Changeset 3412


Ignore:
Timestamp:
May 30, 2007, 5:35:48 PM (14 years ago)
Author:
Martin Svensson
Message:

Fixes #545

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

Legend:

Unmodified
Added
Removed

  • trunk/doc/src/docbook/faq/faqs.xml

    r3402 r3412  
    277277              by marking their checkboxes. Then click on the <guibutton>Pool</guibutton>
    278278              button. For more information see
    279               <xref linkend="sample.manage.createsample.pool" />.
     279              <xref linkend="biomaterials.samples.create" />.
    280280              Pooling can also be applied to extracts and labeled extracts.
    281281            </para>

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

    r3394 r3412  
    314314          <para>Clicking on the <inlinemediaobject>
    315315              <imageobject>
    316                 <imagedata fileref="figures/add.gif" format="GIF"/>
     316                <imagedata fileref="figures/add.png" format="PNG"/>
    317317              </imageobject>
    318318            </inlinemediaobject> add Array batch button available from the
    … …  
    438438          <para>Clicking on the <inlinemediaobject>
    439439              <imageobject>
    440                 <imagedata fileref="figures/add.gif" format="GIF"/>
     440                <imagedata fileref="figures/add.png" format="PNG"/>
    441441              </imageobject>
    442442            </inlinemediaobject> add Array slides button. </para>

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

    r3399 r3412  
    4141      menu again to insist on this natural progression.
    4242    </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>
     43    <itemizedlist>
     44      <listitem>
     45        <simpara>
     46          Biosources correspond to the native biological entity used in an experiment
     47          prior to any treatment.
     48        </simpara>
     49      </listitem>
     50      <listitem>
     51        <simpara>
     52          Samples are central to BASE2 to describe the sample processing. So samples can
     53          be created from other samples if user want to track sample processing event in a
     54          finely granular fashion.
     55        </simpara>
     56      </listitem>
     57      <listitem>
     58        <simpara>
     59          Extracts correspond to nucleic acid material extracted from a tissue sample or a
     60          cell culture sample.
     61        </simpara>
     62      </listitem>
     63      <listitem>
     64        <simpara>
     65          Labeled extracts correspond to nucleic acid materials which have undergone a
     66          marking procedure using a fluorescent or radioactive compound for detection in a
     67          microarray assay.
     68        </simpara>
     69      </listitem>
     70    </itemizedlist>
    6171    <para>
    6272      BASE2 allows users to create any of the these entities fairly freely, however it is
    … …  
    7181    </tip>
    7282  </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
     83  <sect1 id="biomaterials.biosources">
     84    <title>BioSources</title>
     85
     86
     87    <sect2 id="biomaterials.biosources.properties">
     88      <title>Properties</title>
     89      <sect3 id="biomaterials.biosources.properties.biosource">
     90        <title>Biosource</title>
     91        <para>This tab allows users to enter essential information about a biosource.</para>
     92        <variablelist>
     93          <varlistentry>
     94            <term>
     95              <guilabel>Name</guilabel>
     96            </term>
     97            <listitem>
     98              <para>
     99                This is the only mandatory field. BASE2 by default assigns
     100                <replaceable>New biosource</replaceable>
     101                as name but it is advised to provide unique sensible names.
     102              </para>
     103            </listitem>
     104          </varlistentry>
     105          <varlistentry>
     106            <term>
     107              <guilabel>External ID</guilabel>
     108            </term>
     109            <listitem>
     110              <para>
     111                An external reference identifiers (e.g. a patient identification
     112                code) can be supplied using this field.
     113              </para>
     114            </listitem>
     115          </varlistentry>
     116          <varlistentry>
     117            <term>
     118              <guilabel>Description</guilabel>
     119            </term>
     120            <listitem>
     121              <para>A free text description can be supplied using this field.</para>
     122            </listitem>
     123          </varlistentry>
     124        </variablelist>
     125        <figure id="write_docbook_doc.figures.biosource-tab-1">
     126          <title>Biosource properties</title>
     127          <screenshot>
     128            <mediaobject>
     129              <imageobject>
     130                <imagedata contentwidth="10cm" width="10cm"
     131                  fileref="figures/biosource-tab-1.png" format="PNG" />
     132              </imageobject>
     133            </mediaobject>
     134          </screenshot>
     135        </figure>
     136      </sect3>
     137      <sect3 id="biomaterials.biosource.properties.annotations">
     138        <title>Annotations</title>
     139        <para>
     140          This allows BASE2 users to use annotation types to refine biosource description.
     141          More about annotating items can be read in
    173142          <xref linkend="annotations.annotating" />
    174           to get more information on how to set annotation types.
    175         </para>
    176       </listitem>
    177     </itemizedlist>
    178     <para>
    179       Click on the &gbSave; button to store the information in BASE2 or on the &gbCancel;
    180       button to abort.
    181     </para>
    182 
    183     <sect2 id="biomaterial.biosource.manage.detail_view">
    184       <title>Viewing biosources</title>
    185       <para>
    186         From the biosource list view, clicking on the biosource
    187         <guilabel>Name</guilabel>
    188         opens a detailed view for that biosource, showing a summary of all information
    189         available in BASE2 about that particular entity.
    190       </para>
    191       <para>
    192         The default behavior opens the detailed view on the
    193         <guilabel>Properties</guilabel>
    194         tab, which shows a summary information and displays the list of samples derived from
    195         a biosource, if any.
    196       </para>
    197       <figure id="write_docbook_doc.figures.biosource-itemview-prop">
    198         <title>BioSource Item View, properties tab</title>
    199         <screenshot>
    200           <mediaobject>
    201             <imageobject>
    202               <imagedata contentwidth="12cm" width="12cm"
    203                 fileref="figures/biosource-itemview-prop.png" format="PNG" />
    204             </imageobject>
    205           </mediaobject>
    206         </screenshot>
    207       </figure>
    208       <para>
    209         By clicking on the
    210         <guilabel>Annotations</guilabel>
    211         tab, users can display the list of Annotation Types used to annotate a Biosource.
    212       </para>
    213       <figure id="write_docbook_doc.figures.biosource-itemview-annot">
    214         <title>BioSource Item View, annotations tab</title>
    215         <screenshot>
    216           <mediaobject>
    217             <imageobject>
    218               <imagedata contentwidth="13cm" width="13cm"
    219                 fileref="figures/biosource-itemview-annot.png" format="PNG" />
    220             </imageobject>
    221           </mediaobject>
    222         </screenshot>
    223       </figure>
    224       <para>
    225         Clicking the
    226         <inlinemediaobject>
    227           <imageobject>
    228             <imagedata fileref="figures/edit.gif" format="GIF" />
    229           </imageobject>
    230         </inlinemediaobject>
    231         <guiicon>edit icon</guiicon>
    232         in the
    233         <interface>value</interface>
    234         for any of the annotations (e.g. 'antibiotic' in our example), opens an Annotate
    235         window (which is a BioSource Edit window set on the annotation tab) and highlights
    236         the selected Annotation Type, prompting for data entry.
    237       </para>
    238       <figure id="write_docbook_doc.figures.biosource-itemview-annot-edit">
    239         <title>BioSource annotations edit</title>
    240         <screenshot>
    241           <mediaobject>
    242             <imageobject>
    243               <imagedata contentwidth="12cm" width="12cm"
    244                 fileref="figures/biosource-itemview-annot-edit.png" format="PNG" />
    245             </imageobject>
    246           </mediaobject>
    247         </screenshot>
    248       </figure>
    249       <para>
    250         The relevant Annotation Type is highlighted and a list of possible values is
    251         displayed.
    252       </para>
    253       <para>
    254         Again, all Annotation types marked with a
    255         <inlinemediaobject>
    256           <imageobject>
    257             <imagedata fileref="figures/annotated.gif" format="GIF" />
    258           </imageobject>
    259         </inlinemediaobject>
    260         symbol have been used to provided information.
    261       </para>
    262       <para>
    263         Click on the &gbSave; button to store the information in BASE2 or on the &gbCancel;
    264         button to abort.
    265       </para>
     143          .
     144        </para>
     145      </sect3>
    266146    </sect2>
    267147  </sect1>
    268   <sect1 id="sample.manage">
    269     <title>Managing Samples</title>
     148  <sect1 id="biomaterial.samples">
     149    <title>Samples</title>
    270150    <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       .
     151      Samples result from processing events applied to biosource material or other samples
     152      before they are turned into an extract. In other words, samples can be created from
     153      biosource items or from one or more sample items.When a sample is created from several
     154      other samples, a pooling event is performed.
    278155    </para>
    279156    <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
     157      For every step of transformation from biosource to sample, it is possible to provide
    290158      information about the protocol used to perform this task. It is not enforced in BASE2
    291159      but it should serve as guidance when devising the granularity of the sample processing
    … …  
    293161      compliance.
    294162    </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>
     163    <para>
     164      Use
     165      <menuchoice>
     166        <guimenu>View</guimenu>
     167        <guimenuitem>Biosource</guimenuitem>
     168      </menuchoice>
     169      to get to the list of biosources.
     170    </para>
     171    <sect2 id="biomaterials.samples.create">
     172      <title>Create sample</title>
     173      <para>
     174        Beside the common way, using the &gbNew; button, a sample can be created in one of
     175        the following ways:
     176        <variablelist>
     177          <varlistentry>
     178            <term>from either biosource list- or single view- page.</term>
     179            <listitem>
     180              <para>
     181                No matter how complex the sample processing phase is, at least one
     182                sample has to be anchored to a biosource. Therefore, a natural way
     183                to create an sample is to click on
     184                <inlinemediaobject>
     185                  <imageobject>
     186                    <imagedata fileref="figures/add.png" format="PNG" />
     187                  </imageobject>
     188                </inlinemediaobject>
     189                in the sample column of the biosource list view. There is also a
     190                corresponding button,
     191                <guibutton>Create sample&hellip;</guibutton>
     192                in the toolbar when viewing a single biosource.
     193              </para>
     194            </listitem>
     195          </varlistentry>
     196          <varlistentry>
     197            <term>from the sample list page</term>
     198            <listitem>
     199              <para>
     200                Pooled samples can also be created by first selecting the parents
     201                from the list of samples and then press
     202                <guibutton>Pool&hellip;</guibutton>
     203                in the toolbar.
     204              </para>
     205            </listitem>
     206          </varlistentry>
     207        </variablelist>
     208      </para>
     209    </sect2>
     210    <sect2 id="biomaterials.samples.properties">
     211      <title>Properties</title>
     212      <sect3 id="biomaterials.samples.properties.sample">
     213        <title>Sample</title>
     214        <helptext external_id="sample.edit" title="Edit sample">
     215          <variablelist>
     216            <varlistentry>
     217              <term>
     218                <guilabel>Name</guilabel>
     219              </term>
     220              <listitem>
     221                <para>
     222                  The sample's name(required). BASE2 by default assigns names to
     223                  samples (by suffixing
     224                  <replaceable>s#</replaceable>
     225                  when creating a sample from an existing biosource or
     226                  <replaceable>New Sample</replaceable>
     227                  otherwise) but it is possible to edit at will.
