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<?xml version="1.0" encoding="UTF-8"?> |
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<!DOCTYPE chapter PUBLIC |
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"-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN" |
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"../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd"> |
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<!-- |
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$Id$ |
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|
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Copyright (C) 2007 Peter Johansson, Nicklas Nordborg, Philippe Rocca-Serra, Martin Svensson |
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9 |
|
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This file is part of BASE - BioArray Software Environment. |
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Available at http://base.thep.lu.se/ |
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12 |
|
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BASE is free software; you can redistribute it and/or |
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modify it under the terms of the GNU General Public License |
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jari |
as published by the Free Software Foundation; either version 3 |
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nicklas |
of the License, or (at your option) any later version. |
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17 |
|
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BASE is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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nicklas |
GNU General Public License for more details. |
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22 |
|
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You should have received a copy of the GNU General Public License |
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jari |
along with BASE. If not, see <http://www.gnu.org/licenses/>. |
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--> |
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|
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<chapter id="annotations"> |
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<?dbhtml dir="annotations" filename="index.html" ?> |
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|
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<title>Annotations</title> |
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31 |
|
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<sect1 id="annotations.types"> |
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<?dbhtml filename="types.html" ?> |
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<title>Annotation Types</title> |
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|
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<helptext external_id="annotationtype.view.properties" |
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title="Annotation types"> |
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38 |
<para> |
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39 |
BASE has been engineered to closely map the |
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40 |
<ulink |
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41 |
url="http://www.mged.org/Workgroups/MIAME/miame.html"> |
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42 |
MIAME concepts</ulink>. |
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43 |
However, since MIAME is focused on microarray processing |
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44 |
workflow, information about the description biological |
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45 |
samples themselves was left out. BASE users are free to |
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08 Sep 08 |
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46 |
annotate biomaterials (and most BASE items) as they wish, |
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47 |
from basic free text description to more advanced ontology |
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48 |
based terms. To accommodate the annotation needs of users |
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49 |
eager with detailed sample annotations and also the needs of |
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50 |
very different communities, BASE provides a mechanism that |
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51 |
allows a high level of annotation customization. BASE |
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52 |
allows to create descriptive elements for both quantitative |
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annotation and qualitative annotation of Biomaterials via |
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54 |
the <emphasis>Annotation Type mechanism</emphasis>. |
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Actually, annotation types can be used to annotate not |
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only <emphasis>Biomaterials</emphasis> but almost all BASE items, from |
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<emphasis>Plates</emphasis> |
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58 |
to |
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<emphasis>Protocols</emphasis> |
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and |
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<emphasis>Bioassay sets</emphasis>. |
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</para> |
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|
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<nohelp> |
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<para> |
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Go to |
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<menuchoice> |
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68 |
<guimenu>Administrate</guimenu> |
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<guimenuitem>Types</guimenuitem> |
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<guisubmenu>Annotation types</guisubmenu> |
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</menuchoice> |
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to manage your annotation types. |
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73 |
</para> |
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</nohelp> |
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|
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<para> |
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To create a new annotation type, click on the |
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&gbNew; button. This behaves differently |
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than other buttons found elsewhere and you must select |
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one of the 9 different types which can be split in 4 main groups. |
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</para> |
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|
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<itemizedlist> |
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<listitem> |
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<para> |
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<guilabel>Integer</guilabel>, |
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<guilabel>Long</guilabel>, |
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<guilabel>Float</guilabel> and |
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<guilabel>Double</guilabel> |
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for numerical annotation types. |
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</para> |
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</listitem> |
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|
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<listitem> |
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<para> |
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<guilabel>String</guilabel> and |
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<guilabel>Text</guilabel> for textual annotation types. |
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98 |
The difference is that <guilabel>String</guilabel>:s can |
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have a maximum length of 255 characters and can have an attached |
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100 |
list of predefined value. <guilabel>Text</guilabel> |
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101 |
annotation types have no practical limit and are always |
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free-text. |
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103 |
</para> |
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104 |
</listitem> |
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105 |
|
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106 |
<listitem> |
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107 |
<para> |
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<guilabel>Boolean</guilabel> |
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109 |
for declaring annotation types that can take one |
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<constant>TRUE</constant>/<constant>FALSE</constant> |
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111 |
values. |
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112 |
</para> |
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113 |
</listitem> |
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114 |
|
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115 |
<listitem> |
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116 |
<para> |
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117 |
<guilabel>Date</guilabel> and <guilabel>Timestamp</guilabel> |
