Changeset 3399


Ignore:
Timestamp:
May 28, 2007, 5:18:03 PM (16 years ago)
Author:
Martin Svensson
Message:

References #545 Reorganisation, more to come..

Location:
trunk/doc/src/docbook
Files:
2 deleted
1 edited

Legend:

Unmodified
Added
Removed

  • trunk/doc/src/docbook/userdoc/biomaterials.xml

    r3394 r3399  
    33    "-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN"
    44    "../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd">
    5     <!--
    6      $Id$
    7      
    8      Copyright (C) Authors contributing to this file.
    9      
    10      This file is part of BASE - BioArray Software Environment.
    11      Available at http://base.thep.lu.se/
    12      
    13      BASE is free software; you can redistribute it and/or
    14      modify it under the terms of the GNU General Public License
    15      as published by the Free Software Foundation; either version 2
    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     -->             
     5<!--
     6  $Id$
     7 
     8  Copyright (C) Authors contributing to this file.
     9 
     10  This file is part of BASE - BioArray Software Environment.
     11  Available at http://base.thep.lu.se/
     12 
     13  BASE is free software; you can redistribute it and/or
     14  modify it under the terms of the GNU General Public License
     15  as published by the Free Software Foundation; either version 2
     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-->
    2828<chapter id="biomaterials">
    29 <?dbhtml dir="biomaterials"?>
    30  <title>Biomaterials</title>
    31  <sect1 id="biomaterial.introduction">
    32   <title>Introduction</title>
    33   <para> The generic term Biomaterial refers to any biological material used in an Experiment.
    34    Biomaterials are subdivided in 4 components, BioSource, Sample, Extract and Labeled Extract. The
    35    order use in presenting those entities is not inocuous as it represents the sequence of
    36    transformation a source material undergoes until it is in a state compatible with the realization
    37    of a microarray Hybridization. This progression is actually mimicked in the BASE2 View menu again
    38    to insist on this natural progression. </para>
    39   <para>BioSources correspond to the native biological entity used in an experiment prior to any
    40    treatment. </para>
    41   <para>Samples are central to BASE2 to describe the sample processing. So Samples can be created
    42    from other Samples if user want to track sample processing event in a finely granular fashion.</para>
    43   <para>Extracts correspond to nucleic acid material extracted from a tissue sample or a cell
    44    culture sample.</para>
    45   <para>LabeledExtracts correspond to nucleic acid materials which have undergone a marking
    46    procedure using a fluorescent or radioactive compound for detection in a microarray assay.</para>
    47   <para>BASE2 allows users to create any of the these entities fairly freely, however it is expected
    48    that users will follow the natural path of the laboratory workflow.</para>
    49  </sect1>
    50  <sect1 id="biosource.manage">
    51   <title>Managing BioSources</title>
     29  <?dbhtml dir="biomaterials"?>
     30  <title>Biomaterials</title>
     31  <sect1 id="biomaterial.introduction">
     32    <title>Introduction</title>
     33    <para>
     34      The generic term biomaterial refers to any biological material used in an experiment.
     35      biomaterials are subdivided in 4 components, biosource, sample, extract and labeled
     36      extract. The order use in presenting those entities is not inocuous as it represents the
     37      sequence of transformation a source material undergoes until it is in a state compatible
     38      with the realization of a microarray hybridization. This progression is actually
     39      mimicked in the BASE2
     40      <guimenu>View</guimenu>
     41      menu again to insist on this natural progression.
     42    </para>
     43    <para>
     44      Biosources correspond to the native biological entity used in an experiment prior to any
     45      treatment.
     46    </para>
     47    <para>
     48      Samples are central to BASE2 to describe the sample processing. So samples can be
     49      created from other samples if user want to track sample processing event in a finely
     50      granular fashion.
     51    </para>
     52    <para>
     53      Extracts correspond to nucleic acid material extracted from a tissue sample or a cell
     54      culture sample.
     55    </para>
     56    <para>
     57      Labeled extracts correspond to nucleic acid materials which have undergone a marking
     58      procedure using a fluorescent or radioactive compound for detection in a microarray
     59      assay.
     60    </para>
     61    <para>
     62      BASE2 allows users to create any of the these entities fairly freely, however it is
     63      expected that users will follow the natural path of the laboratory workflow.
     64    </para>
     65    <tip>
     66      <para>
     67        It is highly recommended that you have read
     68        <xref linkend="webclient.items" />
     69        before continuing with this chapter.
     70      </para>
     71    </tip>
     72  </sect1>
     73  <sect1 id="biomaterial.biosources">
     74    <title>Biosources</title>
     75    <para>
     76      Go to
     77      <menuchoice>
     78        <guimenu>View</guimenu>
     79        <guimenuitem>Biosources</guimenuitem>
     80      </menuchoice>
     81      .
     82    </para>
     83    <itemizedlist>
     84      <listitem>
     85        <para>
     86          <guilabel>Biosource</guilabel>
     87        </para>
     88        <helptext external_id="biosources.edit" title="Edit biosources">
     89          <para>
     90            This tab allows users to enter essential information about a biosource.
     91          </para>
     92          <variablelist>
     93            <varlistentry>
     94              <term>
     95                <guilabel>Name</guilabel>
     96              </term>
     97              <listitem>
     98                <para>
     99                  This is the only mandatory field. BASE2 by default assigns
     100                  <replaceable>New Biosource</replaceable>
     101                  as name but it is advised to provide unique sensible names.
     102                </para>
     103              </listitem>
     104            </varlistentry>
     105            <varlistentry>
     106              <term>
     107                <guilabel>External id</guilabel>
     108              </term>
     109              <listitem>
     110                <para>
     111                  An external reference identifiers (e.g. a patient identification
     112                  code) can be supplied using this field.
     113                </para>
     114              </listitem>
     115            </varlistentry>
     116            <varlistentry>
     117              <term>
     118                <guilabel>Description</guilabel>
     119              </term>
     120              <listitem>
     121                <para>
     122                  A free text description can be supplied using this field.
     123                </para>
     124              </listitem>
     125            </varlistentry>
     126          </variablelist>
     127          <para>
     128            Change tab to
     129            <guilabel>Annotations</guilabel>
     130            if you want annotate the biosource, otherwise close the pop-up window by
     131            either clicking on the &gbSave; button to store the information in BASE2 or
     132            on the &gbCancel; button to abort.
     133          </para>
     134        </helptext>
     135        <nohelp>
     136          <figure id="write_docbook_doc.figures.biosource-tab-1">
     137            <title>
     138              The
     139              <guilabel>Biosource</guilabel>
     140              tab
     141            </title>
     142            <screenshot>
     143              <mediaobject>
     144                <imageobject>
     145                  <imagedata contentwidth="10cm" width="10cm"
     146                    fileref="figures/biosource-tab-1.png" format="PNG" />
     147                </imageobject>
     148              </mediaobject>
     149            </screenshot>
     150          </figure>
     151        </nohelp>
     152      </listitem>
     153      <listitem>
     154        <para>
     155          <guilabel>Annotations</guilabel>
     156        </para>
     157        <para>
     158          This tab allows BASE2 users to use annotation types to refine biosource
     159          description.
     160        </para>
     161        <para>
     162          A list of annotation types that are owned by or shared to you will be displayed.
     163        </para>
     164        <important>
     165          <para>
     166            In order to use this feature, annotation type must be declared and made
     167            available. To learn more about annotation types, please refer to
     168            <xref linkend="annotations" />
     169          </para>
     170        </important>
     171        <para>
     172          See
     173          <xref linkend="annotations.annotating" />
     174          to get more information on how to set annotation types.
     175        </para>
     176      </listitem>
     177    </itemizedlist>
     178    <para>
     179      Click on the &gbSave; button to store the information in BASE2 or on the &gbCancel;
     180      button to abort.
     181    </para>
    52182
    53   <sect2 id="biosource.manage.create">
    54    <title>Creating BioSources</title>
    55    <para>Go to <menuchoice>
    56      <guimenu>View</guimenu>
    57      <guimenuitem>BioSources</guimenuitem>
    58     </menuchoice> , Click on &gbNew; button </para>
    59    <para> A 'Create' pop-up window opens, it contains 2 tabs: <guilabel>Biosource</guilabel> and
    60      <guilabel>Annotations</guilabel>. </para>
    61    <itemizedlist>
    62     <listitem>
    63      <para>
    64       <guilabel>BioSource</guilabel>
    65      </para>
    66      <para> This tab allows users to enter essential information about a BioSource.</para>
    67      <variablelist>
    68       <varlistentry>
    69        <term>
    70         <guilabel>Name</guilabel>
    71        </term>
    72        <listitem>
    73         <para> This is only mandatory field. BASE2 by default assigns 'New Biosource' as name but it
    74          is advised to provide unique sensible names, as this may impact exporting in tab2mage
    75          format.</para>
    76         <para>For more information about tab2mage format and export, please refer to section <xref
    77           linkend="experiments_analysis.magexport"/> and section <xref
    78           linkend="annotations.bestpractices"/></para>
    79        </listitem>
    80       </varlistentry>
    81       <varlistentry>
    82        <term>
    83         <guilabel>Description</guilabel>
    84        </term>
    85        <listitem>
    86         <para> A free text description can be supplied using this field.</para>
    87        </listitem>
    88       </varlistentry>
    89       <varlistentry>
    90        <term>
    91         <guilabel>External id</guilabel>
    92        </term>
    93        <listitem>
    94         <para> An external reference identifiers (e.g. a patient identification code) can be
    95          supplied using this field.</para>
    96        </listitem>
    97       </varlistentry>
    98      </variablelist>
     183    <sect2 id="biomaterial.biosource.manage.detail_view">
     184      <title>Viewing biosources</title>
     185      <para>
     186        From the biosource list view, clicking on the biosource
     187        <guilabel>Name</guilabel>
     188        opens a detailed view for that biosource, showing a summary of all information
     189        available in BASE2 about that particular entity.
     190      </para>
     191      <para>
     192        The default behavior opens the detailed view on the
     193        <guilabel>Properties</guilabel>
     194        tab, which shows a summary information and displays the list of samples derived from
     195        a biosource, if any.
     196      </para>
     197      <figure id="write_docbook_doc.figures.biosource-itemview-prop">
     198        <title>BioSource Item View, properties tab</title>
     199        <screenshot>
     200          <mediaobject>
     201            <imageobject>
     202              <imagedata contentwidth="12cm" width="12cm"
     203                fileref="figures/biosource-itemview-prop.png" format="PNG" />
     204            </imageobject>
     205          </mediaobject>
     206        </screenshot>
     207      </figure>
     208      <para>
     209        By clicking on the
     210        <guilabel>Annotations</guilabel>
     211        tab, users can display the list of Annotation Types used to annotate a Biosource.
     212      </para>
     213      <figure id="write_docbook_doc.figures.biosource-itemview-annot">
     214        <title>BioSource Item View, annotations tab</title>
     215        <screenshot>
     216          <mediaobject>
     217            <imageobject>
     218              <imagedata contentwidth="13cm" width="13cm"
     219                fileref="figures/biosource-itemview-annot.png" format="PNG" />
     220            </imageobject>
     221          </mediaobject>
     222        </screenshot>
     223      </figure>
     224      <para>
     225        Clicking the
     226        <inlinemediaobject>
     227          <imageobject>
     228            <imagedata fileref="figures/edit.gif" format="GIF" />
     229          </imageobject>
     230        </inlinemediaobject>
     231        <guiicon>edit icon</guiicon>
     232        in the
     233        <interface>value</interface>
     234        for any of the annotations (e.g. 'antibiotic' in our example), opens an Annotate
     235        window (which is a BioSource Edit window set on the annotation tab) and highlights
     236        the selected Annotation Type, prompting for data entry.
     237      </para>
     238      <figure id="write_docbook_doc.figures.biosource-itemview-annot-edit">
     239        <title>BioSource annotations edit</title>
     240        <screenshot>
     241          <mediaobject>
     242            <imageobject>
     243              <imagedata contentwidth="12cm" width="12cm"
     244                fileref="figures/biosource-itemview-annot-edit.png" format="PNG" />
     245            </imageobject>
     246          </mediaobject>
     247        </screenshot>
     248      </figure>
     249      <para>
     250        The relevant Annotation Type is highlighted and a list of possible values is
     251        displayed.
     252      </para>
     253      <para>
     254        Again, all Annotation types marked with a
     255        <inlinemediaobject>
     256          <imageobject>
     257            <imagedata fileref="figures/annotated.gif" format="GIF" />
     258          </imageobject>
     259        </inlinemediaobject>
     260        symbol have been used to provided information.
     261      </para>
     262      <para>
     263        Click on the &gbSave; button to store the information in BASE2 or on the &gbCancel;
     264        button to abort.
     265      </para>
     266    </sect2>
     267  </sect1>
     268  <sect1 id="sample.manage">
     269    <title>Managing Samples</title>
     270    <para>
     271      Samples result from processing events applied to
     272      <guilabel>BioSource</guilabel>
     273      material or other
     274      <guilabel>Samples</guilabel>
     275      before they are turned into an
     276      <guilabel>Extract</guilabel>
     277      .
     278    </para>
     279    <para>
     280      In other words, Samples can be created from BioSource items or from one or more Sample
     281      items.
     282    </para>
     283    <para>
     284      When a Sample is created from several other Samples, a 'pooling' event is performed. A
     285      specific section details how to create pools, refer to
     286      <xref linkend="sample.manage.createsample.pool" />
     287    </para>
     288    <para>
     289      For every step of transformation from BioSource to Sample, it is possible to provide
     290      information about the protocol used to perform this task. It is not enforced in BASE2
     291      but it should serve as guidance when devising the granularity of the sample processing
     292      task. Also, it is good practice to provide protocol information to ensure MIAME
     293      compliance.
     294    </para>
     295    <sect2 id="sample.manage.createsamplefrombiosource">
     296      <title>Creating Samples</title>
     297      <orderedlist>
     298        <listitem>
     299          <para>Creating Samples from the BioSource page</para>
     300          <para>
     301            No matter how complex the sample processing phase is, at least one Sample
     302            has to be anchored to a BioSource.
     303          </para>
     304          <para>
     305            Therefore, a natural way to create a Sample is to click on the
     306            <inlinemediaobject>
     307              <imageobject>
     308                <imagedata fileref="figures/add.gif" format="GIF" />
     309              </imageobject>
     310            </inlinemediaobject>
     311            <guibutton>Create new Sample</guibutton>
     312            from the Sample column of the BioSource list view.
     313          </para>
     314          <figure id="write_docbook_doc.figures.biosource-create-sample">
     315            <title>Creating a Sample from the BioSource list view</title>
     316            <screenshot>
     317              <mediaobject>
     318                <imageobject>
     319                  <imagedata contentwidth="13cm" width="13cm"
     320                    fileref="figures/biosource-create-sample.png" format="PNG" />
     321                </imageobject>
     322              </mediaobject>
     323            </screenshot>
     324          </figure>
     325        </listitem>
     326        <listitem>
     327          <para>Creating Samples from the Sample List view page</para>
     328          <para>
     329            This is the alternative for creating Sample from the BioSource. To do so, go
     330            to
     331            <menuchoice>
     332              <guimenu>View</guimenu>
     333              <guimenuitem>BioSamples</guimenuitem>
     334            </menuchoice>
     335            , Click on &gbNew; button
     336          </para>
     337          <para>
     338            A 'Create' pop-up window opens, it contains 4 tabs:
     339            <guilabel>Sample</guilabel>
     340            ,
     341            <guilabel>Parents</guilabel>
     342            ,
     343            <guilabel>Annotations &amp; parameters</guilabel>
     344            and
     345            <guilabel>Inherited Annotations</guilabel>
     346            .
     347          </para>
     348          <itemizedlist>
     349            <listitem>
     350              <para>The Sample Tab</para>
     351              <para>
     352                This tab contains 1 mandatory field for providing the Sample
     353                <guilabel>Name</guilabel>
     354                . BASE2 by default assigns names to Samples (by suffixing 's#' when
     355                creating a Sample from an existing Biosource or 'New Sample'
     356                otherwise) but it is possible to edit at will.
     357              </para>
     358              <para>
     359                There are 5 optional fields to provide more detailed information
     360              </para>
     361              <itemizedlist>
     362                <listitem>
     363                  <para>
     364                    <guilabel>External ID</guilabel>
     365                    : for instance to report a barcode attached to a Sample
     366                  </para>
     367                </listitem>
     368                <listitem>
     369                  <para>
     370                    <guilabel>Original Quantity (ug)</guilabel>
     371                    : this is meant to report information about the actual mass
     372                    of biomaterial created
     373                  </para>
     374                </listitem>
     375                <listitem>
     376                  <para>
     377                    <guilabel>Created</guilabel>
     378                    : a date should be provided. The information can be
     379                    important when running quality controls on data and account
     380                    for potential confounding factor (e.g. day effect)
     381                  </para>
     382                </listitem>
     383                <listitem>
     384                  <para>
     385                    <guilabel>Protocol</guilabel>
     386                    : this a controled field. A select-list displays protocols
     387                    whose type is
     388                    <guilabel>sampling</guilabel>
     389                    and which are shared to or owned by the logged-in user.
