Changeset 3395
- Timestamp:
- May 28, 2007, 2:22:58 PM (16 years ago)
- Location:
- trunk/doc/src/docbook
- Files:
-
- 3 added
- 6 deleted
- 1 edited
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- Unmodified
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trunk/doc/src/docbook/userdoc/annotations.xml
r3394 r3395 3 3 "-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN" 4 4 "../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd"> 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 --> 5 <!-- 6 $Id$ 7 8 Copyright (C) Authors contributing to this file. 9 10 This file is part of BASE - BioArray Software Environment. 11 Available at http://base.thep.lu.se/ 12 13 BASE is free software; you can redistribute it and/or 14 modify it under the terms of the GNU General Public License 15 as published by the Free Software Foundation; either version 2 16 of the License, or (at your option) any later version. 17 18 BASE is distributed in the hope that it will be useful, 19 but WITHOUT ANY WARRANTY; without even the implied warranty of 20 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 21 GNU General Public License for more details. 22 23 You should have received a copy of the GNU General Public License 24 along with this program; if not, write to the Free Software 25 Foundation, Inc., 59 Temple Place - Suite 330, 26 Boston, MA 02111-1307, USA. 27 --> 28 28 29 29 <chapter id="annotations"> 30 30 <?dbhtml dir="annotations"?> 31 <title>Annotation Types</title> 32 <sect1 id="annotations.introduction"> 33 <title>Introduction</title> 34 <para>BASE2 has been engineered to closely map the <ulink 35 url="http://www.mged.org/Workgroups/MIAME/miame.html">MIAME concepts</ulink>. However, since 36 MIAME is focused on microarray processing workflow, information about the description 37 biological samples themselves was left out. BASE2 users are free to annotate 38 Biomaterials (and most BASE2 items) as they wish, from basic free text description to 39 more advanced ontology based terms. To accomodate the annotation needs of users eager 40 with detailed sample annotations and also the needs of very different communities, BASE2 41 provides a mechanism that allows a high level of annotation customization. BASE2 allows 42 to create descriptive elements for both quantitative annotation and qualitative 43 annotation of Biomaterials via the <guilabel>Annotation Type mechanism</guilabel>. 44 Actually, Annotation Types can be used to annotate not only Biomaterials but almost all 45 BASE2 items, from <guilabel>Plates</guilabel> to <guilabel>Protocols</guilabel> and 46 <guilabel>BioAssaysets</guilabel> This chapter details how to manage and use these 47 elements.</para> 48 </sect1> 49 <sect1 id="annotations.manage"> 50 <title>Managing Annotation Types</title> 51 <para> </para> 52 <sect2 id="annotations.manage.create_at"> 53 <title>Creating Annotation Types</title> 54 <para>Go To <menuchoice> 55 <guimenu>Administrate</guimenu> 56 <guimenuitem>Types</guimenuitem> 57 <guisubmenu>AnnotationTypes</guisubmenu> 58 </menuchoice> 59 </para> 60 <para> Click on &gbNew; and select one of the 8 different 61 types which can be split in 4 main groups</para> 62 <itemizedlist spacing="compact"> 63 <listitem> 64 <para><guilabel>Integer</guilabel>, <guilabel>Long</guilabel>, 65 <guilabel>Float</guilabel> and <guilabel>Double</guilabel> for Numerical 66 Annotation Types.</para> 67 </listitem> 68 69 <listitem> 70 <para><guilabel>String</guilabel> and <guilabel>text</guilabel> for textual 71 Annotation Types .</para> 72 </listitem> 73 74 <listitem> 75 <para><guilabel>Boolean</guilabel> for declaring Annotation Types that can take 76 one of 2 possible values.</para> 77 </listitem> 78 79 <listitem> 80 <para><guilabel>Boolean</guilabel> for declaring Annotation Type used as 81 calendar/time stamps.</para> 82 </listitem> 83 </itemizedlist> 84 <note> 85 <para>These distinctions matter essentially to database administrators who need fine 86 tuning of database settings. Therefore, creation of Annotation Type should be 87 supervised by system administrators.</para> 88 </note> 89 <para> A <guilabel>Create</guilabel> pop-up window opens. It contains 4 different tabs: </para> 90 <orderedlist numeration="loweralpha" spacing="compact"> 91 <listitem> 92 <para> 93 <guilabel>Annotation type</guilabel> 94 </para> 95 <para> It allows definition of core properties of the newly created annotation 96 type. This includes specifying: </para> 97 <itemizedlist spacing="compact"> 98 <listitem> 99 <para>How the <guilabel>Annotation Type</guilabel> should be 100 named.