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118 |
for declaring annotation types used as |
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119 |
calendar/time stamps. |
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120 |
</para> |
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121 |
</listitem> |
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122 |
</itemizedlist> |
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|
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<note> |
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<para> |
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126 |
These distinctions matter essentially to database |
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127 |
administrators who need fine tuning of database |
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128 |
settings. Therefore, creation of annotation type |
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129 |
should be supervised by system administrators. |
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130 |
</para> |
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131 |
</note> |
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132 |
|
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133 |
<seeother> |
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<other external_id="annotationtype.edit">Edit annotation type</other> |
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135 |
</seeother> |
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136 |
</helptext> |
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137 |
|
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138 |
<para> |
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139 |
The <guilabel>Edit annotation type</guilabel> window is opened in a |
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pop-up. It contains several tabs. |
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141 |
</para> |
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142 |
|
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143 |
<sect2 id="annotations.types.properties"> |
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144 |
<title>Properties</title> |
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145 |
|
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146 |
<figure |
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147 |
id="annotations.figures.annotationtype.properties"> |
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148 |
<title>Annotation type properties</title> |
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149 |
<screenshot> |
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150 |
<mediaobject> |
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151 |
<imageobject> |
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152 |
<imagedata |
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153 |
fileref="figures/edit_annotationtype.png" format="PNG" /> |
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154 |
</imageobject> |
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155 |
</mediaobject> |
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156 |
</screenshot> |
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157 |
</figure> |
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158 |
|
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159 |
<helptext external_id="annotationtype.edit" |
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160 |
title="Edit annotation type"> |
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161 |
|
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162 |
<variablelist> |
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163 |
<varlistentry> |
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164 |
<term><guilabel>Name</guilabel></term> |
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165 |
<listitem> |
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166 |
<para> |
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The name of the annotation type. |
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168 |
</para> |
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169 |
</listitem> |
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</varlistentry> |
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171 |
<varlistentry> |
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<term><guilabel>External ID</guilabel></term> |
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173 |
<listitem> |
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174 |
<para> |
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175 |
An ID identifying this annotation type in an external |
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176 |
database. This value can be used by tools that |
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177 |
need to update annotation types in BASE from external |
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sources. The value does not have to be unique and is not |
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used by BASE. |
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</para> |
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181 |
</listitem> |
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182 |
</varlistentry> |
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183 |
<varlistentry> |
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<term><guilabel>Multiplicity</guilabel></term> |
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185 |
<listitem> |
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186 |
<para> |
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187 |
The maximum number of values that can be entered |
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for this annotation type. The default is 1. A value |
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of 0, means that any number of values can be used. |
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</para> |
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nicklas |
191 |
</listitem> |
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nicklas |
192 |
</varlistentry> |
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nicklas |
193 |
<varlistentry> |
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<term><guilabel>Default value</guilabel></term> |
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nicklas |
195 |
<listitem> |
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nicklas |
196 |
<para> |
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A value that can be used as the default when |
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198 |
adding values. |
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199 |
</para> |
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200 |
</listitem> |
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201 |
</varlistentry> |
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202 |
<varlistentry> |
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203 |
<term><guilabel>Is identifier</guilabel></term> |
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04 Mar 19 |
nicklas |
204 |
<listitem> |
| 7620 |
04 Mar 19 |
nicklas |
205 |
<para> |
| 7620 |
04 Mar 19 |
nicklas |
206 |
If this flag is set, the annotation values can be used as identifiers |
| 7620 |
04 Mar 19 |
nicklas |
207 |
for a particualar item. For example, the batch item importers can use |
| 7620 |
04 Mar 19 |
nicklas |
208 |
the annotation type for finding items. Note that BASE doesn't require or |
| 7620 |
04 Mar 19 |
nicklas |
209 |
implement checks that values are unique. |
| 7620 |
04 Mar 19 |
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210 |
</para> |
| 7620 |
04 Mar 19 |
nicklas |
211 |
</listitem> |
| 7620 |
04 Mar 19 |
nicklas |
212 |
</varlistentry> |
| 7620 |
04 Mar 19 |
nicklas |
213 |
<varlistentry> |
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214 |
<term><guilabel>Required for MIAME</guilabel></term> |
| 3395 |
28 May 07 |
nicklas |
215 |
<listitem> |
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28 May 07 |
nicklas |
216 |
<para> |
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28 May 07 |
nicklas |
217 |
If a value must be specified for this annotation type |
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28 May 07 |
nicklas |
218 |
in order for the experiment to be compliant with MIAME. |
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nicklas |
219 |
</para> |
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28 May 07 |
nicklas |
220 |
</listitem> |
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221 |
</varlistentry> |
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28 May 07 |
nicklas |
222 |
<varlistentry> |
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nicklas |
223 |
<term><guilabel>Protocol parameter</guilabel></term> |
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28 May 07 |
nicklas |
224 |
<listitem> |
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28 May 07 |
nicklas |
225 |
<para> |
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28 May 07 |
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226 |
If the annotation type is a protocol parameter. As a protocol |
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28 May 07 |
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227 |
parameter an item can only be annotated if a protocol |
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228 |
that includes this parameter has been used. |
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229 |
<nohelp>See <xref linkend="protocols.parameters" /> |
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230 |
for more information.</nohelp> |
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28 May 07 |
nicklas |
231 |
</para> |
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28 May 07 |
nicklas |
232 |
</listitem> |
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nicklas |