     228                </para>
     229              </listitem>
     230            </varlistentry>
     231            <varlistentry>
     232              <term>
     233                <guilabel>External ID</guilabel>
     234              </term>
     235              <listitem>
     236                <para>
     237                  An identification used to identify the sample outside BASE.
     238                </para>
     239              </listitem>
     240            </varlistentry>
     241            <varlistentry>
     242              <term>
     243                <guilabel>Original quantity</guilabel>
     244              </term>
     245              <listitem>
     246                <para>
     247                  This is meant to report information about the actual mass of
     248                  sample created.
     249                </para>
     250              </listitem>
     251            </varlistentry>
     252            <varlistentry>
     253              <term>
     254                <guilabel>Created</guilabel>
     255              </term>
     256              <listitem>
     257                <para>
     258                  A date when the sample was created. The information can be
     259                  important when running quality controls on data and account for
     260                  potential confounding factor (e.g. day effect).
     261                </para>
     262              </listitem>
     263            </varlistentry>
     264            <varlistentry>
     265              <term>
     266                <guilabel>Registered</guilabel>
     267              </term>
     268              <listitem>
     269                <para>The date at which the sample was entered in BASE2.</para>
     270              </listitem>
     271            </varlistentry>
     272            <varlistentry>
     273              <term>
     274                <guilabel>Protocol</guilabel>
     275              </term>
     276              <listitem>
     277                <para>The protocol used to produce this sample.</para>
     278              </listitem>
     279            </varlistentry>
     280            <varlistentry>
     281              <term>
     282                <guilabel>Description</guilabel>
     283              </term>
     284              <listitem>
     285                <para>
     286                  A text field to report any information that not can be captured
     287                  otherwise.
     288                </para>
     289              </listitem>
     290            </varlistentry>
     291          </variablelist>
     292        </helptext>
     293      </sect3>
     294      <sect3 id="biomaterials.samples.properties.parents">
     295        <title>Parents</title>
     296        <helptext external_id="sample.parents" title="Sample's parents">
    300297          <para>
    301             No matter how complex the sample processing phase is, at least one Sample
    302             has to be anchored to a BioSource.
     298            This is meant to keep track of the sample origin. BASE2 distinguished
     299            between 2 cases which are controled by the
     300            <guilabel>Pooled</guilabel>
     301            radio-button in the edit pop-up window.
    303302          </para>
     303          <itemizedlist>
     304            <listitem>
     305              <para>
     306                If the parent is a biosource the radio-button is set to
     307                <guilabel>No</guilabel>
     308                . This will make the biosource select button active, which allows
     309                users to point to a biosource from which the sample originates from.
     310              </para>
     311            </listitem>
     312            <listitem>
     313              <para>
     314                When the parent is one or several other samples the radio-button is
     315                set to
     316                <guilabel>Yes</guilabel>
     317                . Upon selection, the biosource select button is deactivated and the
     318                samples box and button are activated. This allows users to specify
     319                one or more samples to be selected from a sample list view page.
     320              </para>
     321            </listitem>
     322          </itemizedlist>
     323        </helptext>
     324      </sect3>
     325      <sect3 id="biomaterials.samples.properties.annotation_param">
     326        <title>Annotations &amp; parameters</title>
     327        <para>
     328          As seen in the biosource section, this tab allows users to further supply
     329          information about the sample provided they have defined or shared annotation
     330          types to annotate sample items.
     331        </para>
     332        <para>
     333          To learn more about annotation types and how to define a value for a type,
     334          please refer to
     335          <xref linkend="annotations" />
     336        </para>
     337      </sect3>
     338      <sect3 id="biomaterials.samples.properties.inherited">
     339        <title>Inherited annotations</title>
     340        <para>
     341          This tab contains a list of those annotations that are inherited from the
     342          sample's parents. Information about working with innherited annotations can be
     343          found in
     344          <xref linkend="annotations.inheriting" />
     345          .
     346        </para>
     347      </sect3>
     348    </sect2>
     349  </sect1>
     350
     351  <sect1 id="biomaterials.extracts">
     352    <title>Extracts</title>
     353    <para>
     354      Extract items should be used to describe the events that transform a sample material
     355      into an extract material. An extract can be created from one sample item or from one or
     356      more extract items. When an extract is created from several other extracts, a pooling
     357      event is performed.
     358    </para>
     359    <para>
     360      During the transformation from samples to extracts, it is possible to provide
     361      information about the protocol used to perform this task. It is not enforced in BASE2
     362      but it should serve as guidance when devising the granularity of the sample processing
     363      task. Also, it is good practice to provide protocol information.
     364    </para>
     365    <sect2 id="biomaterials.extracts.create">
     366      <title>Create extract</title>
     367      <para>
     368        Beside the common way, using the &gbNew; button, an extract can be created in one of
     369        the following ways:
     370        <variablelist>
     371          <varlistentry>
     372            <term>from either sample list- or single view- page.</term>
     373            <listitem>
     374              <para>
     375                No matter how complex the extract processing phase is, at least one
     376                extract has to be anchored to a sample. Therefore, a natural way to
     377                create an extract is to click on
     378                <inlinemediaobject>
     379                  <imageobject>
     380                    <imagedata fileref="figures/add.png" format="PNG" />
     381                  </imageobject>
     382                </inlinemediaobject>
     383                in the extracts column for the sample that should be a parent of the
     384                extract.
     385              </para>
     386              <para>
     387                There is also a corresponding button,
     388                <guibutton>Create extract&hellip;</guibutton>
     389                in the toolbar when viewing a single sample.
     390              </para>
     391            </listitem>
     392          </varlistentry>
     393          <varlistentry>
     394            <term>from the extract list page</term>
     395            <listitem>
     396              <para>
     397                Pooled extract can also be created by first selecting the parents
     398                from the list of extracts and then press
     399                <guibutton>Pool&hellip;</guibutton>
     400                in the toolbar. The selected extracts will be put into the parent
     401                property.
     402              </para>
     403            </listitem>
     404          </varlistentry>
     405        </variablelist>
     406      </para>
     407    </sect2>
     408    <sect2 id="biomaterials.extracts.properties">
     409      <title>Properties</title>
     410      <sect3 id="biomaterials.extracts.properties.extract">
     411        <title>Extract</title>
     412        <helptext external_id="extract.edit" title="Edit extract">
     413          <variablelist>
     414            <varlistentry>
     415              <term>
     416                <guilabel>Name</guilabel>
     417              </term>
     418              <listitem>
     419                <para>
     420                  A mandatory field for providing the extract's name. BASE2 by
     421                  default assigns names to extract (by suffixing
     422                  <replaceable>e#</replaceable>
     423                  when creating an extract from an existing sample or
     424                  <replaceable>New extract</replaceable>
     425                  otherwise) but it is possible to edit it at will.
     426                </para>
     427              </listitem>
     428            </varlistentry>
     429            <varlistentry>
     430              <term>
     431                <guilabel>External ID</guilabel>
     432              </term>
     433              <listitem>
     434                <para>The extracts identification outside BASE</para>
     435              </listitem>
     436            </varlistentry>
     437            <varlistentry>
     438              <term>
     439                <guilabel>Original quantity</guilabel>
     440              </term>
     441              <listitem>
     442                <para>
     443                  Holds information about the original mass of the created
     444                  extract.
     445                </para>
     446              </listitem>
     447            </varlistentry>
     448            <varlistentry>
     449              <term>
     450                <guilabel>Created</guilabel>
     451              </term>
     452              <listitem>
     453                <para>
     454                  The date when the extract was created. The information can be
     455                  important when running quality controls on data and account for
     456                  potential confounding factor (e.g. day effect)
     457                </para>
     458              </listitem>
     459            </varlistentry>
     460            <varlistentry>
     461              <term>
     462                <guilabel>Registered</guilabel>
     463              </term>
     464              <listitem>
     465                <para>
     466                  This is automatically populated with a date at which the sample
     467                  was entered in BASE2 system.
     468                </para>
     469              </listitem>
     470            </varlistentry>
     471            <varlistentry>
     472              <term>
     473                <guilabel>Protocol</guilabel>
     474              </term>
     475              <listitem>
     476                <para>
     477                  The extraction protocol that was used to produce the extract.
     478                </para>
     479              </listitem>
     480            </varlistentry>
     481            <varlistentry>
     482              <term>
     483                <guilabel>Description</guilabel>
     484              </term>
     485              <listitem>
     486                <para>
     487                  A text field to report any information that not can be captured
     488                  otherwise.
     489                </para>
     490              </listitem>
     491            </varlistentry>
     492          </variablelist>
     493        </helptext>
     494        <figure id="write_docbook_doc.figures.extract-tab-1">
     495          <title>Extract tab</title>
     496          <screenshot>
     497            <mediaobject>
     498              <imageobject>
     499                <imagedata contentwidth="12cm" width="12cm"
     500                  fileref="figures/extract-tab-1.png" format="PNG" />
     501              </imageobject>
     502            </mediaobject>
     503          </screenshot>
     504        </figure>
     505      </sect3>
     506
     507      <sect3 id="biomaterials.extracts.properties.parents">
     508        <title>Parents</title>
     509        <helptext external_id="extract.parents" title="Extract's parents">
    304510          <para>
    305             Therefore, a natural way to create a Sample is to click on the
    306             <inlinemediaobject>
     511            This important tab allows users to select the extract origin. BASE2
     512            distinguished between 2 cases which are controled by the
     513            <guilabel>Pooled</guilabel>
     514            radio-button.
     515          </para>
     516          <itemizedlist>
     517            <listitem>
     518              <para>
     519                If the parent is a sample the radio-button is set to
     520                <guilabel>No</guilabel>
     521                . The Sample select button is active and allows users to point to
     522                the sample from which the sample originates.
     523              </para>
     524            </listitem>
     525            <listitem>
     526              <para>
     527                The parent is another extract and the radio-button is set to
     528                <guilabel>Yes</guilabel>
     529                . Upon selection, the samples select button is deactivated and the
     530                extracts box and button are activated. This allows users to specify
     531                one or more extracts to be selected from an extract list view page.
     532              </para>
     533            </listitem>
     534          </itemizedlist>
     535        </helptext>
     536        <figure id="write_docbook_doc.figures.extract-tab-2-select-sample">
     537          <title>Parent tab</title>
     538          <screenshot>
     539            <mediaobject>
    307540              <imageobject>
    308                 <imagedata fileref="figures/add.gif" format="GIF" />
     541                <imagedata contentwidth="12cm" width="12cm"
     542                  fileref="figures/extract-tab-2-select-extract.png" format="PNG" />
    309543              </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>
     544            </mediaobject>
     545          </screenshot>
     546        </figure>
     547      </sect3>
     548      <sect3 id="biomaterials.extracts.properties.annotations_param">
     549        <title>Annotations &amp; parameters</title>
     550        <para>
     551          As seen in the biosource and sample sections, this tab allows users to supply
     552          further information about the extract, provided they have defined annotation
     553          types to annotation extract items or have such elements shared to them.