     390                  </para>
     391                  <important>
     392                    <para>
     393                      It is not mandatory to supply protocol in BASE2
     394                      Reporting protocols is a MIAME requirement
     395                    </para>
     396                  </important>
     397                </listitem>
     398                <listitem>
     399                  <para>
     400                    <guilabel>Description</guilabel>
     401                    : a free text field to report any information that not can
     402                    be captured otherwise
     403                  </para>
     404                </listitem>
     405              </itemizedlist>
     406              <para>
     407                Finally, a 7th field,
     408                <guilabel>Registered</guilabel>
     409                is automatically populated with a date at which the Sample was
     410                entered in BASE2 system.
     411              </para>
     412              <figure id="write_docbook_doc.figures.biosample-tab-1">
     413                <title>Sample tab</title>
     414                <screenshot>
     415                  <mediaobject>
     416                    <imageobject>
     417                      <imagedata contentwidth="10cm" width="10cm"
     418                        fileref="figures/biosample-tab-1.png" format="PNG" />
     419                    </imageobject>
     420                  </mediaobject>
     421                </screenshot>
     422              </figure>
     423            </listitem>
     424            <listitem>
     425              <para>The Parents Tab</para>
     426              <para>
     427                This important tab does what it says on the tin: It is meant to keep
     428                track of the Sample origin. BASE2 distinguished between 2 cases
     429                which are controled by the
     430                <guibutton>pooled</guibutton>
     431                radio-button
     432              </para>
     433              <orderedlist>
     434                <listitem>
     435                  <para>The Parent is a BioSource</para>
     436                  <para>
     437                    The
     438                    <guibutton>Pooled</guibutton>
     439                    radio-button is set to
     440                    <guilabel>No</guilabel>
     441                  </para>
     442                  <para>
     443                    The BioSource select button is active and allows users to
     444                    point to one and only one BioSource from which the Sample
     445                    originates from.
     446                  </para>
     447                  <figure
     448                    id="write_docbook_doc.figures.biosample-tab-2-select-biosource">
     449                    <title>
     450                      Parent tab and interaction when pooled button is set to
     451                      No
     452                    </title>
     453                    <screenshot>
     454                      <mediaobject>
     455                        <imageobject>
     456                          <imagedata contentwidth="12cm" width="12cm"
     457                            fileref="figures/biosample-tab-2-select-biosource.png" format="PNG" />
     458                        </imageobject>
     459                      </mediaobject>
     460                    </screenshot>
     461                  </figure>
     462                </listitem>
     463                <listitem>
     464                  <para>The Parent is another Sample</para>
     465                  <para>
     466                    The
     467                    <guibutton>Pooled</guibutton>
     468                    radio-button has to be set to
     469                    <guilabel>Yes</guilabel>
     470                  </para>
     471                  <para>
     472                    Upon selection, the BioSource select button is deactivated
     473                    and the Samples box and button are activated.
     474                  </para>
     475                  <para>
     476                    This allows users to specify one or more Samples to be
     477                    selected from the Sample List View page.
     478                  </para>
     479                  <figure
     480                    id="write_docbook_doc.figures.biosample-tab-2-select-sample">
     481                    <title>
     482                      Parent tab and interaction when pooled button is set to
     483                      Yes
     484                    </title>
     485                    <screenshot>
     486                      <mediaobject>
     487                        <imageobject>
     488                          <imagedata contentwidth="12cm" width="12cm"
     489                            fileref="figures/biosample-tab-2-select-sample.png" format="PNG" />
     490                        </imageobject>
     491                      </mediaobject>
     492                    </screenshot>
     493                  </figure>
     494                </listitem>
     495              </orderedlist>
     496            </listitem>
     497            <listitem>
     498              <para>Annotations &amp; parameters</para>
     499              <para>
     500                As seen in the BioSource section, this tab allows users to further
     501                supply information about the Sample provided they have defined or
     502                shared annotation types to annotate Sample items.
     503              </para>
     504              <para>
     505                The display of Annotation Type can be filtered based on the
     506                Annotation Type Category they belong to.
     507              </para>
     508              <important>
     509                <para>
     510                  In order to use this feature, Annotation Type must be declared
     511                  and made available. To learn more about Annotation Types, please
     512                  refer to
     513                  <xref linkend="annotations" />
     514                </para>
     515              </important>
     516              <para>
     517                To provide a value for a given annotation type, simply click on it
     518                an use the input field or select a value from the drop-down lists or
     519                radio buttons.
     520              </para>
     521              <figure id="write_docbook_doc.figures.biosample-tab-3">
     522                <title>Annotations &amp; parameters</title>
     523                <screenshot>
     524                  <mediaobject>
     525                    <imageobject>
     526                      <imagedata contentwidth="12cm" width="12cm"
     527                        fileref="figures/biosample-tab-3.png" format="PNG" />
     528                    </imageobject>
     529                  </mediaobject>
     530                </screenshot>
     531              </figure>
     532            </listitem>
     533            <listitem>
     534              <para>Inherited Annotations case1</para>
     535              <para>The next picture shows</para>
     536              <figure id="write_docbook_doc.figures.biosample-tab-4">
     537                <title>Inherited Annotations</title>
     538                <screenshot>
     539                  <mediaobject>
     540                    <imageobject>
     541                      <imagedata contentwidth="12cm" width="12cm"
     542                        fileref="figures/biosample-tab-4.png" format="PNG" />
     543                    </imageobject>
     544                  </mediaobject>
     545                </screenshot>
     546              </figure>
     547              <para>Inherited Annotations case2</para>
     548              <figure id="write_docbook_doc.figures.biosample-tab-4bis">
     549                <title>Inherited Annotations</title>
     550                <screenshot>
     551                  <mediaobject>
     552                    <imageobject>
     553                      <imagedata contentwidth="12cm" width="12cm"
     554                        fileref="figures/biosample-tab-4bis.png" format="PNG" />
     555                    </imageobject>
     556                  </mediaobject>
     557                </screenshot>
     558              </figure>
     559            </listitem>
     560          </itemizedlist>
     561        </listitem>
     562      </orderedlist>
     563    </sect2>
     564    <sect2 id="sample.manage.createsample.pool">
     565      <title>Creating Pooled Samples</title>
     566      <para>
     567        It is common practice when biological material is scarce to pool Samples from
     568        equivalent sources. BASE2 provides mechanisms to report on such practice.
     569      </para>
     570      <para>This section details how.</para>
     571      <para>There are 2 ways to create Pooled Samples in BASE2</para>
     572      <orderedlist>
     573        <listitem>
     574          <para>
     575            Using the Pooled radio button option from the Sample Create page, and this
     576            has been shown already
     577          </para>
     578        </listitem>
     579        <listitem>
     580          <para>Using the Pool button in the Menu bar</para>
     581          <para>
     582            The Sample List View page menu bar contains an additionnal button the usage
     583            of which is detailed now.
     584          </para>
     585          <para>
     586            The &gbPool; button
     587            <inlinemediaobject>
     588              <imageobject>
     589                <imagedata fileref="figures/new_pooled.gif" format="GIF" />
     590              </imageobject>
     591            </inlinemediaobject>
     592            allows users to create Pooled Samples by selecting the list of Samples used
     593            to produce that new Sample.
     594          </para>
     595          <para>
     596            Users simply need to tick the select-boxes in front of each relevant Sample
     597            and click the
     598            <inlinemediaobject>
     599              <imageobject>
     600                <imagedata fileref="figures/new_pooled.gif" format="GIF" />
     601              </imageobject>
     602            </inlinemediaobject>
     603            button.
     604          </para>
     605          <para>
     606            This provides an easy and simple way to create Pooled Samples. The result of
     607            such process is the creation of a New Sample, which Parent Samples are
     608            listing and preset in the Parent tab
     609          </para>
     610          <figure id="write_docbook_doc.figures.biosample-tab-2-pool-sample">
     611            <title>Pooling of Samples</title>
     612            <screenshot>
     613              <mediaobject>
     614                <imageobject>
     615                  <imagedata contentwidth="12cm" width="12cm"
     616                    fileref="figures/biosample-tab-2-pool-sample.png" format="PNG" />
     617                </imageobject>
     618              </mediaobject>
     619            </screenshot>
     620          </figure>
     621        </listitem>
     622      </orderedlist>
     623    </sect2>
     624    <sect2 id="sample.manage.delete">
     625      <title>Deleting/Restoring Samples</title>
     626      <para>
     627        As for other items in BASE2, Samples can be removed. For a generic overview on how
     628        to delete and restore items, refer to section
     629        <xref linkend="webclient.items.delete" />
     630      </para>
     631      <para>To delete, do the following</para>
     632      <itemizedlist>
     633        <listitem>
     634          <para>
     635            Select one or more Samples and click &gbDelete; button in the menu bar.
     636          </para>
     637          <para>
     638            All the selected Samples have been marked as deleted and are no longer
     639            available from the interface.
     640          </para>
     641          <para>
     642            From the
     643            <guilabel>view/preset&hellip;</guilabel>
     644            select box, ticking the
     645            <guilabel>Removed</guilabel>
     646            option allows to display those Samples earmarked for deletion. They will be
     647            shown with a symbol
     648            <guiicon>D</guiicon>
     649            in front of them.
     650          </para>
     651        </listitem>
     652        <listitem>
     653          <para>
     654            Alternately, navigating to the Sample Item View, one can hit the &gbDelete;
     655            to performed the task. As showen in the next picture, the Sample is then
     656            flagged with the
     657            <guiicon>This item has been flagged for deletion</guiicon>
     658          </para>
     659          <figure id="write_docbook_doc.figures.sample-delete">
     660            <title>Deleting Samples from the Item View</title>
     661            <screenshot>
     662              <mediaobject>
     663                <imageobject>
     664                  <imagedata contentwidth="12cm" width="12cm"
     665                    fileref="figures/sample-delete.png" format="PNG" />
     666                </imageobject>
     667              </mediaobject>
     668            </screenshot>
     669          </figure>
     670        </listitem>
     671        <listitem>
     672          <para>
     673            Deletion errors can be easily recovered. Select the item to recover from the
     674            List View (be sure to check the
     675            <guilabel>removed</guilabel>
     676            option in the View/preset.. filter) and hit the &gbRestore; to performed the
     677            task.
     678          </para>
     679        </listitem>
     680      </itemizedlist>
     681      <important>
     682        <para>
     683          To really delete an item from the database you must use the trashcan. Items
     684          deleted from the Trashcan can not be recovered. To learn more about the trashcan
     685          function, please refer to
     686          <xref linkend="trashcan" />
     687        </para>
     688      </important>
     689    </sect2>
     690  </sect1>
    99691
    100      <figure id="write_docbook_doc.figures.biosource-tab-1">
    101       <title>The Biosource tab in the Biosource Create Window</title>
    102       <screenshot>
    103       <mediaobject>
    104        <imageobject>
    105         <imagedata contentwidth="10cm" width="10cm" fileref="figures/biosource-tab-1.png" format="PNG"/>
    106        </imageobject>
    107       </mediaobject>
    108      </screenshot>
    109      </figure>
    110     </listitem>
    111     <listitem>
    112      <para>
    113       <guilabel>Annotations</guilabel>
    114      </para>
    115      <para> This tab allows BASE2 users to use Annotation Types to refine BioSource description.</para>
    116      <para>A list of Annotation Type will be displayed only if owned by or shared to the user.</para>
    117      <important>
    118       <para> In order to use this feature, Annotation Type must be declared and made available. To
    119        learn more about Annotation Types, please refer to <xref linkend="annotations"/>
    120       </para>
    121      </important>
    122      <para> Annotation Types can be filtered based on their grouping properties using the
    123        <guilabel>categories</guilabel> select-list feature. For more information about Annotation
    124       Type Categories, refer to section <xref linkend="annotations.manage.create_atcategory"/>. </para>
    125      <figure id="write_docbook_doc.figures.biosource-tab-2">
    126       <title>The Annotation tab from the Biosource Create Window</title>
    127       <screenshot>
    128       <mediaobject>
    129        <imageobject>
    130         <imagedata contentwidth="10cm" width="10cm" fileref="figures/biosource-tab-2.png" format="PNG"/>
    131        </imageobject>
    132       </mediaobject>
    133      </screenshot>
    134      </figure>
    135      <para>To provide a value to a specific Annotation Type, click on it.</para>
    136      <para> Upon selection, the windows is updated to present a drop-down list, an entry box or a
    137       radio-button check box, depending on the type of the Annotation Type.</para>
    138      <para>Once a value has been supplied, an <inlinemediaobject>
    139        <imageobject>
    140         <imagedata fileref="figures/annotated.gif" format="GIF"/>
    141        </imageobject>
    142       </inlinemediaobject> symbol appear in front of the annotation type.</para>
    143      <para>The actual type of the Annotation Type will be reminded between bracket, for instance
    144       appearing in the interface as <guilabel>(float)</guilabel> or <guilabel>(string)</guilabel>.</para>
    145      <para>A validation will be applied upon data entry to match the requirements, i.e. check for
    146       integer,boolean, string... values are provided.</para>
    147      <figure id="write_docbook_doc.figures.biosource-tab-3">
    148       <title>Providing Annotation Type values from the Biosource Create Window</title>
    149       <screenshot>
    150       <mediaobject>
    151        <imageobject>
    152         <imagedata contentwidth="10cm" width="10cm" fileref="figures/biosource-tab-3.png" format="PNG"/>
    153        </imageobject>
    154       </mediaobject>
    155      </screenshot>
    156      </figure>
    157     </listitem>
    158    </itemizedlist>
    159    <para>Click on the <inlinemediaobject>
    160      <imageobject>
    161       <imagedata fileref="figures/save.gif" format="GIF"/>
    162      </imageobject>
    163     </inlinemediaobject> Save button to store the information in BASE2 or on the <inlinemediaobject>
    164      <imageobject>
    165       <imagedata fileref="figures/cancel.gif" format="GIF"/>
    166      </imageobject>
    167     </inlinemediaobject> button to abort. </para>
    168   </sect2>
    169   <sect2 id="biosource.manage.detail_view">
    170    <title>Viewing/Editing BioSources</title>
    171    <para>From the BioSource List View, clicking on the BioSource <guilabel>Name</guilabel> opens a
    172     detailed view for that Biosource, showing a summary of all information available in BASE2 about
    173     that particular entity.</para>
    174    <para> The default behavior opens the detailed view on the <guilabel>Properties</guilabel> tab,
    175     which shows a summary information and displays the list of Samples derived from a BioSource, if
    176     any.</para>
    177    <figure id="write_docbook_doc.figures.biosource-itemview-prop">
    178     <title>BioSource Item View, properties tab</title>
    179     <screenshot>
    180     <mediaobject>
    181      <imageobject>
    182       <imagedata contentwidth="12cm" width="12cm" fileref="figures/biosource-itemview-prop.png" format="PNG"/>
    183      </imageobject>
    184     </mediaobject>
    185    </screenshot>
    186    </figure>
    187    <para>By clicking on the <guilabel>Annotations</guilabel> tab, users can display the list of
    188     Annotation Types used to annotate a Biosource. </para>
    189    <figure id="write_docbook_doc.figures.biosource-itemview-annot">
    190     <title>BioSource Item View, annotations tab</title>
    191     <screenshot>
    192     <mediaobject>
    193      <imageobject>
    194       <imagedata contentwidth="13cm" width="13cm" fileref="figures/biosource-itemview-annot.png" format="PNG"/>
    195      </imageobject>
    196     </mediaobject>
    197    </screenshot>
    198    </figure>
    199    <para>Clicking the <inlinemediaobject>
    200      <imageobject>
    201       <imagedata fileref="figures/edit.gif" format="GIF"/>
    202      </imageobject>
    203     </inlinemediaobject><guiicon> edit icon</guiicon> in the <interface>value</interface> for any of
    204     the annotations (e.g. 'antibiotic' in our example), opens an Annotate window (which is a
    205     BioSource Edit window set on the annotation tab) and highlights the selected Annotation Type,
    206     prompting for data entry.</para>
    207    <figure id="write_docbook_doc.figures.biosource-itemview-annot-edit">
    208     <title>BioSource annotations edit</title>
    209     <screenshot>
    210     <mediaobject>
    211      <imageobject>
    212       <imagedata contentwidth="12cm" width="12cm" fileref="figures/biosource-itemview-annot-edit.png" format="PNG"/>
    213      </imageobject>
    214     </mediaobject>
    215    </screenshot>
    216    </figure>
    217    <para> The relevant Annotation Type is highlighted and a list of possible values is displayed. </para>
    218    <para>Again, all Annotation types marked with a <inlinemediaobject>
    219      <imageobject>
    220       <imagedata fileref="figures/annotated.gif" format="GIF"/>
    221      </imageobject>
    222     </inlinemediaobject> symbol have been used to provided information.</para>
    223    <para>Click on the <inlinemediaobject>
    224      <imageobject>
    225       <imagedata fileref="figures/save.gif" format="GIF"/>
    226      </imageobject>
    227     </inlinemediaobject> Save button to store the information in BASE2 or on the <inlinemediaobject>
    228      <imageobject>
    229       <imagedata fileref="figures/cancel.gif" format="GIF"/>
    230      </imageobject>
    231     </inlinemediaobject> button to abort. </para>
    232   </sect2>
    233   <sect2 id="biosource.manage.delete_restore">
    234    <title>Deleting/Restoring BioSources</title>
    235    <para>As for other items in BASE2, BioSources can be removed. For a generic overview on how to
    236     delete and restore items, refer to section <xref linkend="webclient.items.delete"/>
    237    </para>
    238    <para> To delete, do the following</para>
    239    <itemizedlist>
    240     <listitem>
    241      <para> Select one or more BioSources and click &gbDelete; button in the menu
    242       bar. </para>
    243      <para> All the selected BioSources have been marked as deleted and are no longer available from
    244       the interface. </para>
    245      <para> From the <guilabel>view/preset&hellip;</guilabel> select box, ticking the
    246        <guilabel>Removed</guilabel> option allows to display those of the BioSources earmarked for
    247       deletion. They will be shown with a symbol <inlinemediaobject>
    248        <imageobject>
    249         <imagedata fileref="figures/deleted.gif" format="GIF"/>
    250        </imageobject>
    251       </inlinemediaobject> in front of them. </para>
    252     </listitem>
    253     <listitem>
    254      <para> Alternately, navigating to the BioSource Item View, hitting the
    255       &gbDelete; will perform the task.</para>
    256      <para> As shown in the next picture, the BioSource is then marked with the <inlinemediaobject>
    257        <imageobject>
    258         <imagedata fileref="figures/deleted.gif" format="GIF"/>
    259        </imageobject>
    260       </inlinemediaobject><guilabel>This item has been flagged for deletion</guilabel> label.</para>
    261      <figure id="write_docbook_doc.figures.biosource-delete">
    262       <title>Deleting BioSource from the Item View</title>
    263       <screenshot>
    264      <mediaobject>
    265       <imageobject>
    266        <imagedata contentwidth="12cm" width="12cm" fileref="figures/biosource-delete.png" format="PNG"/>
    267       </imageobject>
    268      </mediaobject>
    269     </screenshot>
    270      </figure>
    271     </listitem>
    272     <listitem>
    273      <para>Deletion errors can be easily recovered. Select the item to recover from the List View
    274       (be sure to check the <guilabel>Removed</guilabel> option in the View/preset.. filter) and hit
    275       the &gbRestore; to performed the task. </para>
    276     </listitem>
    277    </itemizedlist>
    278    <important>
    279     <para>To really delete an item from the database you must use the trashcan. Items deleted from
    280      the Trashcan can not be recovered. To learn more about the trashcan function, please refer to
    281       <xref linkend="trashcan"/>
    282     </para>
    283    </important>
    284   </sect2>
    285  </sect1>
    286  <sect1 id="sample.manage">
    287   <title>Managing Samples</title>
    288   <para>Samples result from processing events applied to <guilabel>BioSource</guilabel> material or
    289    other <guilabel>Samples</guilabel> before they are turned into an <guilabel>Extract</guilabel>.</para>
    290   <para>In other words, Samples can be created from BioSource items or from one or more Sample
    291    items.</para>
    292   <para>When a Sample is created from several other Samples, a 'pooling' event is performed. A
    293    specific section details how to create pools, refer to <xref
    294     linkend="sample.manage.createsample.pool"/></para>
    295   <para>For every step of transformation from BioSource to Sample, it is possible to provide
    296    information about the protocol used to perform this task. It is not enforced in BASE2 but it
    297    should serve as guidance when devising the granularity of the sample processing task. Also, it is
    298    good practice to provide protocol information to ensure MIAME compliance.</para>
    299   <sect2 id="sample.manage.createsamplefrombiosource">
    300    <title>Creating Samples</title>
    301    <orderedlist>
    302     <listitem>
    303      <para>Creating Samples from the BioSource page</para>
    304      <para>No matter how complex the sample processing phase is, at least one Sample has to be
    305       anchored to a BioSource.</para>
    306      <para>Therefore, a natural way to create a Sample is to click on the <inlinemediaobject>
    307        <imageobject>
    308         <imagedata fileref="figures/add.gif" format="GIF"/>
    309        </imageobject>
    310       </inlinemediaobject>
    311       <guibutton>Create new Sample</guibutton> from the Sample column of the BioSource list view.</para>
    312      <figure id="write_docbook_doc.figures.biosource-create-sample">
    313       <title>Creating a Sample from the BioSource list view</title>
    314       <screenshot>
    315        <mediaobject>
    316         <imageobject>
    317          <imagedata contentwidth="13cm" width="13cm" fileref="figures/biosource-create-sample.png" format="PNG"/>
    318         </imageobject>
    319        </mediaobject>
    320       </screenshot>
    321      </figure>
    322     </listitem>
    323     <listitem>
    324      <para>Creating Samples from the Sample List view page</para>
    325      <para> This is the alternative for creating Sample from the BioSource. To do so, go to <menuchoice>
    326        <guimenu>View</guimenu>
    327        <guimenuitem>BioSamples</guimenuitem>
    328       </menuchoice> , Click on &gbNew; button </para>
    329      <para> A 'Create' pop-up window opens, it contains 4 tabs: <guilabel>Sample</guilabel>,
    330        <guilabel>Parents</guilabel>, <guilabel> Annotations &amp; parameters</guilabel> and
    331        <guilabel>Inherited Annotations</guilabel>. </para>
    332      <itemizedlist>
    333       <listitem>
    334        <para>The Sample Tab </para>
    335        <para>This tab contains 1 mandatory field for providing the Sample <guilabel>Name</guilabel>.
