Changeset 3403


Ignore:
Timestamp:
May 29, 2007, 1:26:33 PM (14 years ago)
Author:
Nicklas Nordborg
Message:

Fixes #533.

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

Legend:

Unmodified
Added
Removed
  • trunk/doc/src/docbook/userdoc/reporters.xml

    r3394 r3403  
    33    "-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN"
    44    "../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd">
    5     <!--
    6      $Id$
    7      
    8      Copyright (C) Authors contributing to this file.
    9      
    10      This file is part of BASE - BioArray Software Environment.
    11      Available at http://base.thep.lu.se/
    12      
    13      BASE is free software; you can redistribute it and/or
    14      modify it under the terms of the GNU General Public License
    15      as published by the Free Software Foundation; either version 2
    16      of the License, or (at your option) any later version.
    17      
    18      BASE is distributed in the hope that it will be useful,
    19      but WITHOUT ANY WARRANTY; without even the implied warranty of
    20      MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    21      GNU General Public License for more details.
    22      
    23      You should have received a copy of the GNU General Public License
    24      along with this program; if not, write to the Free Software
    25      Foundation, Inc., 59 Temple Place - Suite 330,
    26      Boston, MA  02111-1307, USA.
    27     -->               
    28 <chapter id="reporters">
    29 <?dbhtml dir="reporters"?>
    30  <title>Reporters</title>
    31  <sect1 id="reporters.introduction">
    32   <title>Introduction</title>
    33   <para>Reporter, a term coined by the MAGE object model refers to spotted DNA sequence on a
    34    microarray. Reporters are therefore usually described by a sequence and a series of database
    35    identifiers qualifying that sequence. Reporters are generally understood as the thing biologists
    36    are interested in when carrying out DNA microarray experiments.</para>
    37   <para>In BASE2, Reporters also refer to Affymetrix Probeset ID but Reporters can be used to
    38    describe genes, transcripts, exons or any other sequence entity of biological relevance. </para>
    39  </sect1>
    40  <sect1 id="reporters.manage">
    41   <title>Managing Reporters</title>
    42   <para> </para>
    43   <sect2 id="reporters.manage.typecreate">
    44    <title>Creating Reporter Types</title>
    45    <para><guilabel>Reporter Type</guilabel> allows classification of reporters based on their usage
    46     and qualification defined during the array design specification. To create a Reporter Type,</para>
    47    <para>Go To <menuchoice>
    48      <guimenu>Administrate</guimenu>
    49      <guimenuitem>Types</guimenuitem>
    50      <guisubmenu>Reporter Type</guisubmenu>
    51     </menuchoice>
    52    </para>
    53    <para> Click on &gbNew;. </para>
    54    <para>A 'Create' pop-up window opens and allow to fill in <guilabel>Name</guilabel> and
    55      <guilabel>Description</guilabel>
    56    </para>
    57    <important>
    58     <para>It is advised to define the Reporter Type <guilabel>Name</guilabel> attribute so that it
    59      is compatible with the <ulink url="http://www.mged.org/Workgroups/MIAME/miame.html">MIAME
    60       requirements</ulink> and recommendations issues by microarray data repositories. Alternately,
    61      the local reporter type could be submitted to those repositories for term inclusion.</para>
    62    </important>
    63    <figure id="write_docbook_doc.figures.reportertype">
    64     <title>The Reporter Type Create Window</title>
    65     <screenshot>
    66     <mediaobject>
    67      <imageobject>
    68       <imagedata contentwidth="7cm" width="7cm" fileref="figures/reportertype.png" format="PNG"/>
    69      </imageobject>
    70     </mediaobject>
    71    </screenshot>
    72    </figure>
    73    <para> One can classically follow the classification between negative control, positive control
    74     and experimental for simplificity. </para>
    75   </sect2>
    76   <sect2 id="reporters.manage.create">
    77    <title>Creating Reporters</title>
    78    <para>Go to <menuchoice>
    79      <guimenu>View</guimenu>
    80      <guimenuitem>Reporter</guimenuitem>
    81     </menuchoice>
    82    </para>
    83    <para>Click on &gbNew;. </para>
    84    <para> A 'Create' pop-up window opens, it contains 2 tabs: <guilabel>Reporter</guilabel> and
    85      <guilabel>Extended properties</guilabel>. </para>
    86    <itemizedlist>
    87     <listitem>
    88      <para>
    89       <guilabel>Reporter</guilabel>
    90      </para>
    91      <para> This tab shows core information that would be common to all base2 instances. Two
    92       mandatory information fields have to be filled in: <guilabel>Name</guilabel> and