     554        </para>
     555        <para>
     556          To learn more about annotation types, please refer to
     557          <xref linkend="annotations" />
     558        </para>
     559      </sect3>
     560      <sect3 id="biomaterials.extracts.properties.inherited">
     561        <title>Inherited Annotations</title>
     562        <para>
     563          This tab contains a list of those annotations that are inherited from the
     564          extract's parents. Information about working with innherited annotations can be
     565          found in
     566          <xref linkend="annotations.inheriting" />
     567          .
     568        </para>
     569      </sect3>
     570    </sect2>
     571  </sect1>
     572
     573  <sect1 id="biomaterials.labels">
     574    <title>Labels</title>
     575    <para>
     576      Before attempting to create labeled extracts, users should make sure that the
     577      appropriate label object is present in BASE2. To browse the list of labels, go to
     578      <menuchoice>
     579        <guimenu>View</guimenu>
     580        <guimenuitem>Labels</guimenuitem>
     581      </menuchoice>
     582    </para>
     583    <sect2 id="biomaterials.labels.properties">
     584      <title>Properties</title>
     585      <helptext external_id="label.edit" title="Edit label">
     586        <para>
     587          The label item is very simple and doesn't need much explanation. There are only
     588          two properties for a label
     589          <variablelist>
     590            <varlistentry>
     591              <term>
     592                <guilabel>Name</guilabel>
     593              </term>
     594              <listitem>
     595                <para>The name of the label(required).</para>
     596              </listitem>
     597            </varlistentry>
     598            <varlistentry>
     599              <term>
     600                <guilabel>Description</guilabel>
     601              </term>
     602              <listitem>
     603                <para>
     604                  An explaining text or other information associated with the
     605                  label.
     606                </para>
     607              </listitem>
     608            </varlistentry>
     609          </variablelist>
     610          .
     611        </para>
     612      </helptext>
     613    </sect2>
     614
     615  </sect1>
     616  <sect1 id="biomaterials.labeledextracts">
     617    <title>Labeled extracts</title>
     618    <para>
     619      Labeled extract items should be used to describe the event that transformed an extract
     620      material in a labeled extract material. Labeled extracts can be created from extract
     621      items or from one or more labeled extract items. When a labeled extract is created from
     622      several other labeled extracts, a pooling event is performed.
     623    </para>
     624    <para>
     625      During the transformation from extracts to labeled extracts, it is possible to provide
     626      information about the protocol used to perform this task. It is not enforced in BASE2
     627      but it should serve as guidance when devising the granularity of the extract processing
     628      task. Also, it is good practice to provide protocol information.
     629    </para>
     630    <sect2 id="biomaterials.labeledextracts.create">
     631      <title>Creating labeled extracts</title>
     632      <para>
     633        Beside the regular way of using the &gbNew; button in
     634        <menuchoice>
     635          <guimenu>View</guimenu>
     636          <guimenuitem>Labeled extracts</guimenuitem>
     637        </menuchoice>
     638        , a labeled extract can be created in one of following ways.
     639      </para>
     640      <variablelist>
     641        <varlistentry>
     642          <term>pooling selected labeled extracts</term>
     643          <listitem>
     644            <para>
     645              The toolbar at the list page of labeled extracts contains an addition
     646              &gbPool; button. This button allows users to create pooled labeled
     647              extracts by selecting the list of labeled extracts used to derived a new
     648              labeled extract and then click on the button.
     649            </para>
     650            <para>
     651              This provides an easy and simple way to create pooled labeled extracts.
     652              The result of such process is the creation of a new labeled extract, in
     653              which, when navigating to the parent tab, shows that all the labeled
     654              extracts involved are already set and listed in the Labeled Extract box
     655              of the tab.
     656            </para>
     657          </listitem>
     658        </varlistentry>
     659        <varlistentry>
     660          <term>from the extract pages.</term>
     661          <listitem>
     662            <para>
     663              Following the laboratory workflow, a natural way to create a labeled
     664              extract from an extract is to click on the
     665              <inlinemediaobject>
    318666                <imageobject>
    319                   <imagedata contentwidth="13cm" width="13cm"
    320                     fileref="figures/biosource-create-sample.png" format="PNG" />
     667                  <imagedata fileref="figures/add.png" format="PNG" />
    321668                </imageobject>
    322               </mediaobject>
    323             </screenshot>
    324           </figure>
    325         </listitem>
    326         <listitem>
    327           <para>Creating Samples from the Sample List view page</para>
     669              </inlinemediaobject>
     670              from the labeled extract column of the extract list view. Corresponding
     671              button,
     672              <guibutton>New labeled extract</guibutton>
     673              is located on the single item view page for each extract. By creating a
     674              labeled extract from an extract page will automatically set the extract
     675              as a parent.
     676            </para>
     677          </listitem>
     678        </varlistentry>
     679        <varlistentry>
     680          <term>from single item view of a label</term>
     681          <listitem>
     682            <para>
     683              Click on the
     684              <guibutton>New labeled extract&hellip;</guibutton>
     685              to use the current label and create a new labeled extract with it
     686              pre-selected as
     687              <guilabel>Label</guilabel>
     688              .
     689            </para>
     690          </listitem>
     691        </varlistentry>
     692      </variablelist>
     693    </sect2>
     694    <sect2 id="biomaterials.labeledextracts.properties">
     695      <title>Properties</title>
     696      <sect3 id="biomaterials.labeledextracts.properties.labeledextract">
     697        <title>Labeled extract</title>
     698        <variablelist>
     699          <varlistentry>
     700            <term>
     701              <guilabel>Name</guilabel>
     702            </term>
     703            <listitem>
     704              <para>
     705                The name of the labeled extract (required). BASE2 by default assigns
     706                names to labeled extract(by suffixing
     707                <replaceable>lbe#</replaceable>
     708                when creating a labeled extract from an existing extract or
     709                <replaceable>New labeled extract</replaceable>
     710                otherwise) but it is possible to edit it at will
     711              </para>
     712            </listitem>
     713          </varlistentry>
     714          <varlistentry>
     715            <term>
     716              <guilabel>Label</guilabel>
     717            </term>
     718            <listitem>
     719              <para>
     720                Used to specify which dye or marker was used in the labeling
     721                reaction (required).
     722              </para>
     723            </listitem>
     724          </varlistentry>
     725          <varlistentry>
     726            <term>
     727              <guilabel>External ID</guilabel>
     728            </term>
     729            <listitem>
     730              <para>An id used to recognize the labeled extract outside BASE.</para>
     731            </listitem>
     732          </varlistentry>
     733          <varlistentry>
     734            <term>
     735              <guilabel>Original quantity</guilabel>
     736            </term>
     737            <listitem>
     738              <para>The mass of labeled extract that was created.</para>
     739            </listitem>
     740          </varlistentry>
     741          <varlistentry>
     742            <term>
     743              <guilabel>Created</guilabel>
     744            </term>
     745            <listitem>
     746              <para>
     747                A date should be provided. The information can be important when
     748                running quality controls on data and account for potential
     749                confounding factor (e.g. day effect).
     750              </para>
     751            </listitem>
     752          </varlistentry>
     753          <varlistentry>
     754            <term>
     755              <guilabel>Registred</guilabel>
     756            </term>
     757            <listitem>
     758              <para>
     759                This is automatically populated with a date at which the labeled
     760                extract was actually entered in BASE2 system.
     761              </para>
     762            </listitem>
     763          </varlistentry>
     764          <varlistentry>
     765            <term>
     766              <guilabel>Protocol</guilabel>
     767            </term>
     768            <listitem>
     769              <para>
     770                The labeling protocol that was used to produce the labeled extract.
     771              </para>
     772            </listitem>
     773          </varlistentry>
     774          <varlistentry>
     775            <term>
     776              <guilabel>Description</guilabel>
     777            </term>
     778            <listitem>
     779              <para>
     780                A free text field to report any information that can not be captured
     781                otherwise.
     782              </para>
     783            </listitem>
     784          </varlistentry>
     785        </variablelist>
     786      </sect3>
     787      <sect3 id="biomaterials.labeledextracts.properties.parents">
     788        <title>Parents</title>
     789        <para>
     790          This important tab allows users to select the labeled extract origin. BASE2
     791          distinguished between 2 cases which are controled by the
     792          <guilabel>Pooled</guilabel>
     793          radio-button.
     794        </para>
     795        <itemizedlist>
     796          <listitem>
     797            <para>The parent is an extract</para>
     798            <para>
     799              The radio-button is set to
     800              <guilabel>No</guilabel>
     801              . The Extract select button is active and allows users to point to one
     802              and only one extract from which the labeled extract originates from.
     803            </para>
     804          </listitem>
     805          <listitem>
     806            <para>The parent is another labeled extract</para>
     807            <para>
     808              The radio-button has to be set to
     809              <guilabel>Yes</guilabel>
     810              . Upon selection, the extract select button is deactivated and the
     811              labeled extracts box and button are activated. This allows users to
     812              specify one or more extracts to be selected from the labeled extract
     813              list view page.
     814            </para>
     815          </listitem>
     816        </itemizedlist>
     817      </sect3>
     818      <sect3 id="biomaterials.labeledextracts.properties.annotations_param">
     819        <title>Annotations &amp; parameters</title>
     820        <para>
     821          As seen in the biosource and sample sections, this tab allows users to further
     822          supply information about the labeled extract provided they have defined
     823          annotation types to annotate labeled extract items or have such elements shared
     824          to them.
     825        </para>
     826        <important>
    328827          <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>
     828            In order to use this feature, annotation type must be declared and made
     829            available. To learn more about annotation types and how these are set,
     830            please refer to
     831            <xref linkend="annotations" />
    346832            .
    347833          </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>
     834        </important>
     835      </sect3>
     836      <sect3 id="biomaterials.labeledextracts.properties.inherited">
     837        <title>Inherited annotations</title>
     838        <para>
     839          This tab contains a list of those annotations that are inherited from the
     840          parents of the labeled extract. Information about dealing with innherited
     841          annotations can be found in
     842          <xref linkend="annotations.inheriting" />
     843          .
     844        </para>
     845      </sect3>
    689846    </sect2>
    690847  </sect1>
    691848
    692   <sect1 id="extract.manage">
    693     <title>Managing Extracts</title>
    694     <para>
    695       Extract items should be used to describe the events that transform a Sample material in
    696       an Extract material.