</para> 101 </listitem> 102 <listitem> 103 <para>If the <guilabel>Annotation Type</guilabel> should be treated as a 104 <guilabel>protocol parameter</guilabel>.</para> 105 </listitem> 106 <listitem> 107 <para>If the <guilabel>Annotation Type</guilabel> should be considered 108 as <guilabel>MIAME required</guilabel>.</para> 109 </listitem> 110 <listitem> 111 <para>If a <guilabel>default value</guilabel> should be 112 available.</para> 113 </listitem> 114 <listitem> 115 <para>If more than one option can be selected by setting the 116 <guilabel>multiplicity</guilabel> to more than one.</para> 117 </listitem> 118 <listitem> 119 <para>Finally, one can add a short textual description of the 120 <guilabel>Annotation Type</guilabel> being created, to clarify 121 its usage.</para> 122 </listitem> 123 </itemizedlist> 124 <figure id="write_docbook_doc.figures.annotationtype"> 125 <title>The Annotation type tab of the Create Window for a String Annotation 126 Type</title> 127 <screenshot> 128 <mediaobject> 129 <imageobject> 130 <imagedata contentwidth="7cm" width="7cm" fileref="figures/annotationtype.png" format="PNG"/> 131 </imageobject> 132 </mediaobject> 133 </screenshot> 134 </figure> 135 </listitem> 136 <listitem> 137 <para> 138 <guilabel>Options</guilabel> 139 </para> 140 <para> The tab allows tuning the interaction options with the Web Graphical User 141 Interface when using Annotation types: <itemizedlist spacing="compact"> 142 <listitem> 143 <para>Choosing <guilabel>text box</guilabel> option allows free text 144 to be entered.</para> 145 </listitem> 146 <listitem> 147 <para>Choosing the <guilabel>selection list</guilabel> option 148 activates the 'value' section. Actual values can be supplied 149 using one line for each value (a return entry is used as 150 separator).</para> 151 <para>It enables administrator to declare the list of possible 152 values using the "values" box.</para> 153 </listitem> 154 <listitem> 155 <para>Choosing the <guilabel>radio button/checkboxes</guilabel> 156 option activates the <guilabel>value</guilabel> section. Actual 157 values can be supplied using one line for each value (a return 158 entry is used as separator).</para> 159 <para>When selecting radio-button instead of selection list, this 160 will alter the interface in order to allow user to tick button 161 instead of selecting from a drop-down list.</para> 162 <tip> 163 <para>In term of usability, drop-down list can be more easily 164 navigated especially when the number of possible values is 165 large, and because selectionlist and drop-down list allow 166 use of arrow and tab for selection.</para> 167 </tip> 168 </listitem> 169 <listitem> 170 <para>GUI Variations depending on the type of Annotation Types: </para> 171 <para>Depending on the nature of the annotation type being created 172 (e.g. whether it is a boolean, a string or a date), the 173 <guilabel>Options</guilabel> tab may display specific 174 fields.</para> 175 <para>When creating an Annotation Type of Type Boolean, the default 176 value field is replaced by the true or false radio-button in 177 order to allow specification of a value.</para> 178 <para>Also, when using numerical AnnotationTypes, upper and lower 179 limit can be defined.</para> 180 </listitem> 181 </itemizedlist> 182 </para> 183 <figure id="write_docbook_doc.figures.annotationtype-option"> 184 <title>The Option tab of the Create Window for a String Annotation Type</title> 185 <screenshot> 186 <mediaobject> 187 <imageobject> 188 <imagedata contentwidth="7cm" width="7cm" fileref="figures/annotationtype-option.png" format="PNG"/> 189 </imageobject> 190 </mediaobject> 191 </screenshot> 192 </figure> 193 </listitem> 194 <listitem> 195 <para> 196 <guilabel>Item types</guilabel> 197 </para> 198 <para> The Item types tab is used to defined which BASE2 entities can be 199 annotated using the newly creating Annotation Type. Simply use 200 <guiicon>arrow left|right</guiicon> to moved items between the 201 <guilabel>disabled for</guilabel> and <guilabel>enabled for</guilabel> 202 <note> 203 <para>Experiment item can not be annotated using Annotation Type</para> 204 </note> 205 </para> 206 <figure id="write_docbook_doc.figures.annotationtype-item"> 207 <title>The Item tab of the Create Window for a String Annotation Type</title> 208 <screenshot> 209 <mediaobject> 210 <imageobject> 211 <imagedata contentwidth="7cm" width="7cm" fileref="figures/annotationtype-item.png" format="PNG"/> 212 </imageobject> 213 </mediaobject> 214 </screenshot> 