    93        <guilabel>External ID</guilabel> e.g. a database identifier. If one requires additional and
    94       more advanced information about the Reporter, the extended properties tab should be used. </para>
    95      <figure id="write_docbook_doc.figures.reporter-1">
    96       <title>The Reporter tab in the Reporter Create Window</title>
    97       <screenshot>
    98       <mediaobject>
    99        <imageobject>
    100         <imagedata contentwidth="7cm" width="7cm" fileref="figures/reporter-1.png" format="PNG"/>
    101        </imageobject>
    102       </mediaobject>
    103      </screenshot>
    104      </figure>
    105     </listitem>
    106     <listitem>
    107      <para>
    108       <guilabel>Extended properties</guilabel>
    109      </para>
    110      <para>In BASE2, the Reporter Items belong to a special class whose properties used to qualify
    111       them can be defined and extended by system administrators. This is done by modifying the
    112       'extended-properties.xml' file during database configuration or upgrade. The file can be found
    113       under <filename class="directory">
    114       \\apache-tomcat-5.5.15\webapps\base\WEB-INF\classes</filename>. </para>
    115      <important>
    116       <para> For more information about database configuration and upgrade process, please refer to
    117         <xref linkend="installation_upgrade.installation"/>. This allow storing of just the right
    118        amount of information. </para>
    119      </important>
    120      <para> This tab displays all kind of reporter properties as defined in the extended_properties </para>
    121      <figure id="write_docbook_doc.figures.reporter-2">
    122       <title>The extended properties tab from the Reporter Create Window</title>
    123       <screenshot>
    124       <mediaobject>
    125        <imageobject>
    126         <imagedata contentwidth="7cm" width="7cm" fileref="figures/reporter-2.png" format="PNG"/>
    127        </imageobject>
    128       </mediaobject>
    129      </screenshot>
    130      </figure>
    131     </listitem>
    132    </itemizedlist>
    133    <para>Click on the <inlinemediaobject>
    134      <imageobject>
    135       <imagedata fileref="figures/save.gif" format="GIF"/>
    136      </imageobject>
    137     </inlinemediaobject> Save button to store the information in BASE2 or on the <inlinemediaobject>
    138      <imageobject>
    139       <imagedata fileref="figures/cancel.gif" format="GIF"/>
    140      </imageobject>
    141     </inlinemediaobject> button to abort. </para>
    142   </sect2>
    143 
    144   <sect2 id="reporter.manage.viewedit">
    145    <title>Viewing/Editing Reporters</title>
    146    <itemizedlist>
    147     <listitem>
    148      <para> Press and hold one of the <keycap>CTRL</keycap>, <keycap>ALT</keycap> or
    149       <keycap>SHIFT</keycap> keys while clicking on the name of a Reporter Item, which is a live
    150       link. </para>
    151     </listitem>
    152     <listitem>
    153      <para> Alternately, navigating to the Reporter Item View, one can hit the
    154        &gbEdit; to performed the task.</para>
    155      <para>In both cases, an Edit pop-up windows opens. It is essentially identical to a Create
    156       window and allows updating information about a particular ArraySlide item stored in BASE2</para>
    157      <figure id="write_docbook_doc.figures.reporter-itemview">
    158       <title>Reporter Item View</title>
    159       <screenshot>
    160        <mediaobject>
    161         <imageobject>
    162          <imagedata contentwidth="10cm" width="10cm" fileref="figures/reporter-itemview.png" format="PNG"/>
    163         </imageobject>
    164        </mediaobject>
    165       </screenshot>
    166      </figure>
    167     </listitem>
    168 
    169     <listitem>
    170      <para>From the Reporter item View, note the <guilabel>extended properties</guilabel> section
    171       which displays biological information and cross-references to external databases. Depending on
    172       the configuration of the extended properties file, backlinks to primary databases can be
    173       established. In the above picture, note the hyperlinks to <guilabel>OMIM</guilabel> and
    174       Unigene <guilabel>Cluster ID</guilabel></para>
    175     </listitem>
    176    </itemizedlist>
    177   </sect2>
    178 
    179   <sect2 id="reporter.manage.delete">
    180    <title>Deleting Reporters</title>
    181    <para>In BASE2, Reporters are treated differently from other items (e.g BioSources or Protocols).</para>
    182    <para>Deleting Reporters from BASE2 does not mark those items for deletion as for other BASE2
    183     items and do not rely on the Trashcan mechanism.</para>
    184    <important>
    185     <para> This specific handling of Reporters means that deletion events are unrecoverable.
