton>
205                in the toolbar.
206              </para>
207            </listitem>
208          </varlistentry>
209        </variablelist>
210      </para>
211    </sect2>
212    <sect2 id="biomaterials.samples.properties">
213      <title>Properties</title>
214      <sect3 id="biomaterials.samples.properties.sample">
215        <title>Sample</title>
216        <helptext external_id="sample.edit" title="Edit sample">
217          <variablelist>
218            <varlistentry>
219              <term>
220                <guilabel>Name</guilabel>
221              </term>
222              <listitem>
223                <para>
224                  The sample's name(required). BASE2 by default assigns names to
225                  samples (by suffixing
226                  <replaceable>s#</replaceable>
227                  when creating a sample from an existing biosource or
228                  <replaceable>New Sample</replaceable>
229                  otherwise) but it is possible to edit at will.
230                </para>
231              </listitem>
232            </varlistentry>
233            <varlistentry>
234              <term>
235                <guilabel>External ID</guilabel>
236              </term>
237              <listitem>
238                <para>
239                  An identification used to identify the sample outside BASE.
240                </para>
241              </listitem>
242            </varlistentry>
243            <varlistentry>
244              <term>
245                <guilabel>Original quantity</guilabel>
246              </term>
247              <listitem>
248                <para>
249                  This is meant to report information about the actual mass of
250                  sample created.
251                </para>
252              </listitem>
253            </varlistentry>
254            <varlistentry>
255              <term>
256                <guilabel>Created</guilabel>
257              </term>
258              <listitem>
259                <para>
260                  A date when the sample was created. The information can be
261                  important when running quality controls on data and account for
262                  potential confounding factor (e.g. day effect).
263                </para>
264              </listitem>
265            </varlistentry>
266            <varlistentry>
267              <term>
268                <guilabel>Registered</guilabel>
269              </term>
270              <listitem>
271                <para>The date at which the sample was entered in BASE2.</para>
272              </listitem>
273            </varlistentry>
274            <varlistentry>
275              <term>
276                <guilabel>Protocol</guilabel>
277              </term>
278              <listitem>
279                <para>The protocol used to produce this sample.</para>
280              </listitem>
281            </varlistentry>
282            <varlistentry>
283              <term>
284                <guilabel>Description</guilabel>
285              </term>
286              <listitem>
287                <para>
288                  A text field to report any information that not can be captured
289                  otherwise.
290                </para>
291              </listitem>
292            </varlistentry>
293          </variablelist>
294        </helptext>
295        <figure id="write_docbook_doc.figures.biosample-tab-1">
296          <title>Sample properties</title>
297          <screenshot>
298            <mediaobject>
299              <imageobject>
300                <imagedata 
301                  fileref="figures/biosample-tab-1.png" format="PNG" />
302              </imageobject>
303            </mediaobject>
304          </screenshot>
305        </figure>
306      </sect3>
307      <sect3 id="biomaterials.samples.properties.parents">
308        <title>Parents</title>
309        <helptext external_id="sample.parents" title="Sample's parents">
310          <para>
311            This is meant to keep track of the sample origin. BASE2 distinguished
312            between 2 cases which are controled by the
313            <guilabel>Pooled</guilabel>
314            radio-button in the edit pop-up window.
315          </para>
316          <itemizedlist>
317            <listitem>
318              <para>
319                If the parent is a biosource the radio-button is set to
320                <guilabel>No</guilabel>
321                . This will make the biosource select button active, which allows
322                users to point to a biosource from which the sample originates from.
323              </para>
324            </listitem>
325            <listitem>
326              <para>
327                When the parent is one or several other samples the radio-button is
328                set to
329                <guilabel>Yes</guilabel>
330                . Upon selection, the biosource select button is deactivated and the
331                samples box and button are activated. This allows users to specify
332                one or more samples to be selected from a sample list view page.