215 </figure> 216 </listitem> 217 <listitem> 218 <para> 219 <guilabel>Categories</guilabel> 220 </para> 221 <para> Annotation Type can be grouped together thanks to the Annotation Category 222 functionality. This enhances display by avoid overcrowding the list of 223 annotation types presented to users. It also allows to improve the display of 224 information. </para> 225 <figure id="write_docbook_doc.figures.annotationtype-categories"> 226 <title>The categories tab of the Create Window for a String Annotation Type</title> 227 <screenshot> 228 <mediaobject> 229 <imageobject> 230 <imagedata contentwidth="7cm" width="7cm" fileref="figures/annotationtype-categories.png" format="PNG"/> 231 </imageobject> 232 </mediaobject> 233 </screenshot> 234 </figure> 235 </listitem> 236 </orderedlist> 237 238 <para>Click on the <inlinemediaobject> 239 <imageobject> 240 <imagedata fileref="figures/save.gif" format="GIF"/> 241 </imageobject> 242 </inlinemediaobject> Save button to store the information in BASE2 or on the <inlinemediaobject> 243 <imageobject> 244 <imagedata fileref="figures/cancel.gif" format="GIF"/> 245 </imageobject> 246 </inlinemediaobject> to abort. </para> 247 248 </sect2> 249 <sect2 id="annotations.manage.update"> 250 <title>Updating Annotation Types</title> 251 <para>Using the <keycap>CTRL</keycap>, <keycap>ALT</keycap>, <keycap>SHIFT</keycap> key 252 combination, click on the Annotation Type to be modified from the Annotation Type 253 List View</para> 254 <para>The <guilabel>Edit</guilabel> pop-up window opens, presenting the various tabs 255 presented in the previous section.</para> 256 <note> 257 <para>Everything is editable except the Annotation Type Type itself, which is 258 immutable and set once and for all upon creation</para> 259 </note> 260 </sect2> 261 <sect2 id="annotations.manage.create_atcategory"> 262 <title>Grouping Annotation Type into Categories</title> 263 <para> 264 <guilabel>Annotation Type Categories</guilabel> allow grouping of related Annotation 265 Types, based on users requirements. </para> 266 <para>For creating a new category, go to: </para> 267 <para> 268 <menuchoice> 269 <guimenu>Administrate</guimenu> 270 <guimenuitem>Types</guimenuitem> 271 <guisubmenu>Annotation Type categories</guisubmenu> 272 </menuchoice> 273 </para> 274 <para>Click on &gbNew;</para> 275 <para>a pop-up window opens.</para> 276 <para>It contains 2 tabs, one for declaring name and description of the newly created 277 category, the second tab is to provide the list of annotation type to be grouped 278 together under this container.</para> 279 <example id="annotation_types.example.atcategory"> 280 <title>A category 'Hematology Descriptors' could be created to group together 281 Annotation Types such as 'Lymphocyte count' and 'Hematocrite' </title> 282 </example> 283 <example id="annotation_types.example.atcategory-2"> 284 <title>A category 'Plasma Clinical Descriptors' could be created to group together 285 Annotation Types such as 'ALT activity (UI/mL)' and 'LDH activity (UI/mL'). 286 </title> 287 </example> 288 </sect2> 289 290 <sect2 id="annotations.manage.batchupload"> 291 <title>Batchloading Annotation Types from file</title> 292 <para>A plugin, CVLoader.jar, has been specially devised with 2 purposes in mind:</para> 293 <orderedlist> 294 <listitem> 295 <para>To speed-up data Annotation Type declaration and upload in the BASE2 296 system.</para> 297 </listitem> 298 <listitem> 299 <para>To enable sharing list of annotation types across BASE2 instances to 300 ensure consistency in data annotation.</para> 301 </listitem> 302 </orderedlist> 303 <para>In order to achieve this functionality, a file format specification was defined 304 and is detailed now</para> 305 306 <sect3 id="annotations.manage.batchupload.fileformat"> 307 <title>Defining the input file: File format definition</title> 308 <para> To use the CV-loader import plugin, users need to create a tab-delimited file 309 complying with the following guidelines. Columns names, order, allowed values 310 and within column separator are important.