source: trunk/doc/src/docbook/userdoc/biomaterials.xml @ 4477

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  Copyright (C) 2007 Peter Johansson, Nicklas Nordborg, Philippe Rocca-Serra, Martin Svensson
  
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<chapter id="biomaterials">
  <?dbhtml dir="biomaterials"?>
  <title>Biomaterials</title>
  <sect1 id="biomaterial.introduction">
    <title>Introduction</title>
    <para>
      The generic term biomaterial refers to any biological material used in an experiment.
      biomaterials are subdivided in 4 components, biosource, sample, extract and labeled
      extract. The order use in presenting those entities is not inocuous as it represents the
      sequence of transformation a source material undergoes until it is in a state compatible
      with the realization of a microarray hybridization. This progression is actually
      mimicked in the BASE2
      <guimenu>View</guimenu>
      menu again to insist on this natural progression.
    </para>
    <itemizedlist>
      <listitem>
        <simpara>
          Biosources correspond to the native biological entity used in an experiment
          prior to any treatment.
        </simpara>
      </listitem>
      <listitem>
        <simpara>
          Samples are central to BASE2 to describe the sample processing. So samples can
          be created from other samples if user want to track sample processing event in a
          finely granular fashion.
        </simpara>
      </listitem>
      <listitem>
        <simpara>
          Extracts correspond to nucleic acid material extracted from a tissue sample or a
          cell culture sample.
        </simpara>
      </listitem>
      <listitem>
        <simpara>
          Labeled extracts correspond to nucleic acid materials which have undergone a
          marking procedure using a fluorescent or radioactive compound for detection in a
          microarray assay.
        </simpara>
      </listitem>
    </itemizedlist>
    <para>
      BASE2 allows users to create any of the these entities fairly freely, however it is
      expected that users will follow the natural path of the laboratory workflow.
    </para>
    <tip>
      <para>
        It is highly recommended that you have read
        <xref linkend="webclient.items" />
        before continuing with this chapter.
      </para>
    </tip>
  </sect1>
  <sect1 id="biomaterials.biosources">
    <title>Biosources</title>