    336         BASE2 by default assigns names to Samples (by suffixing 's#' when creating a Sample from an
    337         existing Biosource or 'New Sample' otherwise) but it is possible to edit at will.</para>
    338        <para>There are 5 optional fields to provide more detailed information</para>
    339        <itemizedlist>
    340         <listitem>
    341          <para><guilabel>External ID</guilabel>: for instance to report a barcode attached to a
    342           Sample</para>
    343         </listitem>
    344         <listitem>
    345          <para><guilabel>Original Quantity (ug)</guilabel>: this is meant to report information
    346           about the actual mass of biomaterial created</para>
    347         </listitem>
    348         <listitem>
    349          <para><guilabel>Created</guilabel>: a date should be provided. The information can be
    350           important when running quality controls on data and account for potential confounding
    351           factor (e.g. day effect)</para>
    352         </listitem>
    353         <listitem>
    354          <para><guilabel>Protocol</guilabel>: this a controled field. A select-list displays
    355           protocols whose type is <guilabel>sampling</guilabel> and which are shared to or owned by
    356           the logged-in user. </para>
    357          <important>
    358           <para>It is not mandatory to supply protocol in BASE2 Reporting protocols is a MIAME
    359            requirement</para>
    360          </important>
    361         </listitem>
    362         <listitem>
    363          <para><guilabel>Description</guilabel>: a free text field to report any information that
    364           not can be captured otherwise</para>
    365         </listitem>
    366        </itemizedlist>
    367        <para>Finally, a 7th field, <guilabel>Registered</guilabel> is automatically populated with a
    368         date at which the Sample was entered in BASE2 system.</para>
    369        <figure id="write_docbook_doc.figures.biosample-tab-1">
    370         <title>Sample tab</title>
    371         <screenshot>
    372          <mediaobject>
    373           <imageobject>
    374            <imagedata contentwidth="10cm" width="10cm" fileref="figures/biosample-tab-1.png" format="PNG"/>
    375           </imageobject>
    376          </mediaobject>
    377         </screenshot>
    378        </figure>
    379       </listitem>
    380       <listitem>
    381        <para>The Parents Tab </para>
    382        <para>This important tab does what it says on the tin: It is meant to keep track of the
    383         Sample origin. BASE2 distinguished between 2 cases which are controled by the
    384          <guibutton>pooled</guibutton> radio-button</para>
    385        <orderedlist>
    386         <listitem>
    387          <para>The Parent is a BioSource</para>
    388          <para> The <guibutton>Pooled</guibutton> radio-button is set to <guilabel>No</guilabel></para>
    389          <para> The BioSource select button is active and allows users to point to one and only one
    390           BioSource from which the Sample originates from.</para>
    391          <figure id="write_docbook_doc.figures.biosample-tab-2-select-biosource">
    392           <title>Parent tab and interaction when pooled button is set to No</title>
    393           <screenshot>
    394            <mediaobject>
    395             <imageobject>
    396              <imagedata contentwidth="12cm" width="12cm" fileref="figures/biosample-tab-2-select-biosource.png" format="PNG"/>
    397             </imageobject>
    398            </mediaobject>
    399           </screenshot>
    400          </figure>
    401         </listitem>
    402         <listitem>
    403          <para>The Parent is another Sample</para>
    404          <para> The <guibutton>Pooled</guibutton> radio-button has to be set to
    405           <guilabel>Yes</guilabel></para>
    406          <para>Upon selection, the BioSource select button is deactivated and the Samples box and
    407           button are activated.</para>
    408          <para>This allows users to specify one or more Samples to be selected from the Sample List
    409           View page. </para>
    410          <figure id="write_docbook_doc.figures.biosample-tab-2-select-sample">
    411           <title>Parent tab and interaction when pooled button is set to Yes</title>
    412           <screenshot>
    413            <mediaobject>
    414             <imageobject>
    415              <imagedata contentwidth="12cm" width="12cm" fileref="figures/biosample-tab-2-select-sample.png" format="PNG"/>
    416             </imageobject>
    417            </mediaobject>
    418           </screenshot>
    419          </figure>
    420         </listitem>
    421        </orderedlist>
    422       </listitem>
    423       <listitem>
    424        <para>Annotations &amp; parameters </para>
    425        <para>As seen in the BioSource section, this tab allows users to further supply information
    426         about the Sample provided they have defined or shared annotation types to annotate Sample
    427         items.</para>
    428        <para>The display of Annotation Type can be filtered based on the Annotation Type Category
    429         they belong to. </para>
    430        <important>
    431         <para> In order to use this feature, Annotation Type must be declared and made available. To
    432          learn more about Annotation Types, please refer to <xref linkend="annotations"/>
    433         </para>
    434        </important>
    435        <para>To provide a value for a given annotation type, simply click on it an use the input
    436         field or select a value from the drop-down lists or radio buttons.</para>
    437        <figure id="write_docbook_doc.figures.biosample-tab-3">
    438         <title>Annotations &amp; parameters</title>
    439         <screenshot>
    440          <mediaobject>
    441           <imageobject>
    442            <imagedata contentwidth="12cm" width="12cm" fileref="figures/biosample-tab-3.png" format="PNG"/>
    443           </imageobject>
    444          </mediaobject>
    445         </screenshot>
    446        </figure>
    447       </listitem>
    448       <listitem>
    449        <para>Inherited Annotations case1 </para>
    450        <para>The next picture shows </para>
    451        <figure id="write_docbook_doc.figures.biosample-tab-4">
    452         <title>Inherited Annotations</title>
    453         <screenshot>
    454          <mediaobject>
    455           <imageobject>
    456            <imagedata contentwidth="12cm" width="12cm" fileref="figures/biosample-tab-4.png" format="PNG"/>
    457           </imageobject>
    458          </mediaobject>
    459         </screenshot>
    460        </figure>
    461        <para>Inherited Annotations case2</para>
    462        <figure id="write_docbook_doc.figures.biosample-tab-4bis">
    463         <title>Inherited Annotations</title>
    464         <screenshot>
    465          <mediaobject>
    466           <imageobject>
    467            <imagedata contentwidth="12cm" width="12cm" fileref="figures/biosample-tab-4bis.png" format="PNG"/>
    468           </imageobject>
    469          </mediaobject>
    470         </screenshot>
    471        </figure>
    472       </listitem>
    473      </itemizedlist>
    474     </listitem>
    475    </orderedlist>
    476   </sect2>
    477   <sect2 id="sample.manage.createsample.pool">
    478    <title>Creating Pooled Samples</title>
    479    <para>It is common practice when biological material is scarce to pool Samples from equivalent
    480     sources. BASE2 provides mechanisms to report on such practice.</para>
    481    <para>This section details how.</para>
    482    <para>There are 2 ways to create Pooled Samples in BASE2</para>
    483    <orderedlist>
    484     <listitem>
    485      <para>Using the Pooled radio button option from the Sample Create page, and this has been shown
    486       already </para>
    487     </listitem>
    488     <listitem>
    489      <para>Using the Pool button in the Menu bar</para>
    490      <para>The Sample List View page menu bar contains an additionnal button the usage of which is
    491       detailed now.</para>
    492      <para>The &gbPool; button <inlinemediaobject>
    493        <imageobject>
    494         <imagedata fileref="figures/new_pooled.gif" format="GIF"/>
    495        </imageobject>
    496       </inlinemediaobject> allows users to create Pooled Samples by selecting the list of Samples
    497       used to produce that new Sample.</para>
    498      <para> Users simply need to tick the select-boxes in front of each relevant Sample and click
    499       the <inlinemediaobject>
    500        <imageobject>
    501         <imagedata fileref="figures/new_pooled.gif" format="GIF"/>
    502        </imageobject>
    503       </inlinemediaobject> button. </para>
    504      <para>This provides an easy and simple way to create Pooled Samples. The result of such process
    505       is the creation of a New Sample, which Parent Samples are listing and preset in the Parent tab</para>
    506      <figure id="write_docbook_doc.figures.biosample-tab-2-pool-sample">
    507       <title>Pooling of Samples</title>
    508       <screenshot>
    509        <mediaobject>
    510         <imageobject>
    511          <imagedata contentwidth="12cm" width="12cm" fileref="figures/biosample-tab-2-pool-sample.png" format="PNG"/>
    512         </imageobject>
    513        </mediaobject>
    514       </screenshot>
    515      </figure>
    516     </listitem>
    517    </orderedlist>
    518   </sect2>
    519   <sect2 id="sample.manage.delete">
    520    <title>Deleting/Restoring Samples</title>
    521    <para>As for other items in BASE2, Samples can be removed. For a generic overview on how to
    522     delete and restore items, refer to section <xref linkend="webclient.items.delete"/></para>
    523    <para>To delete, do the following</para>
    524    <itemizedlist>
    525     <listitem>
    526      <para> Select one or more Samples and click &gbDelete; button in the menu
    527       bar. </para>
    528      <para> All the selected Samples have been marked as deleted and are no longer available from
    529       the interface. </para>
    530      <para> From the <guilabel>view/preset&hellip;</guilabel> select box, ticking the
    531        <guilabel>Removed</guilabel> option allows to display those Samples earmarked for deletion.