233 |
</varlistentry> |
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nicklas |
234 |
<varlistentry> |
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26 Mar 15 |
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235 |
<term><guilabel>Disable change log</guilabel></term> |
| 6805 |
26 Mar 15 |
nicklas |
236 |
<listitem> |
| 6805 |
26 Mar 15 |
nicklas |
237 |
<para> |
| 6805 |
26 Mar 15 |
nicklas |
238 |
If this option is checked, change history logging does not include the |
| 6805 |
26 Mar 15 |
nicklas |
239 |
actual old/new annotation values. Note that the log will still contain |
| 6805 |
26 Mar 15 |
nicklas |
240 |
an entry that the annotation was modified. It is recomended that this |
| 6805 |
26 Mar 15 |
nicklas |
241 |
option is enabled for annotations containing sensitive data since |
| 6805 |
26 Mar 15 |
nicklas |
242 |
access permissions to the change history are different. |
| 6805 |
26 Mar 15 |
nicklas |
243 |
</para> |
| 6805 |
26 Mar 15 |
nicklas |
244 |
</listitem> |
| 6805 |
26 Mar 15 |
nicklas |
245 |
</varlistentry> |
| 6805 |
26 Mar 15 |
nicklas |
246 |
<varlistentry> |
| 6805 |
26 Mar 15 |
nicklas |
247 |
<term><guilabel>Disable inheritance</guilabel></term> |
| 6805 |
26 Mar 15 |
nicklas |
248 |
<listitem> |
| 6805 |
26 Mar 15 |
nicklas |
249 |
<para> |
| 6805 |
26 Mar 15 |
nicklas |
250 |
If this option is checked, annotations of this type are not allowed to be |
| 6805 |
26 Mar 15 |
nicklas |
251 |
inherited to other items. <nohelp>See <xref linkend="annotations.inheriting" /> |
| 6805 |
26 Mar 15 |
nicklas |
252 |
for more information about inheritance.</nohelp> It is recomended that this |
| 6805 |
26 Mar 15 |
nicklas |
253 |
option is enabled for annotations containing sensitive data since |
| 6805 |
26 Mar 15 |
nicklas |
254 |
access permissions to inherited information may be different. |
| 6805 |
26 Mar 15 |
nicklas |
255 |
</para> |
| 6805 |
26 Mar 15 |
nicklas |
256 |
<warning> |
| 6805 |
26 Mar 15 |
nicklas |
257 |
<title>Existing inherited annotations are removed</title> |
| 6805 |
26 Mar 15 |
nicklas |
258 |
<para> |
| 6805 |
26 Mar 15 |
nicklas |
259 |
Be careful when enabling this option for an annotation type |
| 6805 |
26 Mar 15 |
nicklas |
260 |
if there are existing items that already inherit this annotation |
| 6805 |
26 Mar 15 |
nicklas |
261 |
type from their parents. The existing inheritance is automatically |
| 6805 |
26 Mar 15 |
nicklas |
262 |
dropped, and it will not be re-created if resetting this option |
| 6805 |
26 Mar 15 |
nicklas |
263 |
again. |
| 6805 |
26 Mar 15 |
nicklas |
264 |
</para> |
| 6805 |
26 Mar 15 |
nicklas |
265 |
</warning> |
| 6805 |
26 Mar 15 |
nicklas |
266 |
|
| 6805 |
26 Mar 15 |
nicklas |
267 |
</listitem> |
| 6805 |
26 Mar 15 |
nicklas |
268 |
</varlistentry> |
| 6805 |
26 Mar 15 |
nicklas |
269 |
<varlistentry> |
| 7341 |
18 Apr 17 |
nicklas |
270 |
<term><guilabel>Project annotations</guilabel></term> |
| 7341 |
18 Apr 17 |
nicklas |
271 |
<listitem> |
| 7341 |
18 Apr 17 |
nicklas |
272 |
<para> |
| 7341 |
18 Apr 17 |
nicklas |
273 |
If this option is checked, annotations can be set per project. |
| 7341 |
18 Apr 17 |
nicklas |
274 |
A project-specific annotation value is created automatically |
| 7341 |
18 Apr 17 |
nicklas |
275 |
when a project is active. If no project is active only the |
| 7341 |
18 Apr 17 |
nicklas |
276 |
default value value is visible/can be edited. The default |
| 7341 |
18 Apr 17 |
nicklas |
277 |
value is visible also when a project is active unless a |
| 7341 |
18 Apr 17 |
nicklas |
278 |
project-specific value exists. |
| 7341 |
18 Apr 17 |
nicklas |
279 |
</para> |
| 7341 |
18 Apr 17 |
nicklas |
280 |
|
| 7341 |
18 Apr 17 |
nicklas |
281 |
</listitem> |
| 7341 |
18 Apr 17 |
nicklas |
282 |
</varlistentry> |
| 7341 |
18 Apr 17 |
nicklas |
283 |
<varlistentry> |
| 3395 |
28 May 07 |
nicklas |
284 |
<term><guilabel>Description</guilabel></term> |
| 3395 |
28 May 07 |
nicklas |
285 |
<listitem> |
| 3395 |
28 May 07 |
nicklas |
286 |
<para> |
| 5795 |
10 Oct 11 |
nicklas |
287 |
A short textual description |
| 3395 |
28 May 07 |
nicklas |
288 |
to clarify the usage. |
| 3395 |
28 May 07 |
nicklas |
289 |
</para> |
| 3395 |
28 May 07 |
nicklas |
290 |
</listitem> |
| 3395 |
28 May 07 |
nicklas |
291 |
</varlistentry> |
| 3395 |
28 May 07 |
nicklas |
292 |
</variablelist> |
| 3395 |
28 May 07 |
nicklas |
293 |
|
| 3395 |
28 May 07 |
nicklas |
294 |
<seeother> |
| 3395 |
28 May 07 |
nicklas |
295 |
<other external_id="annotationtype.edit.options">Options</other> |
| 3395 |
28 May 07 |
nicklas |
296 |
<other external_id="annotationtype.edit.items">Item types</other> |
| 4561 |
06 Oct 08 |
nicklas |
297 |
<other external_id="annotationtype.edit.units">Units</other> |
| 3395 |
28 May 07 |
nicklas |
298 |
<other external_id="annotationtype.edit.categories">Categories</other> |
| 3395 |
28 May 07 |
nicklas |
299 |
<other external_id="protocol.edit.parameters">Protocol parameters</other> |
| 3395 |
28 May 07 |
nicklas |
300 |
</seeother> |
| 3395 |
28 May 07 |
nicklas |
301 |
</helptext> |
| 3395 |
28 May 07 |
nicklas |
302 |
|
| 3395 |
28 May 07 |
nicklas |
303 |
</sect2> |
| 3372 |
24 May 07 |
philippe |
304 |
|
| 3395 |
28 May 07 |
nicklas |
305 |
<sect2 id="annotations.types.options"> |
| 3395 |
28 May 07 |
nicklas |
306 |
<title>Options</title> |
| 3372 |
24 May 07 |
philippe |
307 |
|
| 3395 |
28 May 07 |
nicklas |
308 |
<figure |
| 3395 |
28 May 07 |
nicklas |
309 |
id="annotations.figures.annotationtype.options"> |
| 3395 |
28 May 07 |
nicklas |
310 |
<title>Annotation type options</title> |
| 3395 |
28 May 07 |
nicklas |
311 |
<screenshot> |
| 3395 |
28 May 07 |
nicklas |
312 |
<mediaobject> |
| 3395 |
28 May 07 |
nicklas |
313 |
<imageobject> |
| 3395 |
28 May 07 |
nicklas |
314 |
<imagedata |
| 3395 |
28 May 07 |
nicklas |
315 |
fileref="figures/annotationtype_options.png" format="PNG" /> |
| 3395 |
28 May 07 |
nicklas |
316 |
</imageobject> |
| 3395 |
28 May 07 |
nicklas |
317 |
</mediaobject> |
| 3395 |
28 May 07 |
nicklas |
318 |
</screenshot> |
| 3395 |
28 May 07 |
nicklas |
319 |
</figure> |
| 3395 |
28 May 07 |
nicklas |
320 |
|
| 3395 |
28 May 07 |
nicklas |
321 |
<helptext external_id="annotationtype.edit.options" |
| 3395 |
28 May 07 |
nicklas |
322 |
title="Annotation type options"> |
| 3395 |
28 May 07 |
nicklas |
323 |
|
| 3395 |
28 May 07 |
nicklas |
324 |
<para> |
| 3395 |
28 May 07 |
nicklas |
325 |
The available options in this tab depends on the type |
| 3395 |
28 May 07 |
nicklas |
326 |
of annotation type, eg. if is a string, numeric or |
| 3395 |
28 May 07 |
nicklas |
327 |
another type. |
| 3395 |
28 May 07 |
nicklas |
328 |
</para> |
| 3395 |
28 May 07 |
nicklas |
329 |
|
| 3395 |
28 May 07 |
nicklas |
330 |
<variablelist> |
| 3395 |
28 May 07 |
nicklas |
331 |
<varlistentry> |
| 3395 |
28 May 07 |
nicklas |
332 |
<term><guilabel>Interface</guilabel></term> |
| 3395 |
28 May 07 |
nicklas |
333 |
<listitem> |
| 3395 |
28 May 07 |
nicklas |
334 |
<para> |
| 3395 |
28 May 07 |
nicklas |
335 |
Select the type of graphical element to use for |
| 3395 |
28 May 07 |
nicklas |
336 |
entering values for the annotation type. You can select |
| 3395 |
28 May 07 |
nicklas |
337 |
between three different options: |
| 3395 |
28 May 07 |
nicklas |
338 |
<itemizedlist> |
| 3395 |
28 May 07 |
nicklas |
339 |
<listitem> |
| 3395 |
28 May 07 |
nicklas |
340 |
<para> |
| 3395 |
28 May 07 |
nicklas |
341 |
<guilabel>text box</guilabel>: The user must enter the value |
| 3395 |
28 May 07 |
nicklas |
342 |
in a free-text box. |
| 3395 |
28 May 07 |
nicklas |
343 |
</para> |
| 3395 |
28 May 07 |
nicklas |
344 |
</listitem> |
| 3395 |
28 May 07 |
nicklas |
345 |
<listitem> |
| 3395 |
28 May 07 |
nicklas |
346 |
<para> |
| 3395 |
28 May 07 |
nicklas |
347 |
<guilabel>selection list</guilabel>: The user must select |
| 3395 |
28 May 07 |
nicklas |
348 |
values from a list of predefined values. |
| 3395 |
28 May 07 |
nicklas |
349 |
</para> |
| 3395 |
28 May 07 |
nicklas |
350 |
</listitem> |
| 3395 |
28 May 07 |
nicklas |
351 |
<listitem> |
| 3395 |
28 May 07 |
nicklas |
352 |
<para> |
| 3395 |
28 May 07 |
nicklas |
353 |
<guilabel>radiobuttons/checkboxes</guilabel>: The user must |
| 3395 |
28 May 07 |
nicklas |
354 |
select values by marking checkboxes or radiobuttons. |
| 3395 |
28 May 07 |
nicklas |
355 |
</para> |
| 3395 |
28 May 07 |
nicklas |
356 |
</listitem> |
| 3395 |
28 May 07 |
nicklas |
357 |
</itemizedlist> |
| 3395 |
28 May 07 |
nicklas |
358 |
|
| 3395 |
28 May 07 |
nicklas |
359 |
The last two options requires that a list of values are |
| 3395 |
28 May 07 |
nicklas |
360 |
available. Enter possible values in the <guilabel>Values</guilabel> |
| 3395 |
28 May 07 |
nicklas |
361 |
which will be activated automatically. |
| 3395 |
28 May 07 |
nicklas |
362 |
</para> |
| 3395 |
28 May 07 |
nicklas |
363 |
<tip> |
| 3395 |
28 May 07 |
nicklas |
364 |
<para> |
| 3395 |
28 May 07 |
nicklas |
365 |
In term of usability, a drop-down |
| 3395 |
28 May 07 |
nicklas |
366 |
list can be more easily |
| 3395 |
28 May 07 |
nicklas |
367 |
navigated especially when the |
| 3395 |
28 May 07 |
nicklas |
368 |
number of possible values is |
| 4487 |
08 Sep 08 |
jari |
369 |
large, and because selection-list |
| 3395 |
28 May 07 |
nicklas |
370 |
and drop-down list allow use of |
| 3395 |
28 May 07 |
nicklas |
371 |
arrow and tab for selection. |
| 3395 |
28 May 07 |
nicklas |
372 |
</para> |
| 3395 |
28 May 07 |
nicklas |
373 |
</tip> |
| 3395 |
28 May 07 |
nicklas |
374 |
</listitem> |
| 3395 |
28 May 07 |
nicklas |
375 |
</varlistentry> |
| 3395 |
28 May 07 |
nicklas |
376 |
|
| 3395 |
28 May 07 |
nicklas |
377 |
<varlistentry> |
| 3395 |
28 May 07 |
nicklas |
378 |
<term><guilabel>Min/max value</guilabel></term> |
| 3395 |
28 May 07 |
nicklas |
379 |
<listitem> |
| 3395 |
28 May 07 |
nicklas |
380 |
<para> |
| 3395 |
28 May 07 |
nicklas |
381 |
Available for numerical annotation types only. |
| 3395 |
28 May 07 |
nicklas |
382 |
Specifies the minimum and maximum allowed value. |