    697     </para>
    698     <para>Extracts can be created from Sample items or from one or more Extract items.</para>
    699     <para>
    700       When an Extract is created from several other Extracts, a Pooling event is performed. A
    701       specific section details how to create pooled Extracts
    702     </para>
    703     <para>
    704       During the transformation from Samples to Extracts, it is possible to provide
    705       information about the protocol used to perform this task.
    706     </para>
    707     <para>
    708       It is not enforced in BASE2 but it should serve as guidance when devising the
    709       granularity of the sample processing task. Also, it is good practice to provide protocol
    710       information.
    711     </para>
    712     <sect2 id="extract.manage.createextractfromsample">
    713       <title>Creating Extracts</title>
    714       <orderedlist>
    715         <listitem>
    716           <para>Creating Extracts from the Sample page</para>
    717           <para>
    718             Following the laboratory workflow, a natural way to create a new Extract is
    719             to click on the
    720             <guibutton>New extract</guibutton>
    721             from the Extract column of the Sample List View.
    722           </para>
    723           <figure id="write_docbook_doc.figures.sample-create-extract">
    724             <title>Creating an Extract from the Sample list view</title>
    725             <screenshot>
    726               <mediaobject>
    727                 <imageobject>
    728                   <imagedata contentwidth="12cm" width="12cm"
    729                     fileref="figures/sample-create-extract.png" format="PNG" />
    730                 </imageobject>
    731               </mediaobject>
    732             </screenshot>
    733           </figure>
    734         </listitem>
    735         <listitem>
    736           <para>Creating Extracts from the Sample List view page</para>
    737           <para>
    738             Alternately, Extracts can be created directly ysing the Extract create page.
    739             To do so, go to
    740             <menuchoice>
    741               <guimenu>View</guimenu>
    742               <guimenuitem>Extracts</guimenuitem>
    743             </menuchoice>
    744             , Click on &gbNew; button
    745           </para>
    746           <para>
    747             A 'Create' pop-up window opens, it contains 4 tabs:
    748             <guilabel>Extract</guilabel>
    749             ,
    750             <guilabel>Parents</guilabel>
    751             ,
    752             <guilabel>Annotations &amp; parameters</guilabel>
    753             and
    754             <guilabel>Inherited Annotations</guilabel>
    755             .
    756           </para>
    757           <itemizedlist>
    758             <listitem>
    759               <para>The Extract Tab</para>
    760               <para>
    761                 This tab contains 1 mandatory field for providing the extract name.
    762               </para>
    763               <para>
    764                 BASE2 by default assigns names to Extract (by suffixing 'e#' when
    765                 creating an Extract from an existing Sample or 'New Extract'
    766                 otherwise) but it is possible to edit it at will
    767               </para>
    768               <para>
    769                 There 5 optional fields to provide more detailed information
    770               </para>
    771               <itemizedlist>
    772                 <listitem>
    773                   <para>
    774                     <guilabel>External ID</guilabel>
    775                     : for instance to report a barcode attached to an extract
    776                   </para>
    777                 </listitem>
    778                 <listitem>
    779                   <para>
    780                     <guilabel>Original Quantity (ug)</guilabel>
    781                     : this is meant to report information about the actual mass
    782                     of biomaterial created
    783                   </para>
    784                 </listitem>
    785                 <listitem>
    786                   <para>
    787                     <guilabel>Created</guilabel>
    788                     : a date should be provided. The information can be
    789                     important when running quality controls on data and account
    790                     for potential confounding factor (e.g. day effect)
    791                   </para>
    792                 </listitem>
    793                 <listitem>
    794                   <para>
    795                     <guilabel>Protocol</guilabel>
    796                     : this a controled field. A select-list displays protocol
    797                     whose type is '
    798                     <guilabel>extraction</guilabel>
    799                     ' and which are shared to or owned by the logged-in user.
    800                     Reporting Protocol should be viewed as a MIAME requirement
    801                   </para>
    802                 </listitem>
    803                 <listitem>
    804                   <para>
    805                     <guilabel>Description</guilabel>
    806                     : a free text field to report any information that not can
    807                     be captured otherwise
    808                   </para>
    809                 </listitem>
    810               </itemizedlist>
    811               <para>
    812                 Finally, a 7th field
    813                 <guilabel>Registered</guilabel>
    814                 is automatically populated with a date at which the sample was
    815                 entered in BASE2 system.
    816               </para>
    817               <figure id="write_docbook_doc.figures.extract-tab-1">
    818                 <title>Extract tab</title>
    819                 <screenshot>
    820                   <mediaobject>
    821                     <imageobject>
    822                       <imagedata contentwidth="12cm" width="12cm"
    823                         fileref="figures/extract-tab-1.png" format="PNG" />
    824                     </imageobject>
    825                   </mediaobject>
    826                 </screenshot>
    827               </figure>
    828             </listitem>
    829             <listitem>
    830               <para>The Parents Tab</para>
    831               <para>
    832                 This important tab allows users to select the Extract origin. BASE2
    833                 distinguished between 2 cases which are controled by the
    834                 <guibutton>'pooled'</guibutton>
    835                 radio-button
    836               </para>
    837               <orderedlist>
    838                 <listitem>
    839                   <para>The Parent is a Sample</para>
    840                   <para>
    841                     The
    842                     <guibutton>pooled</guibutton>
    843                     radio-button is set to
    844                     <guilabel>No</guilabel>
    845                   </para>
    846                   <para>
    847                     The Sample select button is active and allows users to point
    848                     to one and only one Sample from which the sample originates
    849                     from.
    850                   </para>
    851                   <figure
    852                     id="write_docbook_doc.figures.extract-tab-2-select-sample">
    853                     <title>
    854                       Parent tab and interaction when pooled button is set to
    855                       No
    856                     </title>
    857                     <screenshot>
    858                       <mediaobject>
    859                         <imageobject>
    860                           <imagedata contentwidth="12cm" width="12cm"
    861                             fileref="figures/extract-tab-2-select-sample.png" format="PNG" />
    862                         </imageobject>
    863                       </mediaobject>
    864                     </screenshot>
    865                   </figure>
    866                 </listitem>
    867                 <listitem>
    868                   <para>The Parent is another Extract</para>
    869                   <para>
    870                     The
    871                     <guibutton>pooled</guibutton>
    872                     radio-button has to be set to
    873                     <guilabel>Yes</guilabel>
    874                   </para>
    875                   <para>
    876                     Upon selection, the Samples select button is deactivated and
    877                     the Extracts box and button are activated.
    878                   </para>
    879                   <para>
    880                     This allows users to specify one or more extracts to be
    881                     selected from the Extract list View page.
    882                   </para>
    883                   <figure
    884                     id="write_docbook_doc.figures.extract-tab-2-select-extract">
    885                     <title>
    886                       Parent tab and interaction when pooled button is set to
    887                       Yes
    888                     </title>
    889                     <screenshot>
    890                       <mediaobject>
    891                         <imageobject>
    892                           <imagedata contentwidth="12cm" width="12cm"
    893                             fileref="figures/extract-tab-2-select-extract.png" format="PNG" />
    894                         </imageobject>
    895                       </mediaobject>
    896                     </screenshot>
    897                   </figure>
    898                 </listitem>
    899               </orderedlist>
    900             </listitem>
    901             <listitem>
    902               <para>Annotations &amp; parameters</para>
    903               <para>
    904                 As seen in the BioSource and Sample sections, this tab allows users
    905                 to supply further information about the Extract, provided they have
    906                 defined Annotation Types to annotation Extract items or have such
    907                 elements shared to them.
    908               </para>
    909               <para>
    910                 The display of Annotation Type can be filtered based on the
    911                 Annotation Type Category they belong to.
    912               </para>
    913               <important>
    914                 <para>
    915                   In order to use this feature, Annotation Type must be declared
    916                   and made available. To learn more about Annotation Types, please
    917                   refer to
    918                   <xref linkend="annotations" />
    919                 </para>
    920               </important>
    921               <para>
    922                 To provide a value for a given annotation type, simply click on it
    923                 an use the input field or select a value from the drop-down lists or
    924                 radio buttons.
    925               </para>
    926               <figure id="write_docbook_doc.figures.extract-tab-3">
    927                 <title>Annotations &amp; parameters</title>
    928                 <screenshot>
    929                   <mediaobject>
    930                     <imageobject>
    931                       <imagedata contentwidth="12cm" width="12cm"
    932                         fileref="figures/extract-tab-3.png" format="PNG" />
    933                     </imageobject>
    934                   </mediaobject>
    935                 </screenshot>
    936               </figure>
    937             </listitem>
    938             <listitem>
    939               <para>Inherited Annotations case1</para>
    940               <para>The next picture shows</para>
    941               <figure id="write_docbook_doc.figures.extract-tab-4">
    942                 <title>Inherited Annotations</title>
    943                 <screenshot>
    944                   <mediaobject>
    945                     <imageobject>
    946                       <imagedata contentwidth="12cm" width="12cm"
    947                         fileref="figures/extract-tab-4.png" format="PNG" />
    948                     </imageobject>
    949                   </mediaobject>
    950                 </screenshot>
    951               </figure>
    952             </listitem>
    953           </itemizedlist>
    954         </listitem>
    955       </orderedlist>
    956     </sect2>
    957     <sect2 id="extract.manage.createextractpool">
    958       <title>Creating Pooled Extracts</title>
    959       <para>
    960         It is common practice when biological material is scarce to pool extracts from
    961         equivalent sources. BASE2 provides mechanisms to report on such practice. This
    962         section details how.
    963       </para>
    964       <para>There are 2 ways to create pooled samples in BASE2:</para>
    965       <orderedlist>
    966         <listitem>
    967           <para>
    968             Using the Pooled radio button option from the Extract Create page, and this
    969             has been shown already.
    970           </para>
    971         </listitem>
    972         <listitem>
    973           <para>Using the Pool button in the Menu bar</para>
    974           <para>
    975             The Sample List View page menu bar contains an addition &gbPool;
    976             <inlinemediaobject>
    977               <imageobject>
    978                 <imagedata fileref="figures/new_pooled.gif" format="GIF" />
    979               </imageobject>
    980             </inlinemediaobject>
    981             button, the usage of which is detailed now.
    982           </para>
    983           <para>
    984             The &gbPool;
    985             <inlinemediaobject>
    986               <imageobject>
    987                 <imagedata fileref="figures/new_pooled.gif" format="GIF" />
    988               </imageobject>
    989             </inlinemediaobject>
    990             button allows users to create Pooled Extracts by selecting the list of
    991             Extracts used to derived a new Extract. Users simply to tick to boxes in
    992             front of each relevant Extract and click the
    993             <guibutton>Pool...</guibutton>
    994           </para>
    995           <para>
    996             This provides an easy and simple way to create pooled Extracts. The result
    997             of such process is the creation of a New Extract, in which, when navigating
    998             to the Parent tab, shows that all the Extracts involved are already set and
    999             listed in the Extract box of the tab.