</para> 311 <itemizedlist spacing="compact"> 312 <listitem> 313 <para><guilabel>Category Name</guilabel>: free text</para> 314 </listitem> 315 <listitem> 316 <para><guilabel>AnnotationType Name</guilabel>: free text</para> 317 </listitem> 318 <listitem> 319 <para><guilabel>Description</guilabel>: free text</para> 320 </listitem> 321 <listitem> 322 <para><guilabel>ValueType</guilabel>: 323 {string,text,boolean,data,integer,long,double,float}</para> 324 </listitem> 325 <listitem> 326 <para><guilabel>Required for MIAME</guilabel>: true/false</para> 327 </listitem> 328 <listitem> 329 <para><guilabel>Enumeration</guilabel>: true/false</para> 330 </listitem> 331 <listitem> 332 <para><guilabel>Multiplicity</guilabel>: integer</para> 333 </listitem> 334 <listitem> 335 <para><guilabel>Default value</guilabel>: free text</para> 336 </listitem> 337 <listitem> 338 <para><guilabel>Cv values</guilabel>: semi-colon (;) used as 339 separator</para> 340 </listitem> 341 <listitem> 342 <para><guilabel>Item types</guilabel>: semi-colon (;) used as separator 343 {biosource,sample,extract,protocol,arraydesign,array,plate}</para> 344 </listitem> 345 <listitem> 346 <para><guilabel>Parameter</guilabel>: true/false</para> 347 </listitem> 348 </itemizedlist> 349 <para/> 350 </sect3> 351 <sect3 id="annotations.manage.batchupload.pluginconfig"> 352 <title>Configuring the CV loader plugin</title> 353 <para>From the plugin configuration page, Use the &gbImport; 354 button to load the xml configuration file available here. Please refer to <xref 355 linkend="plugins"/> for more ample explanations about plugin configuration.</para> 356 <note> 357 <para>By default the plugin creates <guilabel>selection list</guilabel> for all 358 enumerated values declared in the file. </para> 359 </note> 360 <note> 361 <para><guilabel>external ID</guilabel> field is not supported in the current 362 implementation of the plugin. </para> 363 </note> 364 365 </sect3> 366 <sect3 id="annotations.manage.batchupload.pluginrun"> 367 <title>Running the plugin</title> 368 <para>-From the Annotation Type List View page, click on the 369 &gbImport; Button (which shows up only when the import plugin 370 has been configured).</para> 371 <para>-Supply path to tab delimited file containing the Annotation Type to be 372 imported. Click &gbNext;. </para> 373 <figure id="write_docbook_doc.figures.batchloading-annotationtype-2"> 374 <title>Running the CVloader plugin: specifying the file</title> 375 <screenshot> 376 <mediaobject> 377 <imageobject> 378 <imagedata contentwidth="10cm" width="10cm" fileref="figures/batchloading-annotationtype-2.png" format="PNG"/> 379 </imageobject> 380 </mediaobject> 381 </screenshot> 382 </figure> 383 <para>Define whether or not to update existing Annotation Types and click 384 &gbNext;</para> 385 <figure id="write_docbook_doc.figures.batchloading-annotationtype-3"> 386 <title>Running the CVloader plugin in update mode</title> 387 <screenshot> 388 <mediaobject> 389 <imageobject> 390 <imagedata contentwidth="10cm" width="10cm" fileref="figures/batchloading-annotationtype-3.png" format="PNG"/> 391 </imageobject> 392 </mediaobject> 393 </screenshot> 394 </figure> 395 <para> Click &gbFinish; to launch the plugin execution. If one 396 selects the email notification option, a message will be sent upon job 397 completion detailing success or failure of the import process. </para> 398 <tip> 399 <para>Once an update has been made using the plugin, it can not be undone but 400 one can simply update the file and run the plugin again.</para> 401 </tip> 402 </sect3> 403 </sect2> 404 </sect1> 405 406 <sect1 id="annotations.bestpractices"> 407 <title>Best Practices and Tab2Mage Export functionality</title> 408 409 See <xref linkend="experiments_analysis.magexport" />. 410 411 </sect1> 31 <title>Annotations</title> 32 33 <sect1 id="annotations.types"> 34 <title>Annotation Types</title> 35 36 <helptext id="annotationtype.view.properties" 37 title="Annotation types"> 38 <para> 39 BASE2 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. BASE2 users are free to 46 annotate biomaterials (and most BASE2 items) as they wish, 47 from basic free text description to more advanced ontology 48 based terms. To accomodate the annotation needs of users 49 eager with detailed sample annotations and also the needs of 50 very different communities, BASE2 provides a mechanism that 51 allows a high level of annotation customization. BASE2 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 BASE2 items, from 57 <emphasis>Plates</emphasis> 58 to 59 <emphasis>Protocols</emphasis> 60 and 61 <emphasis>BioAssaysets</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 8 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 practival 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> 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 popup. It contains four different 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 <nohelp> 169 See <xref linkend="experiments_analysis.magexport" /> 170 if you are going to use this annotation type when 171 exporting Tab2Mage files. 