| 3395 |
28 May 07 |
nicklas |
383 |
If left empty, the bound(s) are undefined and any |
| 3395 |
28 May 07 |
nicklas |
384 |
value is allowed. |
| 3395 |
28 May 07 |
nicklas |
385 |
</para> |
| 3395 |
28 May 07 |
nicklas |
386 |
</listitem> |
| 3395 |
28 May 07 |
nicklas |
387 |
</varlistentry> |
| 3395 |
28 May 07 |
nicklas |
388 |
|
| 3395 |
28 May 07 |
nicklas |
389 |
<varlistentry> |
| 3395 |
28 May 07 |
nicklas |
390 |
<term><guilabel>Max length</guilabel></term> |
| 3395 |
28 May 07 |
nicklas |
391 |
<listitem> |
| 3395 |
28 May 07 |
nicklas |
392 |
<para> |
| 3395 |
28 May 07 |
nicklas |
393 |
The maximum allowed length of a string annotation value. |
| 3395 |
28 May 07 |
nicklas |
394 |
If empty, 255 is the maximum length. If you need longer |
| 3395 |
28 May 07 |
nicklas |
395 |
values than that, use a <emphasis>text</emphasis> |
| 3395 |
28 May 07 |
nicklas |
396 |
annotation type. |
| 3395 |
28 May 07 |
nicklas |
397 |
</para> |
| 3395 |
28 May 07 |
nicklas |
398 |
</listitem> |
| 3395 |
28 May 07 |
nicklas |
399 |
</varlistentry> |
| 3395 |
28 May 07 |
nicklas |
400 |
|
| 3395 |
28 May 07 |
nicklas |
401 |
<varlistentry> |
| 3395 |
28 May 07 |
nicklas |
402 |
<term><guilabel>Input box width/height</guilabel></term> |
| 3395 |
28 May 07 |
nicklas |
403 |
<listitem> |
| 3395 |
28 May 07 |
nicklas |
404 |
<para> |
| 3395 |
28 May 07 |
nicklas |
405 |
A suggested display width and height of the element |
| 3395 |
28 May 07 |
nicklas |
406 |
used for input. These values are ignored in the current |
| 3395 |
28 May 07 |
nicklas |
407 |
implementation. |
| 3395 |
28 May 07 |
nicklas |
408 |
</para> |
| 3395 |
28 May 07 |
nicklas |
409 |
</listitem> |
| 3395 |
28 May 07 |
nicklas |
410 |
</varlistentry> |
| 3395 |
28 May 07 |
nicklas |
411 |
|
| 3395 |
28 May 07 |
nicklas |
412 |
<varlistentry> |
| 3395 |
28 May 07 |
nicklas |
413 |
<term><guilabel>Values</guilabel></term> |
| 3395 |
28 May 07 |
nicklas |
414 |
<listitem> |
| 3395 |
28 May 07 |
nicklas |
415 |
<para> |
| 3395 |
28 May 07 |
nicklas |
416 |
A list of predefined values that the user is allowed |
| 3395 |
28 May 07 |
nicklas |
417 |
to select from. This option is only activated if the |
| 3395 |
28 May 07 |
nicklas |
418 |
<guilabel>Interface</guilabel> option is set |
| 3395 |
28 May 07 |
nicklas |
419 |
to <guilabel>selection list</guilabel> or |
| 3395 |
28 May 07 |
nicklas |
420 |
<guilabel>radiobuttons/checkboxes</guilabel>. |
| 3395 |
28 May 07 |
nicklas |
421 |
Actual values can be supplied using one line for each |
| 3395 |
28 May 07 |
nicklas |
422 |
value (a return entry is used as separator). |
| 3395 |
28 May 07 |
nicklas |
423 |
</para> |
| 3395 |
28 May 07 |
nicklas |
424 |
</listitem> |
| 3395 |
28 May 07 |
nicklas |
425 |
</varlistentry> |
| 3395 |
28 May 07 |
nicklas |
426 |
|
| 3395 |
28 May 07 |
nicklas |
427 |
</variablelist> |
| 3395 |
28 May 07 |
nicklas |
428 |
|
| 3395 |
28 May 07 |
nicklas |
429 |
<seeother> |
| 3395 |
28 May 07 |
nicklas |
430 |
<other external_id="annotationtype.edit">Properties</other> |
| 3395 |
28 May 07 |
nicklas |
431 |
<other external_id="annotationtype.edit.items">Item types</other> |
| 4561 |
06 Oct 08 |
nicklas |
432 |
<other external_id="annotationtype.edit.units">Units</other> |
| 3395 |
28 May 07 |
nicklas |
433 |
<other external_id="annotationtype.edit.categories">Categories</other> |
| 3395 |
28 May 07 |
nicklas |
434 |
</seeother> |
| 3395 |
28 May 07 |
nicklas |
435 |
</helptext> |
| 3395 |
28 May 07 |
nicklas |
436 |
</sect2> |
| 3395 |
28 May 07 |
nicklas |
437 |
|
| 3395 |
28 May 07 |
nicklas |
438 |
<sect2 id="annotations.types.items"> |
| 3395 |
28 May 07 |
nicklas |
439 |
<title>Item types</title> |
| 3395 |
28 May 07 |
nicklas |
440 |
|
| 3395 |
28 May 07 |
nicklas |
441 |
<figure |
| 3395 |
28 May 07 |
nicklas |
442 |
id="annotations.figures.annotationtype.items"> |
| 3395 |
28 May 07 |
nicklas |
443 |
<title>Annotation type items</title> |
| 3395 |
28 May 07 |
nicklas |
444 |
<screenshot> |
| 3395 |
28 May 07 |
nicklas |
445 |
<mediaobject> |
| 3395 |
28 May 07 |
nicklas |
446 |
<imageobject> |
| 3395 |
28 May 07 |
nicklas |
447 |
<imagedata |
| 3395 |
28 May 07 |
nicklas |
448 |
fileref="figures/annotationtype_items.png" format="PNG" /> |
| 3395 |
28 May 07 |
nicklas |
449 |
</imageobject> |
| 3395 |
28 May 07 |
nicklas |
450 |
</mediaobject> |
| 3395 |
28 May 07 |
nicklas |
451 |
</screenshot> |
| 3395 |
28 May 07 |
nicklas |
452 |
</figure> |
| 3395 |
28 May 07 |
nicklas |
453 |
|
| 3395 |
28 May 07 |
nicklas |
454 |
<helptext external_id="annotationtype.edit.items" |
| 3395 |
28 May 07 |
nicklas |
455 |
title="Item types"> |
| 3395 |
28 May 07 |
nicklas |
456 |
|
| 3395 |
28 May 07 |
nicklas |
457 |
<para> |
| 3395 |
28 May 07 |
nicklas |
458 |
On this tab you select the item types that you wish to |
| 3395 |
28 May 07 |
nicklas |
459 |
annotate with the annotation type. Simply use |
| 3395 |
28 May 07 |
nicklas |
460 |
left and right buttons to move selection options |
| 3395 |
28 May 07 |
nicklas |
461 |
between the <guilabel>Enabled for</guilabel> |
| 3395 |
28 May 07 |
nicklas |
462 |
and <guilabel>Disabled for</guilabel> lists. |
| 3395 |
28 May 07 |
nicklas |
463 |
</para> |
| 3395 |
28 May 07 |
nicklas |
464 |
|
| 3395 |
28 May 07 |
nicklas |
465 |
<note> |
| 3395 |
28 May 07 |
nicklas |
466 |
<para> |
| 3395 |
28 May 07 |
nicklas |
467 |
If the annotation type has been marked as a |
| 5795 |
10 Oct 11 |
nicklas |
468 |
<guilabel>Protocol parameter</guilabel>, these settings are |
| 3395 |
28 May 07 |
nicklas |
469 |
ignored, with one exception. If you wish to view parameter |
| 3395 |
28 May 07 |
nicklas |
470 |
values in the list view for a specific item type you must select |
| 3395 |
28 May 07 |
nicklas |
471 |
the item type here. Otherwise the parameter will not be present |
| 3395 |
28 May 07 |
nicklas |
472 |
as a displayable column. |
| 3395 |
28 May 07 |
nicklas |
473 |
</para> |
| 3395 |
28 May 07 |
nicklas |
474 |
</note> |
| 3395 |
28 May 07 |
nicklas |
475 |
|
| 3395 |
28 May 07 |
nicklas |
476 |
<seeother> |
| 3395 |
28 May 07 |
nicklas |
477 |
<other external_id="annotationtype.edit">Properties</other> |
| 3395 |
28 May 07 |
nicklas |
478 |
<other external_id="annotationtype.edit.options">Options</other> |
| 4561 |
06 Oct 08 |
nicklas |
479 |
<other external_id="annotationtype.edit.units">Units</other> |
| 3395 |
28 May 07 |
nicklas |
480 |
<other external_id="annotationtype.edit.categories">Categories</other> |
| 3395 |
28 May 07 |
nicklas |
481 |
</seeother> |
| 3395 |
28 May 07 |
nicklas |
482 |
</helptext> |
| 3395 |
28 May 07 |
nicklas |
483 |
</sect2> |
| 3395 |
28 May 07 |
nicklas |
484 |
|
| 4561 |
06 Oct 08 |
nicklas |
485 |
<sect2 id="annotations.types.units"> |
| 4561 |
06 Oct 08 |
nicklas |
486 |
<title>Units</title> |
| 4561 |
06 Oct 08 |
nicklas |
487 |
|
| 4561 |
06 Oct 08 |
nicklas |
488 |
<figure |
| 4561 |
06 Oct 08 |
nicklas |
489 |
id="annotations.figures.annotationtype.units"> |
| 4561 |
06 Oct 08 |
nicklas |
490 |
<title>Annotation type units</title> |
| 4561 |
06 Oct 08 |
nicklas |
491 |
<screenshot> |
| 4561 |
06 Oct 08 |
nicklas |
492 |
<mediaobject> |
| 4561 |
06 Oct 08 |
nicklas |
493 |
<imageobject> |
| 4561 |
06 Oct 08 |
nicklas |
494 |
<imagedata |
| 4561 |
06 Oct 08 |
nicklas |
495 |
fileref="figures/annotationtype_units.png" format="PNG" /> |
| 4561 |
06 Oct 08 |
nicklas |
496 |
</imageobject> |
| 4561 |
06 Oct 08 |
nicklas |
497 |
</mediaobject> |
| 4561 |
06 Oct 08 |
nicklas |
498 |
</screenshot> |
| 4561 |
06 Oct 08 |
nicklas |
499 |
</figure> |
| 4561 |
06 Oct 08 |
nicklas |
500 |
|
| 4561 |
06 Oct 08 |
nicklas |
501 |
<helptext external_id="annotationtype.edit.units" |
| 4561 |
06 Oct 08 |
nicklas |
502 |
title="Units"> |
| 4561 |
06 Oct 08 |
nicklas |
503 |
|
| 4561 |
06 Oct 08 |
nicklas |
504 |
<para> |
| 4561 |
06 Oct 08 |
nicklas |
505 |
Numerical annotation types can optionally be given a quantity and unit. |
| 4561 |
06 Oct 08 |
nicklas |
506 |
</para> |
| 4561 |
06 Oct 08 |
nicklas |
507 |
|
| 4561 |
06 Oct 08 |
nicklas |
508 |
<variablelist> |
| 4561 |
06 Oct 08 |
nicklas |
509 |
<varlistentry> |
| 4561 |
06 Oct 08 |
nicklas |
510 |
<term><guilabel>Quantity</guilabel></term> |
| 4561 |
06 Oct 08 |
nicklas |
511 |
<listitem> |
| 4561 |
06 Oct 08 |
nicklas |
512 |
<para> |
| 4561 |
06 Oct 08 |
nicklas |
513 |
Select which quantity to use for the annotation type. If you |
| 4561 |
06 Oct 08 |
nicklas |
514 |
don't want to use units, select the <emphasis>do not use units</emphasis> |
| 4561 |
06 Oct 08 |
nicklas |
515 |
option. |
| 4561 |
06 Oct 08 |
nicklas |
516 |
</para> |
| 4566 |
07 Oct 08 |
nicklas |
517 |
<note> |
| 4566 |
07 Oct 08 |
nicklas |
518 |
<title>The quantity can't be changed later</title> |
| 4566 |
07 Oct 08 |
nicklas |
519 |
<para> |
| 4566 |
07 Oct 08 |
nicklas |
520 |
Once a quantity has been selected and saved for an |
| 4566 |
07 Oct 08 |
nicklas |
521 |
annotation type, it is not possible to change it to another |
| 4566 |
07 Oct 08 |
nicklas |
522 |
quantity. |
| 4566 |
07 Oct 08 |
nicklas |
523 |
</para> |
| 4566 |
07 Oct 08 |
nicklas |
524 |
</note> |
| 4561 |
06 Oct 08 |
nicklas |
525 |
</listitem> |
| 4561 |
06 Oct 08 |
nicklas |
526 |
</varlistentry> |
| 4561 |
06 Oct 08 |
nicklas |
527 |
<varlistentry> |
| 4561 |
06 Oct 08 |
nicklas |
528 |
<term><guilabel>Default unit</guilabel></term> |
| 4561 |
06 Oct 08 |
nicklas |
529 |
<listitem> |
| 4561 |
06 Oct 08 |
nicklas |
530 |
<para> |
| 4561 |
06 Oct 08 |
nicklas |
531 |
This list will be populated with units from the selected |
| 4561 |
06 Oct 08 |
nicklas |
532 |
quantity. You must select one default unit which is the unit |
| 4561 |
06 Oct 08 |
nicklas |
533 |
that is used if a user leaves out the unit when annotating |
| 4561 |
06 Oct 08 |
nicklas |
534 |
an item. The selected unit is also the unit that is used internally |
| 4561 |
06 Oct 08 |
nicklas |
535 |
when storing the values in the database. |
| 4561 |
06 Oct 08 |
nicklas |
536 |
</para> |
| 4561 |
06 Oct 08 |
nicklas |
537 |
