Changeset 6961


Ignore:
Timestamp:
Oct 1, 2015, 1:23:03 PM (6 years ago)
Author:
Nicklas Nordborg
Message:

References #1941: Store experimental factor values as part experiments

Updated documentation and screen shots related to the new functionality.

Location:
trunk/doc/src/docbook
Files:
4 added
5 edited

Legend:

Unmodified
Added
Removed
  • trunk/doc/src/docbook/user/annotations.xml

    r6805 r6961  
    644644
    645645      <para>
    646         Click on an entry in the list of annotation types to show a
    647         form for entering a value for it to the right. Depending
     646        All possible annotation types are listed under the
     647        <guilabel>Primary annotations</guilabel> section. Click
     648        on an entry in the list to display a form for entering
     649        a value for the annotation. Depending
    648650        on the options set on the annotation type the form may be a simple
    649651        free text field, a list of checkboxes or radiobuttons, or
     
    652654     
    653655      <para>
    654         Annotation types with an <guilabel>X</guilabel> in front
     656        Annotation types with an <guilabel>x</guilabel> in front
    655657        of their names already have a value.
    656658      </para>
     
    659661        Annotation types marked with angle brackets
    660662        <nohelp>
    661           (<guiicon>
    662             <inlinemediaobject>
    663               <imageobject><imagedata fileref="figures/parameter.png" format="PNG"
    664               /></imageobject>
    665             </inlinemediaobject>
    666           </guiicon>)
     663          (<guiicon><inlinemediaobject><imageobject><imagedata fileref="figures/parameter.png" format="PNG"
     664              /></imageobject></inlinemediaobject></guiicon>)
    667665        </nohelp>
    668666        are protocol parameters.
     
    696694      </para>
    697695     
     696     
    698697      <seeother>
    699         <other external_id="annotations.edit.inherited">Inherit annotations</other>
     698        <other external_id="annotations.inherit">Inherit annotations</other>
    700699      </seeother>
    701700     
     
    705704      <title>Inheriting annotations from other items</title>
    706705     
    707       <helptext external_id="annotations.edit.inherited"
     706      <helptext external_id="annotations.inherit"
    708707        title="Inherit annotations">
    709708        <para>
     
    712711          it was created from. This is an important feature to make the
    713712          experimental factors work. Annotations that should be used as
    714           experimental factors must be inherited to the raw bioassay level.
     713          experimental factors must be inherited to the root raw bioassay level.
    715714          <nohelp>See <xref linkend="experiments_analysis.experiment.factors" /> for more
    716           information about experimental factors.</nohelp>
    717         </para>
     715          information about experimental factors.</nohelp> Click on the
     716          <guibutton>Inherit&hellip;</guibutton> button to open a dialog for inheriting
     717          annotations.
     718        </para>
     719       
     720        <para>
     721          Annotations can either be inherited by reference (the default) or as a cloned value. Inheriting
     722          by reference means that if you change the value of the source annotation the new value is automatically
     723          picked up by all items inheriting it. A cloned annotation is a copy
     724          of the original annotation and it is not automatically updated if the original
     725          annotation is modified.
     726        </para>
     727       
     728        <para>
     729          Inherited and cloned annotations are listed under the <guilabel>Inherited &amp; cloned</guilabel>
     730          section. Inherited annotations are marked with <guiicon><inlinemediaobject><imageobject><imagedata
     731            fileref="figures/inherited.png" format="PNG"
     732            /></imageobject></inlinemediaobject></guiicon> and are always a references back to the original
     733          value. Cloned annotations are marked with a double <guilabel>xx</guilabel>. Cloned annotations
     734          that are out-of-sync with their source annotations are marked with <guiicon><inlinemediaobject><imageobject><imagedata
     735            fileref="figures/cloned-outofsync.png" format="PNG"
     736            /></imageobject></inlinemediaobject></guiicon>.
     737        </para>
     738       
     739        <variablelist>
     740          <varlistentry>
     741            <term>
     742              <guilabel>Inherit...</guilabel>
     743            </term>
     744            <listitem>
     745              <para>Opens the <guilabel>Inherit annotations</guilabel> dialog (see below).</para>
     746            </listitem>
     747          </varlistentry>
     748          <varlistentry>
     749            <term>
     750              <guilabel>Delete</guilabel>
     751            </term>
     752            <listitem>
     753              <para>
     754                Will remove values from the checked primary annotations and delete
     755                links to inherited and cloned annotations.
     756              </para>
     757            </listitem>
     758          </varlistentry>
     759          <varlistentry>
     760            <term>
     761              <guilabel>Sync, Clone, Unclone</guilabel>
     762            </term>
     763            <listitem>
     764              <para>
     765                Convert between INHERITED and CLONED annotation and synchronizes
     766                cloned annotations with their source annotation in case the values
     767                have changed.
     768              </para>
     769            </listitem>
     770          </varlistentry>
     771        </variablelist>
    718772       
    719773        <nohelp>
     