    <sect2 id="biomaterials.biosources.properties">
      <title>Properties</title>
      <sect3 id="biomaterials.biosources.properties.biosource">
        <title>Biosource</title>
        <para>This tab allows users to enter essential information about a biosource.</para>
        <variablelist>
          <varlistentry>
            <term>
              <guilabel>Name</guilabel>
            </term>
            <listitem>
              <para>
                This is the only mandatory field. BASE2 by default assigns
                <replaceable>New biosource</replaceable>
                as name but it is advised to provide unique sensible names.
              </para>
            </listitem>
          </varlistentry>
          <varlistentry>
            <term>
              <guilabel>External ID</guilabel>
            </term>
            <listitem>
              <para>
                An external reference identifiers (e.g. a patient identification
                code) can be supplied using this field.
              </para>
            </listitem>
          </varlistentry>
          <varlistentry>
            <term>
              <guilabel>Description</guilabel>
            </term>
            <listitem>
              <para>A free text description can be supplied using this field.</para>
            </listitem>
          </varlistentry>
        </variablelist>
        <figure id="write_docbook_doc.figures.biosource-tab-1">
          <title>Biosource properties</title>
          <screenshot>
            <mediaobject>
              <imageobject>
                <imagedata 
                  fileref="figures/biosource-tab-1.png" format="PNG" />
              </imageobject>
            </mediaobject>
          </screenshot>
        </figure>
      </sect3>
      <sect3 id="biomaterials.biosource.properties.annotations">
        <title>Annotations</title>
        <para>
          This allows BASE2 users to use annotation types to refine biosource description.
          More about annotating items can be read in
          <xref linkend="annotations.annotating" />
          .
        </para>
      </sect3>
    </sect2>
  </sect1>
  <sect1 id="biomaterial.samples">
    <title>Samples</title>
    <para>
      Samples result from processing events applied to biosource material or other samples
      before they are turned into an extract. In other words, samples can be created from
      biosource items or from one or more sample items.When a sample is created from several
      other samples, a pooling event is performed.
    </para>
    <para>
      For every step of transformation from biosource to sample, it is possible to provide
      information about the protocol used to perform this task. It is not enforced in BASE2
      but it should serve as guidance when devising the granularity of the sample processing
      task. Also, it is good practice to provide protocol information to ensure MIAME
      compliance.
    </para>
    <para>
      Use
      <menuchoice>
        <guimenu>View</guimenu>
        <guimenuitem>Biosource</guimenuitem>
      </menuchoice>
      to get to the list of biosources.
    </para>
    <sect2 id="biomaterials.samples.create">
      <title>Create sample</title>
      <para>
        Beside the common way, using the &gbNew; button, a sample can be created in one of
        the following ways:
        <variablelist>
          <varlistentry>
            <term>from either biosource list- or single view- page.</term>
            <listitem>
              <para>
                No matter how complex the sample processing phase is, at least one
                sample has to be anchored to a biosource. Therefore, a natural way
                to create an sample is to click on
                <guiicon>
                  <inlinemediaobject>
                    <imageobject>
                      <imagedata fileref="figures/add.png" format="PNG" />
                    </imageobject>
                  </inlinemediaobject>
                </guiicon>
                in the sample column of the biosource list view. There is also a
                corresponding button,
                <guibutton>Create sample&hellip;</guibutton>
                in the toolbar when viewing a single biosource.
              </para>
            </listitem>
          </varlistentry>
          <varlistentry>
            <term>from the sample list page</term>
            <listitem>
              <para>
                Pooled samples can also be created by first selecting the parents
                from the list of samples and then press
                <guibutton>Pool&hellip;</guibutton>
                in the toolbar.
              </para>
            </listitem>
          </varlistentry>
        </variablelist>
      </para>
    </sect2>
    <sect2 id="biomaterials.samples.properties">
      <title>Properties</title>
      <sect3 id="biomaterials.samples.properties.sample">
        <title>Sample</title>
        <helptext external_id="sample.edit" title="Edit sample">
          <variablelist>
            <varlistentry>
              <term>
                <guilabel>Name</guilabel>
              </term>
              <listitem>
                <para>
                  The sample's name(required). BASE2 by default assigns names to
                  samples (by suffixing
                  <replaceable>s#</replaceable>
                  when creating a sample from an existing biosource or
                  <replaceable>New Sample</replaceable>
                  otherwise) but it is possible to edit at will.
                </para>
              </listitem>
            </varlistentry>
            <varlistentry>
              <term>
                <guilabel>External ID</guilabel>
              </term>
              <listitem>
                <para>
                  An identification used to identify the sample outside BASE.
                </para>
              </listitem>
            </varlistentry>
            <varlistentry>
              <term>
                <guilabel>Original quantity</guilabel>
              </term>
              <listitem>
                <para>
                  This is meant to report information about the actual mass of
                  sample created.
                </para>
              </listitem>
            </varlistentry>
            <varlistentry>
              <term>
                <guilabel>Created</guilabel>
              </term>
              <listitem>
                <para>
                  A date when the sample was created. The information can be
                  important when running quality controls on data and account for
                  potential confounding factor (e.g. day effect).
                </para>
              </listitem>
            </varlistentry>
            <varlistentry>
              <term>
                <guilabel>Registered</guilabel>
              </term>
              <listitem>
                <para>The date at which the sample was entered in BASE2.</para>
              </listitem>
            </varlistentry>
            <varlistentry>
              <term>
                <guilabel>Protocol</guilabel>
              </term>
              <listitem>
                <para>The protocol used to produce this sample.</para>
              </listitem>
            </varlistentry>
            <varlistentry>
              <term>
                <guilabel>Description</guilabel>
              </term>
              <listitem>
                <para>
                  A text field to report any information that not can be captured
                  otherwise.
                </para>
              </listitem>
            </varlistentry>
          </variablelist>
        </helptext>
        <figure id="write_docbook_doc.figures.biosample-tab-1">
          <title>Sample properties</title>
          <screenshot>
            <mediaobject>
              <imageobject>
                <imagedata 
                  fileref="figures/biosample-tab-1.png" format="PNG" />
              </imageobject>
            </mediaobject>
          </screenshot>
        </figure>
      </sect3>
      <sect3 id="biomaterials.samples.properties.parents">
        <title>Parents</title>
        <helptext external_id="sample.parents" title="Sample's parents">
          <para>
            This is meant to keep track of the sample origin. BASE2 distinguished
            between 2 cases which are controled by the
            <guilabel>Pooled</guilabel>
            radio-button in the edit pop-up window.
          </para>
          <itemizedlist>
            <listitem>
              <para>
                If the parent is a biosource the radio-button is set to
                <guilabel>No</guilabel>
                . This will make the biosource select button active, which allows
                users to point to a biosource from which the sample originates from.
              </para>
            </listitem>
            <listitem>
              <para>
                When the parent is one or several other samples the radio-button is
                set to
                <guilabel>Yes</guilabel>
                . Upon selection, the biosource select button is deactivated and the
                samples box and button are activated. This allows users to specify
                one or more samples to be selected from a sample list view page.
              </para>
            </listitem>
          </itemizedlist>
        </helptext>
      </sect3>
      <sect3 id="biomaterials.samples.properties.annotation_param">
        <title>Annotations &amp; parameters</title>
        <para>
          As seen in the biosource section, this tab allows users to further supply
          information about the sample provided they have defined or shared annotation
          types to annotate sample items.
        </para>
        <para>
          To learn more about annotation types and how to define a value for a type,
          please refer to
          <xref linkend="annotations" />
        </para>
      </sect3>
      <sect3 id="biomaterials.samples.properties.inherited">
        <title>Inherited annotations</title>
        <para>
          This tab contains a list of those annotations that are inherited from the
          sample's parents. Information about working with innherited annotations can be
          found in
          <xref linkend="annotations.inheriting" />
          .
        </para>
      </sect3>
    </sect2>
  </sect1>