<warning> |
| 4561 |
06 Oct 08 |
nicklas |
538 |
<title>Do not change the default unit</title> |
| 4561 |
06 Oct 08 |
nicklas |
539 |
<para> |
| 4561 |
06 Oct 08 |
nicklas |
540 |
If you change the default unit for an existing annotation type, |
| 4561 |
06 Oct 08 |
nicklas |
541 |
all annotation values that exists for it, must be converted to the |
| 4561 |
06 Oct 08 |
nicklas |
542 |
new unit. This may result in loss of precision due to rounding/truncation |
| 4561 |
06 Oct 08 |
nicklas |
543 |
errors. |
| 4561 |
06 Oct 08 |
nicklas |
544 |
</para> |
| 4561 |
06 Oct 08 |
nicklas |
545 |
</warning> |
| 4561 |
06 Oct 08 |
nicklas |
546 |
</listitem> |
| 4561 |
06 Oct 08 |
nicklas |
547 |
</varlistentry> |
| 4561 |
06 Oct 08 |
nicklas |
548 |
|
| 4561 |
06 Oct 08 |
nicklas |
549 |
<varlistentry> |
| 4561 |
06 Oct 08 |
nicklas |
550 |
<term><guilabel>Use units</guilabel></term> |
| 4561 |
06 Oct 08 |
nicklas |
551 |
<listitem> |
| 4561 |
06 Oct 08 |
nicklas |
552 |
<para> |
| 4561 |
06 Oct 08 |
nicklas |
553 |
By default, all units of the selected quantity can be used when |
| 4561 |
06 Oct 08 |
nicklas |
554 |
annotating items. If you want, you may force the users to use |
| 4561 |
06 Oct 08 |
nicklas |
555 |
some specific units by moving units into the <emphasis>Use units</emphasis> |
| 4561 |
06 Oct 08 |
nicklas |
556 |
list. This is recommended since the range of available units is usually |
| 4561 |
06 Oct 08 |
nicklas |
557 |
quite large. For example, if the weight of something is normally |
| 4561 |
06 Oct 08 |
nicklas |
558 |
measured in milligrams, it may make sense to leave out kilograms, and |
| 4561 |
06 Oct 08 |
nicklas |
559 |
only use microgram, milligram and gram. |
| 4561 |
06 Oct 08 |
nicklas |
560 |
</para> |
| 4561 |
06 Oct 08 |
nicklas |
561 |
</listitem> |
| 4561 |
06 Oct 08 |
nicklas |
562 |
</varlistentry> |
| 4561 |
06 Oct 08 |
nicklas |
563 |
|
| 4561 |
06 Oct 08 |
nicklas |
564 |
</variablelist> |
| 4561 |
06 Oct 08 |
nicklas |
565 |
|
| 4561 |
06 Oct 08 |
nicklas |
566 |
<seeother> |
| 4561 |
06 Oct 08 |
nicklas |
567 |
<other external_id="annotationtype.edit">Properties</other> |
| 4561 |
06 Oct 08 |
nicklas |
568 |
<other external_id="annotationtype.edit.options">Options</other> |
| 4561 |
06 Oct 08 |
nicklas |
569 |
<other external_id="annotationtype.edit.items">Item types</other> |
| 4561 |
06 Oct 08 |
nicklas |
570 |
<other external_id="annotationtype.edit.categories">Categories</other> |
| 4561 |
06 Oct 08 |
nicklas |
571 |
</seeother> |
| 4561 |
06 Oct 08 |
nicklas |
572 |
|
| 4561 |
06 Oct 08 |
nicklas |
573 |
</helptext> |
| 4561 |
06 Oct 08 |
nicklas |
574 |
</sect2> |
| 4561 |
06 Oct 08 |
nicklas |
575 |
|
| 3395 |
28 May 07 |
nicklas |
576 |
<sect2 id="annotations.types.categories"> |
| 3395 |
28 May 07 |
nicklas |
577 |
<title>Categories</title> |
| 3395 |
28 May 07 |
nicklas |
578 |
|
| 5795 |
10 Oct 11 |
nicklas |
579 |
<figure |
| 5795 |
10 Oct 11 |
nicklas |
580 |
id="annotations.figures.annotationtype.categories"> |
| 5795 |
10 Oct 11 |
nicklas |
581 |
<title>Annotation type categories</title> |
| 5795 |
10 Oct 11 |
nicklas |
582 |
<screenshot> |
| 5795 |
10 Oct 11 |
nicklas |
583 |
<mediaobject> |
| 5795 |
10 Oct 11 |
nicklas |
584 |
<imageobject> |
| 5795 |
10 Oct 11 |
nicklas |
585 |
<imagedata |
| 5795 |
10 Oct 11 |
nicklas |
586 |
fileref="figures/annotationtype_categories.png" format="PNG" /> |
| 5795 |
10 Oct 11 |
nicklas |
587 |
</imageobject> |
| 5795 |
10 Oct 11 |
nicklas |
588 |
</mediaobject> |
| 5795 |
10 Oct 11 |
nicklas |
589 |
</screenshot> |
| 5795 |
10 Oct 11 |
nicklas |
590 |
</figure> |
| 5795 |
10 Oct 11 |
nicklas |
591 |
|
| 3395 |
28 May 07 |
nicklas |
592 |
<helptext external_id="annotationtype.edit.categories" |
| 3395 |
28 May 07 |
nicklas |
593 |
title="Categories"> |
| 3395 |
28 May 07 |
nicklas |
594 |
|
| 3395 |
28 May 07 |
nicklas |
595 |
<para> |
| 3395 |
28 May 07 |
nicklas |
596 |
Annotation type can be grouped together by |
| 3395 |
28 May 07 |
nicklas |
597 |
placing them in one or more categories. This |
| 3395 |
28 May 07 |
nicklas |
598 |
enhances display by avoid overcrowding the list |
| 3395 |
28 May 07 |
nicklas |
599 |
of annotation types presented to users. It also |
| 3395 |
28 May 07 |
nicklas |
600 |
allows to improve the display of information. |
| 3395 |
28 May 07 |
nicklas |
601 |
</para> |
| 3395 |
28 May 07 |
nicklas |
602 |
|
| 3395 |
28 May 07 |
nicklas |
603 |
<para> |
| 3395 |
28 May 07 |
nicklas |
604 |
The <guilabel>Categories</guilabel> list displays |
| 3395 |
28 May 07 |
nicklas |
605 |
the currently associated categories. Use the |
| 3395 |
28 May 07 |
nicklas |
606 |
<guibutton>Add categories</guibutton> button |
| 3395 |
28 May 07 |
nicklas |
607 |
to add more categories, or the <guilabel>Remove</guilabel> |
| 3395 |
28 May 07 |
nicklas |
608 |
button to remove the selected categories. |
| 3395 |
28 May 07 |
nicklas |
609 |
</para> |
| 5795 |
10 Oct 11 |
nicklas |
610 |
|
| 5795 |
10 Oct 11 |
nicklas |
611 |
<tip> |
| 5795 |
10 Oct 11 |
nicklas |
612 |
<title>Create categories with the same name as item subtypes</title> |
| 5795 |
10 Oct 11 |
nicklas |
613 |
<para> |
| 5795 |
10 Oct 11 |
nicklas |
614 |
If you, for example, have defined multiple subtypes of extracts |
| 5795 |
10 Oct 11 |
nicklas |
615 |
(see <xref linkend="subtypes" />), |
| 5795 |
10 Oct 11 |
nicklas |
616 |
it usually so that some annotation types are only intended for |
| 5795 |
10 Oct 11 |
nicklas |
617 |
one subtype while some other annotation types are only intended |
| 5795 |
10 Oct 11 |
nicklas |
618 |
for the other subtype. If you create categories with the same name |
| 5795 |
10 Oct 11 |
nicklas |
619 |
as the item subtypes, BASE will automatically select the corresponding |
| 5795 |
10 Oct 11 |
nicklas |
620 |
category when annotating an extract with a subtype. This makes the interface |
| 5795 |
10 Oct 11 |
nicklas |
621 |
cleaner and easier to use since irrelevant annotation types are hidden. |
| 5795 |
10 Oct 11 |
nicklas |
622 |
Note that it is possible for annotations to be part of more than one |
| 5795 |
10 Oct 11 |
nicklas |
623 |
category so it is also possible to define annotation types that are |
| 5795 |
10 Oct 11 |
nicklas |
624 |
intended for all types of extracts by including them in both categories. |
| 5795 |
10 Oct 11 |
nicklas |
625 |
</para> |
| 5795 |
10 Oct 11 |
nicklas |
626 |
</tip> |
| 5795 |
10 Oct 11 |
nicklas |
627 |
|
| 3395 |
28 May 07 |
nicklas |
628 |
<seeother> |
| 3395 |
28 May 07 |
nicklas |
629 |
<other external_id="annotationtype.edit">Properties</other> |
| 3395 |
28 May 07 |
nicklas |
630 |
<other external_id="annotationtype.edit.options">Options</other> |
| 3395 |
28 May 07 |
nicklas |
631 |
<other external_id="annotationtype.edit.items">Item types</other> |
| 3395 |
28 May 07 |
nicklas |
632 |
</seeother> |
| 3395 |
28 May 07 |
nicklas |
633 |
</helptext> |
| 3395 |
28 May 07 |
nicklas |
634 |
</sect2> |
| 3395 |
28 May 07 |
nicklas |
635 |
</sect1> |
| 3395 |
28 May 07 |
nicklas |
636 |
|
| 3396 |
28 May 07 |
nicklas |
637 |
<sect1 id="annotations.annotating"> |
| 5782 |
04 Oct 11 |
nicklas |
638 |
<?dbhtml filename="annotating.html" ?> |
| 3396 |
28 May 07 |
nicklas |
639 |
<title>Annotating items</title> |
| 3396 |
28 May 07 |
nicklas |
640 |
|
| 3396 |
28 May 07 |
nicklas |
641 |
<para> |
| 3396 |
28 May 07 |
nicklas |
642 |
Entering annotation values follow the same pattern |
| 3396 |
28 May 07 |
nicklas |
643 |
for all items that can have annotations. They all have |
| 3396 |
28 May 07 |
nicklas |
644 |
a <guilabel>Annotations & parameters</guilabel> tab |
| 3396 |
28 May 07 |
nicklas |
645 |
in their edit view. On this tab you can specify values |
| 3396 |
28 May 07 |
nicklas |
646 |
for all annotation types assigned to the type of item, |
| 3396 |
28 May 07 |
nicklas |
647 |
and all parameters that are attached to the protocol |
| 3396 |
28 May 07 |
nicklas |
648 |
used to create the item. Some items, for example |
| 3396 |
28 May 07 |
nicklas |
649 |
<emphasis>biosources</emphasis> and <emphasis>array designs</emphasis> |
| 3487 |
13 Jun 07 |
peter |
650 |
cannot have a protocol. In their case the tab is labelled |
| 3396 |
28 May 07 |
nicklas |
651 |
<guilabel>Annotations</guilabel>. |
| 3396 |
28 May 07 |
nicklas |
652 |
</para> |
| 3396 |
28 May 07 |
nicklas |
653 |
|
| 3396 |
28 May 07 |
nicklas |
654 |
<figure |
| 3396 |
28 May 07 |
nicklas |
655 |
id="annotations.figures.annotate"> |
| 3396 |
28 May 07 |
nicklas |
656 |
<title>Annotating a sample</title> |
| 3396 |
28 May 07 |
nicklas |
657 |
<screenshot> |
| 3396 |
28 May 07 |
nicklas |
658 |
<mediaobject> |
| 3396 |
28 May 07 |
nicklas |
659 |
<imageobject> |
| 3396 |
28 May 07 |
nicklas |
660 |
<imagedata |
| 3396 |
28 May 07 |
nicklas |
661 |
fileref="figures/annotate.png" format="PNG" /> |
| 3396 |
28 May 07 |
nicklas |
662 |
</imageobject> |
| 3396 |
28 May 07 |
nicklas |
663 |
</mediaobject> |
| 3396 |
28 May 07 |
nicklas |
664 |
</screenshot> |
| 3396 |
28 May 07 |
nicklas |
665 |
</figure> |
| 3395 |
28 May 07 |
nicklas |
666 |
|
| 3396 |
28 May 07 |
nicklas |
667 |
<helptext external_id="annotations.edit" |
| 3396 |
28 May 07 |
nicklas |
668 |
title="Annotations & parameters"> |
| 3396 |
28 May 07 |
nicklas |
669 |
|
| 3396 |
28 May 07 |
nicklas |
670 |
<para> |
| 6961 |
01 Oct 15 |
nicklas |
671 |
All possible annotation types are listed under the |
| 6961 |
01 Oct 15 |
nicklas |
672 |
<guilabel>Primary annotations</guilabel> section. Click |
| 6961 |
01 Oct 15 |
nicklas |
673 |
on an entry in the list to display a form for entering |
| 6961 |
01 Oct 15 |
nicklas |
674 |
a value for the annotation. Depending |
| 3396 |
28 May 07 |
nicklas |
675 |
on the options set on the annotation type the form may be a simple |
| 3396 |
28 May 07 |
nicklas |
676 |
free text field, a list of checkboxes or radiobuttons, or |
| 3396 |
28 May 07 |
nicklas |
677 |
something else. |
| 3396 |
28 May 07 |
nicklas |
678 |
</para> |
| 3396 |
28 May 07 |
nicklas |
679 |
|
| 3396 |
28 May 07 |
nicklas |