    1000           </para>
    1001           <figure id="write_docbook_doc.figures.biosample-tab-2-pool-extract">
    1002             <title>Pooling of Extracts</title>
    1003             <screenshot>
    1004               <mediaobject>
    1005                 <imageobject>
    1006                   <imagedata contentwidth="12cm" width="12cm"
    1007                     fileref="figures/extract-tab-2-pool-extract.png" format="PNG" />
    1008                 </imageobject>
    1009               </mediaobject>
    1010             </screenshot>
    1011           </figure>
    1012         </listitem>
    1013       </orderedlist>
    1014     </sect2>
    1015     <sect2 id="extract.manage.delete">
    1016       <title>Deleting/Restoring Extracts</title>
    1017       <para>
    1018         As for other items in BASE2, Extracts can be removed. For a generic overview on how
    1019         to delete and restore items, refer to section
    1020         <xref linkend="webclient.items.delete" />
    1021       </para>
    1022       <para>To delete, do the following</para>
    1023       <itemizedlist>
    1024         <listitem>
    1025           <para>
    1026             Select one or more Extract and click &gbDelete; button in the menu bar.
    1027           </para>
    1028           <para>
    1029             All the selected Extracts have been marked as deleted and are no longer
    1030             available from the interface.
    1031           </para>
    1032           <para>
    1033             Only by selecting from the
    1034             <guilabel>view/preset&hellip;</guilabel>
    1035             select box the
    1036             <guilabel>Removed</guilabel>
    1037             option, one can see those of the Extracts earmarked for deletion. They will
    1038             be shown with a symbol in front of them.
    1039           </para>
    1040         </listitem>
    1041         <listitem>
    1042           <para>
    1043             Alternately, navigating to the Extract Item View, one can hit the &gbDelete;
    1044             to performed the task.
    1045           </para>
    1046           <para>
    1047             As shown in the next picture, the Extract is then marked with the
    1048             <guilabel>This item has been flagged for deletion</guilabel>
    1049           </para>
    1050           <figure id="write_docbook_doc.figures.extract-delete">
    1051             <title>Deleting Extracts from the Item View</title>
    1052             <screenshot>
    1053               <mediaobject>
    1054                 <imageobject>
    1055                   <imagedata contentwidth="12cm" width="12cm"
    1056                     fileref="figures/extract-delete.png" format="PNG" />
    1057                 </imageobject>
    1058               </mediaobject>
    1059             </screenshot>
    1060           </figure>
    1061         </listitem>
    1062         <listitem>
    1063           <para>
    1064             Deletion errors at this stage can be easily recovered. Select the item to
    1065             recover from the List View (be sure to check the
    1066             <guilabel>removed</guilabel>
    1067             option in the View/preset.. filter) and hit the &gbRestore; to performed the
    1068             task.
    1069           </para>
    1070         </listitem>
    1071       </itemizedlist>
    1072       <important>
    1073         <para>
    1074           To really delete an item from the database you must use the trashcan. Items
    1075           deleted from the Trashcan can not be recovered. To learn more about the trashcan
    1076           function, please refer to
    1077           <xref linkend="trashcan" />
    1078         </para>
    1079       </important>
    1080     </sect2>
    1081   </sect1>
    1082 
    1083 
    1084 
    1085   <sect1 id="label">
    1086     <title>Managing Labels</title>
    1087 
    1088     <sect2 id="label.browse">
    1089       <title>Browsing Labels</title>
    1090       <para>
    1091         Before attempting to create Labeled Extracts, users should make sure that the
    1092         appropriate Label object is present in BASE2
    1093       </para>
    1094       <para>
    1095         To browse the list of Labels, go to
    1096         <menuchoice>
    1097           <guimenu>View</guimenu>
    1098           <guimenuitem>Labels</guimenuitem>
    1099         </menuchoice>
    1100         It is wise to select the clear filter option or select the
    1101         <guilabel>shared to me</guilabel>
    1102         option from the view/preset select box in order to view all different dyes.
    1103       </para>
    1104       <para>Clicking on any of item opens an item view page</para>
    1105       <figure id="write_docbook_doc.figures.label-itemview">
    1106         <title>The Label Item View Page</title>
    1107         <screenshot>
    1108           <mediaobject>
    1109             <imageobject>
    1110               <imagedata contentwidth="12cm" width="12cm"
    1111                 fileref="figures/label-itemview.png" format="PNG" />
    1112             </imageobject>
    1113           </mediaobject>
    1114         </screenshot>
    1115       </figure>
    1116       <para>
    1117         Note the
    1118         <guibutton>New labeled extract&hellip;</guibutton>
    1119         button available from this page. For more detailed about creating Labeled extracts,
    1120         see
    1121         <xref linkend="labeledextract.manage" />
    1122       </para>
    1123 
    1124     </sect2>
    1125     <sect2 id="label.create">
    1126       <title>Creating Labels</title>
    1127       <para>
    1128         Click on &gbNew; button, a pop-up window opens. Fill in Name and description if
    1129         required. Label item are very simple object and do not bear association to
    1130         Annotation Type.
    1131       </para>
    1132     </sect2>
    1133   </sect1>
    1134   <sect1 id="labeledextract.manage">
    1135     <title>Managing Labeled Extracts</title>
    1136     <para>
    1137       Labeled Extract items should be used to describe the event that transformed a Extract
    1138       material in a Labeled Extract material.
    1139     </para>
    1140     <para>
    1141       Labeled extracts can be created from Extract items or from one or more Labeled extract
    1142       items.
    1143     </para>
    1144     <para>
    1145       When a Labeled Extract is created from several other Labeled Extracts, a Pooling event
    1146       is performed. A specific section details how to create pooled Labeled Extracts
    1147     </para>
    1148     <para>
    1149       During the transformation from Extracts to Labeled Extracts, it is possible to provide
    1150       information about the protocol used to perform this task.
    1151     </para>
    1152     <para>
    1153       It is not enforced in BASE2 but it should serve as guidance when devising the
    1154       granularity of the extract processing task. Also, it is good practice to provide
    1155       protocol information.
    1156     </para>
    1157     <sect2 id="labeledextract.manage.createlabeledextractfromextract">
    1158       <title>Creating Labeled Extracts</title>
    1159       <orderedlist>
    1160         <listitem>
    1161           <para>Creating Labeled Extracts from the Extract page</para>
    1162           <para>
    1163             Following the laboratory workflow, a natural way to create a Labeled Extract
    1164             is to click on the
    1165             <guibutton>New labeled extract</guibutton>
    1166             from the Labeled Extract column of the Extract List View.
    1167           </para>
    1168           <figure id="write_docbook_doc.figures.sample-create-labeledextract">
    1169             <title>Creating a Labeled Extract from the Extract List View</title>
    1170             <screenshot>
    1171               <mediaobject>
    1172                 <imageobject>
    1173                   <imagedata contentwidth="12cm" width="12cm"
    1174                     fileref="figures/sample-create-labeledextract.png" format="PNG" />
    1175                 </imageobject>
    1176               </mediaobject>
    1177             </screenshot>
    1178           </figure>
    1179         </listitem>
    1180         <listitem>
    1181           <para>Creating Labeled Extracts from the Extract Item View page</para>
    1182           <para>
    1183             Alternately, Labeled Extracts can be created directly using the Labeled
    1184             Extract create page. To do so, go to
    1185             <menuchoice>
    1186               <guimenu>View</guimenu>
    1187               <guimenuitem>Labeled Extracts</guimenuitem>
    1188             </menuchoice>
    1189             , Click on &gbNew; button
    1190           </para>
    1191           <para>
    1192             A 'Create' pop-up window opens, it contains 4 tabs:
    1193             <guilabel>Labeled Extract</guilabel>
    1194             ,
    1195             <guilabel>Parents</guilabel>
    1196             ,
    1197             <guilabel>Annotations &amp; parameters</guilabel>
    1198             and
    1199             <guilabel>Inherited Annotations</guilabel>
    1200             .
    1201           </para>
    1202           <itemizedlist>
    1203             <listitem>
    1204               <para>The Labeled Extract Tab</para>
    1205               <para>
    1206                 This tab contains 2 mandatory fields, one for providing the Labeled
    1207                 Extract
    1208                 <guilabel>Name</guilabel>
    1209                 , the other one
    1210                 <guilabel>Label</guilabel>
    1211                 to specify which dye or marker was used in the labeling reaction.
    1212               </para>
    1213               <para>
    1214                 BASE2 by default assigns names to Labeled Extract(by suffixing
    1215                 'lbe#' when creating a Labeled Extract from an existing Extract or
    1216                 'New labeled extract' otherwise) but it is possible to edit it at
    1217                 will
    1218               </para>
    1219               <para>
    1220                 There 5 optional fields to provide more detailed information
    1221               </para>
    1222               <itemizedlist>
    1223                 <listitem>
    1224                   <para>
    1225                     <guilabel>External ID</guilabel>
    1226                     : for instance to report a barcode attached to an extract
    1227                   </para>
    1228                 </listitem>
    1229                 <listitem>
    1230                   <para>
    1231                     <guilabel>Original Quantity (ug)</guilabel>
    1232                     : this is meant to report information about the actual mass
    1233                     of biomaterial created
    1234                   </para>
    1235                 </listitem>
    1236                 <listitem>
    1237                   <para>
    1238                     <guilabel>Created</guilabel>
    1239                     : a date should be provided. The information can be
    1240                     important when running quality controls on data and account
    1241                     for potential confounding factor (e.g. day effect)
    1242                   </para>
    1243                 </listitem>
    1244                 <listitem>
    1245                   <para>
    1246                     <guilabel>Protocol</guilabel>
    1247                     : this a controled field. A select-list displays protocol
    1248                     whose type is '
    1249                     <guilabel>labeling</guilabel>
    1250                     ' and which are shared to or owned by the logged-in user.
    1251                     Reporting Protocol should be viewed as a MIAME requirement
    1252                   </para>
    1253                 </listitem>
    1254                 <listitem>
    1255                   <para>
    1256                     <guilabel>Description</guilabel>
    1257                     : a free text field to report any information that can not
    1258                     be captured otherwise
    1259                   </para>
    1260                 </listitem>
    1261               </itemizedlist>
    1262               <para>
    1263                 Finally, a 7th field
    1264                 <guilabel>Created</guilabel>
    1265                 is automatically populated with a date at which the Labeled Extract
    1266                 was actually entered in BASE2 system.