  <sect1 id="biomaterials.extracts">
    <title>Extracts</title>
    <para>
      Extract items should be used to describe the events that transform a sample material
      into an extract material. An extract can be created from one sample item or from one or
      more extract items. When an extract is created from several other extracts, a pooling
      event is performed.
    </para>
    <para>
      During the transformation from samples to extracts, it is possible to provide
      information about the protocol used to perform this task. It is not enforced in BASE2
      but it should serve as guidance when devising the granularity of the sample processing
      task. Also, it is good practice to provide protocol information.
    </para>
    <sect2 id="biomaterials.extracts.create">
      <title>Create extract</title>
      <para>
        Beside the common way, using the &gbNew; button, an extract can be created in one of
        the following ways:
        <variablelist>
          <varlistentry>
            <term>from either sample list- or single view- page.</term>
            <listitem>
              <para>
                No matter how complex the extract processing phase is, at least one
                extract has to be anchored to a sample. Therefore, a natural way to
                create an extract is to click on
                <guiicon>
                  <inlinemediaobject>
                    <imageobject>
                      <imagedata fileref="figures/add.png" format="PNG" />
                    </imageobject>
                  </inlinemediaobject>
                </guiicon>
                in the extracts column for the sample that should be a parent of the
                extract.
              </para>
              <para>
                There is also a corresponding button,
                <guibutton>Create extract&hellip;</guibutton>
                in the toolbar when viewing a single sample.
              </para>
            </listitem>
          </varlistentry>
          <varlistentry>
            <term>from the extract list page</term>
            <listitem>
              <para>
                Pooled extract can also be created by first selecting the parents
                from the list of extracts and then press
                <guibutton>Pool&hellip;</guibutton>
                in the toolbar. The selected extracts will be put into the parent
                property.
              </para>
            </listitem>
          </varlistentry>
        </variablelist>
      </para>
    </sect2>
    <sect2 id="biomaterials.extracts.properties">
      <title>Properties</title>
      <sect3 id="biomaterials.extracts.properties.extract">
        <title>Extract</title>
        <helptext external_id="extract.edit" title="Edit extract">
          <variablelist>
            <varlistentry>
              <term>
                <guilabel>Name</guilabel>
              </term>
              <listitem>
                <para>
                  A mandatory field for providing the extract's name. BASE2 by
                  default assigns names to extract (by suffixing
                  <replaceable>e#</replaceable>
                  when creating an extract from an existing sample or
                  <replaceable>New extract</replaceable>
                  otherwise) but it is possible to edit it at will.
                </para>
              </listitem>
            </varlistentry>
            <varlistentry>
              <term>
                <guilabel>External ID</guilabel>
              </term>
              <listitem>
                <para>The extracts identification outside BASE</para>
              </listitem>
            </varlistentry>
            <varlistentry>
              <term>
                <guilabel>Original quantity</guilabel>
              </term>
              <listitem>
                <para>
                  Holds information about the original mass of the created
                  extract.
                </para>
              </listitem>
            </varlistentry>
            <varlistentry>
              <term>
                <guilabel>Created</guilabel>
              </term>
              <listitem>
                <para>
                  The date when the extract was created. The information can be
                  important when running quality controls on data and account for
                  potential confounding factor (e.g. day effect)
                </para>
              </listitem>
            </varlistentry>
            <varlistentry>
              <term>
                <guilabel>Registered</guilabel>
              </term>
              <listitem>
                <para>
                  This is automatically populated with a date at which the sample
                  was entered in BASE2 system.
                </para>
              </listitem>
            </varlistentry>
            <varlistentry>
              <term>
                <guilabel>Protocol</guilabel>
              </term>
              <listitem>
                <para>
                  The extraction protocol that was used to produce the extract.
                </para>
              </listitem>
            </varlistentry>
            <varlistentry>
              <term>
                <guilabel>Description</guilabel>
              </term>
              <listitem>
                <para>
                  A text field to report any information that not can be captured
                  otherwise.
                </para>
              </listitem>
            </varlistentry>
          </variablelist>
        </helptext>
        <figure id="write_docbook_doc.figures.extract-tab-1">
          <title>Extract tab</title>
          <screenshot>
            <mediaobject>
              <imageobject>
                <imagedata 
                  fileref="figures/extract-tab-1.png" format="PNG" />
              </imageobject>
            </mediaobject>
          </screenshot>
        </figure>
      </sect3>