680 |
<para> |
| 6961 |
01 Oct 15 |
nicklas |
681 |
Annotation types with an <guilabel>x</guilabel> in front |
| 3396 |
28 May 07 |
nicklas |
682 |
of their names already have a value. |
| 3396 |
28 May 07 |
nicklas |
683 |
</para> |
| 3396 |
28 May 07 |
nicklas |
684 |
|
| 3396 |
28 May 07 |
nicklas |
685 |
<para> |
| 3400 |
29 May 07 |
nicklas |
686 |
Annotation types marked with angle brackets |
| 3400 |
29 May 07 |
nicklas |
687 |
<nohelp> |
| 6961 |
01 Oct 15 |
nicklas |
688 |
(<guiicon><inlinemediaobject><imageobject><imagedata fileref="figures/parameter.png" format="PNG" |
| 6961 |
01 Oct 15 |
nicklas |
689 |
/></imageobject></inlinemediaobject></guiicon>) |
| 3950 |
12 Nov 07 |
martin |
690 |
</nohelp> |
| 3400 |
29 May 07 |
nicklas |
691 |
are protocol parameters. |
| 3396 |
28 May 07 |
nicklas |
692 |
</para> |
| 3396 |
28 May 07 |
nicklas |
693 |
|
| 3396 |
28 May 07 |
nicklas |
694 |
<para> |
| 3396 |
28 May 07 |
nicklas |
695 |
Select an option in the <guilabel>Categories</guilabel> list to filter the |
| 3396 |
28 May 07 |
nicklas |
696 |
annotation types based on the categories |
| 3396 |
28 May 07 |
nicklas |
697 |
they belong to. This list contains all available |
| 3396 |
28 May 07 |
nicklas |
698 |
categories, and three special ones: |
| 3396 |
28 May 07 |
nicklas |
699 |
<itemizedlist> |
| 3396 |
28 May 07 |
nicklas |
700 |
<listitem> |
| 3396 |
28 May 07 |
nicklas |
701 |
<para> |
| 4487 |
08 Sep 08 |
jari |
702 |
<guilabel>all</guilabel>: Display all annotation types |
| 3396 |
28 May 07 |
nicklas |
703 |
</para> |
| 3396 |
28 May 07 |
nicklas |
704 |
</listitem> |
| 3396 |
28 May 07 |
nicklas |
705 |
<listitem> |
| 3396 |
28 May 07 |
nicklas |
706 |
<para> |
| 3396 |
28 May 07 |
nicklas |
707 |
<guilabel>protocol parameters</guilabel>: Display only |
| 3396 |
28 May 07 |
nicklas |
708 |
those annotation types that are parameters to the current |
| 3396 |
28 May 07 |
nicklas |
709 |
protocol. |
| 3396 |
28 May 07 |
nicklas |
710 |
</para> |
| 3396 |
28 May 07 |
nicklas |
711 |
</listitem> |
| 3396 |
28 May 07 |
nicklas |
712 |
<listitem> |
| 3396 |
28 May 07 |
nicklas |
713 |
<para> |
| 3400 |
29 May 07 |
nicklas |
714 |
<guilabel>uncategorized</guilabel>: Display only annotation types |
| 3487 |
13 Jun 07 |
peter |
715 |
that has not been put into a category. |
| 3396 |
28 May 07 |
nicklas |
716 |
</para> |
| 3396 |
28 May 07 |
nicklas |
717 |
</listitem> |
| 3396 |
28 May 07 |
nicklas |
718 |
</itemizedlist> |
| 3396 |
28 May 07 |
nicklas |
719 |
</para> |
| 3396 |
28 May 07 |
nicklas |
720 |
|
| 6961 |
01 Oct 15 |
nicklas |
721 |
|
| 3400 |
29 May 07 |
nicklas |
722 |
<seeother> |
| 6961 |
01 Oct 15 |
nicklas |
723 |
<other external_id="annotations.inherit">Inherit annotations</other> |
| 7341 |
18 Apr 17 |
nicklas |
724 |
<other external_id="annotations.project-specific">Project-specific annotations</other> |
| 3400 |
29 May 07 |
nicklas |
725 |
</seeother> |
| 3396 |
28 May 07 |
nicklas |
726 |
|
| 3396 |
28 May 07 |
nicklas |
727 |
</helptext> |
| 3396 |
28 May 07 |
nicklas |
728 |
|
| 7341 |
18 Apr 17 |
nicklas |
729 |
<sect2 id="annotations.project-specific"> |
| 7341 |
18 Apr 17 |
nicklas |
730 |
<title>Project-specific annotations</title> |
| 7341 |
18 Apr 17 |
nicklas |
731 |
<para> |
| 7341 |
18 Apr 17 |
nicklas |
732 |
<helptext external_id="annotations.project-specific" |
| 7341 |
18 Apr 17 |
nicklas |
733 |
title="Project-specific annotation values"> |
| 7341 |
18 Apr 17 |
nicklas |
734 |
|
| 7341 |
18 Apr 17 |
nicklas |
735 |
<para> |
| 7341 |
18 Apr 17 |
nicklas |
736 |
An annotation for an annotation type that has the |
| 7341 |
18 Apr 17 |
nicklas |
737 |
<guilabel>Projects annotations</guilabel> |
| 7341 |
18 Apr 17 |
nicklas |
738 |
feature enabled can be edited more or less in the |
| 7341 |
18 Apr 17 |
nicklas |
739 |
same way as any other annotation. If an item is edited when |
| 7341 |
18 Apr 17 |
nicklas |
740 |
no project is active only the <guilabel>default value</guilabel> |
| 7341 |
18 Apr 17 |
nicklas |
741 |
is accessible. It can be created, modified and deleted just as |
| 7341 |
18 Apr 17 |
nicklas |
742 |
any other annotation, but note that deleting the default value |
| 7341 |
18 Apr 17 |
nicklas |
743 |
will not delete any existing project-specific values. |
| 7341 |
18 Apr 17 |
nicklas |
744 |
</para> |
| 7341 |
18 Apr 17 |
nicklas |
745 |
|
| 7341 |
18 Apr 17 |
nicklas |
746 |
<para> |
| 7341 |
18 Apr 17 |
nicklas |
747 |
If an item is edited when a project is active, and it doesn't |
| 7341 |
18 Apr 17 |
nicklas |
748 |
yet have a project-specific value, the default value is visible. |
| 7341 |
18 Apr 17 |
nicklas |
749 |
If the value is modified, a project-specific annotation is automatically |
| 7341 |
18 Apr 17 |
nicklas |
750 |
created (the default value is never modified when a project is |
| 7341 |
18 Apr 17 |
nicklas |
751 |
active). The project-specific value may be deleted to bring back |
| 7341 |
18 Apr 17 |
nicklas |
752 |
the default value again. Note that changing the project-specific |
| 7341 |
18 Apr 17 |
nicklas |
753 |
value back to the original value (=same as the default) will not |
| 7341 |
18 Apr 17 |
nicklas |
754 |
remove the project-specific value. |
| 7341 |
18 Apr 17 |
nicklas |
755 |
</para> |
| 7341 |
18 Apr 17 |
nicklas |
756 |
|
| 7341 |
18 Apr 17 |
nicklas |
757 |
<seeother> |
| 7341 |
18 Apr 17 |
nicklas |
758 |
<other external_id="annotations.edit">Annotations and parameters</other> |
| 7341 |
18 Apr 17 |
nicklas |
759 |
<other external_id="annotationtype.edit"></other> |
| 7341 |
18 Apr 17 |
nicklas |
760 |
</seeother> |
| 7341 |
18 Apr 17 |
nicklas |
761 |
</helptext> |
| 7341 |
18 Apr 17 |
nicklas |
762 |
</para> |
| 7341 |
18 Apr 17 |
nicklas |
763 |
</sect2> |
| 7341 |
18 Apr 17 |
nicklas |
764 |
|
| 3396 |
28 May 07 |
nicklas |
765 |
<sect2 id="annotations.inheriting"> |
| 3396 |
28 May 07 |
nicklas |
766 |
<title>Inheriting annotations from other items</title> |
| 3400 |
29 May 07 |
nicklas |
767 |
|
| 6961 |
01 Oct 15 |
nicklas |
768 |
<helptext external_id="annotations.inherit" |
| 3400 |
29 May 07 |
nicklas |
769 |
title="Inherit annotations"> |
| 3400 |
29 May 07 |
nicklas |
770 |
<para> |
| 3400 |
29 May 07 |
nicklas |
771 |
An item may inherit annotations from any of it's parent items. |
| 3400 |
29 May 07 |
nicklas |
772 |
E.g. an extract can inherit annotations from the sample or biosource |
| 3400 |
29 May 07 |
nicklas |
773 |
it was created from. This is an important feature to make the |
| 3400 |
29 May 07 |
nicklas |
774 |
experimental factors work. Annotations that should be used as |
| 6961 |
01 Oct 15 |
nicklas |
775 |
experimental factors must be inherited to the root raw bioassay level. |
| 3400 |
29 May 07 |
nicklas |
776 |
<nohelp>See <xref linkend="experiments_analysis.experiment.factors" /> for more |
| 6961 |
01 Oct 15 |
nicklas |
777 |
information about experimental factors.</nohelp> Click on the |
| 6961 |
01 Oct 15 |
nicklas |
778 |
<guibutton>Inherit…</guibutton> button to open a dialog for inheriting |
| 6961 |
01 Oct 15 |
nicklas |
779 |
annotations. |
| 3400 |
29 May 07 |
nicklas |
780 |
</para> |
| 3400 |
29 May 07 |
nicklas |
781 |
|
| 6961 |
01 Oct 15 |
nicklas |
782 |
<para> |
| 6961 |
01 Oct 15 |
nicklas |
783 |
Annotations can either be inherited by reference (the default) or as a cloned value. Inheriting |
| 6961 |
01 Oct 15 |
nicklas |
784 |
by reference means that if you change the value of the source annotation the new value is automatically |
| 6961 |
01 Oct 15 |
nicklas |
785 |
picked up by all items inheriting it. A cloned annotation is a copy |
| 6961 |
01 Oct 15 |
nicklas |
786 |
of the original annotation and it is not automatically updated if the original |
| 6961 |
01 Oct 15 |
nicklas |
787 |
annotation is modified. |
| 6961 |
01 Oct 15 |
nicklas |
788 |
</para> |
| 6961 |
01 Oct 15 |
nicklas |
789 |
|
| 6961 |
01 Oct 15 |
nicklas |
790 |
<para> |
| 6961 |
01 Oct 15 |
nicklas |
791 |
Inherited and cloned annotations are listed under the <guilabel>Inherited & cloned</guilabel> |
| 6961 |
01 Oct 15 |
nicklas |
792 |
section. Inherited annotations are marked with <guiicon><inlinemediaobject><imageobject><imagedata |
| 6961 |
01 Oct 15 |
nicklas |
793 |
fileref="figures/inherited.png" format="PNG" |
| 6961 |
01 Oct 15 |
nicklas |
794 |
/></imageobject></inlinemediaobject></guiicon> and are always a references back to the original |
| 6961 |
01 Oct 15 |
nicklas |
795 |
value. Cloned annotations are marked with a double <guilabel>xx</guilabel>. Cloned annotations |
| 6961 |
01 Oct 15 |
nicklas |
796 |
that are out-of-sync with their source annotations are marked with <guiicon><inlinemediaobject><imageobject><imagedata |
| 6961 |
01 Oct 15 |
nicklas |
797 |
fileref="figures/cloned-outofsync.png" format="PNG" |
| 6961 |
01 Oct 15 |
nicklas |
798 |
/></imageobject></inlinemediaobject></guiicon>. |
| 6961 |
01 Oct 15 |
nicklas |
799 |
</para> |
| 6961 |
01 Oct 15 |
nicklas |
800 |
|
| 6961 |
01 Oct 15 |
nicklas |
801 |
<variablelist> |
| 6961 |
01 Oct 15 |
nicklas |
802 |
<varlistentry> |
| 6961 |
01 Oct 15 |
nicklas |
803 |
<term> |
| 6961 |
01 Oct 15 |
nicklas |
804 |
<guilabel>Inherit...</guilabel> |
| 6961 |
01 Oct 15 |
nicklas |
805 |
</term> |
| 6961 |
01 Oct 15 |
nicklas |
806 |
<listitem> |
| 6961 |
01 Oct 15 |
nicklas |
807 |
<para>Opens the <guilabel>Inherit annotations</guilabel> dialog (see below).</para> |
| 6961 |
01 Oct 15 |
nicklas |
808 |
</listitem> |
| 6961 |
01 Oct 15 |
nicklas |
809 |
</varlistentry> |
| 6961 |
01 Oct 15 |
nicklas |
810 |
<varlistentry> |
| 6961 |
01 Oct 15 |
nicklas |
811 |
<term> |
| 6961 |
01 Oct 15 |
nicklas |
812 |
<guilabel>Delete</guilabel> |
| 6961 |
01 Oct 15 |
nicklas |
813 |
</term> |
| 6961 |
01 Oct 15 |
nicklas |
814 |
<listitem> |
| 6961 |
01 Oct 15 |
nicklas |
815 |
<para> |
| 6961 |
01 Oct 15 |
nicklas |
816 |
Will remove values from the checked primary annotations and delete |
| 6961 |
01 Oct 15 |
nicklas |
817 |
links to inherited and cloned annotations. |
| 6961 |
01 Oct 15 |
nicklas |