333              </para>
334            </listitem>
335          </itemizedlist>
336        </helptext>
337      </sect3>
338      <sect3 id="biomaterials.samples.properties.annotation_param">
339        <title>Annotations &amp; parameters</title>
340        <para>
341          As seen in the biosource section, this tab allows users to further supply
342          information about the sample provided they have defined or shared annotation
343          types to annotate sample items.
344        </para>
345        <para>
346          To learn more about annotation types and how to define a value for a type,
347          please refer to
348          <xref linkend="annotations" />
349        </para>
350      </sect3>
351      <sect3 id="biomaterials.samples.properties.inherited">
352        <title>Inherited annotations</title>
353        <para>
354          This tab contains a list of those annotations that are inherited from the
355          sample's parents. Information about working with innherited annotations can be
356          found in
357          <xref linkend="annotations.inheriting" />
358          .
359        </para>
360      </sect3>
361    </sect2>
362  </sect1>
363
364  <sect1 id="biomaterials.extracts">
365    <title>Extracts</title>
366    <para>
367      Extract items should be used to describe the events that transform a sample material
368      into an extract material. An extract can be created from one sample item or from one or
369      more extract items. When an extract is created from several other extracts, a pooling
370      event is performed.
371    </para>
372    <para>
373      During the transformation from samples to extracts, it is possible to provide
374      information about the protocol used to perform this task. It is not enforced in BASE2
375      but it should serve as guidance when devising the granularity of the sample processing
376      task. Also, it is good practice to provide protocol information.
377    </para>
378    <sect2 id="biomaterials.extracts.create">
379      <title>Create extract</title>
380      <para>
381        Beside the common way, using the &gbNew; button, an extract can be created in one of
382        the following ways:
383        <variablelist>
384          <varlistentry>
385            <term>from either sample list- or single view- page.</term>
386            <listitem>
387              <para>
388                No matter how complex the extract processing phase is, at least one
389                extract has to be anchored to a sample. Therefore, a natural way to
390                create an extract is to click on
391                <guiicon>
392                  <inlinemediaobject>
393                    <imageobject>
394                      <imagedata fileref="figures/add.png" format="PNG" />
395                    </imageobject>
396                  </inlinemediaobject>
397                </guiicon>
398                in the extracts column for the sample that should be a parent of the
399                extract.
400              </para>
401              <para>
402                There is also a corresponding button,
403                <guibutton>Create extract&hellip;</guibutton>
404                in the toolbar when viewing a single sample.
405              </para>
406            </listitem>
407          </varlistentry>
408          <varlistentry>
409            <term>from the extract list page</term>
410            <listitem>
411              <para>
412                Pooled extract can also be created by first selecting the parents
413                from the list of extracts and then press
414                <guibutton>Pool&hellip;</guibutton>
415                in the toolbar. The selected extracts will be put into the parent
416                property.
417              </para>
418            </listitem>
419          </varlistentry>
420        </variablelist>
421      </para>
422    </sect2>
423    <sect2 id="biomaterials.extracts.properties">
424      <title>Properties</title>
425      <sect3 id="biomaterials.extracts.properties.extract">
426        <title>Extract</title>
427        <helptext external_id="extract.edit" title="Edit extract">
428          <variablelist>
429            <varlistentry>
430              <term>
431                <guilabel>Name</guilabel>
432              </term>
433              <listitem>
434                <para>
435                  A mandatory field for providing the extract's name. BASE2 by
436                  default assigns names to extract (by suffixing
437                  <replaceable>e#</replaceable>
438                  when creating an extract from an existing sample or
439                  <replaceable>New extract</replaceable>
440                  otherwise) but it is possible to edit it at will.
441                </para>
442              </listitem>
443            </varlistentry>
444            <varlistentry>
445              <term>
446                <guilabel>External ID</guilabel>
447              </term>
448              <listitem>
449                <para>The extracts identification outside BASE</para>
450              </listitem>
451            </varlistentry>
452            <varlistentry>
453              <term>
454                <guilabel>Original quantity</guilabel>
455              </term>
456              <listitem>
457                <para>
458                  Holds information about the original mass of the created
459                  extract.