      <sect3 id="biomaterials.extracts.properties.parents">
        <title>Parents</title>
        <helptext external_id="extract.parents" title="Extract's parents">
          <para>
            This important tab allows users to select the extract origin. BASE2
            distinguished between 2 cases which are controled by the
            <guilabel>Pooled</guilabel>
            radio-button.
          </para>
          <itemizedlist>
            <listitem>
              <para>
                If the parent is a sample the radio-button is set to
                <guilabel>No</guilabel>
                . The Sample select button is active and allows users to point to
                the sample from which the sample originates.
              </para>
            </listitem>
            <listitem>
              <para>
                The parent is another extract and the radio-button is set to
                <guilabel>Yes</guilabel>
                . Upon selection, the samples select button is deactivated and the
                extracts box and button are activated. This allows users to specify
                one or more extracts to be selected from an extract list view page.
              </para>
            </listitem>
          </itemizedlist>
        </helptext>
      </sect3>
      <sect3 id="biomaterials.extracts.properties.annotations_param">
        <title>Annotations &amp; parameters</title>
        <para>
          As seen in the biosource and sample sections, this tab allows users to supply
          further information about the extract, provided they have defined annotation
          types to annotation extract items or have such elements shared to them.
        </para>
        <para>
          To learn more about annotation types, please refer to
          <xref linkend="annotations" />
        </para>
      </sect3>
      <sect3 id="biomaterials.extracts.properties.inherited">
        <title>Inherited Annotations</title>
        <para>
          This tab contains a list of those annotations that are inherited from the
          extract's parents. Information about working with innherited annotations can be
          found in
          <xref linkend="annotations.inheriting" />
          .
        </para>
      </sect3>
    </sect2>
  </sect1>

  <sect1 id="biomaterials.labels">
    <title>Labels</title>
    <para>
      Before attempting to create labeled extracts, users should make sure that the
      appropriate label object is present in BASE2. To browse the list of labels, go to
      <menuchoice>
        <guimenu>View</guimenu>
        <guimenuitem>Labels</guimenuitem>
      </menuchoice>
    </para>
    <sect2 id="biomaterials.labels.properties">
      <title>Properties</title>
      <helptext external_id="label.edit" title="Edit label">
        <para>
          The label item is very simple and does not need much explanation. There are only
          two properties for a label
          <variablelist>
            <varlistentry>
              <term>
                <guilabel>Name</guilabel>
              </term>
              <listitem>
                <para>The name of the label(required).</para>
              </listitem>
            </varlistentry>
            <varlistentry>
              <term>
                <guilabel>Description</guilabel>
              </term>
              <listitem>
                <para>
                  An explaining text or other information associated with the
                  label.
                </para>
              </listitem>
            </varlistentry>
          </variablelist>
          .
        </para>
      </helptext>
    </sect2>