818 |
</para> |
| 6961 |
01 Oct 15 |
nicklas |
819 |
</listitem> |
| 6961 |
01 Oct 15 |
nicklas |
820 |
</varlistentry> |
| 6961 |
01 Oct 15 |
nicklas |
821 |
<varlistentry> |
| 6961 |
01 Oct 15 |
nicklas |
822 |
<term> |
| 6961 |
01 Oct 15 |
nicklas |
823 |
<guilabel>Sync, Clone, Unclone</guilabel> |
| 6961 |
01 Oct 15 |
nicklas |
824 |
</term> |
| 6961 |
01 Oct 15 |
nicklas |
825 |
<listitem> |
| 6961 |
01 Oct 15 |
nicklas |
826 |
<para> |
| 6961 |
01 Oct 15 |
nicklas |
827 |
Convert between INHERITED and CLONED annotation and synchronizes |
| 6961 |
01 Oct 15 |
nicklas |
828 |
cloned annotations with their source annotation in case the values |
| 6961 |
01 Oct 15 |
nicklas |
829 |
have changed. |
| 6961 |
01 Oct 15 |
nicklas |
830 |
</para> |
| 6961 |
01 Oct 15 |
nicklas |
831 |
</listitem> |
| 6961 |
01 Oct 15 |
nicklas |
832 |
</varlistentry> |
| 6961 |
01 Oct 15 |
nicklas |
833 |
</variablelist> |
| 6961 |
01 Oct 15 |
nicklas |
834 |
|
| 3400 |
29 May 07 |
nicklas |
835 |
<nohelp> |
| 3400 |
29 May 07 |
nicklas |
836 |
<figure |
| 3400 |
29 May 07 |
nicklas |
837 |
id="annotations.figures.inherit"> |
| 3400 |
29 May 07 |
nicklas |
838 |
<title>Inheriting annotations from a parent item</title> |
| 3400 |
29 May 07 |
nicklas |
839 |
<screenshot> |
| 3400 |
29 May 07 |
nicklas |
840 |
<mediaobject> |
| 3400 |
29 May 07 |
nicklas |
841 |
<imageobject> |
| 3400 |
29 May 07 |
nicklas |
842 |
<imagedata |
| 3400 |
29 May 07 |
nicklas |
843 |
fileref="figures/inherit_annotations.png" format="PNG" /> |
| 3400 |
29 May 07 |
nicklas |
844 |
</imageobject> |
| 3400 |
29 May 07 |
nicklas |
845 |
</mediaobject> |
| 3400 |
29 May 07 |
nicklas |
846 |
</screenshot> |
| 3400 |
29 May 07 |
nicklas |
847 |
</figure> |
| 3400 |
29 May 07 |
nicklas |
848 |
</nohelp> |
| 3400 |
29 May 07 |
nicklas |
849 |
|
| 3400 |
29 May 07 |
nicklas |
850 |
<para> |
| 6961 |
01 Oct 15 |
nicklas |
851 |
In this dialog there is a tree-like structure in two levels to the left. |
| 6961 |
01 Oct 15 |
nicklas |
852 |
The first level |
| 6961 |
01 Oct 15 |
nicklas |
853 |
lists all parent items which has at least one annotation. The second |
| 3400 |
29 May 07 |
nicklas |
854 |
level lists the annotations and protocol parameters for the item. |
| 3400 |
29 May 07 |
nicklas |
855 |
Selecting an item in the first level will inherit all annotations |
| 6961 |
01 Oct 15 |
nicklas |
856 |
from that item. Selecting an annotation or protocol parameter at |
| 6961 |
01 Oct 15 |
nicklas |
857 |
the second level will inherit only the selected one. |
| 3400 |
29 May 07 |
nicklas |
858 |
</para> |
| 3400 |
29 May 07 |
nicklas |
859 |
|
| 6724 |
12 Feb 15 |
nicklas |
860 |
<para> |
| 6724 |
12 Feb 15 |
nicklas |
861 |
The filter field on the top of the dialog is a simple search filter to |
| 6724 |
12 Feb 15 |
nicklas |
862 |
make it easier to find a specific annotation. In large projects, the |
| 6724 |
12 Feb 15 |
nicklas |
863 |
parent tree may contain lots of items having hundreds of different |
| 6724 |
12 Feb 15 |
nicklas |
864 |
annotations. Use the filter to find annotations containing the |
| 6724 |
12 Feb 15 |
nicklas |
865 |
same text. The search is case-insensitive and will match anywhere |
| 6724 |
12 Feb 15 |
nicklas |
866 |
on the name of the annotation type, but not values. The filter only |
| 6724 |
12 Feb 15 |
nicklas |
867 |
affects what is displayed. Changes that have been made to hidden items |
| 6724 |
12 Feb 15 |
nicklas |
868 |
are still saved. |
| 6724 |
12 Feb 15 |
nicklas |
869 |
</para> |
| 6724 |
12 Feb 15 |
nicklas |
870 |
|
| 6981 |
08 Oct 15 |
nicklas |
871 |
<para> |
| 6981 |
08 Oct 15 |
nicklas |
872 |
Use the <guibutton>Inherit</guibutton> button to inherit the selected |
| 6981 |
08 Oct 15 |
nicklas |
873 |
annotations by reference, and the <guibutton>Clone</guibutton> button |
| 6981 |
08 Oct 15 |
nicklas |
874 |
to clone the values of the selected annotations. |
| 6981 |
08 Oct 15 |
nicklas |
875 |
</para> |
| 6981 |
08 Oct 15 |
nicklas |
876 |
|
| 3400 |
29 May 07 |
nicklas |
877 |
<note> |
| 3400 |
29 May 07 |
nicklas |
878 |
<itemizedlist> |
| 3400 |
29 May 07 |
nicklas |
879 |
<listitem> |
| 3400 |
29 May 07 |
nicklas |
880 |
<para> |
| 6981 |
08 Oct 15 |
nicklas |
881 |
Already inherited or cloned annotations are not shown in the dialog. |
| 3400 |
29 May 07 |
nicklas |
882 |
</para> |
| 3400 |
29 May 07 |
nicklas |
883 |
</listitem> |
| 3400 |
29 May 07 |
nicklas |
884 |
<listitem> |
| 3400 |
29 May 07 |
nicklas |
885 |
<para> |
| 6981 |
08 Oct 15 |
nicklas |
886 |
Annotations that are inherited by reference can easily be converted to |
| 6981 |
08 Oct 15 |
nicklas |
887 |
cloned annotations. Select the annotation in the list and click on the |
| 6981 |
08 Oct 15 |
nicklas |
888 |
<guilabel>clone</guilabel> link. |
| 6961 |
01 Oct 15 |
nicklas |
889 |
<nohelp> |
| 6961 |
01 Oct 15 |
nicklas |
890 |
<figure> |
| 6961 |
01 Oct 15 |
nicklas |
891 |
<title>Convert to a cloned annotation</title> |
| 6961 |
01 Oct 15 |
nicklas |
892 |
<screenshot> |
| 6961 |
01 Oct 15 |
nicklas |
893 |
<mediaobject> |
| 6961 |
01 Oct 15 |
nicklas |
894 |
<imageobject> |
| 6961 |
01 Oct 15 |
nicklas |
895 |
<imagedata |
| 6961 |
01 Oct 15 |
nicklas |
896 |
fileref="figures/clone_annotation.png" format="PNG" /> |
| 6961 |
01 Oct 15 |
nicklas |
897 |
</imageobject> |
| 6961 |
01 Oct 15 |
nicklas |
898 |
</mediaobject> |
| 6961 |
01 Oct 15 |
nicklas |
899 |
</screenshot> |
| 6961 |
01 Oct 15 |
nicklas |
900 |
</figure> |
| 6961 |
01 Oct 15 |
nicklas |
901 |
</nohelp> |
| 3400 |
29 May 07 |
nicklas |
902 |
</para> |
| 3400 |
29 May 07 |
nicklas |
903 |
</listitem> |
| 3400 |
29 May 07 |
nicklas |
904 |
<listitem> |
| 3400 |
29 May 07 |
nicklas |
905 |
<para> |
| 3400 |
29 May 07 |
nicklas |
906 |
If you delete an annotation from a parent item, the inheritance will |
| 3400 |
29 May 07 |
nicklas |
907 |
be lost, even if you later add a value again. |
| 3400 |
29 May 07 |
nicklas |
908 |
</para> |
| 3400 |
29 May 07 |
nicklas |
909 |
</listitem> |
| 3400 |
29 May 07 |
nicklas |
910 |
</itemizedlist> |
| 3400 |
29 May 07 |
nicklas |
911 |
</note> |
| 3400 |
29 May 07 |
nicklas |
912 |
|
| 3400 |
29 May 07 |
nicklas |
913 |
<warning> |
| 3400 |
29 May 07 |
nicklas |
914 |
<para> |
| 3400 |
29 May 07 |
nicklas |
915 |
If you rearrange links to parent items after you have |
| 3400 |
29 May 07 |
nicklas |
916 |
specified inheritance, it may happen that you are inheriting |
| 3400 |
29 May 07 |
nicklas |
917 |
annotation from non-parent items. This will be flagged with a warning |
| 4771 |
19 Feb 09 |
nicklas |
918 |
icon in the list, and must be fixed manually. The item overview |
| 3400 |
29 May 07 |
nicklas |
919 |
tool is an excellent help for locating this kind of problems. |
| 4771 |
19 Feb 09 |
nicklas |
920 |
<nohelp>See <xref linkend="webclient.itemoverview" />.</nohelp> |
| 3400 |
29 May 07 |
nicklas |
921 |
</para> |
| 3400 |
29 May 07 |
nicklas |
922 |
</warning> |
| 3400 |
29 May 07 |
nicklas |
923 |
|
| 3400 |
29 May 07 |
nicklas |
924 |
<seeother> |
| 3400 |
29 May 07 |
nicklas |
925 |
<other external_id="annotations.edit">Annotations and parameters</other> |
| 3400 |
29 May 07 |
nicklas |
926 |
<other external_id="experiment.edit.factors">Experimental factors</other> |
| 6725 |
12 Feb 15 |
nicklas |
927 |
<other external_id="annotations.batch_inherit">Batch inherit annotations</other> |
| 4772 |
19 Feb 09 |
nicklas |
928 |
<other external_id="item.overview">Item overview tool</other> |
| 3400 |
29 May 07 |
nicklas |
929 |
</seeother> |
| 3400 |
29 May 07 |
nicklas |
930 |
|
| 3400 |
29 May 07 |
nicklas |
931 |
</helptext> |
| 3400 |
29 May 07 |
nicklas |
932 |
|
| 3396 |
28 May 07 |
nicklas |
933 |
</sect2> |
| 3396 |
28 May 07 |
nicklas |
934 |
|
| 6725 |
12 Feb 15 |
nicklas |
935 |
<sect2 id="annotations.batch-inherit"> |
| 6725 |
12 Feb 15 |
nicklas |
936 |
<title>Batch inherit annotations</title> |
| 6725 |
12 Feb 15 |
nicklas |
937 |
|
| 6725 |
12 Feb 15 |
nicklas |
938 |
<helptext external_id="annotations.batch_inherit" |
| 6725 |
12 Feb 15 |
nicklas |
939 |
title="Batch inherit annotations"> |
| 6725 |
12 Feb 15 |
nicklas |
940 |
<para> |
| 6725 |
12 Feb 15 |
nicklas |
941 |
Manually inheriting annotations on a per-item basis will quickly become a time-consuming |
| 6725 |
12 Feb 15 |
nicklas |
942 |
and boring task as the project gets larger. Typically, there is a given set of annotations |
| 6725 |
12 Feb 15 |
nicklas |
943 |
that should be inherited from different levels in the parent chain. This is possible |
| 6725 |
12 Feb 15 |
nicklas |
944 |
with the batch inherit feature. Open this dialog by selecting at least one item in the |
| 6725 |
12 Feb 15 |
nicklas |
945 |
list-view and then use the <guibutton>Inherit annotations…</guibutton> button |
| 6725 |
12 Feb 15 |
nicklas |
946 |
in the toolbar. |
| 6725 |
12 Feb 15 |
nicklas |
947 |
</para> |
| 6725 |
12 Feb 15 |
nicklas |
948 |
|
| 6725 |
12 Feb 15 |
nicklas |
949 |
<nohelp> |
| 6725 |
12 Feb 15 |
nicklas |
950 |
<figure |
| 6725 |
12 Feb 15 |
nicklas |
951 |
id="annotations.figures.batch_inherit"> |
| 6725 |
12 Feb 15 |
nicklas |
952 |
<title>Batch inherit annotations</title> |
| 6725 |
12 Feb 15 |
nicklas |
953 |
<screenshot> |
| 6725 |
12 Feb 15 |
nicklas |
954 |
<mediaobject> |
| 6725 |
12 Feb 15 |
nicklas |
955 |
<imageobject> |
| 6725 |
12 Feb 15 |
nicklas |
956 |
<imagedata |
| 6725 |
12 Feb 15 |
nicklas |
957 |
fileref="figures/batch_inherit_annotations.png" format="PNG" /> |
| 6725 |
12 Feb 15 |
nicklas |
958 |
</imageobject> |
| 6725 |
12 Feb 15 |
nicklas |
959 |
</mediaobject> |
| 6725 |
12 Feb 15 |
nicklas |
960 |
</screenshot> |
| 6725 |
12 Feb 15 |
nicklas |
961 |
</figure> |
| 6725 |
12 Feb 15 |
nicklas |
962 |
</nohelp> |
| 6725 |
12 Feb 15 |
nicklas |
963 |
|
| 6725 |
12 Feb 15 |
nicklas |
964 |
|
| 6725 |
12 Feb 15 |
nicklas |
965 |
<variablelist> |
| 6725 |
12 Feb 15 |
nicklas |
966 |
<varlistentry> |
| 6725 |
12 Feb 15 |
nicklas |
967 |
<term><guilabel>Select annotation types</guilabel></term> |
| 6725 |
12 Feb 15 |