    532       They will be shown with a symbol <guiicon>D</guiicon> in front of them. </para>
    533     </listitem>
    534     <listitem>
    535      <para> Alternately, navigating to the Sample Item View, one can hit the
    536       &gbDelete; to performed the task. As showen in the next picture, the Sample
    537       is then flagged with the <guiicon>This item has been flagged for deletion</guiicon>
    538      </para>
    539      <figure id="write_docbook_doc.figures.sample-delete">
    540       <title>Deleting Samples from the Item View</title>
    541       <screenshot>
    542      <mediaobject>
    543       <imageobject>
    544        <imagedata contentwidth="12cm" width="12cm" fileref="figures/sample-delete.png" format="PNG"/>
    545       </imageobject>
    546      </mediaobject>
    547     </screenshot>
    548      </figure>
    549     </listitem>
    550     <listitem>
    551      <para>Deletion errors can be easily recovered. Select the item to recover from the List View
    552       (be sure to check the <guilabel>removed</guilabel> option in the View/preset.. filter) and hit
    553       the &gbRestore; to performed the task. </para>
    554     </listitem>
    555    </itemizedlist>
    556    <important>
    557     <para>To really delete an item from the database you must use the trashcan. Items deleted from
    558      the Trashcan can not be recovered. To learn more about the trashcan function, please refer to
    559       <xref linkend="trashcan"/>
    560     </para>
    561    </important>
    562   </sect2>
    563  </sect1>
    564 
    565  <sect1 id="extract.manage">
    566   <title>Managing Extracts</title>
    567   <para>Extract items should be used to describe the events that transform a Sample material in an
    568    Extract material.</para>
    569   <para>Extracts can be created from Sample items or from one or more Extract items.</para>
    570   <para>When an Extract is created from several other Extracts, a Pooling event is performed. A
    571    specific section details how to create pooled Extracts</para>
    572   <para>During the transformation from Samples to Extracts, it is possible to provide information
    573    about the protocol used to perform this task.</para>
    574   <para>It is not enforced in BASE2 but it should serve as guidance when devising the granularity of
    575    the sample processing task. Also, it is good practice to provide protocol information.</para>
    576   <sect2 id="extract.manage.createextractfromsample">
    577    <title>Creating Extracts</title>
    578    <orderedlist>
    579     <listitem>
    580      <para>Creating Extracts from the Sample page</para>
    581      <para>Following the laboratory workflow, a natural way to create a new Extract is to click on
    582       the <guibutton>New extract</guibutton> from the Extract column of the Sample List View.</para>
    583      <figure id="write_docbook_doc.figures.sample-create-extract">
    584       <title>Creating an Extract from the Sample list view</title>
    585       <screenshot>
    586        <mediaobject>
    587         <imageobject>
    588          <imagedata contentwidth="12cm" width="12cm" fileref="figures/sample-create-extract.png" format="PNG"/>
    589         </imageobject>
    590        </mediaobject>
    591       </screenshot>
    592      </figure>
    593     </listitem>
    594     <listitem>
    595      <para>Creating Extracts from the Sample List view page</para>
    596      <para> Alternately, Extracts can be created directly ysing the Extract create page. To do so,
    597       go to <menuchoice>
    598        <guimenu>View</guimenu>
    599        <guimenuitem>Extracts</guimenuitem>
    600       </menuchoice> , Click on &gbNew; button </para>
    601      <para> A 'Create' pop-up window opens, it contains 4 tabs: <guilabel>Extract</guilabel>,
    602        <guilabel>Parents</guilabel>, <guilabel> Annotations &amp; parameters</guilabel> and
    603        <guilabel>Inherited Annotations</guilabel>. </para>
    604      <itemizedlist>
    605       <listitem>
    606        <para>The Extract Tab </para>
    607        <para>This tab contains 1 mandatory field for providing the extract name. </para>
    608        <para>BASE2 by default assigns names to Extract (by suffixing 'e#' when creating an Extract
    609         from an existing Sample or 'New Extract' otherwise) but it is possible to edit it at will</para>
    610        <para>There 5 optional fields to provide more detailed information</para>
    611        <itemizedlist>
    612         <listitem>
    613          <para><guilabel>External ID</guilabel>: for instance to report a barcode attached to an
    614           extract</para>
    615         </listitem>
    616         <listitem>
    617          <para><guilabel>Original Quantity (ug)</guilabel>: this is meant to report information
    618           about the actual mass of biomaterial created</para>
    619         </listitem>
    620         <listitem>
    621          <para><guilabel>Created</guilabel>: a date should be provided. The information can be
    622           important when running quality controls on data and account for potential confounding
    623           factor (e.g. day effect)</para>
    624         </listitem>
    625         <listitem>
    626          <para><guilabel>Protocol</guilabel>: this a controled field. A select-list displays
    627           protocol whose type is '<guilabel>extraction</guilabel>' and which are shared to or owned
    628           by the logged-in user. Reporting Protocol should be viewed as a MIAME requirement</para>
    629         </listitem>
    630         <listitem>
    631          <para><guilabel>Description</guilabel>: a free text field to report any information that
    632           not can be captured otherwise</para>
    633         </listitem>
    634        </itemizedlist>
    635        <para>Finally, a 7th field <guilabel>Registered</guilabel> is automatically populated with a
    636         date at which the sample was entered in BASE2 system.</para>
    637        <figure id="write_docbook_doc.figures.extract-tab-1">
    638         <title>Extract tab</title>
    639         <screenshot>
    640          <mediaobject>
    641           <imageobject>
    642            <imagedata contentwidth="12cm" width="12cm" fileref="figures/extract-tab-1.png" format="PNG"/>
    643           </imageobject>
    644          </mediaobject>
    645         </screenshot>
    646        </figure>
    647       </listitem>
    648       <listitem>
    649        <para>The Parents Tab </para>
    650        <para>This important tab allows users to select the Extract origin. BASE2 distinguished
    651         between 2 cases which are controled by the <guibutton>'pooled'</guibutton> radio-button</para>
    652        <orderedlist>
    653         <listitem>
    654          <para>The Parent is a Sample</para>
    655          <para> The <guibutton>pooled</guibutton> radio-button is set to <guilabel>No</guilabel></para>
    656          <para> The Sample select button is active and allows users to point to one and only one
    657           Sample from which the sample originates from.</para>
    658          <figure id="write_docbook_doc.figures.extract-tab-2-select-sample">
    659           <title>Parent tab and interaction when pooled button is set to No</title>
    660           <screenshot>
    661            <mediaobject>
    662             <imageobject>
    663              <imagedata contentwidth="12cm" width="12cm" fileref="figures/extract-tab-2-select-sample.png" format="PNG"/>
    664             </imageobject>
    665            </mediaobject>
    666           </screenshot>
    667          </figure>
    668         </listitem>
    669         <listitem>
    670          <para>The Parent is another Extract</para>
    671          <para> The <guibutton>pooled</guibutton> radio-button has to be set to
    672           <guilabel>Yes</guilabel></para>
    673          <para>Upon selection, the Samples select button is deactivated and the Extracts box and
    674           button are activated.</para>
    675          <para>This allows users to specify one or more extracts to be selected from the Extract
    676           list View page.</para>
    677          <figure id="write_docbook_doc.figures.extract-tab-2-select-extract">
    678           <title>Parent tab and interaction when pooled button is set to Yes</title>
    679           <screenshot>
    680            <mediaobject>
    681             <imageobject>
    682               <imagedata contentwidth="12cm" width="12cm" fileref="figures/extract-tab-2-select-extract.png" format="PNG"/>
    683             </imageobject>
    684            </mediaobject>
    685           </screenshot>
    686          </figure>
    687         </listitem>
    688        </orderedlist>
    689       </listitem>
    690       <listitem>
    691        <para>Annotations &amp; parameters </para>
    692        <para>As seen in the BioSource and Sample sections, this tab allows users to supply further
    693         information about the Extract, provided they have defined Annotation Types to annotation
    694         Extract items or have such elements shared to them.</para>
    695        <para>The display of Annotation Type can be filtered based on the Annotation Type Category
    696         they belong to.</para>
    697        <important>
    698         <para> In order to use this feature, Annotation Type must be declared and made available. To
    699          learn more about Annotation Types, please refer to <xref linkend="annotations"/>
    700         </para>
    701        </important>
    702        <para>To provide a value for a given annotation type, simply click on it an use the input
    703         field or select a value from the drop-down lists or radio buttons.</para>
    704        <figure id="write_docbook_doc.figures.extract-tab-3">
    705         <title>Annotations &amp; parameters</title>
    706         <screenshot>
    707          <mediaobject>
    708           <imageobject>
    709            <imagedata contentwidth="12cm" width="12cm" fileref="figures/extract-tab-3.png" format="PNG"/>
    710           </imageobject>
    711          </mediaobject>
    712         </screenshot>
    713        </figure>
    714       </listitem>
    715       <listitem>
    716        <para>Inherited Annotations case1 </para>
    717        <para>The next picture shows </para>
    718        <figure id="write_docbook_doc.figures.extract-tab-4">
    719         <title>Inherited Annotations</title>
    720         <screenshot>
    721          <mediaobject>
    722           <imageobject>
    723            <imagedata contentwidth="12cm" width="12cm" fileref="figures/extract-tab-4.png" format="PNG"/>
    724           </imageobject>
    725          </mediaobject>
    726         </screenshot>
    727        </figure>
    728       </listitem>
    729      </itemizedlist>
    730     </listitem>
    731    </orderedlist>
    732   </sect2>
    733   <sect2 id="extract.manage.createextractpool">
    734    <title>Creating Pooled Extracts</title>
    735    <para>It is common practice when biological material is scarce to pool extracts from equivalent
    736     sources. BASE2 provides mechanisms to report on such practice. This section details how.</para>
    737    <para>There are 2 ways to create pooled samples in BASE2:</para>
    738    <orderedlist>
    739     <listitem>
    740      <para>Using the Pooled radio button option from the Extract Create page, and this has been
    741       shown already.</para>
    742     </listitem>
    743     <listitem>
    744      <para>Using the Pool button in the Menu bar</para>
    745      <para>The Sample List View page menu bar contains an addition &gbPool;
    746       <inlinemediaobject>
    747        <imageobject>
    748         <imagedata fileref="figures/new_pooled.gif" format="GIF"/>
    749        </imageobject>
    750       </inlinemediaobject> button, the usage of which is detailed now.</para>
    751      <para>The &gbPool;
    752       <inlinemediaobject>
    753        <imageobject>
    754         <imagedata fileref="figures/new_pooled.gif" format="GIF"/>
    755        </imageobject>
    756       </inlinemediaobject> button allows users to create Pooled Extracts by selecting the list of
    757       Extracts used to derived a new Extract. Users simply to tick to boxes in front of each
    758       relevant Extract and click the <guibutton>Pool...</guibutton></para>
    759      <para>This provides an easy and simple way to create pooled Extracts. The result of such
    760       process is the creation of a New Extract, in which, when navigating to the Parent tab, shows
    761       that all the Extracts involved are already set and listed in the Extract box of the tab.</para>
    762      <figure id="write_docbook_doc.figures.biosample-tab-2-pool-extract">
    763       <title>Pooling of Extracts</title>
    764       <screenshot>
    765        <mediaobject>
    766         <imageobject>
    767          <imagedata contentwidth="12cm" width="12cm" fileref="figures/extract-tab-2-pool-extract.png" format="PNG"/>
    768         </imageobject>
    769        </mediaobject>
    770       </screenshot>
    771      </figure>
    772     </listitem>
    773    </orderedlist>
    774   </sect2>
    775   <sect2 id="extract.manage.delete">
    776    <title>Deleting/Restoring Extracts</title>
    777    <para>As for other items in BASE2, Extracts can be removed. For a generic overview on how to
    778     delete and restore items, refer to section <xref linkend="webclient.items.delete"/>
    779    </para>
    780    <para>To delete, do the following</para>
    781    <itemizedlist>
    782     <listitem>
    783      <para> Select one or more Extract and click &gbDelete; button in the menu
    784       bar.</para>
    785      <para> All the selected Extracts have been marked as deleted and are no longer available from
    786       the interface.</para>
    787      <para> Only by selecting from the <guilabel>view/preset&hellip;</guilabel> select box the
    788        <guilabel>Removed</guilabel> option, one can see those of the Extracts earmarked for
    789       deletion. They will be shown with a symbol in front of them.</para>
    790     </listitem>
    791     <listitem>
    792      <para> Alternately, navigating to the Extract Item View, one can hit the
    793       &gbDelete; to performed the task.</para>
    794      <para> As shown in the next picture, the Extract is then marked with the <guilabel>This item
    795        has been flagged for deletion</guilabel>
    796      </para>
    797      <figure id="write_docbook_doc.figures.extract-delete">
    798       <title>Deleting Extracts from the Item View</title>
    799       <screenshot>
    800        <mediaobject>
    801         <imageobject>
    802          <imagedata contentwidth="12cm" width="12cm" fileref="figures/extract-delete.png" format="PNG"/>
    803         </imageobject>
    804        </mediaobject>
    805       </screenshot>
    806      </figure>
    807     </listitem>
    808     <listitem>
    809      <para>Deletion errors at this stage can be easily recovered. Select the item to recover from
    810       the List View (be sure to check the <guilabel>removed</guilabel> option in the View/preset..
    811       filter) and hit the &gbRestore; to performed the task. </para>
    812     </listitem>
    813    </itemizedlist>
    814    <important>
    815     <para>To really delete an item from the database you must use the trashcan. Items deleted from
    816      the Trashcan can not be recovered. To learn more about the trashcan function, please refer to
    817       <xref linkend="trashcan"/>
    818     </para>
    819    </important>
    820   </sect2>
    821  </sect1>
     692  <sect1 id="extract.manage">
     693    <title>Managing Extracts</title>
     694    <para>
     695      Extract items should be used to describe the events that transform a Sample material in
     696      an Extract material.
     697    </para>
     698    <para>Extracts can be created from Sample items or from one or more Extract items.</para>
     699    <para>
     700      When an Extract is created from several other Extracts, a Pooling event is performed. A
     701      specific section details how to create pooled Extracts
     702    </para>
     703    <para>
     704      During the transformation from Samples to Extracts, it is possible to provide
     705      information about the protocol used to perform this task.
     706    </para>
     707    <para>
     708      It is not enforced in BASE2 but it should serve as guidance when devising the
     709      granularity of the sample processing task. Also, it is good practice to provide protocol
     710      information.
     711    </para>
     712    <sect2 id="extract.manage.createextractfromsample">
     713      <title>Creating Extracts</title>
     714      <orderedlist>
     715        <listitem>
     716          <para>Creating Extracts from the Sample page</para>
     717          <para>
     718            Following the laboratory workflow, a natural way to create a new Extract is
     719            to click on the
     720            <guibutton>New extract</guibutton>
     721            from the Extract column of the Sample List View.
     722          </para>
     723          <figure id="write_docbook_doc.figures.sample-create-extract">
     724            <title>Creating an Extract from the Sample list view</title>
     725            <screenshot>
     726              <mediaobject>
     727                <imageobject>
     728                  <imagedata contentwidth="12cm" width="12cm"
     729                    fileref="figures/sample-create-extract.png" format="PNG" />
     730                </imageobject>
     731              </mediaobject>
     732            </screenshot>
     733          </figure>
     734        </listitem>
     735        <listitem>
     736          <para>Creating Extracts from the Sample List view page</para>
     737          <para>
     738            Alternately, Extracts can be created directly ysing the Extract create page.
     739            To do so, go to
     740            <menuchoice>
     741              <guimenu>View</guimenu>
     742              <guimenuitem>Extracts</guimenuitem>
     743            </menuchoice>
     744            , Click on &gbNew; button
     745          </para>
     746          <para>
     747            A 'Create' pop-up window opens, it contains 4 tabs:
     748            <guilabel>Extract</guilabel>
     749            ,
     750            <guilabel>Parents</guilabel>
     751            ,
     752            <guilabel>Annotations &amp; parameters</guilabel>
     753            and
     754            <guilabel>Inherited Annotations</guilabel>
     755            .
     756          </para>
     757          <itemizedlist>
     758            <listitem>
     759              <para>The Extract Tab</para>
     760              <para>
     761                This tab contains 1 mandatory field for providing the extract name.
     762              </para>
     763              <para>
     764                BASE2 by default assigns names to Extract (by suffixing 'e#' when
     765                creating an Extract from an existing Sample or 'New Extract'
     766                otherwise) but it is possible to edit it at will
     767              </para>
     768              <para>
     769                There 5 optional fields to provide more detailed information
     770              </para>
     771              <itemizedlist>
     772                <listitem>
     773                  <para>
     774                    <guilabel>External ID</guilabel>
     775                    : for instance to report a barcode attached to an extract
     776                  </para>
     777                </listitem>
     778                <listitem>
     779                  <para>
     780                    <guilabel>Original Quantity (ug)</guilabel>
     781                    : this is meant to report information about the actual mass
     782                    of biomaterial created
     783                  </para>
     784                </listitem>
     785                <listitem>
     786                  <para>
     787                    <guilabel>Created</guilabel>
     788                    : a date should be provided. The information can be
     789                    important when running quality controls on data and account
     790                    for potential confounding factor (e.g. day effect)
     791                  </para>
     792                </listitem>
     793                <listitem>
     794                  <para>
     795                    <guilabel>Protocol</guilabel>
     796                    : this a controled field. A select-list displays protocol
     797                    whose type is '
     798                    <guilabel>extraction</guilabel>
     799                    ' and which are shared to or owned by the logged-in user.
     800                    Reporting Protocol should be viewed as a MIAME requirement
     801                  </para>
     802                </listitem>
     803                <listitem>
     804                  <para>
     805                    <guilabel>Description</guilabel>
     806                    : a free text field to report any information that not can
     807                    be captured otherwise
     808                  </para>
     809                </listitem>
     810              </itemizedlist>
     811              <para>
     812                Finally, a 7th field
     813                <guilabel>Registered</guilabel>
     814                is automatically populated with a date at which the sample was
     815                entered in BASE2 system.
     816              </para>
     817              <figure id="write_docbook_doc.figures.extract-tab-1">
     818                <title>Extract tab</title>
     819                <screenshot>
     820                  <mediaobject>
     821                    <imageobject>
     822                      <imagedata contentwidth="12cm" width="12cm"
     823                        fileref="figures/extract-tab-1.png" format="PNG" />
     824                    </imageobject>
     825                  </mediaobject>
     826                </screenshot>
     827              </figure>
     828            </listitem>
     829            <listitem>
     830              <para>The Parents Tab</para>
     831              <para>
     832                This important tab allows users to select the Extract origin. BASE2
     833                distinguished between 2 cases which are controled by the
     834                <guibutton>'pooled'</guibutton>
     835                radio-button
     836              </para>
     837              <orderedlist>
     838                <listitem>
     839                  <para>The Parent is a Sample</para>
     840                  <para>
     841                    The
     842                    <guibutton>pooled</guibutton>
     843                    radio-button is set to
     844                    <guilabel>No</guilabel>
     845                  </para>
     846                  <para>
     847                    The Sample select button is active and allows users to point
     848                    to one and only one Sample from which the sample originates
     849                    from.
     850                  </para>
     851                  <figure
     852                    id="write_docbook_doc.figures.extract-tab-2-select-sample">
     853                    <title>
     854                      Parent tab and interaction when pooled button is set to
     855                      No
     856                    </title>
     857                    <screenshot>
     858                      <mediaobject>
     859                        <imageobject>
     860                          <imagedata contentwidth="12cm" width="12cm"
     861                            fileref="figures/extract-tab-2-select-sample.png" format="PNG" />
     862                        </imageobject>
     863                      </mediaobject>
     864                    </screenshot>
     865                  </figure>
     866                </listitem>
     867                <listitem>
     868                  <para>The Parent is another Extract</para>
     869                  <para>
     870                    The
     871                    <guibutton>pooled</guibutton>
     872                    radio-button has to be set to
     873                    <guilabel>Yes</guilabel>
     874                  </para>
     875                  <para>
     876                    Upon selection, the Samples select button is deactivated and
     877                    the Extracts box and button are activated.
     878                  </para>
     879                  <para>
     880                    This allows users to specify one or more extracts to be
     881                    selected from the Extract list View page.
     882                  </para>
     883                  <figure
     884                    id="write_docbook_doc.figures.extract-tab-2-select-extract">
     885                    <title>
     886                      Parent tab and interaction when pooled button is set to
     887                      Yes
     888                    </title>
     889                    <screenshot>
     890                      <mediaobject>
     891                        <imageobject>
     892                          <imagedata contentwidth="12cm" width="12cm"
     893                            fileref="figures/extract-tab-2-select-extract.png" format="PNG" />
     894                        </imageobject>
     895                      </mediaobject>
     896                    </screenshot>
     897                  </figure>
     898                </listitem>
     899              </orderedlist>
     900            </listitem>
     901            <listitem>
     902              <para>Annotations &amp; parameters</para>
     903              <para>
     904                As seen in the BioSource and Sample sections, this tab allows users
     905                to supply further information about the Extract, provided they have
     906                defined Annotation Types to annotation Extract items or have such
     907                elements shared to them.