    186      Therefore, pressing the &gbDelete; button will always prompt for a
    187      confirmation message as illustrated below. </para>
    188 
    189     <figure id="write_docbook_doc.figures.reporter-delele-msg">
    190      <title>The Final Warning message when attempting to delete Reporters</title>
    191      <screenshot>
    192     <mediaobject>
    193      <imageobject>
    194       <imagedata contentwidth="7cm" width="7cm" fileref="figures/reporter-delete-msg.png" format="PNG"/>
    195      </imageobject>
    196     </mediaobject>
    197    </screenshot>
    198     </figure>
    199    </important>
    200    <para> Select one or more reporters and click &gbDelete; button in the menu
    201     bar. </para>
    202   </sect2>
    203   <sect2 id="reporter.import">
    204    <title>Importing Reporters from files</title>
    205    <para> Reporters are used to represent genes, transcripts, exons and therefore come in their
    206     thousands. To solve this problem, BASE2 relies on <guilabel>Reporter import plugins</guilabel>.
    207     Those need to be specifically configured to deal with a particular input file. This input file
    208     can be typically be an Axon gal file which is a tab delimited file providing information about
    209     Reporters and their annotations. </para>
    210 
    211    <tip>
    212     <para>As for any other plugin, configuration parameters can be saved as an xml file and
    213      exchanged with another BASE2 instance, thereby reducing configuration burden (provided the 2
    214      instances have identical extended properties xml files). </para>
    215    </tip>
    216 
    217    <para> Dealing with Affymetrix Probesets: </para>
    218    <para> In BASE2, Affymetrix Probesets (when they exist) should be treated as Reporters.</para>
    219    <para> The Affymetrix Probeset ID could be stored in both the name and the reporter external id
    220     fields of the reporter table.</para>
    221    <tip>
    222     <para> Note that Affymetrix serves files containing Annotation about the Probesets ids from the
    223      NetAffx web site. A plugin configuration can be defined to upload these files directly into the
    224      Reporter table provided it has been modified to accomodate the relevant information. In order
    225      to be able to deal with the Affymetrix NetAffx native files (<ulink
    226       url="http://www.affymetrix.com/Auth/analysis/downloads/na22/ivt/HG-U133A_2.na22.annot.csv.zip/"
    227       >Affymetrix HG-133A_2 annotations in csv format</ulink>) one would have to select the
    228      separator as <guilabel>comma between "</guilabel> in order to avoid splitting on 'comma'
    229      present in the Affymetrix annotation file, an event that would alter the import. </para>
    230    </tip>
    231 
    232    <tip>
    233     <para>Storing the Affymetrix Probeset ID should be enough as most analysis tools allow retrieval
    234      of updated information based on the Affymetrix probeset id from web resources. </para>
    235    </tip>
    236 
    237   </sect2>
    238 
    239   <sect2 id="reporterlist.create">
    240    <title>Creating List of Reporters</title>
    241    <para> BASE2 allows for defining sets of reporters for a particular use, for instance to define a
    242     list of reporters to be used on an array. There are 2 ways to do so: </para>
    243    <orderedlist>
    244     <listitem>
    245      <para>From the Reporter ListView page:</para>
    246      <para>Click on the <guibutton>New Reporter List</guibutton> button.</para>
    247      <para/>
    248      <figure id="write_docbook_doc.figures.reporterlist-1">
    249       <title>The ReporterList Create Window called from the Reporter page</title>
    250       <screenshot>
    251       <mediaobject>
    252        <imageobject>
    253         <imagedata contentwidth="7cm" width="7cm" fileref="figures/reporterlist-1.png" format="PNG"/>
    254        </imageobject>
    255       </mediaobject>