    1267               </para>
    1268               <figure id="write_docbook_doc.figures.labeledextract-tab-1">
    1269                 <title>Labeled Extract tab</title>
    1270                 <screenshot>
    1271                   <mediaobject>
    1272                     <imageobject>
    1273                       <imagedata contentwidth="12cm" width="12cm"
    1274                         fileref="figures/labeledextract-tab-1.png" format="PNG" />
    1275                     </imageobject>
    1276                   </mediaobject>
    1277                 </screenshot>
    1278               </figure>
    1279             </listitem>
    1280             <listitem>
    1281               <para>The Parents Tab</para>
    1282               <para>
    1283                 This important tab allows users to select the Labeled Extract
    1284                 origin. BASE2 distinguished between 2 cases which are controled by
    1285                 the
    1286                 <guibutton>'pooled'</guibutton>
    1287                 radio-button
    1288               </para>
    1289               <orderedlist>
    1290                 <listitem>
    1291                   <para>The Parent is an Extract</para>
    1292                   <para>
    1293                     The
    1294                     <guibutton>pooled</guibutton>
    1295                     radio-button is set to
    1296                     <guilabel>No</guilabel>
    1297                   </para>
    1298                   <para>
    1299                     The Extract select button is active and allows users to
    1300                     point to one and only one Extract from which the Labeled
    1301                     Extract originates from.
    1302                   </para>
    1303                   <figure
    1304                     id="write_docbook_doc.figures.labeledextract-tab-2-select-extract">
    1305                     <title>
    1306                       Parent tab and interaction when pooled button is set to
    1307                       No
    1308                     </title>
    1309                     <screenshot>
    1310                       <mediaobject>
    1311                         <imageobject>
    1312                           <imagedata contentwidth="12cm" width="12cm"
    1313                             fileref="figures/labeledextract-tab-2-select-extract.png" format="PNG" />
    1314                         </imageobject>
    1315                       </mediaobject>
    1316                     </screenshot>
    1317                   </figure>
    1318                 </listitem>
    1319                 <listitem>
    1320                   <para>The Parent is another Labeled Extract</para>
    1321                   <para>
    1322                     The
    1323                     <guibutton>pooled</guibutton>
    1324                     radio-button has to be set to
    1325                     <guilabel>Yes</guilabel>
    1326                   </para>
    1327                   <para>
    1328                     Upon selection, the Extract select button is deactivated and
    1329                     the Labeled Extracts box and button are activated.
    1330                   </para>
    1331                   <para>
    1332                     This allows users to specify one or more extracts to be
    1333                     selected from the Labeled Extract list View page.
    1334                   </para>
    1335                   <figure
    1336                     id="write_docbook_doc.figures.labeledextract-tab-2-select-labeledextract">
    1337                     <title>
    1338                       Parent tab and interaction when pooled button is set to
    1339                       Yes
    1340                     </title>
    1341                     <screenshot>
    1342                       <mediaobject>
    1343                         <imageobject>
    1344                           <imagedata contentwidth="12cm" width="12cm"
    1345                             fileref="figures/labeledextract-tab-2-select-labeledextract.png" format="PNG" />
    1346                         </imageobject>
    1347                       </mediaobject>
    1348                     </screenshot>
    1349                   </figure>
    1350                 </listitem>
    1351               </orderedlist>
    1352             </listitem>
    1353             <listitem>
    1354               <para>Annotations &amp; parameters</para>
    1355               <para>
    1356                 As seen in the BioSource and Sample sections, this tab allows users
    1357                 to further supply information about the labeled extract provided
    1358                 they have defined annotation types to annotate Labeled Extract items
    1359                 or have such elements shared to them.
    1360               </para>
    1361               <para>
    1362                 The display of Annotation Types can be filtered based on the
    1363                 Annotation Type Categories they belong to.
    1364               </para>
    1365               <important>
    1366                 <para>
    1367                   In order to use this feature, Annotation Type must be declared
    1368                   and made available. To learn more about Annotation Types, please
    1369                   refer to
    1370                   <xref linkend="annotations" />
    1371                 </para>
    1372               </important>
    1373               <para>
    1374                 To provide a value for a given annotation type, simply click on it
    1375                 an use the input field or select a value from the drop-down lists or
    1376                 radio buttons.
    1377               </para>
    1378               <figure id="write_docbook_doc.figures.labeledextract-tab-3">
    1379                 <title>Annotations &amp; parameters</title>
    1380                 <screenshot>
    1381                   <mediaobject>
    1382                     <imageobject>
    1383                       <imagedata contentwidth="12cm" width="12cm"
    1384                         fileref="figures/labeledextract-tab-3.png" format="PNG" />
    1385                     </imageobject>
    1386                   </mediaobject>
    1387                 </screenshot>
    1388               </figure>
    1389             </listitem>
    1390             <listitem>
    1391               <para>Inherited Annotations case1</para>
    1392               <para>The next picture shows</para>
    1393               <figure id="write_docbook_doc.figures.labeledextract-tab-4">
    1394                 <title>Inherited Annotations</title>
    1395                 <screenshot>
    1396                   <mediaobject>
    1397                     <imageobject>
    1398                       <imagedata contentwidth="12cm" width="12cm"
    1399                         fileref="figures/labeledextract-tab-4.png" format="PNG" />
    1400                     </imageobject>
    1401                   </mediaobject>
    1402                 </screenshot>
    1403               </figure>
    1404             </listitem>
    1405           </itemizedlist>
    1406         </listitem>
    1407       </orderedlist>
    1408     </sect2>
    1409     <sect2 id="labeledextract.manage.createelabeledxtract.pool">
    1410       <title>Creating Pooled Labeled Extracts</title>
    1411       <para>
    1412         It is common practice when biological material is scarce to pool extracts from
    1413         equivalent sources. BASE2 provides mechanisms to report on such practice.
    1414       </para>
    1415       <para>This section details how.</para>
    1416       <para>There are 2 ways to create pooled Labeled Extracts in BASE2</para>
    1417       <orderedlist>
    1418         <listitem>
    1419           <para>
    1420             Using the Pooled radio button option from the Labeled Extract Create page,
    1421             and this has been shown already
    1422           </para>
    1423         </listitem>
    1424         <listitem>
    1425           <para>Using the Pool button in the Menu bar</para>
    1426           <para>
    1427             The Labeled Extracts List View page menu bar contains an addition &gbPool;
    1428             button, the usage of which is detailed now.
    1429           </para>
    1430           <para>
    1431             The &gbPool; button
    1432             <inlinemediaobject>
    1433               <imageobject>
    1434                 <imagedata fileref="figures/new_pooled.gif" format="GIF" />
    1435               </imageobject>
    1436             </inlinemediaobject>
    1437             allows users to create Pooled Labeled Extracts by selecting the list of
    1438             Labeled Extracts used to derived a new Labeled Extract. Users simply have to
    1439             tick to boxes in front of each relevant Labeled Extract and click the
    1440             <guibutton>Pool...</guibutton>
    1441           </para>
    1442           <para>
    1443             This provides an easy and simple way to create pooled Labeled Extracts. The
    1444             result of such process is the creation of a New Labeled Extract, in which,
    1445             when navigating to the Parent tab, shows that all the Labeled Extracts
    1446             involved are already set and listed in the Labeled Extract box of the tab.
    1447           </para>
    1448           <figure
    1449             id="write_docbook_doc.figures.labeledextract-tab-2-pool-labeledextract">
    1450             <title>Pooling of Labeled Extracts:</title>
    1451             <screenshot>
    1452               <mediaobject>
    1453                 <imageobject>
    1454                   <imagedata contentwidth="12cm" width="12cm"
    1455                     fileref="figures/labeledextract-tab-2-pool-labeledextract.png" format="PNG" />
    1456                 </imageobject>
    1457               </mediaobject>
    1458             </screenshot>
    1459           </figure>
    1460         </listitem>
    1461       </orderedlist>
    1462     </sect2>
    1463     <sect2 id="labeledextract.manage.delete">
    1464       <title>Deleting/Restoring Labeled Extracts</title>
    1465       <para>
    1466         As for other items in BASE2, Labeled Extracts can be deleted. For a generic overview
    1467         on how to delete and restore items, refer to section
    1468         <xref linkend="webclient.items.delete" />
    1469       </para>
    1470       <para>To delete, do the following</para>
    1471       <itemizedlist>
    1472         <listitem>
    1473           <para>
    1474             Select one or more Labeled Extract and click &gbDelete; button in the menu
    1475             bar.
    1476           </para>
    1477           <para>
    1478             All the selected Labeled Extracts have been marked as deleted and are no
    1479             longer available from the interface.
    1480           </para>
    1481           <para>
    1482             Only by selecting from the
    1483             <guilabel>view/preset&hellip;</guilabel>
    1484             select box the
    1485             <guilabel>Removed</guilabel>
    1486             option, one can see those of the Labeled Extracts earmarked for deletion.
    1487             They will be shown with a symbol in front of them.
    1488           </para>
    1489         </listitem>
    1490         <listitem>
    1491           <para>
    1492             Alternately, navigating to the Labeled Extract Item View, one can hit the
    1493             &gbDelete; to performed the task. As showed in the next picture, the Labeled
    1494             Extract is then marked with the
    1495             <inlinemediaobject>
    1496               <imageobject>
    1497                 <imagedata fileref="figures/deleted.gif" format="GIF" />
    1498               </imageobject>
    1499             </inlinemediaobject>
    1500             <guiicon>This item has been flagged for deletion</guiicon>
    1501           </para>
    1502           <figure id="write_docbook_doc.figures.labeledextract-delete">
    1503             <title>Deleting Labeled Extracts from the Item View</title>
    1504             <screenshot>
    1505               <mediaobject>
    1506                 <imageobject>
    1507                   <imagedata contentwidth="12cm" width="12cm"
    1508                     fileref="figures/labeledextract-delete.png" format="PNG" />
    1509                 </imageobject>
    1510               </mediaobject>
    1511             </screenshot>
    1512           </figure>
    1513         </listitem>
    1514         <listitem>
    1515           <para>
    1516             Deletion errors at this stage can be easily recovered. Select the item to
    1517             recover from the List View (be sure to check the
    1518             <guilabel>Removed</guilabel>
    1519             option in the View/preset.. filter) and hit the &gbRestore; to performed the
    1520             task.
    1521           </para>
    1522         </listitem>
    1523       </itemizedlist>
    1524       <important>
    1525         <para>
    1526           To really delete an item from the database you must use the trashcan. Items
    1527           deleted from the Trashcan can not be recovered. To learn more about the trashcan
    1528           function, please refer to
    1529           <xref linkend="trashcan" />
    1530         </para>
    1531       </important>
    1532     </sect2>
    1533   </sect1>
    1534   <sect1 id="hybridization.manage">
    1535     <title>Managing Hybridizations</title>
     849  <sect1 id="biomaterials.hybridizations">
     850    <title>Hybridizations</title>
    1536851    <para>
    1537852      An hybridization event corresponds to the application of one or more labeled extracts
    1538853      materials to a microarray slide under conditions detailed in hybridization protocols.
     854      Use
     855      <menuchoice>
     856        <guimenu>View</guimenu>
     857        <guimenuitem>Hybridizatons</guimenuitem>
     858      </menuchoice>
     859      to get to the hybridizations.