     908              </para>
     909              <para>
     910                The display of Annotation Type can be filtered based on the
     911                Annotation Type Category they belong to.
     912              </para>
     913              <important>
     914                <para>
     915                  In order to use this feature, Annotation Type must be declared
     916                  and made available. To learn more about Annotation Types, please
     917                  refer to
     918                  <xref linkend="annotations" />
     919                </para>
     920              </important>
     921              <para>
     922                To provide a value for a given annotation type, simply click on it
     923                an use the input field or select a value from the drop-down lists or
     924                radio buttons.
     925              </para>
     926              <figure id="write_docbook_doc.figures.extract-tab-3">
     927                <title>Annotations &amp; parameters</title>
     928                <screenshot>
     929                  <mediaobject>
     930                    <imageobject>
     931                      <imagedata contentwidth="12cm" width="12cm"
     932                        fileref="figures/extract-tab-3.png" format="PNG" />
     933                    </imageobject>
     934                  </mediaobject>
     935                </screenshot>
     936              </figure>
     937            </listitem>
     938            <listitem>
     939              <para>Inherited Annotations case1</para>
     940              <para>The next picture shows</para>
     941              <figure id="write_docbook_doc.figures.extract-tab-4">
     942                <title>Inherited Annotations</title>
     943                <screenshot>
     944                  <mediaobject>
     945                    <imageobject>
     946                      <imagedata contentwidth="12cm" width="12cm"
     947                        fileref="figures/extract-tab-4.png" format="PNG" />
     948                    </imageobject>
     949                  </mediaobject>
     950                </screenshot>
     951              </figure>
     952            </listitem>
     953          </itemizedlist>
     954        </listitem>
     955      </orderedlist>
     956    </sect2>
     957    <sect2 id="extract.manage.createextractpool">
     958      <title>Creating Pooled Extracts</title>
     959      <para>
     960        It is common practice when biological material is scarce to pool extracts from
     961        equivalent sources. BASE2 provides mechanisms to report on such practice. This
     962        section details how.
     963      </para>
     964      <para>There are 2 ways to create pooled samples in BASE2:</para>
     965      <orderedlist>
     966        <listitem>
     967          <para>
     968            Using the Pooled radio button option from the Extract Create page, and this
     969            has been shown already.
     970          </para>
     971        </listitem>
     972        <listitem>
     973          <para>Using the Pool button in the Menu bar</para>
     974          <para>
     975            The Sample List View page menu bar contains an addition &gbPool;
     976            <inlinemediaobject>
     977              <imageobject>
     978                <imagedata fileref="figures/new_pooled.gif" format="GIF" />
     979              </imageobject>
     980            </inlinemediaobject>
     981            button, the usage of which is detailed now.
     982          </para>
     983          <para>
     984            The &gbPool;
     985            <inlinemediaobject>
     986              <imageobject>
     987                <imagedata fileref="figures/new_pooled.gif" format="GIF" />
     988              </imageobject>
     989            </inlinemediaobject>
     990            button allows users to create Pooled Extracts by selecting the list of
     991            Extracts used to derived a new Extract. Users simply to tick to boxes in
     992            front of each relevant Extract and click the
     993            <guibutton>Pool...</guibutton>
     994          </para>
     995          <para>
     996            This provides an easy and simple way to create pooled Extracts. The result
     997            of such process is the creation of a New Extract, in which, when navigating
     998            to the Parent tab, shows that all the Extracts involved are already set and
     999            listed in the Extract box of the tab.
     1000          </para>
     1001          <figure id="write_docbook_doc.figures.biosample-tab-2-pool-extract">
     1002            <title>Pooling of Extracts</title>
     1003            <screenshot>
     1004              <mediaobject>
     1005                <imageobject>
     1006                  <imagedata contentwidth="12cm" width="12cm"
     1007                    fileref="figures/extract-tab-2-pool-extract.png" format="PNG" />
     1008                </imageobject>
     1009              </mediaobject>
     1010            </screenshot>
     1011          </figure>
     1012        </listitem>
     1013      </orderedlist>
     1014    </sect2>
     1015    <sect2 id="extract.manage.delete">
     1016      <title>Deleting/Restoring Extracts</title>
     1017      <para>
     1018        As for other items in BASE2, Extracts can be removed. For a generic overview on how
     1019        to delete and restore items, refer to section
     1020        <xref linkend="webclient.items.delete" />
     1021      </para>
     1022      <para>To delete, do the following</para>
     1023      <itemizedlist>
     1024        <listitem>
     1025          <para>
     1026            Select one or more Extract and click &gbDelete; button in the menu bar.
     1027          </para>
     1028          <para>
     1029            All the selected Extracts have been marked as deleted and are no longer
     1030            available from the interface.
     1031          </para>
     1032          <para>
     1033            Only by selecting from the
     1034            <guilabel>view/preset&hellip;</guilabel>
     1035            select box the
     1036            <guilabel>Removed</guilabel>
     1037            option, one can see those of the Extracts earmarked for deletion. They will
     1038            be shown with a symbol in front of them.
     1039          </para>
     1040        </listitem>
     1041        <listitem>
     1042          <para>
     1043            Alternately, navigating to the Extract Item View, one can hit the &gbDelete;
     1044            to performed the task.
     1045          </para>
     1046          <para>
     1047            As shown in the next picture, the Extract is then marked with the
     1048            <guilabel>This item has been flagged for deletion</guilabel>
     1049          </para>
     1050          <figure id="write_docbook_doc.figures.extract-delete">
     1051            <title>Deleting Extracts from the Item View</title>
     1052            <screenshot>
     1053              <mediaobject>
     1054                <imageobject>
     1055                  <imagedata contentwidth="12cm" width="12cm"
     1056                    fileref="figures/extract-delete.png" format="PNG" />
     1057                </imageobject>
     1058              </mediaobject>
     1059            </screenshot>
     1060          </figure>
     1061        </listitem>
     1062        <listitem>
     1063          <para>
     1064            Deletion errors at this stage can be easily recovered. Select the item to
     1065            recover from the List View (be sure to check the
     1066            <guilabel>removed</guilabel>
     1067            option in the View/preset.. filter) and hit the &gbRestore; to performed the
     1068            task.
     1069          </para>
     1070        </listitem>
     1071      </itemizedlist>
     1072      <important>
     1073        <para>
     1074          To really delete an item from the database you must use the trashcan. Items
     1075          deleted from the Trashcan can not be recovered. To learn more about the trashcan
     1076          function, please refer to
     1077          <xref linkend="trashcan" />
     1078        </para>
     1079      </important>
     1080    </sect2>
     1081  </sect1>
    8221082
    8231083
    8241084
    825  <sect1 id="label">
    826   <title>Managing Labels</title>
     1085  <sect1 id="label">
     1086    <title>Managing Labels</title>
    8271087
    828   <sect2 id="label.browse">
    829    <title>Browsing Labels</title>
    830    <para>Before attempting to create Labeled Extracts, users should make sure that the appropriate
    831     Label object is present in BASE2</para>
    832    <para>To browse the list of Labels, go to <menuchoice>
    833      <guimenu>View</guimenu>
    834      <guimenuitem>Labels</guimenuitem>
    835     </menuchoice> It is wise to select the clear filter option or select the <guilabel>shared to
    836     me</guilabel> option from the view/preset select box in order to view all different dyes.</para>
    837    <para>Clicking on any of item opens an item view page</para>
    838    <figure id="write_docbook_doc.figures.label-itemview">
    839     <title>The Label Item View Page</title>
    840     <screenshot>
    841      <mediaobject>
    842       <imageobject>
    843        <imagedata contentwidth="12cm" width="12cm" fileref="figures/label-itemview.png" format="PNG"/>
    844       </imageobject>
    845      </mediaobject>
    846     </screenshot>
    847    </figure>
    848    <para>Note the <guibutton>New labeled extract&hellip;</guibutton> button available from this page. For
    849     more detailed about creating Labeled extracts, see <xref linkend="labeledextract.manage"/></para>
     1088    <sect2 id="label.browse">
     1089      <title>Browsing Labels</title>
     1090      <para>
     1091        Before attempting to create Labeled Extracts, users should make sure that the
     1092        appropriate Label object is present in BASE2
     1093      </para>
     1094      <para>
     1095        To browse the list of Labels, go to
     1096        <menuchoice>
     1097          <guimenu>View</guimenu>
     1098          <guimenuitem>Labels</guimenuitem>
     1099        </menuchoice>
     1100        It is wise to select the clear filter option or select the
     1101        <guilabel>shared to me</guilabel>
     1102        option from the view/preset select box in order to view all different dyes.
     1103      </para>
     1104      <para>Clicking on any of item opens an item view page</para>
     1105      <figure id="write_docbook_doc.figures.label-itemview">
     1106        <title>The Label Item View Page</title>
     1107        <screenshot>
     1108          <mediaobject>
     1109            <imageobject>
     1110              <imagedata contentwidth="12cm" width="12cm"
     1111                fileref="figures/label-itemview.png" format="PNG" />
     1112            </imageobject>
     1113          </mediaobject>
     1114        </screenshot>
     1115      </figure>
     1116      <para>
     1117        Note the
     1118        <guibutton>New labeled extract&hellip;</guibutton>
     1119        button available from this page. For more detailed about creating Labeled extracts,
     1120        see
     1121        <xref linkend="labeledextract.manage" />
     1122      </para>
    8501123
    851   </sect2>
    852   <sect2 id="label.create">
    853    <title>Creating Labels</title>
    854    <para> Click on &gbNew; button, a pop-up window opens. Fill in
    855     Name and description if required. Label item are very simple object and do not bear association
    856     to Annotation Type. </para>
    857   </sect2>
    858  </sect1>
    859  <sect1 id="labeledextract.manage">
    860   <title>Managing Labeled Extracts</title>
    861   <para>Labeled Extract items should be used to describe the event that transformed a Extract
    862    material in a Labeled Extract material.</para>
    863   <para>Labeled extracts can be created from Extract items or from one or more Labeled extract
    864    items.</para>
    865   <para>When a Labeled Extract is created from several other Labeled Extracts, a Pooling event is
    866    performed. A specific section details how to create pooled Labeled Extracts</para>
    867   <para>During the transformation from Extracts to Labeled Extracts, it is possible to provide
    868    information about the protocol used to perform this task.</para>
    869   <para>It is not enforced in BASE2 but it should serve as guidance when devising the granularity of
    870    the extract processing task. Also, it is good practice to provide protocol information.</para>
    871   <sect2 id="labeledextract.manage.createlabeledextractfromextract">
    872    <title>Creating Labeled Extracts</title>
    873    <orderedlist>
    874     <listitem>
    875      <para>Creating Labeled Extracts from the Extract page</para>
    876      <para>Following the laboratory workflow, a natural way to create a Labeled Extract is to click
    877       on the <guibutton>New labeled extract</guibutton> from the Labeled Extract column of the
    878       Extract List View.</para>
    879      <figure id="write_docbook_doc.figures.sample-create-labeledextract">
    880       <title>Creating a Labeled Extract from the Extract List View</title>
    881       <screenshot>
    882        <mediaobject>
    883         <imageobject>
    884          <imagedata contentwidth="12cm" width="12cm" fileref="figures/sample-create-labeledextract.png" format="PNG"/>
    885         </imageobject>
    886        </mediaobject>
    887       </screenshot>
    888      </figure>
    889     </listitem>
    890     <listitem>
    891      <para>Creating Labeled Extracts from the Extract Item View page</para>
    892      <para> Alternately, Labeled Extracts can be created directly using the Labeled Extract create
    893       page. To do so, go to <menuchoice>
    894        <guimenu>View</guimenu>
    895        <guimenuitem>Labeled Extracts</guimenuitem>
    896       </menuchoice> , Click on &gbNew; button </para>
    897      <para> A 'Create' pop-up window opens, it contains 4 tabs: <guilabel>Labeled
    898       Extract</guilabel>, <guilabel>Parents</guilabel>, <guilabel> Annotations &amp;
    899       parameters</guilabel> and <guilabel>Inherited Annotations</guilabel>. </para>
    900      <itemizedlist>
    901       <listitem>
    902        <para>The Labeled Extract Tab </para>
    903        <para>This tab contains 2 mandatory fields, one for providing the Labeled Extract
    904          <guilabel>Name</guilabel>, the other one <guilabel>Label</guilabel> to specify which dye or
    905         marker was used in the labeling reaction.</para>
    906        <para> BASE2 by default assigns names to Labeled Extract(by suffixing 'lbe#' when creating a
    907         Labeled Extract from an existing Extract or 'New labeled extract' otherwise) but it is
    908         possible to edit it at will</para>
    909        <para>There 5 optional fields to provide more detailed information</para>
    910        <itemizedlist>
    911         <listitem>
    912          <para><guilabel>External ID</guilabel>: for instance to report a barcode attached to an
    913           extract</para>
    914         </listitem>
    915         <listitem>
    916          <para><guilabel>Original Quantity (ug)</guilabel>: this is meant to report information
    917           about the actual mass of biomaterial created</para>
    918         </listitem>
    919         <listitem>
    920          <para><guilabel>Created</guilabel>: a date should be provided. The information can be
    921           important when running quality controls on data and account for potential confounding
    922           factor (e.g. day effect)</para>
    923         </listitem>
    924         <listitem>
    925          <para><guilabel>Protocol</guilabel>: this a controled field. A select-list displays
    926           protocol whose type is '<guilabel>labeling</guilabel>' and which are shared to or owned by
    927           the logged-in user. Reporting Protocol should be viewed as a MIAME requirement</para>
    928         </listitem>
    929         <listitem>
    930          <para><guilabel>Description</guilabel>: a free text field to report any information that
    931           can not be captured otherwise</para>
    932         </listitem>
    933        </itemizedlist>
    934        <para>Finally, a 7th field <guilabel>Created</guilabel> is automatically populated with a
    935         date at which the Labeled Extract was actually entered in BASE2 system.</para>
    936        <figure id="write_docbook_doc.figures.labeledextract-tab-1">
    937         <title>Labeled Extract tab</title>
    938         <screenshot>
    939          <mediaobject>
    940           <imageobject>
    941            <imagedata contentwidth="12cm" width="12cm" fileref="figures/labeledextract-tab-1.png" format="PNG"/>
    942           </imageobject>
    943          </mediaobject>
    944         </screenshot>
    945        </figure>
    946       </listitem>
    947       <listitem>
    948        <para>The Parents Tab </para>
    949        <para>This important tab allows users to select the Labeled Extract origin. BASE2
    950         distinguished between 2 cases which are controled by the <guibutton>'pooled'</guibutton>
    951         radio-button</para>
    952        <orderedlist>
    953         <listitem>
    954          <para>The Parent is an Extract</para>
    955          <para> The <guibutton>pooled</guibutton> radio-button is set to <guilabel>No</guilabel></para>
    956          <para> The Extract select button is active and allows users to point to one and only one
    957           Extract from which the Labeled Extract originates from.</para>
    958          <figure id="write_docbook_doc.figures.labeledextract-tab-2-select-extract">
    959           <title>Parent tab and interaction when pooled button is set to No</title>
    960           <screenshot>
    961            <mediaobject>
    962             <imageobject>
    963              <imagedata contentwidth="12cm" width="12cm" fileref="figures/labeledextract-tab-2-select-extract.png" format="PNG"/>
    964             </imageobject>
    965            </mediaobject>
    966           </screenshot>
    967          </figure>
    968         </listitem>
    969         <listitem>
    970          <para>The Parent is another Labeled Extract</para>
    971          <para> The <guibutton>pooled</guibutton> radio-button has to be set to
    972           <guilabel>Yes</guilabel></para>
    973          <para>Upon selection, the Extract select button is deactivated and the Labeled Extracts box
    974           and button are activated. </para>
    975          <para>This allows users to specify one or more extracts to be selected from the Labeled
    976           Extract list View page. </para>
    977          <figure id="write_docbook_doc.figures.labeledextract-tab-2-select-labeledextract">
    978           <title>Parent tab and interaction when pooled button is set to Yes</title>
    979           <screenshot>
    980            <mediaobject>
    981             <imageobject>
    982              <imagedata contentwidth="12cm" width="12cm" fileref="figures/labeledextract-tab-2-select-labeledextract.png" format="PNG"/>
    983             </imageobject>
    984            </mediaobject>
    985           </screenshot>
    986          </figure>
    987         </listitem>
    988        </orderedlist>
    989       </listitem>
    990       <listitem>
    991        <para>Annotations &amp; parameters </para>
    992        <para>As seen in the BioSource and Sample sections, this tab allows users to further supply
    993         information about the labeled extract provided they have defined annotation types to
    994         annotate Labeled Extract items or have such elements shared to them.</para>
    995        <para>The display of Annotation Types can be filtered based on the Annotation Type Categories
    996         they belong to.</para>
    997        <important>
    998         <para> In order to use this feature, Annotation Type must be declared and made available. To
    999          learn more about Annotation Types, please refer to <xref linkend="annotations"/>
    1000         </para>
    1001        </important>