460                </para>
461              </listitem>
462            </varlistentry>
463            <varlistentry>
464              <term>
465                <guilabel>Created</guilabel>
466              </term>
467              <listitem>
468                <para>
469                  The date when the extract was created. The information can be
470                  important when running quality controls on data and account for
471                  potential confounding factor (e.g. day effect)
472                </para>
473              </listitem>
474            </varlistentry>
475            <varlistentry>
476              <term>
477                <guilabel>Registered</guilabel>
478              </term>
479              <listitem>
480                <para>
481                  This is automatically populated with a date at which the sample
482                  was entered in BASE2 system.
483                </para>
484              </listitem>
485            </varlistentry>
486            <varlistentry>
487              <term>
488                <guilabel>Protocol</guilabel>
489              </term>
490              <listitem>
491                <para>
492                  The extraction protocol that was used to produce the extract.
493                </para>
494              </listitem>
495            </varlistentry>
496            <varlistentry>
497              <term>
498                <guilabel>Description</guilabel>
499              </term>
500              <listitem>
501                <para>
502                  A text field to report any information that not can be captured
503                  otherwise.
504                </para>
505              </listitem>
506            </varlistentry>
507          </variablelist>
508        </helptext>
509        <figure id="write_docbook_doc.figures.extract-tab-1">
510          <title>Extract tab</title>
511          <screenshot>
512            <mediaobject>
513              <imageobject>
514                <imagedata 
515                  fileref="figures/extract-tab-1.png" format="PNG" />
516              </imageobject>
517            </mediaobject>
518          </screenshot>
519        </figure>
520      </sect3>
521
522      <sect3 id="biomaterials.extracts.properties.parents">
523        <title>Parents</title>
524        <helptext external_id="extract.parents" title="Extract's parents">
525          <para>
526            This important tab allows users to select the extract origin. BASE2
527            distinguished between 2 cases which are controled by the
528            <guilabel>Pooled</guilabel>
529            radio-button.
530          </para>
531          <itemizedlist>
532            <listitem>
533              <para>
534                If the parent is a sample the radio-button is set to
535                <guilabel>No</guilabel>
536                . The Sample select button is active and allows users to point to
537                the sample from which the sample originates.
538              </para>
539            </listitem>
540            <listitem>
541              <para>
542                The parent is another extract and the radio-button is set to
543                <guilabel>Yes</guilabel>
544                . Upon selection, the samples select button is deactivated and the
545                extracts box and button are activated. This allows users to specify
546                one or more extracts to be selected from an extract list view page.
547              </para>
548            </listitem>
549          </itemizedlist>
550        </helptext>
551      </sect3>
552      <sect3 id="biomaterials.extracts.properties.annotations_param">
553        <title>Annotations &amp; parameters</title>
554        <para>
555          As seen in the biosource and sample sections, this tab allows users to supply
556          further information about the extract, provided they have defined annotation
557          types to annotation extract items or have such elements shared to them.
558        </para>
559        <para>
560          To learn more about annotation types, please refer to
561          <xref linkend="annotations" />
562        </para>
563      </sect3>
564      <sect3 id="biomaterials.extracts.properties.inherited">
565        <title>Inherited Annotations</title>
566        <para>
567          This tab contains a list of those annotations that are inherited from the
568          extract's parents. Information about working with innherited annotations can be
569          found in
570          <xref linkend="annotations.inheriting" />
571          .