nicklas |
968 |
<listitem> |
| 6725 |
12 Feb 15 |
nicklas |
969 |
<para> |
| 6725 |
12 Feb 15 |
nicklas |
970 |
Use this button to select one or more annotation types that you want to inherit. |
| 6725 |
12 Feb 15 |
nicklas |
971 |
Once the selection has been made, the selected annotation types will be added to |
| 6725 |
12 Feb 15 |
nicklas |
972 |
the table in the dialog as shown on the screen shot. |
| 6725 |
12 Feb 15 |
nicklas |
973 |
</para> |
| 6725 |
12 Feb 15 |
nicklas |
974 |
</listitem> |
| 6725 |
12 Feb 15 |
nicklas |
975 |
</varlistentry> |
| 6725 |
12 Feb 15 |
nicklas |
976 |
<varlistentry> |
| 6725 |
12 Feb 15 |
nicklas |
977 |
<term><guilabel>Action</guilabel></term> |
| 6725 |
12 Feb 15 |
nicklas |
978 |
<listitem> |
| 6725 |
12 Feb 15 |
nicklas |
979 |
<para> |
| 6725 |
12 Feb 15 |
nicklas |
980 |
For each annotation type you can select if you want to |
| 6961 |
01 Oct 15 |
nicklas |
981 |
<guilabel>inherit</guilabel> or <guilabel>clone</guilabel> new annotations, |
| 6961 |
01 Oct 15 |
nicklas |
982 |
<guilabel>remove</guilabel> existing inherited annotations or |
| 6961 |
01 Oct 15 |
nicklas |
983 |
<guilabel>resync</guilabel> existing cloned annotation. It is possible to use different |
| 6725 |
12 Feb 15 |
nicklas |
984 |
actions for different annotation types. |
| 6725 |
12 Feb 15 |
nicklas |
985 |
</para> |
| 6725 |
12 Feb 15 |
nicklas |
986 |
</listitem> |
| 6725 |
12 Feb 15 |
nicklas |
987 |
</varlistentry> |
| 6725 |
12 Feb 15 |
nicklas |
988 |
<varlistentry> |
| 6725 |
12 Feb 15 |
nicklas |
989 |
<term><guilabel>Parent item type</guilabel></term> |
| 6725 |
12 Feb 15 |
nicklas |
990 |
<listitem> |
| 6725 |
12 Feb 15 |
nicklas |
991 |
<para> |
| 6725 |
12 Feb 15 |
nicklas |
992 |
In this list you can select if you want to inherit from |
| 6725 |
12 Feb 15 |
nicklas |
993 |
any type of parent or only from a specific type. This is |
| 6725 |
12 Feb 15 |
nicklas |
994 |
useful if the same annotation is present on multiple parent |
| 6725 |
12 Feb 15 |
nicklas |
995 |
levels. If the annotation type has been added to a category, |
| 6725 |
12 Feb 15 |
nicklas |
996 |
BASE will automatically try to guess the parent type (=the |
| 6725 |
12 Feb 15 |
nicklas |
997 |
parent type that has the same name as the category). This |
| 6725 |
12 Feb 15 |
nicklas |
998 |
option is disabled when removing annotations. |
| 6725 |
12 Feb 15 |
nicklas |
999 |
</para> |
| 6725 |
12 Feb 15 |
nicklas |
1000 |
</listitem> |
| 6725 |
12 Feb 15 |
nicklas |
1001 |
</varlistentry> |
| 6725 |
12 Feb 15 |
nicklas |
1002 |
<varlistentry> |
| 6725 |
12 Feb 15 |
nicklas |
1003 |
<term><guilabel>Options</guilabel></term> |
| 6725 |
12 Feb 15 |
nicklas |
1004 |
<listitem> |
| 6725 |
12 Feb 15 |
nicklas |
1005 |
<para> |
| 6725 |
12 Feb 15 |
nicklas |
1006 |
You may specify if existing inherited annotations should be |
| 6725 |
12 Feb 15 |
nicklas |
1007 |
replaced and if duplicate inheritance should be allowed or not. |
| 6725 |
12 Feb 15 |
nicklas |
1008 |
The default is to replace existing annotations and not allow |
| 6725 |
12 Feb 15 |
nicklas |
1009 |
duplicates. |
| 6725 |
12 Feb 15 |
nicklas |
1010 |
</para> |
| 6725 |
12 Feb 15 |
nicklas |
1011 |
</listitem> |
| 6725 |
12 Feb 15 |
nicklas |
1012 |
</varlistentry> |
| 6725 |
12 Feb 15 |
nicklas |
1013 |
</variablelist> |
| 6725 |
12 Feb 15 |
nicklas |
1014 |
|
| 6725 |
12 Feb 15 |
nicklas |
1015 |
<para> |
| 6725 |
12 Feb 15 |
nicklas |
1016 |
Click on <guibutton>Ok</guibutton> to finish. The work is performed as a background job |
| 6725 |
12 Feb 15 |
nicklas |
1017 |
on the server. The progress can be followed in the dialog. It may take a while to |
| 6725 |
12 Feb 15 |
nicklas |
1018 |
complete if several items was selected since BASE will need to look up all parents |
| 6725 |
12 Feb 15 |
nicklas |
1019 |
and determine if they have any annotations that match the critera that was set up. |
| 6725 |
12 Feb 15 |
nicklas |
1020 |
</para> |
| 6725 |
12 Feb 15 |
nicklas |
1021 |
</helptext> |
| 6725 |
12 Feb 15 |
nicklas |
1022 |
|
| 6725 |
12 Feb 15 |
nicklas |
1023 |
</sect2> |
| 6725 |
12 Feb 15 |
nicklas |
1024 |
|
| 3588 |
23 Jul 07 |
nicklas |
1025 |
<sect2 id="annotations.massimport"> |
| 3588 |
23 Jul 07 |
nicklas |
1026 |
<title>Mass annotation import plug-in</title> |
| 3588 |
23 Jul 07 |
nicklas |
1027 |
|
| 3588 |
23 Jul 07 |
nicklas |
1028 |
<para> |
| 3588 |
23 Jul 07 |
nicklas |
1029 |
BASE includes a plug-in for importing annotations to multiple items |
| 3588 |
23 Jul 07 |
nicklas |
1030 |
in one go. The plug-in read annotation values from a simple column-based |
| 5706 |
23 Aug 11 |
nicklas |
1031 |
text file. Usually, a tab is used as the delimiter between columns, but this |
| 5706 |
23 Aug 11 |
nicklas |
1032 |
is configurable. |
| 3588 |
23 Jul 07 |
nicklas |
1033 |
The first row should contain the column headers. One column should contain |
| 7620 |
04 Mar 19 |
nicklas |
1034 |
a value that can be used to identify items. Typically, the name or the external ID |
| 7620 |
04 Mar 19 |
nicklas |
1035 |
is used, but it is also possible to use the internal ID or an annotation type that |
| 7620 |
04 Mar 19 |
nicklas |
1036 |
has been flagged as an <property>identifier</property>. The rest of the columns can each be |
| 3588 |
23 Jul 07 |
nicklas |
1037 |
mapped to an annotation type and contains the annotation values. If a column |
| 3588 |
23 Jul 07 |
nicklas |
1038 |
header exactly match the name of an annotation type, the plug-in will automatically |
| 3588 |
23 Jul 07 |
nicklas |
1039 |
create the mapping, otherwise you must do it manually. You don't have to map |
| 3588 |
23 Jul 07 |
nicklas |
1040 |
all columns if you don't want to. |
| 3588 |
23 Jul 07 |
nicklas |
1041 |
</para> |
| 3588 |
23 Jul 07 |
nicklas |
1042 |
|
| 3588 |
23 Jul 07 |
nicklas |
1043 |
<para> |
| 3588 |
23 Jul 07 |
nicklas |
1044 |
Each column can only contain a single annotation value for each row. |
| 3588 |
23 Jul 07 |
nicklas |
1045 |
If you have annotation types that accept multiple values you can map |
| 3588 |
23 Jul 07 |
nicklas |
1046 |
two or more columns to the same annotation type, or you can add an |
| 3588 |
23 Jul 07 |
nicklas |
1047 |
extra row only giving the name and the extra annotation value. |
| 3588 |
23 Jul 07 |
nicklas |
1048 |
Here is a simple example of a valid file with comma as column separator: |
| 3588 |
23 Jul 07 |
nicklas |
1049 |
</para> |
| 3588 |
23 Jul 07 |
nicklas |
1050 |
|
| 3588 |
23 Jul 07 |
nicklas |
1051 |
<programlisting> |
| 3588 |
23 Jul 07 |
nicklas |
1052 |
# 'Time' and 'Age' are integer types |
| 3588 |
23 Jul 07 |
nicklas |
1053 |
# 'Subtype' is a string enumeration |
| 3588 |
23 Jul 07 |
nicklas |
1054 |
# 'Comment' is a text type that accept multiple values |
| 3588 |
23 Jul 07 |
nicklas |
1055 |
Name,Time (hours),Age (years),Subtype,Comment |
| 3588 |
23 Jul 07 |
nicklas |
1056 |
Sample #1,0,0,alfa,Very good |
| 3588 |
23 Jul 07 |
nicklas |
1057 |
Sample #2,24,0,beta,Not so bad |
| 3588 |
23 Jul 07 |
nicklas |
1058 |
Sample #2,,,,Yet another comment |
| 3588 |
23 Jul 07 |
nicklas |
1059 |
</programlisting> |
| 3588 |
23 Jul 07 |
nicklas |
1060 |
|
| 3588 |
23 Jul 07 |
nicklas |
1061 |
<para> |
| 3588 |
23 Jul 07 |
nicklas |
1062 |
The plug-in can be used with or without a configuration. The configuration |
| 3588 |
23 Jul 07 |
nicklas |
1063 |
keeps the regular expressions and other settings used to parse the file. If |
| 3588 |
23 Jul 07 |
nicklas |
1064 |
you often import annotations from the same file format, we recommend that |
| 3588 |
23 Jul 07 |
nicklas |
1065 |
you use a configuration. The mapping from file columns to annotation types |
| 3588 |
23 Jul 07 |
nicklas |
1066 |
is not part of the configuration, it must be done each time the plug-in is used. |
| 3588 |
23 Jul 07 |
nicklas |
1067 |
</para> |
| 3588 |
23 Jul 07 |
nicklas |
1068 |
|
| 3588 |
23 Jul 07 |
nicklas |
1069 |
<para> |
| 3588 |
23 Jul 07 |
nicklas |
1070 |
The plug-in can be used from the list view of all annotatable items. |
| 3588 |
23 Jul 07 |
nicklas |
1071 |
Using the plug-in is a three-step wizard: |
| 3588 |
23 Jul 07 |
nicklas |
1072 |
</para> |
| 3588 |
23 Jul 07 |
nicklas |
1073 |
|
| 3588 |
23 Jul 07 |
nicklas |
1074 |
<orderedlist> |
| 3588 |
23 Jul 07 |
nicklas |
1075 |
<listitem> |
| 3588 |
23 Jul 07 |
nicklas |
1076 |
<para> |
| 3588 |
23 Jul 07 |
nicklas |
1077 |
Select a file to import from and the regular expressions and other |
| 3588 |
23 Jul 07 |
nicklas |
1078 |
settings used to parse the file. In this step you also select the column |
| 3588 |
23 Jul 07 |
nicklas |
1079 |
that contains the name or external ID the items. If a configuration is used |
| 3588 |
23 Jul 07 |
nicklas |
1080 |
all settings on this page, except the file to import from, already has values. |
| 3588 |
23 Jul 07 |
nicklas |
1081 |
</para> |
| 3588 |
23 Jul 07 |
nicklas |
1082 |
</listitem> |
| 3588 |
23 Jul 07 |
nicklas |
1083 |
|
| 3588 |
23 Jul 07 |
nicklas |
1084 |
<listitem> |
| 3588 |
23 Jul 07 |
nicklas |
1085 |
<para> |
| 3588 |
23 Jul 07 |
nicklas |
1086 |
The plug-in will start parsing the file until it finds the column headers. |
| 3588 |
23 Jul 07 |
nicklas |
1087 |
You are asked to select an annotation type for each column. |
| 3588 |
23 Jul 07 |
nicklas |
1088 |
</para> |
| 3588 |
23 Jul 07 |
nicklas |
1089 |
</listitem> |
| 3588 |
23 Jul 07 |
nicklas |
1090 |
|
| 3588 |
23 Jul 07 |
nicklas |
1091 |
<listitem> |
| 3588 |
23 Jul 07 |
nicklas |
1092 |
<para> |
| 3588 |
23 Jul 07 |
nicklas |
1093 |
Set error handling options and some other import options. |
| 3588 |
23 Jul 07 |
nicklas |
1094 |
</para> |
| 3588 |
23 Jul 07 |
nicklas |
1095 |
</listitem> |
| 3588 |
23 Jul 07 |
nicklas |
1096 |
|
| 3588 |
23 Jul 07 |
nicklas |
1097 |
</orderedlist> |
| 3588 |
23 Jul 07 |
nicklas |
1098 |
|
| 3588 |
23 Jul 07 |
nicklas |
1099 |
</sect2> |
| 3588 |
23 Jul 07 |
nicklas |
1100 |
|
| 3396 |
28 May 07 |
nicklas |
1101 |
</sect1> |
| 3396 |
28 May 07 |
nicklas |
1102 |
|
| 3372 |
24 May 07 |
philippe |
1103 |
</chapter> |