source: trunk/doc/src/docbook/user/annotations.xml @ 5971

Last change on this file since 5971 was 5971, checked in by Nicklas Nordborg, 10 years ago

References #1655: GUI improvements

  • Started to create screen shots with the new design for the user documentation.
  • Got rid of old .gif icons in the documentation and replaced them with .png versions.
  • Fixed some issues with placement of 'required information' in two dialogs.
  • Property svn:eol-style set to native
  • Property svn:keywords set to Id
File size: 26.2 KB
Line 
1<?xml version="1.0" encoding="UTF-8"?>
2<!DOCTYPE chapter PUBLIC
3    "-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN"
4    "../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd">
5<!--
6  $Id: annotations.xml 5971 2012-02-17 10:30:22Z nicklas $
7 
8  Copyright (C) 2007 Peter Johansson, Nicklas Nordborg, Philippe Rocca-Serra, Martin Svensson
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 3
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 BASE. If not, see <http://www.gnu.org/licenses/>.
25-->
26
27<chapter id="annotations">
28  <?dbhtml dir="annotations" filename="index.html" ?>
29 
30  <title>Annotations</title>
31 
32  <sect1 id="annotations.types">
33    <?dbhtml filename="types.html" ?>
34    <title>Annotation Types</title>
35
36    <helptext external_id="annotationtype.view.properties" 
37      title="Annotation types">
38    <para>
39      BASE has been engineered to closely map the
40      <ulink
41        url="http://www.mged.org/Workgroups/MIAME/miame.html">
42        MIAME concepts</ulink>.
43      However, since MIAME is focused on microarray processing
44      workflow, information about the description biological
45      samples themselves was left out. BASE users are free to
46      annotate biomaterials (and most BASE items) as they wish,
47      from basic free text description to more advanced ontology
48      based terms. To accommodate the annotation needs of users
49      eager with detailed sample annotations and also the needs of
50      very different communities, BASE provides a mechanism that
51      allows a high level of annotation customization. BASE
52      allows to create descriptive elements for both quantitative
53      annotation and qualitative annotation of Biomaterials via
54      the <emphasis>Annotation Type mechanism</emphasis>.
55      Actually, annotation types can be used to annotate not
56      only <emphasis>Biomaterials</emphasis> but almost all BASE items, from
57      <emphasis>Plates</emphasis>
58      to
59      <emphasis>Protocols</emphasis>
60      and
61      <emphasis>Bioassay sets</emphasis>.
62    </para>
63
64    <nohelp>
65    <para>
66      Go to
67      <menuchoice>
68        <guimenu>Administrate</guimenu>
69        <guimenuitem>Types</guimenuitem>
70        <guisubmenu>Annotation types</guisubmenu>
71      </menuchoice>
72      to manage your annotation types.
73    </para>
74    </nohelp>
75
76    <para>
77      To create a new annotation type, click on the
78      &gbNew; button. This behaves differently
79      than other buttons found elsewhere and you must select
80      one of the 9 different types which can be split in 4 main groups.
81    </para>
82
83    <itemizedlist>
84    <listitem>
85      <para>
86        <guilabel>Integer</guilabel>,
87        <guilabel>Long</guilabel>,
88        <guilabel>Float</guilabel> and
89        <guilabel>Double</guilabel>
90        for numerical annotation types.
91      </para>
92    </listitem>
93
94    <listitem>
95      <para>
96        <guilabel>String</guilabel> and
97        <guilabel>Text</guilabel> for textual annotation types.
98        The difference is that <guilabel>String</guilabel>:s can
99        have a maximum length of 255 characters and can have an attached
100        list of predefined value. <guilabel>Text</guilabel>
101        annotation types have no practical limit and are always
102        free-text.
103      </para>
104    </listitem>
105
106    <listitem>
107      <para>
108        <guilabel>Boolean</guilabel>
109        for declaring annotation types that can take one
110        <constant>TRUE</constant>/<constant>FALSE</constant>
111        values.
112      </para>
113    </listitem>
114
115    <listitem>
116      <para>
117        <guilabel>Date</guilabel> and <guilabel>Timestamp</guilabel>
118        for declaring annotation types used as
119        calendar/time stamps.
120      </para>
121    </listitem>
122    </itemizedlist>
123
124    <note>
125      <para>
126        These distinctions matter essentially to database
127        administrators who need fine tuning of database
128        settings. Therefore, creation of annotation type
129        should be supervised by system administrators.