572        </para>
573      </sect3>
574    </sect2>
575  </sect1>
576
577  <sect1 id="biomaterials.labels">
578    <title>Labels</title>
579    <para>
580      Before attempting to create labeled extracts, users should make sure that the
581      appropriate label object is present in BASE2. To browse the list of labels, go to
582      <menuchoice>
583        <guimenu>View</guimenu>
584        <guimenuitem>Labels</guimenuitem>
585      </menuchoice>
586    </para>
587    <sect2 id="biomaterials.labels.properties">
588      <title>Properties</title>
589      <helptext external_id="label.edit" title="Edit label">
590        <para>
591          The label item is very simple and does not need much explanation. There are only
592          two properties for a label
593          <variablelist>
594            <varlistentry>
595              <term>
596                <guilabel>Name</guilabel>
597              </term>
598              <listitem>
599                <para>The name of the label(required).</para>
600              </listitem>
601            </varlistentry>
602            <varlistentry>
603              <term>
604                <guilabel>Description</guilabel>
605              </term>
606              <listitem>
607                <para>
608                  An explaining text or other information associated with the
609                  label.
610                </para>
611              </listitem>
612            </varlistentry>
613          </variablelist>
614          .
615        </para>
616      </helptext>
617    </sect2>
618
619  </sect1>
620  <sect1 id="biomaterials.labeledextracts">
621    <title>Labeled extracts</title>
622    <para>
623      Labeled extract items should be used to describe the event that transformed an extract
624      material in a labeled extract material. Labeled extracts can be created from extract
625      items or from one or more labeled extract items. When a labeled extract is created from
626      several other labeled extracts, a pooling event is performed.
627    </para>
628    <para>
629      During the transformation from extracts to labeled extracts, it is possible to provide
630      information about the protocol used to perform this task. It is not enforced in BASE2
631      but it should serve as guidance when devising the granularity of the extract processing
632      task. Also, it is good practice to provide protocol information.
633    </para>
634    <sect2 id="biomaterials.labeledextracts.create">
635      <title>Creating labeled extracts</title>
636      <para>
637        Beside the regular way of using the &gbNew; button in
638        <menuchoice>
639          <guimenu>View</guimenu>
640          <guimenuitem>Labeled extracts</guimenuitem>
641        </menuchoice>
642        , a labeled extract can be created in one of following ways.
643      </para>
644      <variablelist>
645        <varlistentry>
646          <term>pooling selected labeled extracts</term>
647          <listitem>
648            <para>
649              The toolbar at the list page of labeled extracts contains an addition
650              &gbPool; button. This button allows users to create pooled labeled
651              extracts by selecting the list of labeled extracts used to derived a new
652              labeled extract and then click on the button.
653            </para>
654            <para>
655              This provides an easy and simple way to create pooled labeled extracts.
656              The result of such process is the creation of a new labeled extract, in
657              which, when navigating to the parent tab, shows that all the labeled
658              extracts involved are already set and listed in the Labeled Extract box
659              of the tab.
660            </para>
661          </listitem>
662        </varlistentry>
663        <varlistentry>
664          <term>from the extract pages.</term>
665          <listitem>
666            <para>
667              Following the laboratory workflow, a natural way to create a labeled
668              extract from an extract is to click on the
669              <guiicon>
670                <inlinemediaobject>
671                  <imageobject>
672                    <imagedata fileref="figures/add.png" format="PNG" />
673                  </imageobject>
674                </inlinemediaobject>
675              </guiicon>
676              from the labeled extract column of the extract list view. Corresponding
677              button,
678              <guibutton>New labeled extract</guibutton>
679              is located on the single item view page for each extract. By creating a
680              labeled extract from an extract page will automatically set the extract
681              as a parent.
682            </para>
683          </listitem>
684        </varlistentry>
685        <varlistentry>
686          <term>from single item view of a label</term>
687          <listitem>
688            <para>
689              Click on the
690              <guibutton>New labeled extract&hellip;</guibutton>
691              to use the current label and create a new labeled extract with it
692              pre-selected as
693              <guilabel>Label</guilabel>
694              .