    256      </screenshot>
    257      </figure>
    258     </listitem>
    259     <listitem>
    260      <para>From View Menu:</para>
    261      <para>Go to <menuchoice>
    262        <guimenu>View</guimenu>
    263        <guimenuitem>Reporter List</guimenuitem>
    264       </menuchoice>
    265      </para>
    266      <para> Click on &gbNew; button from the ReporterList ListView </para>
    267      <para> A 'Create' pop-up window opens allowing to fill-in Name and a short text description of
    268       the newly created Reporter list </para>
    269      <figure id="write_docbook_doc.figures.reporterlist-2">
    270       <title>The ReporterList Create Window called from the ReporterList page</title>
    271       <screenshot>
    272       <mediaobject>
    273        <imageobject>
    274         <imagedata contentwidth="7cm" width="7cm" fileref="figures/reporterlist-2.png" format="PNG"/>
    275        </imageobject>
    276       </mediaobject>
    277      </screenshot>
    278      </figure>
    279     </listitem>
    280    </orderedlist>
    281    <para>Click on the <inlinemediaobject>
    282      <imageobject>
    283       <imagedata fileref="figures/save.gif" format="GIF"/>
    284      </imageobject>
    285     </inlinemediaobject> Save button to store the information in BASE2 or on the <inlinemediaobject>
    286      <imageobject>
    287       <imagedata fileref="figures/cancel.gif" format="GIF"/>
    288      </imageobject>
    289     </inlinemediaobject> button to abort. </para>
    290   </sect2>
    291  </sect1>
     5<!--
     6  $Id$
     7 
     8  Copyright (C) Authors contributing to this file.
     9 
     10  This file is part of BASE - BioArray Software Environment.
     11  Available at http://base.thep.lu.se/
     12 
     13  BASE is free software; you can redistribute it and/or
     14  modify it under the terms of the GNU General Public License
     15  as published by the Free Software Foundation; either version 2
     16  of the License, or (at your option) any later version.
     17 
     18  BASE is distributed in the hope that it will be useful,
     19  but WITHOUT ANY WARRANTY; without even the implied warranty of
     20  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
     21  GNU General Public License for more details.
     22 
     23  You should have received a copy of the GNU General Public License
     24  along with this program; if not, write to the Free Software
     25  Foundation, Inc., 59 Temple Place - Suite 330,
     26  Boston, MA  02111-1307, USA.
     27-->
     28<chapter id="reporters" chunked="0">
     29  <?dbhtml dir="reporters"?>
     30  <title>Reporters</title>
     31  <sect1 id="reporters.introduction">
     32    <title>Introduction</title>
     33    <helptext external_id="reporter.view.properties"
     34      title="About reporters">
     35    <para>
     36      Reporter, a term coined by the MAGE object model refers to
     37      spotted DNA sequence on a microarray. Reporters are
     38      therefore usually described by a sequence and a series of
     39      database identifiers qualifying that sequence. Reporters are
     40      generally understood as the thing biologists are interested
     41      in when carrying out DNA microarray experiments.
     42    </para>
     43    <para>
     44      In BASE2, reporters also refer to Affymetrix Probeset ID but
     45      reporters can be used to describe genes, transcripts, exons
     46      or any other sequence entity of biological relevance.
     47    </para>
     48    </helptext>
     49  </sect1>
     50 
     51  <sect1 id="reportertypes">
     52    <title>Reporter types</title>
     53   
     54    <helptext external_id="reportertype.view.properties"
     55      title="About reporter types">
     56    <para>
     57      <guilabel>Reporter Type</guilabel>
     58      allows classification of reporters based on their usage
     59      and qualification defined during the array design
     60      specification.