    1002        <para>To provide a value for a given annotation type, simply click on it an use the input
    1003         field or select a value from the drop-down lists or radio buttons.</para>
    1004        <figure id="write_docbook_doc.figures.labeledextract-tab-3">
    1005         <title>Annotations &amp; parameters</title>
    1006         <screenshot>
    1007          <mediaobject>
    1008           <imageobject>
    1009            <imagedata contentwidth="12cm" width="12cm" fileref="figures/labeledextract-tab-3.png" format="PNG"/>
    1010           </imageobject>
    1011          </mediaobject>
    1012         </screenshot>
    1013        </figure>
    1014       </listitem>
    1015       <listitem>
    1016        <para>Inherited Annotations case1 </para>
    1017        <para>The next picture shows </para>
    1018        <figure id="write_docbook_doc.figures.labeledextract-tab-4">
    1019         <title>Inherited Annotations</title>
    1020         <screenshot>
    1021          <mediaobject>
    1022           <imageobject>
    1023            <imagedata contentwidth="12cm" width="12cm" fileref="figures/labeledextract-tab-4.png" format="PNG"/>
    1024           </imageobject>
    1025          </mediaobject>
    1026         </screenshot>
    1027        </figure>
    1028       </listitem>
    1029      </itemizedlist>
    1030     </listitem>
    1031    </orderedlist>
    1032   </sect2>
    1033   <sect2 id="labeledextract.manage.createelabeledxtract.pool">
    1034    <title>Creating Pooled Labeled Extracts</title>
    1035    <para>It is common practice when biological material is scarce to pool extracts from equivalent
    1036     sources. BASE2 provides mechanisms to report on such practice.</para>
    1037    <para>This section details how.</para>
    1038    <para>There are 2 ways to create pooled Labeled Extracts in BASE2</para>
    1039    <orderedlist>
    1040     <listitem>
    1041      <para>Using the Pooled radio button option from the Labeled Extract Create page, and this has
    1042       been shown already </para>
    1043     </listitem>
    1044     <listitem>
    1045      <para>Using the Pool button in the Menu bar</para>
    1046      <para>The Labeled Extracts List View page menu bar contains an addition
    1047        &gbPool; button, the usage of which is detailed now.</para>
    1048      <para>The &gbPool; button <inlinemediaobject>
    1049        <imageobject>
    1050         <imagedata fileref="figures/new_pooled.gif" format="GIF"/>
    1051        </imageobject>
    1052       </inlinemediaobject> allows users to create Pooled Labeled Extracts by selecting the list of
    1053       Labeled Extracts used to derived a new Labeled Extract. Users simply have to tick to boxes in
    1054       front of each relevant Labeled Extract and click the <guibutton>Pool...</guibutton></para>
    1055      <para>This provides an easy and simple way to create pooled Labeled Extracts. The result of
    1056       such process is the creation of a New Labeled Extract, in which, when navigating to the Parent
    1057       tab, shows that all the Labeled Extracts involved are already set and listed in the Labeled
    1058       Extract box of the tab.</para>
    1059      <figure id="write_docbook_doc.figures.labeledextract-tab-2-pool-labeledextract">
    1060       <title>Pooling of Labeled Extracts:</title>
    1061       <screenshot>
    1062        <mediaobject>
    1063         <imageobject>
    1064          <imagedata contentwidth="12cm" width="12cm" fileref="figures/labeledextract-tab-2-pool-labeledextract.png" format="PNG"/>
    1065         </imageobject>
    1066        </mediaobject>
    1067       </screenshot>
    1068      </figure>
    1069     </listitem>
    1070    </orderedlist>
    1071   </sect2>
    1072   <sect2 id="labeledextract.manage.delete">
    1073    <title>Deleting/Restoring Labeled Extracts</title>
    1074    <para>As for other items in BASE2, Labeled Extracts can be deleted. For a generic overview on how
    1075     to delete and restore items, refer to section <xref linkend="webclient.items.delete"/></para>
    1076    <para>To delete, do the following</para>
    1077    <itemizedlist>
    1078     <listitem>
    1079      <para> Select one or more Labeled Extract and click &gbDelete; button in the
    1080       menu bar. </para>
    1081      <para> All the selected Labeled Extracts have been marked as deleted and are no longer
    1082       available from the interface. </para>
    1083      <para> Only by selecting from the <guilabel>view/preset&hellip;</guilabel> select box the
    1084        <guilabel>Removed</guilabel> option, one can see those of the Labeled Extracts earmarked for
    1085       deletion. They will be shown with a symbol in front of them. </para>
    1086     </listitem>
    1087     <listitem>
    1088      <para> Alternately, navigating to the Labeled Extract Item View, one can hit the
    1089        &gbDelete; to performed the task. As showed in the next picture, the
    1090       Labeled Extract is then marked with the <inlinemediaobject>
    1091        <imageobject>
    1092         <imagedata fileref="figures/deleted.gif" format="GIF"/>
    1093        </imageobject>
    1094       </inlinemediaobject>
    1095       <guiicon>This item has been flagged for deletion</guiicon>
    1096      </para>
    1097      <figure id="write_docbook_doc.figures.labeledextract-delete">
    1098       <title>Deleting Labeled Extracts from the Item View</title>
    1099       <screenshot>
    1100        <mediaobject>
    1101         <imageobject>
    1102          <imagedata contentwidth="12cm" width="12cm" fileref="figures/labeledextract-delete.png" format="PNG"/>
    1103         </imageobject>
    1104        </mediaobject>
    1105       </screenshot>
    1106      </figure>
    1107     </listitem>
    1108     <listitem>
    1109      <para>Deletion errors at this stage can be easily recovered. Select the item to recover from
    1110       the List View (be sure to check the <guilabel>Removed</guilabel> option in the View/preset..
    1111       filter) and hit the &gbRestore; to performed the task. </para>
    1112     </listitem>
    1113    </itemizedlist>
    1114    <important>
    1115     <para>To really delete an item from the database you must use the trashcan. Items deleted from
    1116      the Trashcan can not be recovered. To learn more about the trashcan function, please refer to
    1117       <xref linkend="trashcan"/>
    1118     </para>
    1119    </important>
    1120   </sect2>
    1121  </sect1>
    1122  <sect1 id="hybridization.manage">
    1123   <title>Managing Hybridizations</title>
    1124   <para> An hybridization event corresponds to the application of one or more labeled extracts
    1125    materials to a microarray slide under conditions detailed in hybridization protocols. </para>
    1126   <para>In BASE2, there are 3 possible routes to create an hybridization object.</para>
    1127   <sect2 id="hybridization.manage.create">
    1128    <title>Creating Hybridizations</title>
    1129    <orderedlist>
    1130     <listitem>
    1131      <para>Creating Hybridization from the Labeled Extract List View page</para>
    1132      <para>Select at least one Labeled Extract by ticking to selection boxes before the name field.</para>
    1133      <para>Click on the <guibutton>New hybridzation (to be changed)</guibutton> from the menu bar of
    1134       Labeled Extract list view.</para>
    1135      <figure id="write_docbook_doc.figures.hyb-create-labeledlistview">
    1136       <title>Creating a Hybridization from the Labeled Extract List View</title>
    1137       <screenshot>
    1138        <mediaobject>
    1139         <imageobject>
    1140          <imagedata contentwidth="12cm" width="12cm" fileref="figures/hyb-create-labeledlistview.png" format="PNG"/>
    1141         </imageobject>
    1142        </mediaobject>
    1143       </screenshot>
    1144      </figure>
    1145     </listitem>
    1146     <listitem>
    1147      <para>Creating Hybridization from the Labeled Extract Item View page</para>
    1148      <para>After having selected a Labeled Extract and displayed it in the Item View, Click on the
    1149        <guibutton>New hybridization</guibutton> button from the Menu bar of the Labeled Extract Item
    1150       View.</para>
    1151      <figure id="write_docbook_doc.figures.hyb-create-labeleditemview">
    1152       <title>Creating a Hybridization from the Labeled Extract Item View</title>
    1153       <screenshot>
    1154        <mediaobject>
    1155         <imageobject>
    1156          <imagedata contentwidth="12cm" width="12cm" fileref="figures/hyb-create-labeleditemview.png" format="PNG"/>
    1157         </imageobject>
    1158        </mediaobject>
    1159       </screenshot>
    1160      </figure>
    1161     </listitem>
    1162     <listitem>
    1163      <para>Creating Hybridizations from the Hybridization List View page</para>
    1164      <para> Hybridizations can be created directly using the Hybridization create page. To do so, go
    1165       to <menuchoice>
    1166        <guimenu>View</guimenu>
    1167        <guimenuitem>Hybridizations</guimenuitem>
    1168       </menuchoice> , Click on &gbNew;
    1169      </para>
    1170      <figure id="write_docbook_doc.figures.hyb-create">
    1171       <title>Creating Hybridizations from the Hybridization List View</title>
    1172       <screenshot>
    1173        <mediaobject>
    1174         <imageobject>
    1175          <imagedata contentwidth="12cm" width="12cm" fileref="figures/hyb-create.png" format="PNG"/>
    1176         </imageobject>
    1177        </mediaobject>
    1178       </screenshot>
    1179      </figure>
    1180      <para> Irrespective of the methods chosen to create the Hybridization item, A 'Create' pop-up
    1181       window will open. It contains 4 distinct tabs: <guilabel>Hybridization</guilabel>,
    1182        <guilabel>Parents</guilabel>, <guilabel> Annotations &amp; parameters</guilabel> and
    1183        <guilabel>Inherited Annotations</guilabel>. </para>
    1184      <itemizedlist>
    1185       <listitem>
    1186        <para>The Hybridization Tab </para>
     1124    </sect2>
     1125    <sect2 id="label.create">
     1126      <title>Creating Labels</title>
     1127      <para>
     1128        Click on &gbNew; button, a pop-up window opens. Fill in Name and description if
     1129        required. Label item are very simple object and do not bear association to
     1130        Annotation Type.
     1131      </para>
     1132    </sect2>
     1133  </sect1>
     1134  <sect1 id="labeledextract.manage">
     1135    <title>Managing Labeled Extracts</title>
     1136    <para>
     1137      Labeled Extract items should be used to describe the event that transformed a Extract
     1138      material in a Labeled Extract material.
     1139    </para>
     1140    <para>
     1141      Labeled extracts can be created from Extract items or from one or more Labeled extract
     1142      items.
     1143    </para>
     1144    <para>
     1145      When a Labeled Extract is created from several other Labeled Extracts, a Pooling event
     1146      is performed. A specific section details how to create pooled Labeled Extracts
     1147    </para>
     1148    <para>
     1149      During the transformation from Extracts to Labeled Extracts, it is possible to provide
     1150      information about the protocol used to perform this task.
     1151    </para>
     1152    <para>
     1153      It is not enforced in BASE2 but it should serve as guidance when devising the
     1154      granularity of the extract processing task. Also, it is good practice to provide
     1155      protocol information.
     1156    </para>
     1157    <sect2 id="labeledextract.manage.createlabeledextractfromextract">
     1158      <title>Creating Labeled Extracts</title>
     1159      <orderedlist>
     1160        <listitem>
     1161          <para>Creating Labeled Extracts from the Extract page</para>
     1162          <para>
     1163            Following the laboratory workflow, a natural way to create a Labeled Extract
     1164            is to click on the
     1165            <guibutton>New labeled extract</guibutton>
     1166            from the Labeled Extract column of the Extract List View.
     1167          </para>
     1168          <figure id="write_docbook_doc.figures.sample-create-labeledextract">
     1169            <title>Creating a Labeled Extract from the Extract List View</title>
     1170            <screenshot>
     1171              <mediaobject>
     1172                <imageobject>
     1173                  <imagedata contentwidth="12cm" width="12cm"
     1174                    fileref="figures/sample-create-labeledextract.png" format="PNG" />
     1175                </imageobject>
     1176              </mediaobject>
     1177            </screenshot>
     1178          </figure>
     1179        </listitem>
     1180        <listitem>
     1181          <para>Creating Labeled Extracts from the Extract Item View page</para>
     1182          <para>
     1183            Alternately, Labeled Extracts can be created directly using the Labeled
     1184            Extract create page. To do so, go to
     1185            <menuchoice>
     1186              <guimenu>View</guimenu>
     1187              <guimenuitem>Labeled Extracts</guimenuitem>
     1188            </menuchoice>
     1189            , Click on &gbNew; button
     1190          </para>
     1191          <para>
     1192            A 'Create' pop-up window opens, it contains 4 tabs:
     1193            <guilabel>Labeled Extract</guilabel>
     1194            ,
     1195            <guilabel>Parents</guilabel>
     1196            ,
     1197            <guilabel>Annotations &amp; parameters</guilabel>
     1198            and
     1199            <guilabel>Inherited Annotations</guilabel>
     1200            .
     1201          </para>
     1202          <itemizedlist>
     1203            <listitem>
     1204              <para>The Labeled Extract Tab</para>
     1205              <para>
     1206                This tab contains 2 mandatory fields, one for providing the Labeled
     1207                Extract
     1208                <guilabel>Name</guilabel>
     1209                , the other one
     1210                <guilabel>Label</guilabel>
     1211                to specify which dye or marker was used in the labeling reaction.
     1212              </para>
     1213              <para>
     1214                BASE2 by default assigns names to Labeled Extract(by suffixing
     1215                'lbe#' when creating a Labeled Extract from an existing Extract or
     1216                'New labeled extract' otherwise) but it is possible to edit it at
     1217                will
     1218              </para>
     1219              <para>
     1220                There 5 optional fields to provide more detailed information
     1221              </para>
     1222              <itemizedlist>
     1223                <listitem>
     1224                  <para>
     1225                    <guilabel>External ID</guilabel>
     1226                    : for instance to report a barcode attached to an extract
     1227                  </para>
     1228                </listitem>
     1229                <listitem>
     1230                  <para>
     1231                    <guilabel>Original Quantity (ug)</guilabel>
     1232                    : this is meant to report information about the actual mass
     1233                    of biomaterial created
     1234                  </para>
     1235                </listitem>
     1236                <listitem>
     1237                  <para>
     1238                    <guilabel>Created</guilabel>
     1239                    : a date should be provided. The information can be
     1240                    important when running quality controls on data and account
     1241                    for potential confounding factor (e.g. day effect)
     1242                  </para>
     1243                </listitem>
     1244                <listitem>
     1245                  <para>
     1246                    <guilabel>Protocol</guilabel>
     1247                    : this a controled field. A select-list displays protocol
     1248                    whose type is '
     1249                    <guilabel>labeling</guilabel>
     1250                    ' and which are shared to or owned by the logged-in user.
     1251                    Reporting Protocol should be viewed as a MIAME requirement
     1252                  </para>
     1253                </listitem>
     1254                <listitem>
     1255                  <para>
     1256                    <guilabel>Description</guilabel>
     1257                    : a free text field to report any information that can not
     1258                    be captured otherwise
     1259                  </para>
     1260                </listitem>
     1261              </itemizedlist>
     1262              <para>
     1263                Finally, a 7th field
     1264                <guilabel>Created</guilabel>
     1265                is automatically populated with a date at which the Labeled Extract
     1266                was actually entered in BASE2 system.
     1267              </para>
     1268              <figure id="write_docbook_doc.figures.labeledextract-tab-1">
     1269                <title>Labeled Extract tab</title>
     1270                <screenshot>
     1271                  <mediaobject>
     1272                    <imageobject>
     1273                      <imagedata contentwidth="12cm" width="12cm"
     1274                        fileref="figures/labeledextract-tab-1.png" format="PNG" />
     1275                    </imageobject>
     1276                  </mediaobject>
     1277                </screenshot>
     1278              </figure>
     1279            </listitem>
     1280            <listitem>
     1281              <para>The Parents Tab</para>
     1282              <para>
     1283                This important tab allows users to select the Labeled Extract
     1284                origin. BASE2 distinguished between 2 cases which are controled by
     1285                the
     1286                <guibutton>'pooled'</guibutton>
     1287                radio-button
     1288              </para>
     1289              <orderedlist>
     1290                <listitem>
     1291                  <para>The Parent is an Extract</para>
     1292                  <para>
     1293                    The
     1294                    <guibutton>pooled</guibutton>
     1295                    radio-button is set to
     1296                    <guilabel>No</guilabel>
     1297                  </para>
     1298                  <para>
     1299                    The Extract select button is active and allows users to
     1300                    point to one and only one Extract from which the Labeled
     1301                    Extract originates from.
     1302                  </para>
     1303                  <figure
     1304                    id="write_docbook_doc.figures.labeledextract-tab-2-select-extract">
     1305                    <title>
     1306                      Parent tab and interaction when pooled button is set to
     1307                      No
     1308                    </title>
     1309                    <screenshot>
     1310                      <mediaobject>
     1311                        <imageobject>
     1312                          <imagedata contentwidth="12cm" width="12cm"
     1313                            fileref="figures/labeledextract-tab-2-select-extract.png" format="PNG" />
     1314                        </imageobject>
     1315                      </mediaobject>
     1316                    </screenshot>
     1317                  </figure>
     1318                </listitem>
     1319                <listitem>
     1320                  <para>The Parent is another Labeled Extract</para>
     1321                  <para>
     1322                    The
     1323                    <guibutton>pooled</guibutton>
     1324                    radio-button has to be set to
     1325                    <guilabel>Yes</guilabel>
     1326                  </para>
     1327                  <para>
     1328                    Upon selection, the Extract select button is deactivated and
     1329                    the Labeled Extracts box and button are activated.