695            </para>
696          </listitem>
697        </varlistentry>
698      </variablelist>
699    </sect2>
700    <sect2 id="biomaterials.labeledextracts.properties">
701      <title>Properties</title>
702      <sect3 id="biomaterials.labeledextracts.properties.labeledextract">
703        <title>Labeled extract</title>
704        <variablelist>
705          <varlistentry>
706            <term>
707              <guilabel>Name</guilabel>
708            </term>
709            <listitem>
710              <para>
711                The name of the labeled extract (required). BASE2 by default assigns
712                names to labeled extract(by suffixing
713                <replaceable>lbe#</replaceable>
714                when creating a labeled extract from an existing extract or
715                <replaceable>New labeled extract</replaceable>
716                otherwise) but it is possible to edit it at will
717              </para>
718            </listitem>
719          </varlistentry>
720          <varlistentry>
721            <term>
722              <guilabel>Label</guilabel>
723            </term>
724            <listitem>
725              <para>
726                Used to specify which dye or marker was used in the labeling
727                reaction (required).
728              </para>
729            </listitem>
730          </varlistentry>
731          <varlistentry>
732            <term>
733              <guilabel>External ID</guilabel>
734            </term>
735            <listitem>
736              <para>An id used to recognize the labeled extract outside BASE.</para>
737            </listitem>
738          </varlistentry>
739          <varlistentry>
740            <term>
741              <guilabel>Original quantity</guilabel>
742            </term>
743            <listitem>
744              <para>The mass of labeled extract that was created.</para>
745            </listitem>
746          </varlistentry>
747          <varlistentry>
748            <term>
749              <guilabel>Created</guilabel>
750            </term>
751            <listitem>
752              <para>
753                A date should be provided. The information can be important when
754                running quality controls on data and account for potential
755                confounding factor (e.g. day effect).
756              </para>
757            </listitem>
758          </varlistentry>
759          <varlistentry>
760            <term>
761              <guilabel>Registred</guilabel>
762            </term>
763            <listitem>
764              <para>
765                This is automatically populated with a date at which the labeled
766                extract was actually entered in BASE2 system.
767              </para>
768            </listitem>
769          </varlistentry>
770          <varlistentry>
771            <term>
772              <guilabel>Protocol</guilabel>
773            </term>
774            <listitem>
775              <para>
776                The labeling protocol that was used to produce the labeled extract.
777              </para>
778            </listitem>
779          </varlistentry>
780          <varlistentry>
781            <term>
782              <guilabel>Description</guilabel>
783            </term>
784            <listitem>
785              <para>
786                A free text field to report any information that can not be captured
787                otherwise.
788              </para>
789            </listitem>
790          </varlistentry>
791        </variablelist>
792        <figure id="write_docbook_doc.figures.labeledextract-properties">
793          <title>Labeled extract properties</title>
794          <screenshot>
795            <mediaobject>
796              <imageobject>
797                <imagedata contentwidth="10cm" width="10cm"
798                  fileref="figures/labeledextract-properties.png" format="PNG" />
799              </imageobject>
800            </mediaobject>
801          </screenshot>
802        </figure>
803      </sect3>
804      <sect3 id="biomaterials.labeledextracts.properties.parents">
805        <title>Parents</title>
806        <para>
807          This important tab allows users to select the labeled extract origin. BASE2
808          distinguished between 2 cases which are controled by the
809          <guilabel>Pooled</guilabel>
810          radio-button.
811        </para>
812        <itemizedlist>
813          <listitem>
814            <para>The parent is an extract</para>
815            <para>
816              The radio-button is set to
817              <guilabel>No</guilabel>
818              . The Extract select button is active and allows users to point to one
819              and only one extract from which the labeled extract originates from.
820            </para>
821          </listitem>
822          <listitem>
823            <para>The parent is another labeled extract</para>
824            <para>
825              The radio-button has to be set to
826              <guilabel>Yes</guilabel>
827              . Upon selection, the extract select button is deactivated and the
828              labeled extracts box and button are activated. This allows users to
829              specify one or more extracts to be selected from the labeled extract
830              list view page.