     61    </para>
     62    </helptext>
     63   
     64    <para>
     65      You can manage the reporter types by going to
     66      <menuchoice>
     67        <guimenu>Administrate</guimenu>
     68        <guimenuitem>Types</guimenuitem>
     69        <guisubmenu>Reporter types</guisubmenu>
     70      </menuchoice>.
     71    </para>
     72   
     73    <figure
     74      id="protocols.figures.protocoltype">
     75      <title>Reporter type properties</title>
     76      <screenshot>
     77        <mediaobject>
     78          <imageobject>
     79            <imagedata
     80              fileref="figures/reportertype.png" format="PNG" />
     81          </imageobject>
     82        </mediaobject>
     83      </screenshot>
     84    </figure>
     85   
     86    <helptext external_id="reportertype.edit"
     87      title="Reporter type properties">
     88     
     89      <variablelist>
     90      <varlistentry>
     91        <term><guilabel>Name</guilabel></term>
     92        <listitem>
     93          <para>
     94          The name of the reporter type. It is advised to define the name
     95          so that it is compatible with the
     96          <ulink url="http://www.mged.org/Workgroups/MIAME/miame.html"
     97            >MIAME requirements</ulink>
     98          and recommendations issues by microarray data
     99          repositories. Alternately, the local reporter type
     100          could be submitted to those repositories for term
     101          inclusion.
     102          </para>
     103        </listitem>
     104      </varlistentry>
     105      <varlistentry>
     106        <term><guilabel>Description</guilabel></term>
     107        <listitem>
     108          <para>
     109          A description of the reporter type.
     110          </para>
     111        </listitem>
     112      </varlistentry>
     113      </variablelist>
     114    </helptext>
     115   
     116  </sect1>
     117
     118
     119  <sect1 id="reporter.manage">
     120    <title>Reporters</title>
     121   
     122    <para>
     123      Go to
     124      <menuchoice>
     125        <guimenu>View</guimenu>
     126        <guimenuitem>Reporter</guimenuitem>
     127      </menuchoice> to view and manage the reporters.
     128    </para>
     129   
     130    <sect2 id="reporters.import">
     131      <title>Import/update reporter from files</title>
     132     
     133      <para>
     134        Reporters are used to represent genes, transcripts,
     135        exons and therefore come in their thousands. To solve
     136        this problem, BASE2 relies on
     137        <emphasis>Reporter import plug-ins</emphasis>.
     138        Those need to be specifically configured to deal with
     139        a particular input file format. This input file can be
     140        typically be an Axon GAL file or an Affymetrix CSV file
     141        which both provide information about reporters and their
     142        annotations. See <xref linkend="import_export_data.import" />
     143        for more information about importing and <xref
     144        linkend="plugins.configuration" />
     145        for more information about configuring file formats.
     146      </para>
     147     
     148      <tip>
     149        <title>Exchanging plug-in configurations</title>
     150        <para>
     151          As for any other plug-in, configuration parameters
     152          can be saved as an XML file and exchanged with
     153          another BASE2 instance, thereby reducing
     154          configuration burden (provided the 2 instances have
     155          identical <filename>extended-properties.xml</filename> files).
     156          See <xref linkend="resources.coreplugins" /> for information
     157          about available configuration files.
     158        </para>
     159      </tip>
     160
     161      <note>
     162        <title>Dealing with Affymetrix probesets</title>
     163        <para>
     164        In BASE2, Affymetrix probesets should be treated as reporters.
     165        The probeset ID could be stored in both the
     166        <guilabel>Name</guilabel> and the <guilabel>External ID</guilabel>
     167        fields of the reporter table.
     168        Storing the probeset ID should be enough
     169        as most analysis tools allow retrieval of updated
     170        information based on the probeset ID from
     171        web resources.
     172        </para>
     173      </note>
     174     
     175    </sect2>
     176   
     177    <sect2 id="reporters.create">
     178      <title>Manual management of reporters</title>
     179     
     180      <para>
     181        Reporters can also be created or edited manually
     182        one-by-one. This follows the same pattern as for
     183        all other items and is described in general terms
     184        in <xref linkend="webclient.items"/>.