130      </para>
131    </note>
132   
133      <seeother>
134        <other external_id="annotationtype.edit">Edit annotation type</other>
135      </seeother>
136    </helptext>
137 
138    <para>
139      The <guilabel>Edit annotation type</guilabel> window is opened in a
140      pop-up. It contains several tabs.
141    </para>
142 
143    <sect2 id="annotations.types.properties">
144      <title>Properties</title>
145     
146      <figure
147        id="annotations.figures.annotationtype.properties">
148        <title>Annotation type properties</title>
149        <screenshot>
150          <mediaobject>
151            <imageobject>
152              <imagedata
153                fileref="figures/edit_annotationtype.png" format="PNG" />
154            </imageobject>
155          </mediaobject>
156        </screenshot>
157      </figure>
158     
159      <helptext external_id="annotationtype.edit" 
160        title="Edit annotation type">
161       
162        <variablelist>
163        <varlistentry>
164          <term><guilabel>Name</guilabel></term>
165          <listitem>
166            <para>
167            The name of the annotation type.
168            </para>
169          </listitem>
170        </varlistentry>
171        <varlistentry>
172          <term><guilabel>External ID</guilabel></term>
173          <listitem>
174            <para>
175            An ID identifying this annotation type in an external
176            database. This value can be used by tools that
177            need to update annotation types in BASE from external
178            sources. The value does not have to be unique and is not
179            used by BASE.
180            </para>
181          </listitem>
182        </varlistentry>
183        <varlistentry>
184          <term><guilabel>Multiplicity</guilabel></term>
185          <listitem>
186            <para>
187              The maximum number of values that can be entered
188              for this annotation type. The default is 1. A value
189              of 0, means that any number of values can be used.
190            </para>
191          </listitem>
192        </varlistentry>
193        <varlistentry>
194          <term><guilabel>Default value</guilabel></term>
195          <listitem>
196            <para>
197              A value that can be used as the default when
198              adding values.
199            </para>
200          </listitem>
201        </varlistentry>
202        <varlistentry>
203          <term><guilabel>Required for MIAME</guilabel></term>
204          <listitem>
205            <para>
206              If a value must be specified for this annotation type
207              in order for the experiment to be compliant with MIAME.
208            </para>
209          </listitem>
210        </varlistentry>
211        <varlistentry>
212          <term><guilabel>Protocol parameter</guilabel></term>
213          <listitem>
214            <para>
215              If the annotation type is a protocol parameter. As a protocol
216              parameter an item can only be annotated if a protocol
217              that includes this parameter has been used.
218              <nohelp>See <xref linkend="protocols.parameters" /> 
219              for more information.</nohelp>
220            </para>
221          </listitem>
222        </varlistentry>
223        <varlistentry>
224          <term><guilabel>Description</guilabel></term>
225          <listitem>
226            <para>
227              A short textual description
228              to clarify the usage.
229            </para>
230          </listitem>
231        </varlistentry>
232        </variablelist>
233       
234        <seeother>
235          <other external_id="annotationtype.edit.options">Options</other>
236          <other external_id="annotationtype.edit.items">Item types</other>
237          <other external_id="annotationtype.edit.units">Units</other>
238          <other external_id="annotationtype.edit.categories">Categories</other>
239          <other external_id="protocol.edit.parameters">Protocol parameters</other>
240        </seeother>
241      </helptext>
242   
243    </sect2>
244
245    <sect2 id="annotations.types.options">
246      <title>Options</title>
247
248      <figure
249        id="annotations.figures.annotationtype.options">
250        <title>Annotation type options</title>
251        <screenshot>
252          <mediaobject>
253            <imageobject>
254              <imagedata
255                fileref="figures/annotationtype_options.png" format="PNG" />
256            </imageobject>
257          </mediaobject>
258        </screenshot>
259      </figure>
260     
261      <helptext external_id="annotationtype.edit.options" 
262        title="Annotation type options">
263       
264        <para>
265          The available options in this tab depends on the type
266          of annotation type, eg. if is a string, numeric or
267          another type.
268        </para>
269       
270        <variablelist>
271        <varlistentry>
272          <term><guilabel>Interface</guilabel></term>
273          <listitem>
274            <para>
275            Select the type of graphical element to use for
276            entering values for the annotation type. You can select
277            between three different options:
278            <itemizedlist>
279            <listitem>
280              <para>
281              <guilabel>text box</guilabel>: The user must enter the value
282              in a free-text box.