  </sect1>
  <sect1 id="biomaterials.labeledextracts">
    <title>Labeled extracts</title>
    <para>
      Labeled extract items should be used to describe the event that transformed an extract
      material in a labeled extract material. Labeled extracts can be created from extract
      items or from one or more labeled extract items. When a labeled extract is created from
      several other labeled extracts, a pooling event is performed.
    </para>
    <para>
      During the transformation from extracts to labeled extracts, it is possible to provide
      information about the protocol used to perform this task. It is not enforced in BASE2
      but it should serve as guidance when devising the granularity of the extract processing
      task. Also, it is good practice to provide protocol information.
    </para>
    <sect2 id="biomaterials.labeledextracts.create">
      <title>Creating labeled extracts</title>
      <para>
        Beside the regular way of using the &gbNew; button in
        <menuchoice>
          <guimenu>View</guimenu>
          <guimenuitem>Labeled extracts</guimenuitem>
        </menuchoice>
        , a labeled extract can be created in one of following ways.
      </para>
      <variablelist>
        <varlistentry>
          <term>pooling selected labeled extracts</term>
          <listitem>
            <para>
              The toolbar at the list page of labeled extracts contains an addition
              &gbPool; button. This button allows users to create pooled labeled
              extracts by selecting the list of labeled extracts used to derived a new
              labeled extract and then click on the button.
            </para>
            <para>
              This provides an easy and simple way to create pooled labeled extracts.
              The result of such process is the creation of a new labeled extract, in
              which, when navigating to the parent tab, shows that all the labeled
              extracts involved are already set and listed in the Labeled Extract box
              of the tab.
            </para>
          </listitem>
        </varlistentry>
        <varlistentry>
          <term>from the extract pages.</term>
          <listitem>
            <para>
              Following the laboratory workflow, a natural way to create a labeled
              extract from an extract is to click on the
              <guiicon>
                <inlinemediaobject>
                  <imageobject>
                    <imagedata fileref="figures/add.png" format="PNG" />
                  </imageobject>
                </inlinemediaobject>
              </guiicon>
              from the labeled extract column of the extract list view. Corresponding
              button,
              <guibutton>New labeled extract</guibutton>
              is located on the single item view page for each extract. By creating a
              labeled extract from an extract page will automatically set the extract
              as a parent.
            </para>
          </listitem>
        </varlistentry>
        <varlistentry>
          <term>from single item view of a label</term>
          <listitem>
            <para>
              Click on the
              <guibutton>New labeled extract&hellip;</guibutton>
              to use the current label and create a new labeled extract with it
              pre-selected as
              <guilabel>Label</guilabel>
              .
            </para>
          </listitem>
        </varlistentry>
      </variablelist>
    </sect2>
    <sect2 id="biomaterials.labeledextracts.properties">
      <title>Properties</title>
      <sect3 id="biomaterials.labeledextracts.properties.labeledextract">
        <title>Labeled extract</title>
        <variablelist>
          <varlistentry>
            <term>
              <guilabel>Name</guilabel>
            </term>
            <listitem>
              <para>
                The name of the labeled extract (required). BASE2 by default assigns
                names to labeled extract(by suffixing
                <replaceable>lbe#</replaceable>
                when creating a labeled extract from an existing extract or
                <replaceable>New labeled extract</replaceable>
                otherwise) but it is possible to edit it at will
              </para>
            </listitem>
          </varlistentry>
          <varlistentry>
            <term>
              <guilabel>Label</guilabel>
            </term>
            <listitem>
              <para>
                Used to specify which dye or marker was used in the labeling
                reaction (required).
              </para>
            </listitem>
          </varlistentry>
          <varlistentry>
            <term>
              <guilabel>External ID</guilabel>
            </term>
            <listitem>
              <para>An id used to recognize the labeled extract outside BASE.</para>
            </listitem>
          </varlistentry>
          <varlistentry>
            <term>
              <guilabel>Original quantity</guilabel>
            </term>
            <listitem>
              <para>The mass of labeled extract that was created.</para>
            </listitem>
          </varlistentry>
          <varlistentry>
            <term>
              <guilabel>Created</guilabel>
            </term>
            <listitem>
              <para>
                A date should be provided. The information can be important when
                running quality controls on data and account for potential
                confounding factor (e.g. day effect).
              </para>
            </listitem>
          </varlistentry>
          <varlistentry>
            <term>
              <guilabel>Registred</guilabel>
            </term>
            <listitem>
              <para>
                This is automatically populated with a date at which the labeled
                extract was actually entered in BASE2 system.
              </para>
            </listitem>
          </varlistentry>
          <varlistentry>
            <term>
              <guilabel>Protocol</guilabel>
            </term>
            <listitem>
              <para>
                The labeling protocol that was used to produce the labeled extract.
              </para>
            </listitem>
          </varlistentry>
          <varlistentry>
            <term>
              <guilabel>Description</guilabel>
            </term>
            <listitem>
              <para>
                A free text field to report any information that can not be captured
                otherwise.
              </para>
            </listitem>
          </varlistentry>
        </variablelist>
        <figure id="write_docbook_doc.figures.labeledextract-properties">
          <title>Labeled extract properties</title>
          <screenshot>
            <mediaobject>
              <imageobject>
                <imagedata contentwidth="10cm" width="10cm"
                  fileref="figures/labeledextract-properties.png" format="PNG" />
              </imageobject>
            </mediaobject>
          </screenshot>
        </figure>
      </sect3>
      <sect3 id="biomaterials.labeledextracts.properties.parents">
        <title>Parents</title>
        <para>
          This important tab allows users to select the labeled extract origin. BASE2
          distinguished between 2 cases which are controled by the
          <guilabel>Pooled</guilabel>
          radio-button.
        </para>
        <itemizedlist>
          <listitem>
            <para>The parent is an extract</para>
            <para>
              The radio-button is set to
              <guilabel>No</guilabel>
              . The Extract select button is active and allows users to point to one
              and only one extract from which the labeled extract originates from.
            </para>
          </listitem>
          <listitem>
            <para>The parent is another labeled extract</para>
            <para>
              The radio-button has to be set to
              <guilabel>Yes</guilabel>
              . Upon selection, the extract select button is deactivated and the
              labeled extracts box and button are activated. This allows users to
              specify one or more extracts to be selected from the labeled extract
              list view page.
            </para>
          </listitem>
        </itemizedlist>
      </sect3>
      <sect3 id="biomaterials.labeledextracts.properties.annotations_param">
        <title>Annotations &amp; parameters</title>
        <para>
          As seen in the biosource and sample sections, this tab allows users to further
          supply information about the labeled extract provided they have defined
          annotation types to annotate labeled extract items or have such elements shared
          to them.
        </para>
        <important>
          <para>
            In order to use this feature, annotation type must be declared and made
            available. To learn more about annotation types and how these are set,
            please refer to
            <xref linkend="annotations" />
            .
          </para>
        </important>
      </sect3>
      <sect3 id="biomaterials.labeledextracts.properties.inherited">
        <title>Inherited annotations</title>
        <para>
          This tab contains a list of those annotations that are inherited from the
          parents of the labeled extract. Information about dealing with innherited
          annotations can be found in
          <xref linkend="annotations.inheriting" />
          .
        </para>
      </sect3>
    </sect2>
  </sect1>