     185      </para>
     186     
     187      <sect3 id="reporters.properties">
     188        <title>Reporter properties</title>
     189       
     190        <figure id="reporters.figures.properties">
     191          <title>Reporter properties</title>
     192          <screenshot>
     193            <mediaobject>
     194              <imageobject>
     195                <imagedata fileref="figures/reporter-1.png" format="PNG" />
     196              </imageobject>
     197            </mediaobject>
     198          </screenshot>
     199        </figure>
     200       
     201        <helptext external_id="reporter.edit"
     202          title="Reporer properties">
     203         
     204          <para>
     205            This tab shows core information that would be
     206            common to all BASE instances.
     207          </para>
     208         
     209          <variablelist>
     210          <varlistentry>
     211            <term><guilabel>Name</guilabel></term>
     212            <listitem>
     213              <para>
     214              The name of the reporter. This is often the same
     215              as the <guilabel>External ID</guilabel>.
     216              </para>
     217            </listitem>
     218          </varlistentry>
     219          <varlistentry>
     220            <term><guilabel>External ID</guilabel></term>
     221            <listitem>
     222              <para>
     223              The external ID of the reporter as it is defined in
     224              some database. The ID must be unique within BASE. The
     225              external ID is what plug-ins uses to match reporter
     226              information found in raw data files, array design files,
     227              etc.
     228              </para>
     229            </listitem>
     230          </varlistentry>
     231          <varlistentry>
     232            <term><guilabel>Type</guilabel></term>
     233            <listitem>
     234              <para>
     235              Optionally select a reporter type.
     236              </para>
     237            </listitem>
     238          </varlistentry>
     239          <varlistentry>
     240            <term><guilabel>Gene symbol</guilabel></term>
     241            <listitem>
     242              <para>
     243              The gene this reporter represents.
     244              </para>
     245            </listitem>
     246          </varlistentry>
     247          </variablelist>
     248         
     249          <seeother>
     250            <other external_id="reporter.view.properties">About reporters</other>
     251            <other external_id="reporter.edit.extended">Extended properties</other>
     252          </seeother>
     253        </helptext>
     254      </sect3>
     255     
     256      <sect3 id="reporters.extended_properties">
     257        <title>Extended properties</title>
     258       
     259        <figure id="reporters.figures.extended_properties">
     260          <title>Extended reporter properties</title>
     261          <screenshot>
     262            <mediaobject>
     263              <imageobject>
     264                <imagedata fileref="figures/reporter-2.png" format="PNG" />
     265              </imageobject>
     266            </mediaobject>
     267          </screenshot>
     268        </figure>
     269       
     270        <helptext external_id="reporter.edit.extended"
     271          title="Extended reporter properties">
     272       
     273          <para>
     274            Reporters belong to a special class whose properties
     275            can be defined and extended by system
     276            administrators. This is done by modifying the
     277            <filename>extended-properties.xml</filename> file during
     278            database configuration or upgrade. All fields on
     279            this tab are automatically generated based on this
     280            configuration and can be different from one server
     281            to the next.     
     282            <nohelp>
     283            See <xref linkend="installation_upgrade.installation" />
     284            and <xref linkend="appendix.extendedproperties" />
     285            for more information.
     286            </nohelp>
     287           
     288            <note>
     289              <para>
     290                It is possible to configure the extended properties
     291                so that links to the primary external databases can
     292                be made. For example, the <guilabel>Cluster ID</guilabel>
     293                is linked to the <ulink
     294                  url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene"
     295                  >Unigene database at NCBI</ulink>.
     296              </para>
     297            </note>
     298          </para>
     299       
     300          <seeother>
     301            <other external_id="reporter.edit">Reporter properties</other>
     302          </seeother>
     303        </helptext>
     304      </sect3>
     305    </sect2>
     306 
     307
     308    <sect2 id="reporter.delete">
     309      <title>Deleting reporters</title>
     310     
     311      <important>
     312        <title>Deleted reporters can't be restored</title>
     313        <para>
     314          Reporters are treated differently from other
     315          items (e.g biosources or protocols) since they
     316          doesn't use the trashcan mechanism (see <xref linkend="trashcan" />).