831            </para>
832          </listitem>
833        </itemizedlist>
834      </sect3>
835      <sect3 id="biomaterials.labeledextracts.properties.annotations_param">
836        <title>Annotations &amp; parameters</title>
837        <para>
838          As seen in the biosource and sample sections, this tab allows users to further
839          supply information about the labeled extract provided they have defined
840          annotation types to annotate labeled extract items or have such elements shared
841          to them.
842        </para>
843        <important>
844          <para>
845            In order to use this feature, annotation type must be declared and made
846            available. To learn more about annotation types and how these are set,
847            please refer to
848            <xref linkend="annotations" />
849            .
850          </para>
851        </important>
852      </sect3>
853      <sect3 id="biomaterials.labeledextracts.properties.inherited">
854        <title>Inherited annotations</title>
855        <para>
856          This tab contains a list of those annotations that are inherited from the
857          parents of the labeled extract. Information about dealing with innherited
858          annotations can be found in
859          <xref linkend="annotations.inheriting" />
860          .
861        </para>
862      </sect3>
863    </sect2>
864  </sect1>
865
866  <sect1 id="biomaterials.hybridizations">
867    <title>Hybridizations</title>
868    <para>
869      An hybridization event corresponds to the application of one or more labeled extracts
870      materials to a microarray slide under conditions detailed in hybridization protocols.
871      Use
872      <menuchoice>
873        <guimenu>View</guimenu>
874        <guimenuitem>Hybridizatons</guimenuitem>
875      </menuchoice>
876      to get to the hybridizations.
877    </para>
878    <sect2 id="biomaterials.hybridizations.create">
879      <title>Creating hybridizations</title>
880      <para>
881        In BASE2, there are 2 possible routes to create an hybridization object except the
882        common way with the &gbNew; button at hybridization list page.
883      </para>
884      <variablelist>
885        <varlistentry>
886          <term>from the labeled extract list view page</term>
887          <listitem>
888            <para>
889              Select at least one labeled extract, to create a hybridization from, by
890              ticking the selection boxes before the name field.
891            </para>
892            <para>
893              Click on the
894              <guibutton>New hybridzation&hellip;</guibutton>
895              from the toolbar of labeled extract list view.
896            </para>
897          </listitem>
898        </varlistentry>
899        <varlistentry>
900          <term>from a labeled extract single item page</term>
901          <listitem>
902            <para>
903              When viewing a label extract in single item view, click on the
904              <guibutton>New hybridization&hellip;</guibutton>
905              button from the toolbar of the labeled extract item view.
906            </para>
907          </listitem>
908        </varlistentry>
909      </variablelist>
910    </sect2>
911    <sect2 id="biomaterials.hybridizations.properties">
912      <title>Properties</title>
913
914      <sect3 id="biomaterials.hybridizations.hybridization">
915        <title>Hybridization</title>
916 
917        <figure id="write_docbook_doc.figures.hybridization-tab-1">
918          <title>Hybridization tab</title>
919          <screenshot>
920            <mediaobject>
921              <imageobject>
922                <imagedata 
923                  fileref="figures/hybridization-tab-1.png" format="PNG" />
924              </imageobject>
925            </mediaobject>
926          </screenshot>
927        </figure> 
928       
929        <helptext external_id="hybridization.edit" title="Edit hybridization">
930        <variablelist>
931          <varlistentry>
932            <term>
933              <guilabel>Name</guilabel>
934            </term>
935            <listitem>
936              <para>
937                <replaceable>New hybridization</replaceable>
938                is BASE2 default name but it is strongly advise to provide a
939                meaningful and unique name (required).
940              </para>
941            </listitem>
942          </varlistentry>
943          <varlistentry>
944            <term>
945              <guilabel>Arrays</guilabel>
946            </term>
947            <listitem>
948              <para>
949                The number of sub-arrays on the slide that was used in
950                this hybridization. The default value is 1, but some
951                platforms, for example Illumina, has slides
952                with 6 or 8 arrays.