  <sect1 id="biomaterials.hybridizations">
    <title>Hybridizations</title>
    <para>
      An hybridization event corresponds to the application of one or more labeled extracts
      materials to a microarray slide under conditions detailed in hybridization protocols.
      Use
      <menuchoice>
        <guimenu>View</guimenu>
        <guimenuitem>Hybridizatons</guimenuitem>
      </menuchoice>
      to get to the hybridizations.
    </para>
    <sect2 id="biomaterials.hybridizations.create">
      <title>Creating hybridizations</title>
      <para>
        In BASE2, there are 2 possible routes to create an hybridization object except the
        common way with the &gbNew; button at hybridization list page.
      </para>
      <variablelist>
        <varlistentry>
          <term>from the labeled extract list view page</term>
          <listitem>
            <para>
              Select at least one labeled extract, to create a hybridization from, by
              ticking the selection boxes before the name field.
            </para>
            <para>
              Click on the
              <guibutton>New hybridzation&hellip;</guibutton>
              from the toolbar of labeled extract list view.
            </para>
          </listitem>
        </varlistentry>
        <varlistentry>
          <term>from a labeled extract single item page</term>
          <listitem>
            <para>
              When viewing a label extract in single item view, click on the
              <guibutton>New hybridization&hellip;</guibutton>
              button from the toolbar of the labeled extract item view.
            </para>
          </listitem>
        </varlistentry>
      </variablelist>
    </sect2>
    <sect2 id="biomaterials.hybridizations.properties">
      <title>Properties</title>

      <sect3 id="biomaterials.hybridizations.hybridization">
        <title>Hybridization</title>
  