283              </para>
284            </listitem>
285            <listitem>
286              <para>
287              <guilabel>selection list</guilabel>: The user must select
288              values from a list of predefined values.
289              </para>
290            </listitem>
291            <listitem>
292              <para>
293              <guilabel>radiobuttons/checkboxes</guilabel>: The user must
294              select values by marking checkboxes or radiobuttons.
295              </para>
296            </listitem>
297            </itemizedlist>
298           
299            The last two options requires that a list of values are
300            available. Enter possible values in the <guilabel>Values</guilabel>
301            which will be activated automatically.
302            </para>
303            <tip>
304              <para>
305                In term of usability, a drop-down
306                list can be more easily
307                navigated especially when the
308                number of possible values is
309                large, and because selection-list
310                and drop-down list allow use of
311                arrow and tab for selection.
312              </para>
313            </tip>
314          </listitem>
315        </varlistentry>
316       
317        <varlistentry>
318          <term><guilabel>Min/max value</guilabel></term>
319          <listitem>
320            <para>
321              Available for numerical annotation types only.
322              Specifies the minimum and maximum allowed value.
323              If left empty, the bound(s) are undefined and any
324              value is allowed.
325            </para>
326          </listitem>
327        </varlistentry>
328       
329        <varlistentry>
330          <term><guilabel>Max length</guilabel></term>
331          <listitem>
332            <para>
333              The maximum allowed length of a string annotation value.
334              If empty, 255 is the maximum length. If you need longer
335              values than that, use a <emphasis>text</emphasis> 
336              annotation type.
337            </para>
338          </listitem>
339        </varlistentry>
340
341        <varlistentry>
342          <term><guilabel>Input box width/height</guilabel></term>
343          <listitem>
344            <para>
345              A suggested display width and height of the element
346              used for input. These values are ignored in the current
347              implementation.
348            </para>
349          </listitem>
350        </varlistentry>
351
352        <varlistentry>
353          <term><guilabel>Values</guilabel></term>
354          <listitem>
355            <para>
356              A list of predefined values that the user is allowed
357              to select from. This option is only activated if the
358              <guilabel>Interface</guilabel> option is set
359              to <guilabel>selection list</guilabel> or
360              <guilabel>radiobuttons/checkboxes</guilabel>.
361              Actual values can be supplied using one line for each
362              value (a return entry is used as separator).
363            </para>
364          </listitem>
365        </varlistentry>
366
367        </variablelist>
368       
369        <seeother>
370          <other external_id="annotationtype.edit">Properties</other>
371          <other external_id="annotationtype.edit.items">Item types</other>
372          <other external_id="annotationtype.edit.units">Units</other>
373          <other external_id="annotationtype.edit.categories">Categories</other>
374        </seeother>
375      </helptext>
376    </sect2>
377   
378    <sect2 id="annotations.types.items">
379      <title>Item types</title>
380     
381      <figure
382        id="annotations.figures.annotationtype.items">
383        <title>Annotation type items</title>
384        <screenshot>
385          <mediaobject>
386            <imageobject>
387              <imagedata
388                fileref="figures/annotationtype_items.png" format="PNG" />
389            </imageobject>
390          </mediaobject>
391        </screenshot>
392      </figure>
393   
394      <helptext external_id="annotationtype.edit.items" 
395        title="Item types">
396       
397        <para>
398          On this tab you select the item types that you wish to
399          annotate with the annotation type. Simply use
400          left and right buttons to move selection options
401          between the <guilabel>Enabled for</guilabel>
402          and <guilabel>Disabled for</guilabel> lists.
403        </para>
404       
405        <note>
406          <para>
407          If the annotation type has been marked as a
408          <guilabel>Protocol parameter</guilabel>, these settings are
409          ignored, with one exception. If you wish to view parameter
410          values in the list view for a specific item type you must select
411          the item type here. Otherwise the parameter will not be present
412          as a displayable column.