953              </para>
954            </listitem>
955          </varlistentry>
956
957          <varlistentry>
958            <term>
959              <guilabel>Created</guilabel>
960            </term>
961            <listitem>
962              <para>
963                A date should be provided. The information can be important when
964                running quality controls on data and account for potential
965                confounding factor (e.g. to account for a day effect)
966              </para>
967            </listitem>
968          </varlistentry>
969
970          <varlistentry>
971            <term>
972              <guilabel>Registered</guilabel>
973            </term>
974            <listitem>
975              <para>
976                This field is automatically populated with a date at which the
977                hybridization was entered in BASE2 system.
978              </para>
979            </listitem>
980          </varlistentry>
981
982          <varlistentry>
983            <term>
984              <guilabel>Protocol</guilabel>
985            </term>
986            <listitem>
987              <para>
988                The hybridization protocol that was used to do the hybridization.
989              </para>
990            </listitem>
991          </varlistentry>
992
993          <varlistentry>
994            <term>
995              <guilabel>Hardware</guilabel>
996            </term>
997            <listitem>
998              <para>
999                The hybridization-station that was used during the hybridization.
1000              </para>
1001            </listitem>
1002          </varlistentry>
1003
1004          <varlistentry>
1005            <term>
1006              <guilabel>Array slide</guilabel>
1007            </term>
1008            <listitem>
1009              <para>The array slide that was used in the hybridization.</para>
1010              <note>
1011                <para>
1012                  Ideally, The Array Slides should have been created but for those
1013                  users with permission to do, Array Slides could be generated at
1014                  that point.
1015                </para>
1016              </note>
1017            </listitem>
1018          </varlistentry>
1019
1020          <varlistentry>
1021            <term>
1022              <guilabel>Description</guilabel>
1023            </term>
1024            <listitem>
1025              <para>
1026                A free text field to report any information that can not be captured
1027                otherwise
1028              </para>
1029            </listitem>
1030          </varlistentry>
1031        </variablelist>
1032        <seeother>
1033          <other external_id="hybridization.labeledextracts">Labeled extracts</other>
1034        </seeother>
1035        </helptext>
1036       
1037      </sect3>
1038     
1039      <sect3 id="biomaterials.hybridizations.properties.labeledextracts">
1040        <title>Labeled extracts</title>
1041       
1042        <helptext external_id="hybridization.labeledextracts" title="Labeled extracts">
1043        <para>
1044          This important tab allows users to select the labeled extracts applied to an
1045          array slide, and specify the amount of material used, expressed in microgram.
1046        </para>
1047        <para>
1048          Use the <guibutton>Add labeled extracts</guibutton> button to add
1049          items and the <guibutton>Remove</guibutton> button to remove items.
1050          Select one or several labeled extracts in the list and write the used
1051          mass and sub-array index in the fields below.
1052        </para>
1053       
1054        <seeother>
1055          <other external_id="hybridization.edit">Edit hybridization</other>
1056        </seeother>
1057        </helptext>
1058       
1059      </sect3>
1060      <sect3 id="biomaterials.hybridizations.properties.annotations_param">
1061        <title>Annotations &amp; parameters</title>
1062        <para>
1063          As seen in the biosource and sample sections, this tab allows users to supply
1064          further information about the hybridization provided annotation types have been
1065          defined or shared to annotate hybridization items.
1066        </para>
1067        <important>
1068          <para>
1069            In order to use this feature, annotation type must be declared and made
1070            available. To learn more about annotation types and how these are set,
1071            please refer to
1072            <xref linkend="annotations" />
1073          </para>
1074        </important>
1075      </sect3>
1076      <sect3 id="biomaterials.hybridizations.properties.inherited">
1077        <title>Inherited annotations</title>
1078        <para>
1079          This tab contains a list of those annotations that are inherited from the
1080          labeled extracts. Information about dealing with innherited annotations can be
1081          found in
1082          <xref linkend="annotations.inheriting" />
1083          .
1084        </para>
1085      </sect3>
1086    </sect2>
1087  </sect1>
1088</chapter>
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