     317          The deletion happens immediately and is an unrecoverable
     318          event. BASE will always show a warning message which you must
     319          confirm before the reporters are deleted.
     320        </para>
     321      </important>
     322     
     323      <para>
     324        Reporters which has been referenced to from raw data, array
     325        designs, plates or any other item can't be deleted.
     326      </para>
     327    </sect2>
     328
     329  </sect1>
     330
     331  <sect1 id="reporterlists">
     332    <title>Reporter lists</title>
     333    <para>
     334      BASE2 allows for defining sets of reporters for a
     335      particular use, for instance to define a list of
     336      reporters to be used on an array. There are 2 ways to do
     337      so:
     338    </para>
     339    <orderedlist>
     340      <listitem>
     341        <para>
     342          Use the <guibutton>New reporter list</guibutton> button on the
     343          <menuchoice>
     344            <guimenu>View</guimenu>
     345            <guimenuitem>Reporters</guimenuitem>
     346          </menuchoice> page.
     347        </para>
     348      </listitem>
     349     
     350      <listitem>
     351        <para>
     352          Use the <guibutton>New</guibutton> button on the
     353          <menuchoice>
     354            <guimenu>View</guimenu>
     355            <guimenuitem>Reporter lists</guimenuitem>
     356          </menuchoice> page.
     357        </para>
     358      </listitem>
     359      </orderedlist>
     360     
     361      <figure
     362        id="reporterlists.figures.create">
     363        <title>
     364          The Create reporter list called from
     365          the reporters page.
     366        </title>
     367        <screenshot>
     368          <mediaobject>
     369            <imageobject>
     370              <imagedata fileref="figures/reporterlist-1.png" format="PNG" />
     371            </imageobject>
     372          </mediaobject>
     373        </screenshot>
     374      </figure>
     375   
     376      <helptext external_id="reporterlist.edit"
     377        title="Create reporter list">
     378       
     379        <variablelist>
     380        <varlistentry>
     381          <term><guilabel>Name</guilabel></term>
     382          <listitem>
     383            <para>
     384            The name of the reporter list.
     385            </para>
     386          </listitem>
     387        </varlistentry>
     388        <varlistentry>
     389          <term><guilabel>Exernal ID</guilabel></term>
     390          <listitem>
     391            <para>
     392            An optional external ID. This value is useful,
     393            for example, for a tool that automatically
     394            updates the reporter list from som external source.
     395            It is not used by BASE.
     396            </para>
     397          </listitem>
     398        </varlistentry>
     399        <varlistentry>
     400          <term><guilabel>Which reporters</guilabel></term>
     401          <listitem>
     402            <para>
     403            Select one of the options for specifying which reporters
     404            should be included in the list.
     405            <note>
     406              This option is only available when creating a
     407              reporter list from the
     408              <menuchoice>
     409                <guimenu>View</guimenu>
     410                <guimenuitem>Reporters</guimenuitem>
     411              </menuchoice> page, not when editing
     412              an existing list or creating it from the
     413              <menuchoice>
     414                <guimenu>View</guimenu>
     415                <guimenuitem>Reporter lists</guimenuitem>
     416              </menuchoice> page.
     417            </note>
     418           
     419            <tip>
     420              <para>
     421              To add or remove reporters to the list use the
     422              <guilabel>Reporters</guilabel> tab on the single-item
     423              view page of a reporter list. This tab lists all
     424              reporters in the list and there are functions for
     425              removing, adding and importing reporters to the list.
     426              </para>
     427            </tip>
     428           
     429            </para>
     430          </listitem>
     431        </varlistentry>
     432        <varlistentry>
     433          <term><guilabel>Description</guilabel></term>
     434          <listitem>
     435            <para>
     436            A description of the reporter list.
     437            </para>
     438          </listitem>
     439        </varlistentry>
     440        </variablelist>
     441      </helptext>
     442
     443  </sect1>
    292444</chapter>
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