413          </para>
414        </note>
415       
416        <seeother>
417          <other external_id="annotationtype.edit">Properties</other>
418          <other external_id="annotationtype.edit.options">Options</other>
419          <other external_id="annotationtype.edit.units">Units</other>
420          <other external_id="annotationtype.edit.categories">Categories</other>
421        </seeother>
422      </helptext>
423    </sect2>
424 
425    <sect2 id="annotations.types.units">
426      <title>Units</title>
427       
428      <figure
429        id="annotations.figures.annotationtype.units">
430        <title>Annotation type units</title>
431        <screenshot>
432          <mediaobject>
433            <imageobject>
434              <imagedata
435                fileref="figures/annotationtype_units.png" format="PNG" />
436            </imageobject>
437          </mediaobject>
438        </screenshot>
439      </figure>
440 
441      <helptext external_id="annotationtype.edit.units" 
442        title="Units">
443 
444        <para>
445        Numerical annotation types can optionally be given a quantity and unit.
446        </para>
447       
448        <variablelist>
449        <varlistentry>
450          <term><guilabel>Quantity</guilabel></term>
451          <listitem>
452            <para>
453            Select which quantity to use for the annotation type. If you
454            don't want to use units, select the <emphasis>do not use units</emphasis>
455            option.
456            </para>
457            <note>
458              <title>The quantity can't be changed later</title>
459              <para>
460              Once a quantity has been selected and saved for an
461              annotation type, it is not possible to change it to another
462              quantity.
463              </para>
464            </note>
465          </listitem>
466        </varlistentry>
467        <varlistentry>
468          <term><guilabel>Default unit</guilabel></term>
469          <listitem>
470            <para>
471            This list will be populated with units from the selected
472            quantity. You must select one default unit which is the unit
473            that is used if a user leaves out the unit when annotating
474            an item. The selected unit is also the unit that is used internally
475            when storing the values in the database.
476            </para>
477            <warning>
478              <title>Do not change the default unit</title>
479              <para>
480                If you change the default unit for an existing annotation type,
481                all annotation values that exists for it, must be converted to the
482                new unit. This may result in loss of precision due to rounding/truncation
483                errors.
484              </para>
485            </warning>
486          </listitem>
487        </varlistentry>
488       
489        <varlistentry>
490          <term><guilabel>Use units</guilabel></term>
491          <listitem>
492            <para>
493            By default, all units of the selected quantity can be used when
494            annotating items. If you want, you may force the users to use
495            some specific units by moving units into the <emphasis>Use units</emphasis>
496            list. This is recommended since the range of available units is usually
497            quite large. For example, if the weight of something is normally
498            measured in milligrams, it may make sense to leave out kilograms, and
499            only use microgram, milligram and gram.
500            </para>
501          </listitem>
502        </varlistentry>
503       
504        </variablelist>
505       
506        <seeother>
507          <other external_id="annotationtype.edit">Properties</other>
508          <other external_id="annotationtype.edit.options">Options</other>
509          <other external_id="annotationtype.edit.items">Item types</other>
510          <other external_id="annotationtype.edit.categories">Categories</other>
511        </seeother>
512       
513      </helptext>
514    </sect2>
515 
516    <sect2 id="annotations.types.categories">
517      <title>Categories</title>
518   
519      <figure
520        id="annotations.figures.annotationtype.categories">
521        <title>Annotation type categories</title>
522        <screenshot>
523          <mediaobject>
524            <imageobject>
525              <imagedata
526                fileref="figures/annotationtype_categories.png" format="PNG" />
527            </imageobject>
528          </mediaobject>
529        </screenshot>
530      </figure>
531     
532      <helptext external_id="annotationtype.edit.categories" 
533        title="Categories">
534       
535        <para>
536          Annotation type can be grouped together by
537          placing them in one or more categories. This
538          enhances display by avoid overcrowding the list
539          of annotation types presented to users. It also
540          allows to improve the display of information.
541        </para>
542       
543        <para>
544          The <guilabel>Categories</guilabel> list displays
545          the currently associated categories. Use the
546          <guibutton>Add categories</guibutton> button
547          to add more categories, or the <guilabel>Remove</guilabel>
548          button to remove the selected categories.
549        </para>
550       
551        <tip>
552          <title>Create categories with the same name as item subtypes</title>
553          <para>
554            If you, for example, have defined multiple subtypes of extracts
555            (see <xref linkend="subtypes" />),
556            it usually so that some annotation types are only intended for
557            one subtype while some other annotation types are only intended
558            for the other subtype. If you create categories with the same name
559            as the item subtypes, BASE will automatically select the corresponding
560            category when annotating an extract with a subtype. This makes the interface
561            cleaner and easier to use since irrelevant annotation types are hidden.