    1539860    </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>
     861    <sect2 id="biomaterials.hybridizations.create">
     862      <title>Creating hybridizations</title>
     863      <para>
     864        In BASE2, there are 2 possible routes to create an hybridization object except the
     865        common way with the &gbNew; button at hybridization list page.
     866      </para>
     867      <variablelist>
     868        <varlistentry>
     869          <term>from the labeled extract list view page</term>
     870          <listitem>
     871            <para>
     872              Select at least one labeled extract, to create a hybridization from, by
     873              ticking the selection boxes before the name field.
     874            </para>
     875            <para>
     876              Click on the
     877              <guibutton>New hybridzation&hellip;</guibutton>
     878              from the toolbar of labeled extract list view.
     879            </para>
     880          </listitem>
     881        </varlistentry>
     882        <varlistentry>
     883          <term>from a labeled extract single item page</term>
     884          <listitem>
     885            <para>
     886              When viewing a label extract in single item view, click on the
     887              <guibutton>New hybridization&hellip;</guibutton>
     888              button from the toolbar of the labeled extract item view.
     889            </para>
     890          </listitem>
     891        </varlistentry>
     892      </variablelist>
     893    </sect2>
     894    <sect2 id="biomaterials.hybridizations.properties">
     895      <title>Properties</title>
     896
     897      <sect3 id="biomaterials.hybridizations.hybridization">
     898        <title>Hybridization</title>
     899        <variablelist>
     900          <varlistentry>
     901            <term>
     902              <guilabel>Name</guilabel>
     903            </term>
     904            <listitem>
     905              <para>
     906                <replaceable>New hybridization</replaceable>
     907                is BASE2 default name but it is strongly advise to provide a
     908                meaningful and unique name (required).
     909              </para>
     910            </listitem>
     911          </varlistentry>
     912
     913          <varlistentry>
     914            <term>
     915              <guilabel>Created</guilabel>
     916            </term>
     917            <listitem>
     918              <para>
     919                A date should be provided. The information can be important when
     920                running quality controls on data and account for potential
     921                confounding factor (e.g. to account for a day effect)
     922              </para>
     923            </listitem>
     924          </varlistentry>
     925
     926          <varlistentry>
     927            <term>
     928              <guilabel>Registered</guilabel>
     929            </term>
     930            <listitem>
     931              <para>
     932                This field is automatically populated with a date at which the
     933                hybridization was entered in BASE2 system.
     934              </para>
     935            </listitem>
     936          </varlistentry>
     937
     938          <varlistentry>
     939            <term>
     940              <guilabel>Protocol</guilabel>
     941            </term>
     942            <listitem>
     943              <para>
     944                The hybridization protocol that was used to do the hybridization.
     945              </para>
     946            </listitem>
     947          </varlistentry>
     948
     949          <varlistentry>
     950            <term>
     951              <guilabel>Hardware</guilabel>
     952            </term>
     953            <listitem>
     954              <para>
     955                The hybridization-station that was used during the hybridization.
     956              </para>
     957            </listitem>
     958          </varlistentry>
     959
     960          <varlistentry>
     961            <term>
     962              <guilabel>Array slide</guilabel>
     963            </term>
     964            <listitem>
     965              <para>The array slide that was used in the hybridization.</para>
     966              <note>
     967                <para>
     968                  Ideally, The Array Slides should have been created but for those
     969                  users with permission to do, Array Slides could be generated at
     970                  that point.
     971                </para>
     972              </note>
     973            </listitem>
     974          </varlistentry>
     975
     976          <varlistentry>
     977            <term>
     978              <guilabel>Description</guilabel>
     979            </term>
     980            <listitem>
     981              <para>
     982                A free text field to report any information that can not be captured
     983                otherwise
     984              </para>
     985            </listitem>
     986          </varlistentry>
     987        </variablelist>
     988        <figure id="write_docbook_doc.figures.hybridization-tab-1">
     989          <title>Hybridization tab</title>
     990          <screenshot>
     991            <mediaobject>
     992              <imageobject>
     993                <imagedata contentwidth="12cm" width="12cm"
     994                  fileref="figures/hybridization-tab-1.png" format="PNG" />
     995              </imageobject>
     996            </mediaobject>
     997          </screenshot>
     998        </figure>
     999      </sect3>
     1000      <sect3 id="biomaterials.hybridizations.properties.labeledextracts">
     1001        <title>Labeled extracts</title>
     1002        <figure id="write_docbook_doc.figures.hybridization-tab-2">
     1003          <title>Labeled Extract tab</title>
     1004          <screenshot>
     1005            <mediaobject>
     1006              <imageobject>
     1007                <imagedata contentwidth="12cm" width="12cm"
     1008                  fileref="figures/hybridization-tab-2.png" format="PNG" />
     1009              </imageobject>
     1010            </mediaobject>
     1011          </screenshot>
     1012        </figure>
     1013        <para>
     1014          This important tab allows users to select the labeled extracts applied to an
     1015          array slide, and specify the amount of material used, expressed in microgram.
     1016        </para>
     1017        <para>
     1018          Use the buttons to the right for adding and removing the items in the list.
     1019          Select one or several labeled extracts in the list and write the used mass in
     1020          the field below.
     1021        </para>
     1022      </sect3>
     1023      <sect3 id="biomaterials.hybridizations.properties.annotations_param">
     1024        <title>Annotations &amp; parameters</title>
     1025        <para>
     1026          As seen in the biosource and sample sections, this tab allows users to supply
     1027          further information about the hybridization provided annotation types have been
     1028          defined or shared to annotate hybridization items.
     1029        </para>
     1030        <important>
    15461031          <para>
    1547             Select at least one Labeled Extract by ticking to selection boxes before the
    1548             name field.
     1032            In order to use this feature, annotation type must be declared and made
     1033            available. To learn more about annotation types and how these are set,
     1034            please refer to
     1035            <xref linkend="annotations" />
    15491036          </para>
    1550           <para>
    1551             Click on the
    1552             <guibutton>New hybridzation (to be changed)</guibutton>
    1553             from the menu bar of Labeled Extract list view.
    1554           </para>
    1555           <figure id="write_docbook_doc.figures.hyb-create-labeledlistview">
    1556             <title>Creating a Hybridization from the Labeled Extract List View</title>
    1557             <screenshot>
    1558               <mediaobject>
    1559                 <imageobject>
    1560                   <imagedata contentwidth="12cm" width="12cm"
    1561                     fileref="figures/hyb-create-labeledlistview.png" format="PNG" />
    1562                 </imageobject>
    1563               </mediaobject>
    1564             </screenshot>
    1565           </figure>
    1566         </listitem>
    1567         <listitem>
    1568           <para>Creating Hybridization from the Labeled Extract Item View page</para>
    1569           <para>
    1570             After having selected a Labeled Extract and displayed it in the Item View,
    1571             Click on the
    1572             <guibutton>New hybridization</guibutton>
    1573             button from the Menu bar of the Labeled Extract Item View.
    1574           </para>
    1575           <figure id="write_docbook_doc.figures.hyb-create-labeleditemview">
    1576             <title>Creating a Hybridization from the Labeled Extract Item View</title>
    1577             <screenshot>
    1578               <mediaobject>
    1579                 <imageobject>
    1580                   <imagedata contentwidth="12cm" width="12cm"
    1581                     fileref="figures/hyb-create-labeleditemview.png" format="PNG" />
    1582                 </imageobject>
    1583               </mediaobject>
    1584             </screenshot>
    1585           </figure>
    1586         </listitem>
    1587         <listitem>
    1588           <para>Creating Hybridizations from the Hybridization List View page</para>
    1589           <para>
    1590             Hybridizations can be created directly using the Hybridization create page.
    1591             To do so, go to
    1592             <menuchoice>
    1593               <guimenu>View</guimenu>
    1594               <guimenuitem>Hybridizations</guimenuitem>
    1595             </menuchoice>
    1596             , Click on &gbNew;
    1597           </para>
    1598           <figure id="write_docbook_doc.figures.hyb-create">
    1599             <title>Creating Hybridizations from the Hybridization List View</title>
    1600             <screenshot>
    1601               <mediaobject>
    1602                 <imageobject>
    1603                   <imagedata contentwidth="12cm" width="12cm"
    1604                     fileref="figures/hyb-create.png" format="PNG" />
    1605                 </imageobject>
    1606               </mediaobject>
    1607             </screenshot>
    1608           </figure>
    1609           <para>
    1610             Irrespective of the methods chosen to create the Hybridization item, A
    1611             'Create' pop-up window will open. It contains 4 distinct tabs:
    1612             <guilabel>Hybridization</guilabel>
    1613             ,
    1614             <guilabel>Parents</guilabel>
    1615             ,
    1616             <guilabel>Annotations &amp; parameters</guilabel>
    1617             and
    1618             <guilabel>Inherited Annotations</guilabel>
    1619             .
    1620           </para>
    1621           <itemizedlist>
    1622             <listitem>
    1623               <para>The Hybridization Tab</para>
    1624 
    1625               <variablelist>
    1626                 <varlistentry>
    1627                   <term>
    1628                     <interface>Name</interface>
    1629                   </term>
    1630                   <listitem>
    1631                     <para>
    1632                       New Hybridization is BASE2 default name but it is
    1633                       strongly advise to provide a meaningful and unique name
    1634                       as it matters for tab2mage export to function properly.
    1635                     </para>
    1636                     <para>
    1637                       There are 5 optional fields to provide more detailed
    1638                       information
    1639                     </para>
    1640 
    1641                   </listitem>
    1642                 </varlistentry>
    1643 
    1644                 <varlistentry>
    1645                   <term>
    1646                     <guilabel>Created</guilabel>
    1647                   </term>
    1648                   <listitem>
    1649                     <para>
    1650                       A date should be provided. The information can be
    1651                       important when running quality controls on data and
    1652                       account for potential confounding factor (e.g. to
    1653                       account for a day effect)
    1654                     </para>
    1655                   </listitem>
    1656                 </varlistentry>
    1657 
    1658                 <varlistentry>
    1659                   <term>
    1660                     <guilabel>Protocol</guilabel>
    1661                   </term>
    1662                   <listitem>
    1663                     <para>
    1664                       This is a controled field. A select-list displays
    1665                       protocol whose type is '
    1666                       <guilabel>hybridization</guilabel>
    1667                       ' and which are shared to or owned by the logged-in
    1668                       user.
    1669                     </para>
    1670                     <important>
    1671                       <para>
    1672                         Reporting Protocols should be viewed as a MIAME
    1673                         requirement
    1674                       </para>
    1675                     </important>
    1676                   </listitem>
    1677                 </varlistentry>
    1678 
    1679                 <varlistentry>
    1680                   <term>
    1681                     <guilabel>Hardware</guilabel>
    1682                   </term>
    1683                   <listitem>
    1684                     <para>
    1685                       This is a controled field. A select-list displays
    1686                       Hardware whose type is '
    1687                       <guilabel>Hybridization station</guilabel>
    1688                       ' and which are shared to or owned by the logged-in
    1689                       user.