     1330                  </para>
     1331                  <para>
     1332                    This allows users to specify one or more extracts to be
     1333                    selected from the Labeled Extract list View page.
     1334                  </para>
     1335                  <figure
     1336                    id="write_docbook_doc.figures.labeledextract-tab-2-select-labeledextract">
     1337                    <title>
     1338                      Parent tab and interaction when pooled button is set to
     1339                      Yes
     1340                    </title>
     1341                    <screenshot>
     1342                      <mediaobject>
     1343                        <imageobject>
     1344                          <imagedata contentwidth="12cm" width="12cm"
     1345                            fileref="figures/labeledextract-tab-2-select-labeledextract.png" format="PNG" />
     1346                        </imageobject>
     1347                      </mediaobject>
     1348                    </screenshot>
     1349                  </figure>
     1350                </listitem>
     1351              </orderedlist>
     1352            </listitem>
     1353            <listitem>
     1354              <para>Annotations &amp; parameters</para>
     1355              <para>
     1356                As seen in the BioSource and Sample sections, this tab allows users
     1357                to further supply information about the labeled extract provided
     1358                they have defined annotation types to annotate Labeled Extract items
     1359                or have such elements shared to them.
     1360              </para>
     1361              <para>
     1362                The display of Annotation Types can be filtered based on the
     1363                Annotation Type Categories they belong to.
     1364              </para>
     1365              <important>
     1366                <para>
     1367                  In order to use this feature, Annotation Type must be declared
     1368                  and made available. To learn more about Annotation Types, please
     1369                  refer to
     1370                  <xref linkend="annotations" />
     1371                </para>
     1372              </important>
     1373              <para>
     1374                To provide a value for a given annotation type, simply click on it
     1375                an use the input field or select a value from the drop-down lists or
     1376                radio buttons.
     1377              </para>
     1378              <figure id="write_docbook_doc.figures.labeledextract-tab-3">
     1379                <title>Annotations &amp; parameters</title>
     1380                <screenshot>
     1381                  <mediaobject>
     1382                    <imageobject>
     1383                      <imagedata contentwidth="12cm" width="12cm"
     1384                        fileref="figures/labeledextract-tab-3.png" format="PNG" />
     1385                    </imageobject>
     1386                  </mediaobject>
     1387                </screenshot>
     1388              </figure>
     1389            </listitem>
     1390            <listitem>
     1391              <para>Inherited Annotations case1</para>
     1392              <para>The next picture shows</para>
     1393              <figure id="write_docbook_doc.figures.labeledextract-tab-4">
     1394                <title>Inherited Annotations</title>
     1395                <screenshot>
     1396                  <mediaobject>
     1397                    <imageobject>
     1398                      <imagedata contentwidth="12cm" width="12cm"
     1399                        fileref="figures/labeledextract-tab-4.png" format="PNG" />
     1400                    </imageobject>
     1401                  </mediaobject>
     1402                </screenshot>
     1403              </figure>
     1404            </listitem>
     1405          </itemizedlist>
     1406        </listitem>
     1407      </orderedlist>
     1408    </sect2>
     1409    <sect2 id="labeledextract.manage.createelabeledxtract.pool">
     1410      <title>Creating Pooled Labeled Extracts</title>
     1411      <para>
     1412        It is common practice when biological material is scarce to pool extracts from
     1413        equivalent sources. BASE2 provides mechanisms to report on such practice.
     1414      </para>
     1415      <para>This section details how.</para>
     1416      <para>There are 2 ways to create pooled Labeled Extracts in BASE2</para>
     1417      <orderedlist>
     1418        <listitem>
     1419          <para>
     1420            Using the Pooled radio button option from the Labeled Extract Create page,
     1421            and this has been shown already
     1422          </para>
     1423        </listitem>
     1424        <listitem>
     1425          <para>Using the Pool button in the Menu bar</para>
     1426          <para>
     1427            The Labeled Extracts List View page menu bar contains an addition &gbPool;
     1428            button, the usage of which is detailed now.
     1429          </para>
     1430          <para>
     1431            The &gbPool; button
     1432            <inlinemediaobject>
     1433              <imageobject>
     1434                <imagedata fileref="figures/new_pooled.gif" format="GIF" />
     1435              </imageobject>
     1436            </inlinemediaobject>
     1437            allows users to create Pooled Labeled Extracts by selecting the list of
     1438            Labeled Extracts used to derived a new Labeled Extract. Users simply have to
     1439            tick to boxes in front of each relevant Labeled Extract and click the
     1440            <guibutton>Pool...</guibutton>
     1441          </para>
     1442          <para>
     1443            This provides an easy and simple way to create pooled Labeled Extracts. The
     1444            result of such process is the creation of a New Labeled Extract, in which,
     1445            when navigating to the Parent tab, shows that all the Labeled Extracts
     1446            involved are already set and listed in the Labeled Extract box of the tab.
     1447          </para>
     1448          <figure
     1449            id="write_docbook_doc.figures.labeledextract-tab-2-pool-labeledextract">
     1450            <title>Pooling of Labeled Extracts:</title>
     1451            <screenshot>
     1452              <mediaobject>
     1453                <imageobject>
     1454                  <imagedata contentwidth="12cm" width="12cm"
     1455                    fileref="figures/labeledextract-tab-2-pool-labeledextract.png" format="PNG" />
     1456                </imageobject>
     1457              </mediaobject>
     1458            </screenshot>
     1459          </figure>
     1460        </listitem>
     1461      </orderedlist>
     1462    </sect2>
     1463    <sect2 id="labeledextract.manage.delete">
     1464      <title>Deleting/Restoring Labeled Extracts</title>
     1465      <para>
     1466        As for other items in BASE2, Labeled Extracts can be deleted. For a generic overview
     1467        on how to delete and restore items, refer to section
     1468        <xref linkend="webclient.items.delete" />
     1469      </para>
     1470      <para>To delete, do the following</para>
     1471      <itemizedlist>
     1472        <listitem>
     1473          <para>
     1474            Select one or more Labeled Extract and click &gbDelete; button in the menu
     1475            bar.
     1476          </para>
     1477          <para>
     1478            All the selected Labeled Extracts have been marked as deleted and are no
     1479            longer available from the interface.
     1480          </para>
     1481          <para>
     1482            Only by selecting from the
     1483            <guilabel>view/preset&hellip;</guilabel>
     1484            select box the
     1485            <guilabel>Removed</guilabel>
     1486            option, one can see those of the Labeled Extracts earmarked for deletion.
     1487            They will be shown with a symbol in front of them.
     1488          </para>
     1489        </listitem>
     1490        <listitem>
     1491          <para>
     1492            Alternately, navigating to the Labeled Extract Item View, one can hit the
     1493            &gbDelete; to performed the task. As showed in the next picture, the Labeled
     1494            Extract is then marked with the
     1495            <inlinemediaobject>
     1496              <imageobject>
     1497                <imagedata fileref="figures/deleted.gif" format="GIF" />
     1498              </imageobject>
     1499            </inlinemediaobject>
     1500            <guiicon>This item has been flagged for deletion</guiicon>
     1501          </para>
     1502          <figure id="write_docbook_doc.figures.labeledextract-delete">
     1503            <title>Deleting Labeled Extracts from the Item View</title>
     1504            <screenshot>
     1505              <mediaobject>
     1506                <imageobject>
     1507                  <imagedata contentwidth="12cm" width="12cm"
     1508                    fileref="figures/labeledextract-delete.png" format="PNG" />
     1509                </imageobject>
     1510              </mediaobject>
     1511            </screenshot>
     1512          </figure>
     1513        </listitem>
     1514        <listitem>
     1515          <para>
     1516            Deletion errors at this stage can be easily recovered. Select the item to
     1517            recover from the List View (be sure to check the
     1518            <guilabel>Removed</guilabel>
     1519            option in the View/preset.. filter) and hit the &gbRestore; to performed the
     1520            task.
     1521          </para>
     1522        </listitem>
     1523      </itemizedlist>
     1524      <important>
     1525        <para>
     1526          To really delete an item from the database you must use the trashcan. Items
     1527          deleted from the Trashcan can not be recovered. To learn more about the trashcan
     1528          function, please refer to
     1529          <xref linkend="trashcan" />
     1530        </para>
     1531      </important>
     1532    </sect2>
     1533  </sect1>
     1534  <sect1 id="hybridization.manage">
     1535    <title>Managing Hybridizations</title>
     1536    <para>
     1537      An hybridization event corresponds to the application of one or more labeled extracts
     1538      materials to a microarray slide under conditions detailed in hybridization protocols.
     1539    </para>
     1540    <para>In BASE2, there are 3 possible routes to create an hybridization object.</para>
     1541    <sect2 id="hybridization.manage.create">
     1542      <title>Creating Hybridizations</title>
     1543      <orderedlist>
     1544        <listitem>
     1545          <para>Creating Hybridization from the Labeled Extract List View page</para>
     1546          <para>
     1547            Select at least one Labeled Extract by ticking to selection boxes before the
     1548            name field.
     1549          </para>
     1550          <para>
     1551            Click on the
     1552            <guibutton>New hybridzation (to be changed)</guibutton>
     1553            from the menu bar of Labeled Extract list view.
     1554          </para>
     1555          <figure id="write_docbook_doc.figures.hyb-create-labeledlistview">
     1556            <title>Creating a Hybridization from the Labeled Extract List View</title>
     1557            <screenshot>
     1558              <mediaobject>
     1559                <imageobject>
     1560                  <imagedata contentwidth="12cm" width="12cm"
     1561                    fileref="figures/hyb-create-labeledlistview.png" format="PNG" />
     1562                </imageobject>
     1563              </mediaobject>
     1564            </screenshot>
     1565          </figure>
     1566        </listitem>
     1567        <listitem>
     1568          <para>Creating Hybridization from the Labeled Extract Item View page</para>
     1569          <para>
     1570            After having selected a Labeled Extract and displayed it in the Item View,
     1571            Click on the
     1572            <guibutton>New hybridization</guibutton>
     1573            button from the Menu bar of the Labeled Extract Item View.
     1574          </para>
     1575          <figure id="write_docbook_doc.figures.hyb-create-labeleditemview">
     1576            <title>Creating a Hybridization from the Labeled Extract Item View</title>
     1577            <screenshot>
     1578              <mediaobject>
     1579                <imageobject>
     1580                  <imagedata contentwidth="12cm" width="12cm"
     1581                    fileref="figures/hyb-create-labeleditemview.png" format="PNG" />
     1582                </imageobject>
     1583              </mediaobject>
     1584            </screenshot>
     1585          </figure>
     1586        </listitem>
     1587        <listitem>
     1588          <para>Creating Hybridizations from the Hybridization List View page</para>
     1589          <para>
     1590            Hybridizations can be created directly using the Hybridization create page.
     1591            To do so, go to
     1592            <menuchoice>
     1593              <guimenu>View</guimenu>
     1594              <guimenuitem>Hybridizations</guimenuitem>
     1595            </menuchoice>
     1596            , Click on &gbNew;
     1597          </para>
     1598          <figure id="write_docbook_doc.figures.hyb-create">
     1599            <title>Creating Hybridizations from the Hybridization List View</title>
     1600            <screenshot>
     1601              <mediaobject>
     1602                <imageobject>
     1603                  <imagedata contentwidth="12cm" width="12cm"
     1604                    fileref="figures/hyb-create.png" format="PNG" />
     1605                </imageobject>
     1606              </mediaobject>
     1607            </screenshot>
     1608          </figure>
     1609          <para>
     1610            Irrespective of the methods chosen to create the Hybridization item, A
     1611            'Create' pop-up window will open. It contains 4 distinct tabs:
     1612            <guilabel>Hybridization</guilabel>
     1613            ,
     1614            <guilabel>Parents</guilabel>
     1615            ,
     1616            <guilabel>Annotations &amp; parameters</guilabel>
     1617            and
     1618            <guilabel>Inherited Annotations</guilabel>
     1619            .
     1620          </para>
     1621          <itemizedlist>
     1622            <listitem>
     1623              <para>The Hybridization Tab</para>
    11871624
    1188        <variablelist>
    1189         <varlistentry>
    1190          <term>
    1191           <interface>Name</interface>
    1192          </term>
    1193          <listitem>
    1194           <para> New Hybridization is BASE2 default name but it is strongly advise to provide a
    1195            meaningful and unique name as it matters for tab2mage export to function properly. </para>
    1196           <para>There are 5 optional fields to provide more detailed information</para>
     1625              <variablelist>
     1626                <varlistentry>
     1627                  <term>
     1628                    <interface>Name</interface>
     1629                  </term>
     1630                  <listitem>
     1631                    <para>
     1632                      New Hybridization is BASE2 default name but it is
     1633                      strongly advise to provide a meaningful and unique name
     1634                      as it matters for tab2mage export to function properly.
     1635                    </para>
     1636                    <para>
     1637                      There are 5 optional fields to provide more detailed
     1638                      information
     1639                    </para>
    11971640
    1198          </listitem>
    1199         </varlistentry>
     1641                  </listitem>
     1642                </varlistentry>
    12001643
    1201         <varlistentry>
    1202          <term>
    1203           <guilabel>Created</guilabel>
    1204          </term>
    1205          <listitem>
    1206           <para>A date should be provided. The information can be important when running quality
    1207            controls on data and account for potential confounding factor (e.g. to account for a day
    1208            effect)</para>
    1209          </listitem>
    1210         </varlistentry>
     1644                <varlistentry>
     1645                  <term>
     1646                    <guilabel>Created</guilabel>
     1647                  </term>
     1648                  <listitem>
     1649                    <para>
     1650                      A date should be provided. The information can be
     1651                      important when running quality controls on data and
     1652                      account for potential confounding factor (e.g. to
     1653                      account for a day effect)
     1654                    </para>
     1655                  </listitem>
     1656                </varlistentry>
    12111657
    1212         <varlistentry>
    1213          <term>
    1214           <guilabel>Protocol</guilabel>
    1215          </term>
    1216          <listitem>
    1217           <para>This is a controled field. A select-list displays protocol whose type is
    1218             '<guilabel>hybridization</guilabel>' and which are shared to or owned by the logged-in
    1219            user.</para>
    1220           <important>
    1221            <para> Reporting Protocols should be viewed as a MIAME requirement </para>
    1222           </important>
    1223          </listitem>
    1224         </varlistentry>
     1658                <varlistentry>
     1659                  <term>
     1660                    <guilabel>Protocol</guilabel>
     1661                  </term>
     1662                  <listitem>
     1663                    <para>
     1664                      This is a controled field. A select-list displays
     1665                      protocol whose type is '
     1666                      <guilabel>hybridization</guilabel>
     1667                      ' and which are shared to or owned by the logged-in
     1668                      user.
     1669                    </para>
     1670                    <important>
     1671                      <para>
     1672                        Reporting Protocols should be viewed as a MIAME
     1673                        requirement
     1674                      </para>
     1675                    </important>
     1676                  </listitem>
     1677                </varlistentry>
    12251678
    1226         <varlistentry>
    1227          <term>
    1228           <guilabel>Hardware</guilabel>
    1229          </term>
    1230          <listitem>
    1231           <para>This is a controled field. A select-list displays Hardware whose type is
    1232             '<guilabel>Hybridization station</guilabel>' and which are shared to or owned by the
    1233            logged-in user.</para>
    1234          </listitem>
    1235         </varlistentry>
     1679                <varlistentry>
     1680                  <term>
     1681                    <guilabel>Hardware</guilabel>
     1682                  </term>
     1683                  <listitem>
     1684                    <para>
     1685                      This is a controled field. A select-list displays
     1686                      Hardware whose type is '
     1687                      <guilabel>Hybridization station</guilabel>
     1688                      ' and which are shared to or owned by the logged-in
     1689                      user.
     1690                    </para>
     1691                  </listitem>
     1692                </varlistentry>
    12361693
    1237         <varlistentry>
    1238          <term>
    1239           <guilabel>Array Slide</guilabel>
    1240          </term>
    1241          <listitem>
    1242           <para>This is meant to specify the actual microarray slide.</para>
    1243           <note>
    1244            <para>Ideally, The Array Slides should have been created but for those users with
    1245             permission to do, Array Slides could be generated at that point.</para>
    1246           </note>
    1247          </listitem>
    1248         </varlistentry>
     1694                <varlistentry>
     1695                  <term>
     1696                    <guilabel>Array Slide</guilabel>
     1697                  </term>
     1698                  <listitem>
     1699                    <para>
     1700                      This is meant to specify the actual microarray slide.
     1701                    </para>
     1702                    <note>
     1703                      <para>
     1704                        Ideally, The Array Slides should have been created
     1705                        but for those users with permission to do, Array
     1706                        Slides could be generated at that point.
     1707                      </para>
     1708                    </note>
     1709                  </listitem>
     1710                </varlistentry>
    12491711
    1250         <varlistentry>
    1251          <term>
    1252           <guilabel>Description</guilabel>
    1253          </term>
    1254          <listitem>
    1255           <para>A free text field to report any information that can not be captured
    1256           otherwise</para>
    1257          </listitem>
    1258         </varlistentry>
     1712                <varlistentry>
     1713                  <term>
     1714                    <guilabel>Description</guilabel>
     1715                  </term>
     1716                  <listitem>
     1717                    <para>
     1718                      A free text field to report any information that can not
     1719                      be captured otherwise
     1720                    </para>
     1721                  </listitem>
     1722                </varlistentry>
    12591723
    1260         <varlistentry>
    1261          <term>
    1262           <guilabel>Registered</guilabel>
    1263          </term>
    1264          <listitem>
    1265           <para>This 7th field is automatically populated with a date at which the sample was
    1266            entered in BASE2 system.</para>
    1267          </listitem>
    1268         </varlistentry>
    1269        </variablelist>
     1724                <varlistentry>
     1725                  <term>
     1726                    <guilabel>Registered</guilabel>
     1727                  </term>
     1728                  <listitem>
     1729                    <para>
     1730                      This 7th field is automatically populated with a date at
     1731                      which the sample was entered in BASE2 system.