    733787   
    734788        <para>
    735           On this screen is a tree-like structure in two levels. The first level
    736           lists all parent items which has at least one annotations. The second
     789          In this dialog there is a tree-like structure in two levels to the left.
     790          The first level
     791          lists all parent items which has at least one annotation. The second
    737792          level lists the annotations and protocol parameters for the item.
    738793          Selecting an item in the first level will inherit all annotations
    739           from that item, including those that you maybe add later.
    740           Selecting an annotation or protocol parameter at the second level
    741           will inherit only the selected one.
     794          from that item. Selecting an annotation or protocol parameter at
     795          the second level will inherit only the selected one.
    742796        </para>
    743797       
     
    757811          <listitem>
    758812            <para>
    759             The inheritance is implemented by reference. This means that if
    760             you change the value of an annotation the new value is automatically
    761             picked up by those inheriting it.
    762             </para>
    763           </listitem>
    764           <listitem>
    765             <para>
    766             You cannot inherit annotations from an item which does not have
    767             annotations.
     813            Already inherited annotations are not shown in the dialog.
     814            </para>
     815          </listitem>
     816          <listitem>
     817            <para>
     818            By default, the inheritance is implemented by reference. To convert
     819            it to a cloned annotation select it in the list and click on <guilabel>clone</guilabel>.
     820            <nohelp>
     821            <figure>
     822              <title>Convert to a cloned annotation</title>
     823              <screenshot>
     824                <mediaobject>
     825                  <imageobject>
     826                    <imagedata
     827                      fileref="figures/clone_annotation.png" format="PNG" />
     828                  </imageobject>
     829                </mediaobject>
     830              </screenshot>
     831            </figure>
     832            </nohelp>
     833
    768834            </para>
    769835          </listitem>
     
    845911            <para>
    846912              For each annotation type you can select if you want to
    847               <guilabel>inherit</guilabel> new annotations or <guilabel>remove</guilabel>
    848               existing inherited annotations. It is possible to use different
     913              <guilabel>inherit</guilabel> or <guilabel>clone</guilabel> new annotations,
     914              <guilabel>remove</guilabel> existing inherited annotations or
     915              <guilabel>resync</guilabel> existing cloned annotation. It is possible to use different
    849916              actions for different annotation types.
    850917            </para>
  • trunk/doc/src/docbook/user/experiments.xml

    r5800 r6961  
    291291        To be able to use the values of the experimental factors
    292292        in the analysis of your data the values must be accessible
    293         from the raw bioassays. Since most of your annotations are
    294         probably made at the sample or biosource level the raw bioassays
    295         must inherit those annotations.
    296         <nohelp>Read <xref linkend="annotations.inheriting" />
    297         for more information about this.</nohelp>
    298       </para>
    299      
     293        from the <guilabel>root raw bioassays</guilabel>. A root raw bioassay
     294        is a wrapper around a raw bioassay that is part of the experiment and
     295        it has two purposes:
     296      </para>
     297     
     298      <itemizedlist>
     299        <listitem>
     300          <para>
     301          Hold experimental factor values for the raw bioassay in the
     302          context of the current experiment without affecting other
     303          experiments were the same raw bioassay is used.
     304          </para>
     305        </listitem>
     306        <listitem>
     307          <para>
     308          Give the owner of the experiment control over the experimental factor
     309          values used. In a multi-project setting this is important since the
     310          owner of the raw bioassay may not permit changes to the raw bioassay.
     311          Use the <guilabel>clone</guilabel> feature when inheriting
     312          annotations to the root raw bioassay to make sure that downstream
     313          analysis is not affected by changes made to the original parent
     314          annotations (unless you do a manual <guilabel>resync</guilabel>).
     315          </para>
     316        </listitem>
     317      </itemizedlist>
     318       
     319      <para>
     320        Since most of your annotations are probably made at the sample or biosource
     321        level the root raw bioassays must inherit or clone those annotations.
     322        The experiment view page lists all experimental factors and their current
     323        values for each root raw bioassay.
     324      </para>
     325
     326      <para>
     327        There is a quick access to the <link linkend="annotations.batch-inherit">batch inherit</link>
     328        function that makes it easy to inherit any annotations that are missing.
     329        <nohelp>See also <xref linkend="annotations.inheriting" /> for more information about inheriting annotations.</nohelp>
     330      </para>
     331     
     332      <nohelp>
     333      <figure id="experiments_analysis.figures.experiment_factor_values">
     334        <title>Experimental factor values</title>
     335        <screenshot>
     336          <mediaobject>
     337            <imageobject><imagedata
     338              fileref="figures/experiment_factor_values.png" format="PNG"
     339              /></imageobject>
     340          </mediaobject>
     341        </screenshot>
     342      </figure>
     343      </nohelp>
     344
    300345      <tip>
    301346        <para>
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