    1690                     </para>
    1691                   </listitem>
    1692                 </varlistentry>
    1693 
    1694                 <varlistentry>
    1695                   <term>
    1696                     <guilabel>Array Slide</guilabel>
    1697                   </term>
    1698                   <listitem>
    1699                     <para>
    1700                       This is meant to specify the actual microarray slide.
    1701                     </para>
    1702                     <note>
    1703                       <para>
    1704                         Ideally, The Array Slides should have been created
    1705                         but for those users with permission to do, Array
    1706                         Slides could be generated at that point.
    1707                       </para>
    1708                     </note>
    1709                   </listitem>
    1710                 </varlistentry>
    1711 
    1712                 <varlistentry>
    1713                   <term>
    1714                     <guilabel>Description</guilabel>
    1715                   </term>
    1716                   <listitem>
    1717                     <para>
    1718                       A free text field to report any information that can not
    1719                       be captured otherwise
    1720                     </para>
    1721                   </listitem>
    1722                 </varlistentry>
    1723 
    1724                 <varlistentry>
    1725                   <term>
    1726                     <guilabel>Registered</guilabel>
    1727                   </term>
    1728                   <listitem>
    1729                     <para>
    1730                       This 7th field is automatically populated with a date at
    1731                       which the sample was entered in BASE2 system.
    1732                     </para>
    1733                   </listitem>
    1734                 </varlistentry>
    1735               </variablelist>
    1736 
    1737               <figure id="write_docbook_doc.figures.hybridization-tab-1">
    1738                 <title>Hybridization tab</title>
    1739                 <screenshot>
    1740                   <mediaobject>
    1741                     <imageobject>
    1742                       <imagedata contentwidth="12cm" width="12cm"
    1743                         fileref="figures/hybridization-tab-1.png" format="PNG" />
    1744                     </imageobject>
    1745                   </mediaobject>
    1746                 </screenshot>
    1747               </figure>
    1748             </listitem>
    1749             <listitem>
    1750               <para>The Labeled Extract Tab</para>
    1751               <para>
    1752                 This important tab allows users to select the Labeled Extracts
    1753                 applied to an Array Slide, and specify the amount of material used,
    1754                 expressed in microgram.
    1755               </para>
    1756               <figure id="write_docbook_doc.figures.hybridization-tab-2">
    1757                 <title>Labeled Extract tab</title>
    1758                 <screenshot>
    1759                   <mediaobject>
    1760                     <imageobject>
    1761                       <imagedata contentwidth="12cm" width="12cm"
    1762                         fileref="figures/hybridization-tab-2.png" format="PNG" />
    1763                     </imageobject>
    1764                   </mediaobject>
    1765                 </screenshot>
    1766               </figure>
    1767             </listitem>
    1768             <listitem>
    1769               <para>Annotations &amp; parameters</para>
    1770               <para>
    1771                 As seen in the BioSource and Sample sections, this tab allows users
    1772                 to supply further information about the hybridization provided
    1773                 annotation types have been defined or shared to annotate
    1774                 Hybridization items. The display of Annotation Types can be filtered
    1775                 based on the Annotation Type Category they belong to.
    1776               </para>
    1777               <important>
    1778                 <para>
    1779                   In order to use this feature, Annotation Type must be declared
    1780                   and made available. To learn more about Annotation Types, please
    1781                   refer to
    1782                   <xref linkend="annotations" />
    1783                 </para>
    1784               </important>
    1785               <para>
    1786                 To provide a value for a given annotation type, simply click on it
    1787                 and use the input field or select a value from the drop-down lists
    1788                 or radio buttons.
    1789               </para>
    1790               <para>
    1791                 A caption also reminds users if Annotation Types are parameters
    1792                 <inlinemediaobject>
    1793                   <imageobject>
    1794                     <imagedata fileref="figures/parameter.gif" format="GIF" />
    1795                   </imageobject>
    1796                 </inlinemediaobject>
    1797                 and if annotation values have already been supplied, marked by the
    1798                 <inlinemediaobject>
    1799                   <imageobject>
    1800                     <imagedata fileref="figures/annotated.gif" format="GIF" />
    1801                   </imageobject>
    1802                 </inlinemediaobject>
    1803                 logo.
    1804               </para>
    1805               <figure id="write_docbook_doc.figures.hybridization-tab-3">
    1806                 <title>Annotations &amp; parameters</title>
    1807                 <screenshot>
    1808                   <mediaobject>
    1809                     <imageobject>
    1810                       <imagedata contentwidth="12cm" width="12cm"
    1811                         fileref="figures/hybridization-tab-3.png" format="PNG" />
    1812                     </imageobject>
    1813                   </mediaobject>
    1814                 </screenshot>
    1815               </figure>
    1816             </listitem>
    1817             <listitem>
    1818               <para>Inherited Annotations</para>
    1819               <para>
    1820                 The next screenshot shows a typical view of the functionality.
    1821               </para>
    1822               <figure id="write_docbook_doc.figures.hybridization-tab-4">
    1823                 <title>Inherited Annotations</title>
    1824                 <screenshot>
    1825                   <mediaobject>
    1826                     <imageobject>
    1827                       <imagedata contentwidth="12cm" width="12cm"
    1828                         fileref="figures/hybridization-tab-4.png" format="PNG" />
    1829                     </imageobject>
    1830                   </mediaobject>
    1831                 </screenshot>
    1832               </figure>
    1833               <para>
    1834                 Note the tags used to distinguish between Annotation Types which are
    1835                 parameters noted
    1836                 <inlinemediaobject>
    1837                   <imageobject>
    1838                     <imagedata fileref="figures/parameter.gif" format="GIF" />
    1839                   </imageobject>
    1840                 </inlinemediaobject>
    1841                 and those which are Biomaterial Characteristics,noted
    1842                 <inlinemediaobject>
    1843                   <imageobject>
    1844                     <imagedata fileref="figures/annotation.gif" format="GIF" />
    1845                   </imageobject>
    1846                 </inlinemediaobject>
    1847               </para>
    1848             </listitem>
    1849           </itemizedlist>
    1850         </listitem>
    1851       </orderedlist>
    1852     </sect2>
    1853     <sect2 id="hybridization.manage.viewedit">
    1854       <title>Viewing/Editing Hybridizations</title>
    1855       <para>
    1856         As for other items in BASE2, Hybridizations can be edited. To do so, do the
    1857         following
    1858       </para>
    1859       <itemizedlist>
    1860         <listitem>
    1861           <para>
    1862             Press and hold one of the
    1863             <keycap>CTRL</keycap>
    1864             ,
    1865             <keycap>ALT</keycap>
    1866             or
    1867             <keycap>SHIFT</keycap>
    1868             keys while clicking on the name of an Hybridization Item, which is a live
    1869             link.
    1870           </para>
    1871         </listitem>
    1872         <listitem>
    1873           <para>
    1874             Alternately, navigating to the Hybridization Item View, one can hit the
    1875             <guibutton>Edit</guibutton>
    1876             to performed the task.
    1877           </para>
    1878         </listitem>
    1879 
    1880         <listitem>
    1881           <para>
    1882             The Hybridization item View summarizes key information such as the list of
    1883             <guilabel>Labeled Extracts</guilabel>
    1884             , and the list of associated
    1885             <guilabel>Scans</guilabel>
    1886             . Both are available as hyperlinks to allow quick and easy navigation.
    1887           </para>
    1888           <figure id="write_docbook_doc.figures.hybridization-itemview">
    1889             <title>Hardware Item View</title>
    1890             <screenshot>
    1891               <mediaobject>
    1892                 <imageobject>
    1893                   <imagedata contentwidth="10cm" width="10cm"
    1894                     fileref="figures/hybridization-itemview.png" format="PNG" />
    1895                 </imageobject>
    1896               </mediaobject>
    1897             </screenshot>
    1898           </figure>
    1899         </listitem>
    1900       </itemizedlist>
    1901 
    1902     </sect2>
    1903 
    1904     <sect2 id="hybridization.manage.delete">
    1905       <title>Deleting/Restoring Hybridizations</title>
    1906       <para>
    1907         As for other items in BASE2, Hybridizations can be deleted. For a generic overview
    1908         on how to delete and restore items, refer to section
    1909         <xref linkend="webclient.items.delete" />
    1910       </para>
    1911 
    1912       <para>To delete, do the following</para>
    1913       <itemizedlist>
    1914         <listitem>
    1915           <para>
    1916             Select one or more Hybridization Items and click on the &gbDelete; button in
    1917             the menu bar.
    1918           </para>
    1919           <para>
    1920             All the selected Hybridizations have been marked as deleted and are no
    1921             longer available from the interface.
    1922           </para>
    1923           <para>
    1924             Only by selecting from the
    1925             <guilabel>view/preset&hellip;</guilabel>
    1926             select box the
    1927             <guilabel>Removed</guilabel>
    1928             option, one can see those of the Hybridizations earmarked for deletion. They
    1929             will be shown with a symbol in front of them.
    1930           </para>
    1931         </listitem>
    1932         <listitem>
    1933           <para>
    1934             Alternately, navigating to the Hybridization Item View, one can hit the
    1935             &gbDelete; to performed the task. As shown in the next picture, the
    1936             Hybridization is then marked with the
    1937             <inlinemediaobject>
    1938               <imageobject>
    1939                 <imagedata fileref="figures/deleted.gif" format="GIF" />
    1940               </imageobject>
    1941             </inlinemediaobject>
    1942             <guilabel>This item has been flagged for deletion</guilabel>
    1943           </para>
    1944           <figure id="write_docbook_doc.figures.hybridization-delete">
    1945             <title>Deleting Hybridizations from the Hybridization Item View</title>
    1946             <screenshot>
    1947               <mediaobject>
    1948                 <imageobject>
    1949                   <imagedata contentwidth="10cm" width="10cm"
    1950                     fileref="figures/hybridization-delete.png" format="PNG" />
    1951                 </imageobject>
    1952               </mediaobject>
    1953             </screenshot>
    1954           </figure>
    1955         </listitem>
    1956       </itemizedlist>
    1957       <important>
    1958         <para>
    1959           To really delete an item from the database you must use the trashcan. Items
    1960           deleted from the Trashcan can not be recovered. To learn more about the trashcan
    1961           function, please refer to
    1962           <xref linkend="trashcan" />
    1963         </para>
    1964       </important>
     1037        </important>
     1038      </sect3>
     1039      <sect3 id="biomaterials.hybridizations.properties.inherited">
     1040        <title>Inherited annotations</title>
     1041        <para>
     1042          This tab contains a list of those annotations that are inherited from the
     1043          labeled extracts. Information about dealing with innherited annotations can be
     1044          found in
     1045          <xref linkend="annotations.inheriting" />
     1046          .
     1047        </para>
     1048      </sect3>
    19651049    </sect2>
    19661050  </sect1>
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