     1732                    </para>
     1733                  </listitem>
     1734                </varlistentry>
     1735              </variablelist>
    12701736
    1271        <figure id="write_docbook_doc.figures.hybridization-tab-1">
    1272         <title>Hybridization tab</title>
    1273         <screenshot>
    1274          <mediaobject>
    1275           <imageobject>
    1276            <imagedata contentwidth="12cm" width="12cm" fileref="figures/hybridization-tab-1.png" format="PNG"/>
    1277           </imageobject>
    1278          </mediaobject>
    1279         </screenshot>
    1280        </figure>
    1281       </listitem>
    1282       <listitem>
    1283        <para>The Labeled Extract Tab </para>
    1284        <para>This important tab allows users to select the Labeled Extracts applied to an Array
    1285         Slide, and specify the amount of material used, expressed in microgram.</para>
    1286        <figure id="write_docbook_doc.figures.hybridization-tab-2">
    1287         <title>Labeled Extract tab</title>
    1288         <screenshot>
    1289          <mediaobject>
    1290           <imageobject>
    1291            <imagedata contentwidth="12cm" width="12cm" fileref="figures/hybridization-tab-2.png" format="PNG"/>
    1292           </imageobject>
    1293          </mediaobject>
    1294         </screenshot>
    1295        </figure>
    1296       </listitem>
    1297       <listitem>
    1298        <para>Annotations &amp; parameters </para>
    1299        <para>As seen in the BioSource and Sample sections, this tab allows users to supply further
    1300         information about the hybridization provided annotation types have been defined or shared to
    1301         annotate Hybridization items. The display of Annotation Types can be filtered based on the
    1302         Annotation Type Category they belong to.</para>
    1303        <important>
    1304         <para> In order to use this feature, Annotation Type must be declared and made available. To
    1305          learn more about Annotation Types, please refer to <xref linkend="annotations"/>
    1306         </para>
    1307        </important>
    1308        <para>To provide a value for a given annotation type, simply click on it and use the input
    1309         field or select a value from the drop-down lists or radio buttons.</para>
    1310        <para>A caption also reminds users if Annotation Types are parameters <inlinemediaobject>
    1311          <imageobject>
    1312           <imagedata fileref="figures/parameter.gif" format="GIF"/>
    1313          </imageobject>
    1314         </inlinemediaobject>and if annotation values have already been supplied, marked by the <inlinemediaobject>
    1315          <imageobject>
    1316           <imagedata fileref="figures/annotated.gif" format="GIF"/>
    1317          </imageobject>
    1318         </inlinemediaobject> logo.</para>
    1319        <figure id="write_docbook_doc.figures.hybridization-tab-3">
    1320         <title>Annotations &amp; parameters</title>
    1321         <screenshot>
    1322          <mediaobject>
    1323           <imageobject>
    1324            <imagedata contentwidth="12cm" width="12cm" fileref="figures/hybridization-tab-3.png" format="PNG"/>
    1325           </imageobject>
    1326          </mediaobject>
    1327         </screenshot>
    1328        </figure>
    1329       </listitem>
    1330       <listitem>
    1331        <para>Inherited Annotations </para>
    1332        <para>The next screenshot shows a typical view of the functionality.</para>
    1333        <figure id="write_docbook_doc.figures.hybridization-tab-4">
    1334         <title>Inherited Annotations</title>
    1335         <screenshot>
    1336          <mediaobject>
    1337           <imageobject>
    1338            <imagedata contentwidth="12cm" width="12cm" fileref="figures/hybridization-tab-4.png" format="PNG"/>
    1339           </imageobject>
    1340          </mediaobject>
    1341         </screenshot>
    1342        </figure>
    1343        <para> Note the tags used to distinguish between Annotation Types which are parameters noted <inlinemediaobject>
    1344          <imageobject>
    1345           <imagedata fileref="figures/parameter.gif" format="GIF"/>
    1346          </imageobject>
    1347         </inlinemediaobject> and those which are Biomaterial Characteristics,noted <inlinemediaobject>
    1348          <imageobject>
    1349           <imagedata fileref="figures/annotation.gif" format="GIF"/>
    1350          </imageobject>
    1351         </inlinemediaobject></para>
    1352       </listitem>
    1353      </itemizedlist>
    1354     </listitem>
    1355    </orderedlist>
    1356   </sect2>
    1357   <sect2 id="hybridization.manage.viewedit">
    1358    <title>Viewing/Editing Hybridizations</title>
    1359    <para>As for other items in BASE2, Hybridizations can be edited. To do so, do the following</para>
    1360    <itemizedlist>
    1361     <listitem>
    1362      <para> Press and hold one of the <keycap>CTRL</keycap>, <keycap>ALT</keycap> or
    1363       <keycap>SHIFT</keycap> keys while clicking on the name of an Hybridization Item, which is a
    1364       live link. </para>
    1365     </listitem>
    1366     <listitem>
    1367      <para> Alternately, navigating to the Hybridization Item View, one can hit the
    1368       <guibutton>Edit</guibutton> to performed the task.</para>
    1369     </listitem>
     1737              <figure id="write_docbook_doc.figures.hybridization-tab-1">
     1738                <title>Hybridization tab</title>
     1739                <screenshot>
     1740                  <mediaobject>
     1741                    <imageobject>
     1742                      <imagedata contentwidth="12cm" width="12cm"
     1743                        fileref="figures/hybridization-tab-1.png" format="PNG" />
     1744                    </imageobject>
     1745                  </mediaobject>
     1746                </screenshot>
     1747              </figure>
     1748            </listitem>
     1749            <listitem>
     1750              <para>The Labeled Extract Tab</para>
     1751              <para>
     1752                This important tab allows users to select the Labeled Extracts
     1753                applied to an Array Slide, and specify the amount of material used,
     1754                expressed in microgram.
     1755              </para>
     1756              <figure id="write_docbook_doc.figures.hybridization-tab-2">
     1757                <title>Labeled Extract tab</title>
     1758                <screenshot>
     1759                  <mediaobject>
     1760                    <imageobject>
     1761                      <imagedata contentwidth="12cm" width="12cm"
     1762                        fileref="figures/hybridization-tab-2.png" format="PNG" />
     1763                    </imageobject>
     1764                  </mediaobject>
     1765                </screenshot>
     1766              </figure>
     1767            </listitem>
     1768            <listitem>
     1769              <para>Annotations &amp; parameters</para>
     1770              <para>
     1771                As seen in the BioSource and Sample sections, this tab allows users
     1772                to supply further information about the hybridization provided
     1773                annotation types have been defined or shared to annotate
     1774                Hybridization items. The display of Annotation Types can be filtered
     1775                based on the Annotation Type Category they belong to.
     1776              </para>
     1777              <important>
     1778                <para>
     1779                  In order to use this feature, Annotation Type must be declared
     1780                  and made available. To learn more about Annotation Types, please
     1781                  refer to
     1782                  <xref linkend="annotations" />
     1783                </para>
     1784              </important>
     1785              <para>
     1786                To provide a value for a given annotation type, simply click on it
     1787                and use the input field or select a value from the drop-down lists
     1788                or radio buttons.
     1789              </para>
     1790              <para>
     1791                A caption also reminds users if Annotation Types are parameters
     1792                <inlinemediaobject>
     1793                  <imageobject>
     1794                    <imagedata fileref="figures/parameter.gif" format="GIF" />
     1795                  </imageobject>
     1796                </inlinemediaobject>
     1797                and if annotation values have already been supplied, marked by the
     1798                <inlinemediaobject>
     1799                  <imageobject>
     1800                    <imagedata fileref="figures/annotated.gif" format="GIF" />
     1801                  </imageobject>
     1802                </inlinemediaobject>
     1803                logo.
     1804              </para>
     1805              <figure id="write_docbook_doc.figures.hybridization-tab-3">
     1806                <title>Annotations &amp; parameters</title>
     1807                <screenshot>
     1808                  <mediaobject>
     1809                    <imageobject>
     1810                      <imagedata contentwidth="12cm" width="12cm"
     1811                        fileref="figures/hybridization-tab-3.png" format="PNG" />
     1812                    </imageobject>
     1813                  </mediaobject>
     1814                </screenshot>
     1815              </figure>
     1816            </listitem>
     1817            <listitem>
     1818              <para>Inherited Annotations</para>
     1819              <para>
     1820                The next screenshot shows a typical view of the functionality.
     1821              </para>
     1822              <figure id="write_docbook_doc.figures.hybridization-tab-4">
     1823                <title>Inherited Annotations</title>
     1824                <screenshot>
     1825                  <mediaobject>
     1826                    <imageobject>
     1827                      <imagedata contentwidth="12cm" width="12cm"
     1828                        fileref="figures/hybridization-tab-4.png" format="PNG" />
     1829                    </imageobject>
     1830                  </mediaobject>
     1831                </screenshot>
     1832              </figure>
     1833              <para>
     1834                Note the tags used to distinguish between Annotation Types which are
     1835                parameters noted
     1836                <inlinemediaobject>
     1837                  <imageobject>
     1838                    <imagedata fileref="figures/parameter.gif" format="GIF" />
     1839                  </imageobject>
     1840                </inlinemediaobject>
     1841                and those which are Biomaterial Characteristics,noted
     1842                <inlinemediaobject>
     1843                  <imageobject>
     1844                    <imagedata fileref="figures/annotation.gif" format="GIF" />
     1845                  </imageobject>
     1846                </inlinemediaobject>
     1847              </para>
     1848            </listitem>
     1849          </itemizedlist>
     1850        </listitem>
     1851      </orderedlist>
     1852    </sect2>
     1853    <sect2 id="hybridization.manage.viewedit">
     1854      <title>Viewing/Editing Hybridizations</title>
     1855      <para>
     1856        As for other items in BASE2, Hybridizations can be edited. To do so, do the
     1857        following
     1858      </para>
     1859      <itemizedlist>
     1860        <listitem>
     1861          <para>
     1862            Press and hold one of the
     1863            <keycap>CTRL</keycap>
     1864            ,
     1865            <keycap>ALT</keycap>
     1866            or
     1867            <keycap>SHIFT</keycap>
     1868            keys while clicking on the name of an Hybridization Item, which is a live
     1869            link.
     1870          </para>
     1871        </listitem>
     1872        <listitem>
     1873          <para>
     1874            Alternately, navigating to the Hybridization Item View, one can hit the
     1875            <guibutton>Edit</guibutton>
     1876            to performed the task.
     1877          </para>
     1878        </listitem>
    13701879
    1371     <listitem>
    1372      <para>The Hybridization item View summarizes key information such as the list of
    1373        <guilabel>Labeled Extracts</guilabel>, and the list of associated <guilabel>Scans</guilabel>.
    1374       Both are available as hyperlinks to allow quick and easy navigation.</para>
    1375      <figure id="write_docbook_doc.figures.hybridization-itemview">
    1376       <title>Hardware Item View</title>
    1377       <screenshot>
    1378        <mediaobject>
    1379         <imageobject>
    1380          <imagedata contentwidth="10cm" width="10cm" fileref="figures/hybridization-itemview.png" format="PNG"/>
    1381         </imageobject>
    1382        </mediaobject>
    1383       </screenshot>
    1384      </figure>
    1385     </listitem>
    1386    </itemizedlist>
     1880        <listitem>
     1881          <para>
     1882            The Hybridization item View summarizes key information such as the list of
     1883            <guilabel>Labeled Extracts</guilabel>
     1884            , and the list of associated
     1885            <guilabel>Scans</guilabel>
     1886            . Both are available as hyperlinks to allow quick and easy navigation.
     1887          </para>
     1888          <figure id="write_docbook_doc.figures.hybridization-itemview">
     1889            <title>Hardware Item View</title>
     1890            <screenshot>
     1891              <mediaobject>
     1892                <imageobject>
     1893                  <imagedata contentwidth="10cm" width="10cm"
     1894                    fileref="figures/hybridization-itemview.png" format="PNG" />
     1895                </imageobject>
     1896              </mediaobject>
     1897            </screenshot>
     1898          </figure>
     1899        </listitem>
     1900      </itemizedlist>
    13871901
    1388   </sect2>
     1902    </sect2>
    13891903
    1390   <sect2 id="hybridization.manage.delete">
    1391    <title>Deleting/Restoring Hybridizations</title>
    1392    <para>As for other items in BASE2, Hybridizations can be deleted. For a generic overview on how
    1393     to delete and restore items, refer to section <xref linkend="webclient.items.delete"/>
    1394    </para>
     1904    <sect2 id="hybridization.manage.delete">
     1905      <title>Deleting/Restoring Hybridizations</title>
     1906      <para>
     1907        As for other items in BASE2, Hybridizations can be deleted. For a generic overview
     1908        on how to delete and restore items, refer to section
     1909        <xref linkend="webclient.items.delete" />
     1910      </para>
    13951911
    1396    <para>To delete, do the following</para>
    1397    <itemizedlist>
    1398     <listitem>
    1399      <para> Select one or more Hybridization Items and click on the &gbDelete;
    1400       button in the menu bar. </para>
    1401      <para> All the selected Hybridizations have been marked as deleted and are no longer available
    1402       from the interface. </para>
    1403      <para> Only by selecting from the <guilabel>view/preset&hellip;</guilabel> select box the
    1404        <guilabel>Removed</guilabel> option, one can see those of the Hybridizations earmarked for
    1405       deletion. They will be shown with a symbol in front of them. </para>
    1406     </listitem>
    1407     <listitem>
    1408      <para> Alternately, navigating to the Hybridization Item View, one can hit the
    1409        &gbDelete; to performed the task. As shown in the next picture, the
    1410       Hybridization is then marked with the <inlinemediaobject>
    1411        <imageobject>
    1412         <imagedata fileref="figures/deleted.gif" format="GIF"/>
    1413        </imageobject>
    1414       </inlinemediaobject><guilabel>This item has been flagged for deletion</guilabel>
    1415      </para>
    1416      <figure id="write_docbook_doc.figures.hybridization-delete">
    1417       <title>Deleting Hybridizations from the Hybridization Item View</title>
    1418       <screenshot>
    1419        <mediaobject>
    1420         <imageobject>
    1421          <imagedata contentwidth="10cm" width="10cm" fileref="figures/hybridization-delete.png" format="PNG"/>
    1422         </imageobject>
    1423        </mediaobject>
    1424       </screenshot>
    1425      </figure>
    1426     </listitem>
    1427    </itemizedlist>
    1428    <important>
    1429     <para>To really delete an item from the database you must use the trashcan. Items deleted from
    1430      the Trashcan can not be recovered. To learn more about the trashcan function, please refer to
    1431       <xref linkend="trashcan"/>
    1432     </para>
    1433    </important>
    1434   </sect2>
    1435  </sect1>
     1912      <para>To delete, do the following</para>
     1913      <itemizedlist>
     1914        <listitem>
     1915          <para>
     1916            Select one or more Hybridization Items and click on the &gbDelete; button in
     1917            the menu bar.
     1918          </para>
     1919          <para>
     1920            All the selected Hybridizations have been marked as deleted and are no
     1921            longer available from the interface.
     1922          </para>
     1923          <para>
     1924            Only by selecting from the
     1925            <guilabel>view/preset&hellip;</guilabel>
     1926            select box the
     1927            <guilabel>Removed</guilabel>
     1928            option, one can see those of the Hybridizations earmarked for deletion. They
     1929            will be shown with a symbol in front of them.
     1930          </para>
     1931        </listitem>
     1932        <listitem>
     1933          <para>
     1934            Alternately, navigating to the Hybridization Item View, one can hit the
     1935            &gbDelete; to performed the task. As shown in the next picture, the
     1936            Hybridization is then marked with the
     1937            <inlinemediaobject>
     1938              <imageobject>
     1939                <imagedata fileref="figures/deleted.gif" format="GIF" />
     1940              </imageobject>
     1941            </inlinemediaobject>
     1942            <guilabel>This item has been flagged for deletion</guilabel>
     1943          </para>
     1944          <figure id="write_docbook_doc.figures.hybridization-delete">
     1945            <title>Deleting Hybridizations from the Hybridization Item View</title>
     1946            <screenshot>
     1947              <mediaobject>
     1948                <imageobject>
     1949                  <imagedata contentwidth="10cm" width="10cm"
     1950                    fileref="figures/hybridization-delete.png" format="PNG" />
     1951                </imageobject>
     1952              </mediaobject>
     1953            </screenshot>
     1954          </figure>
     1955        </listitem>
     1956      </itemizedlist>
     1957      <important>
     1958        <para>
     1959          To really delete an item from the database you must use the trashcan. Items
     1960          deleted from the Trashcan can not be recovered. To learn more about the trashcan
     1961          function, please refer to
     1962          <xref linkend="trashcan" />
     1963        </para>
     1964      </important>
     1965    </sect2>
     1966  </sect1>
    14361967</chapter>
Note: See TracChangeset for help on using the changeset viewer.