562            Note that it is possible for annotations to be part of more than one
563            category so it is also possible to define annotation types that are
564            intended for all types of extracts by including them in both categories.
565          </para>
566        </tip>
567       
568        <seeother>
569          <other external_id="annotationtype.edit">Properties</other>
570          <other external_id="annotationtype.edit.options">Options</other>
571          <other external_id="annotationtype.edit.items">Item types</other>
572        </seeother>
573      </helptext>
574    </sect2>
575  </sect1>
576 
577  <sect1 id="annotations.annotating">
578    <?dbhtml filename="annotating.html" ?>
579    <title>Annotating items</title>
580   
581    <para>
582      Entering annotation values follow the same pattern
583      for all items that can have annotations. They all have
584      a <guilabel>Annotations &amp; parameters</guilabel> tab
585      in their edit view. On this tab you can specify values
586      for all annotation types assigned to the type of item,
587      and all parameters that are attached to the protocol
588      used to create the item. Some items, for example
589      <emphasis>biosources</emphasis> and <emphasis>array designs</emphasis> 
590      cannot have a protocol. In their case the tab is labelled
591      <guilabel>Annotations</guilabel>.
592    </para>
593   
594    <figure
595      id="annotations.figures.annotate">
596      <title>Annotating a sample</title>
597      <screenshot>
598        <mediaobject>
599          <imageobject>
600            <imagedata
601              fileref="figures/annotate.png" format="PNG" />
602          </imageobject>
603        </mediaobject>
604      </screenshot>
605    </figure>
606
607    <helptext external_id="annotations.edit" 
608      title="Annotations &amp; parameters">
609
610      <para>
611        Click on an entry in the list of annotation types to show a
612        form for entering a value for it to the right. Depending
613        on the options set on the annotation type the form may be a simple
614        free text field, a list of checkboxes or radiobuttons, or
615        something else.
616      </para>
617     
618      <para>
619        Annotation types with an <guilabel>X</guilabel> in front
620        of their names already have a value.
621      </para>
622     
623      <para>
624        Annotation types marked with angle brackets
625        <nohelp>
626          (<guiicon>
627            <inlinemediaobject>
628              <imageobject><imagedata fileref="figures/parameter.png" format="PNG"
629              /></imageobject>
630            </inlinemediaobject>
631          </guiicon>)
632        </nohelp>
633        are protocol parameters.
634      </para>
635     
636      <para>
637        Select an option in the <guilabel>Categories</guilabel> list to filter the
638        annotation types based on the categories
639        they belong to. This list contains all available
640        categories, and three special ones:
641        <itemizedlist>
642        <listitem>
643          <para>
644          <guilabel>all</guilabel>: Display all annotation types
645          </para>
646        </listitem>
647        <listitem>
648          <para>
649          <guilabel>protocol parameters</guilabel>: Display only
650          those annotation types that are parameters to the current
651          protocol.
652          </para>
653        </listitem>
654        <listitem>
655          <para>
656          <guilabel>uncategorized</guilabel>: Display only annotation types
657          that has not been put into a category.
658          </para>
659        </listitem>
660        </itemizedlist>
661      </para>
662     
663      <seeother>
664        <other external_id="annotations.edit.inherited">Inherit annotations</other>
665      </seeother>
666     
667    </helptext>
668   
669    <sect2 id="annotations.inheriting">
670      <title>Inheriting annotations from other items</title>
671     
672      <helptext external_id="annotations.edit.inherited" 
673        title="Inherit annotations">
674        <para>
675          An item may inherit annotations from any of it's parent items.
676          E.g. an extract can inherit annotations from the sample or biosource
677          it was created from. This is an important feature to make the
678          experimental factors work. Annotations that should be used as
679          experimental factors must be inherited to the raw bioassay level.
680          <nohelp>See <xref linkend="experiments_analysis.experiment.factors" /> for more
681          information about experimental factors.</nohelp>
682        </para>
683       
684        <nohelp>
685        <figure
686          id="annotations.figures.inherit">
687          <title>Inheriting annotations from a parent item</title>
688          <screenshot>
689            <mediaobject>
690              <imageobject>
691                <imagedata
692                  fileref="figures/inherit_annotations.png" format="PNG" />
693              </imageobject>
694            </mediaobject>
695          </screenshot>
696        </figure>
697        </nohelp>
698   
699        <para>
700          On this screen is a tree-like structure in two levels. The first level
701          lists all parent items which has at least one annotations. The second
702          level lists the annotations and protocol parameters for the item.