        <figure id="write_docbook_doc.figures.hybridization-tab-1">
          <title>Hybridization tab</title>
          <screenshot>
            <mediaobject>
              <imageobject>
                <imagedata 
                  fileref="figures/hybridization-tab-1.png" format="PNG" />
              </imageobject>
            </mediaobject>
          </screenshot>
        </figure> 
        
        <helptext external_id="hybridization.edit" title="Edit hybridization">
        <variablelist>
          <varlistentry>
            <term>
              <guilabel>Name</guilabel>
            </term>
            <listitem>
              <para>
                <replaceable>New hybridization</replaceable>
                is BASE2 default name but it is strongly advise to provide a
                meaningful and unique name (required).
              </para>
            </listitem>
          </varlistentry>
          <varlistentry>
            <term>
              <guilabel>Arrays</guilabel>
            </term>
            <listitem>
              <para>
                The number of sub-arrays on the slide that was used in
                this hybridization. The default value is 1, but some
                platforms, for example Illumina, has slides
                with 6 or 8 arrays.
              </para>
            </listitem>
          </varlistentry>

          <varlistentry>
            <term>
              <guilabel>Created</guilabel>
            </term>
            <listitem>
              <para>
                A date should be provided. The information can be important when
                running quality controls on data and account for potential
                confounding factor (e.g. to account for a day effect)
              </para>
            </listitem>
          </varlistentry>

          <varlistentry>
            <term>
              <guilabel>Registered</guilabel>
            </term>
            <listitem>
              <para>
                This field is automatically populated with a date at which the
                hybridization was entered in BASE2 system.
              </para>
            </listitem>
          </varlistentry>

          <varlistentry>
            <term>
              <guilabel>Protocol</guilabel>
            </term>
            <listitem>
              <para>
                The hybridization protocol that was used to do the hybridization.
              </para>
            </listitem>
          </varlistentry>

          <varlistentry>
            <term>
              <guilabel>Hardware</guilabel>
            </term>
            <listitem>
              <para>
                The hybridization-station that was used during the hybridization.
              </para>
            </listitem>
          </varlistentry>

          <varlistentry>
            <term>
              <guilabel>Array slide</guilabel>
            </term>
            <listitem>
              <para>The array slide that was used in the hybridization.</para>
              <note>
                <para>
                  Ideally, The Array Slides should have been created but for those
                  users with permission to do, Array Slides could be generated at
                  that point.
                </para>
              </note>
            </listitem>
          </varlistentry>

          <varlistentry>
            <term>
              <guilabel>Description</guilabel>
            </term>
            <listitem>
              <para>
                A free text field to report any information that can not be captured
                otherwise
              </para>
            </listitem>
          </varlistentry>
        </variablelist>
        <seeother>
          <other external_id="hybridization.labeledextracts">Labeled extracts</other>
        </seeother>
        </helptext>
        
      </sect3>
      
      <sect3 id="biomaterials.hybridizations.properties.labeledextracts">
        <title>Labeled extracts</title>
        
        <helptext external_id="hybridization.labeledextracts" title="Labeled extracts">
        <para>
          This important tab allows users to select the labeled extracts applied to an
          array slide, and specify the amount of material used, expressed in microgram.
        </para>
        <para>
          Use the <guibutton>Add labeled extracts</guibutton> button to add
          items and the <guibutton>Remove</guibutton> button to remove items.
          Select one or several labeled extracts in the list and write the used 
          mass and sub-array index in the fields below.
        </para>
        
        <seeother>
          <other external_id="hybridization.edit">Edit hybridization</other>
        </seeother>
        </helptext>
        
      </sect3>
      <sect3 id="biomaterials.hybridizations.properties.annotations_param">
        <title>Annotations &amp; parameters</title>
        <para>
          As seen in the biosource and sample sections, this tab allows users to supply
          further information about the hybridization provided annotation types have been
          defined or shared to annotate hybridization items.
        </para>
        <important>
          <para>
            In order to use this feature, annotation type must be declared and made
            available. To learn more about annotation types and how these are set,
            please refer to
            <xref linkend="annotations" />
          </para>
        </important>
      </sect3>
      <sect3 id="biomaterials.hybridizations.properties.inherited">
        <title>Inherited annotations</title>
        <para>
          This tab contains a list of those annotations that are inherited from the
          labeled extracts. Information about dealing with innherited annotations can be
          found in
          <xref linkend="annotations.inheriting" />
          .
        </para>
      </sect3>
    </sect2>
  </sect1>
</chapter>