703          Selecting an item in the first level will inherit all annotations
704          from that item, including those that you maybe add later.
705          Selecting an annotation or protocol parameter at the second level
706          will inherit only the selected one.
707        </para>
708       
709        <note>
710          <itemizedlist>
711          <listitem>
712            <para>
713            The inheritance is implemented by reference. This means that if
714            you change the value of an annotation the new value is automatically
715            picked up by those inheriting it.
716            </para>
717          </listitem>
718          <listitem>
719            <para>
720            You cannot inherit annotations from an item which does not have
721            annotations.
722            </para>
723          </listitem>
724          <listitem>
725            <para>
726            If you delete an annotation from a parent item, the inheritance will
727            be lost, even if you later add a value again.
728            </para>
729          </listitem>
730          </itemizedlist>
731        </note>
732       
733        <warning>
734          <para>
735          If you rearrange links to parent items after you have
736          specified inheritance, it may happen that you are inheriting
737          annotation from non-parent items. This will be flagged with a warning
738          icon in the list, and must be fixed manually. The item overview
739          tool is an excellent help for locating this kind of problems.
740          <nohelp>See <xref linkend="webclient.itemoverview" />.</nohelp>
741          </para>
742        </warning>
743   
744        <seeother>
745          <other external_id="annotations.edit">Annotations and parameters</other>
746          <other external_id="experiment.edit.factors">Experimental factors</other>
747          <other external_id="item.overview">Item overview tool</other>
748        </seeother>
749     
750      </helptext>     
751     
752    </sect2>
753   
754    <sect2 id="annotations.massimport">
755      <title>Mass annotation import plug-in</title>
756     
757      <para>
758        BASE includes a plug-in for importing annotations to multiple items
759        in one go. The plug-in read annotation values from a simple column-based
760        text file. Usually, a tab is used as the delimiter between columns, but this
761        is configurable.
762        The first row should contain the column headers. One column should contain
763        the name or the external ID of the item. The rest of the columns can each be
764        mapped to an annotation type and contains the annotation values. If a column
765        header exactly match the name of an annotation type, the plug-in will automatically
766        create the mapping, otherwise you must do it manually. You don't have to map
767        all columns if you don't want to.
768      </para>
769     
770      <para>
771        Each column can only contain a single annotation value for each row.
772        If you have annotation types that accept multiple values you can map
773        two or more columns to the same annotation type, or you can add an
774        extra row only giving the name and the extra annotation value.
775        Here is a simple example of a valid file with comma as column separator:
776      </para>
777     
778      <programlisting>
779# 'Time' and 'Age' are integer types
780# 'Subtype' is a string enumeration
781# 'Comment' is a text type that accept multiple values
782Name,Time (hours),Age (years),Subtype,Comment
783Sample #1,0,0,alfa,Very good
784Sample #2,24,0,beta,Not so bad
785Sample #2,,,,Yet another comment
786</programlisting>
787     
788      <para>
789        The plug-in can be used with or without a configuration. The configuration
790        keeps the regular expressions and other settings used to parse the file. If
791        you often import annotations from the same file format, we recommend that
792        you use a configuration. The mapping from file columns to annotation types
793        is not part of the configuration, it must be done each time the plug-in is used.
794      </para>
795     
796      <para>
797        The plug-in can be used from the list view of all annotatable items.
798        Using the plug-in is a three-step wizard:
799      </para>
800     
801      <orderedlist>
802      <listitem>
803        <para>
804        Select a file to import from and the regular expressions and other
805        settings used to parse the file. In this step you also select the column
806        that contains the name or external ID the items. If a configuration is used
807        all settings on this page, except the file to import from, already has values.
808        </para>
809      </listitem>
810     
811      <listitem>
812        <para>
813        The plug-in will start parsing the file until it finds the column headers.
814        You are asked to select an annotation type for each column.
815        </para>
816      </listitem>
817     
818      <listitem>
819        <para>
820        Set error handling options and some other import options.
821        </para>
822      </listitem>
823     
824      </orderedlist>
825     
826    </sect2>
827   
828  </sect1>
829
830</chapter>
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