172 </nohelp> 173 </para> 174 </listitem> 175 </varlistentry> 176 <varlistentry> 177 <term><guilabel>External ID</guilabel></term> 178 <listitem> 179 <para> 180 An ID identifying this annotation type in an external 181 database. This value can be used by tools that 182 need to update annotation types in BASE from external 183 sources. The value doesn't have to be unique. 184 </para> 185 </listitem> 186 </varlistentry> 187 <varlistentry> 188 <term><guilabel>Multiplicity</guilabel></term> 189 <listitem> 190 <para> 191 The maximum number of values that can be entered 192 for this annotation type. The default is 1. A value 193 of 0, means that any number of values can be used. 194 </para> 195 </listitem> 196 </varlistentry> 197 <varlistentry> 198 <term><guilabel>Default value</guilabel></term> 199 <listitem> 200 <para> 201 A value that can be used as the default when 202 adding values. 203 </para> 204 </listitem> 205 </varlistentry> 206 <varlistentry> 207 <term><guilabel>Required for MIAME</guilabel></term> 208 <listitem> 209 <para> 210 If a value must be specified for this annotation type 211 in order for the experiment to be compliant with MIAME. 212 </para> 213 </listitem> 214 </varlistentry> 215 <varlistentry> 216 <term><guilabel>Protocol parameter</guilabel></term> 217 <listitem> 218 <para> 219 If the annotation type is a protocol parameter. As a protocol 220 parameter an item can only be annotated if a protocol 221 that includes this parameter has been used. 222 <nohelp>See <xref linkend="protocols.parameters" /> 223 for more information.</nohelp> 224 </para> 225 </listitem> 226 </varlistentry> 227 <varlistentry> 228 <term><guilabel>Description</guilabel></term> 229 <listitem> 230 <para> 231 A short textual description of the 232 to clarify the usage. 233 </para> 234 </listitem> 235 </varlistentry> 236 </variablelist> 237 238 <seeother> 239 <other external_id="annotationtype.edit.options">Options</other> 240 <other external_id="annotationtype.edit.items">Item types</other> 241 <other external_id="annotationtype.edit.categories">Categories</other> 242 <other external_id="protocol.edit.parameters">Protocol parameters</other> 243 </seeother> 244 </helptext> 245 246 </sect2> 247 248 <sect2 id="annotations.types.options"> 249 <title>Options</title> 250 251 <figure 252 id="annotations.figures.annotationtype.options"> 253 <title>Annotation type options</title> 254 <screenshot> 255 <mediaobject> 256 <imageobject> 257 <imagedata 258 fileref="figures/annotationtype_options.png" format="PNG" /> 259 </imageobject> 260 </mediaobject> 261 </screenshot> 262 </figure> 263 264 <helptext external_id="annotationtype.edit.options" 265 title="Annotation type options"> 266 267 <para> 268 The available options in this tab depends on the type 269 of annotation type, eg. if is a string, numeric or 270 another type. 271 </para> 272 273 <variablelist> 274 <varlistentry> 275 <term><guilabel>Interface</guilabel></term> 276 <listitem> 277 <para> 278 Select the type of graphical element to use for 279 entering values for the annotation type. You can select 280 between three different options: 281 <itemizedlist> 282 <listitem> 283 <para> 284 <guilabel>text box</guilabel>: The user must enter the value 285 in a free-text box. 286 </para> 287 </listitem> 288 <listitem> 289 <para> 290 <guilabel>selection list</guilabel>: The user must select 291 values from a list of predefined values. 292 </para> 293 </listitem> 294 <listitem> 295 <para> 296 <guilabel>radiobuttons/checkboxes</guilabel>: The user must 297 select values by marking checkboxes or radiobuttons. 298 </para> 299 </listitem> 300 </itemizedlist> 301 302 The last two options requires that a list of values are 303 available. Enter possible values in the <guilabel>Values</guilabel> 304 which will be activated automatically. 305 </para> 306 <tip> 307 <para> 308 In term of usability, a drop-down 309 list can be more easily 310 navigated especially when the 311 number of possible values is 312 large, and because selectionlist 313 and drop-down list allow use of 314 arrow and tab for selection. 315 </para> 316 </tip> 317 </listitem> 318 </varlistentry> 319 320 <varlistentry> 321 <term><guilabel>Min/max value</guilabel></term> 322 <listitem> 323 <para> 324 Available for numerical annotation types only. 325 Specifies the minimum and maximum allowed value. 326 If left empty, the bound(s) are undefined and any 327 value is allowed. 328 </para> 329 </listitem> 330 </varlistentry> 331 332 <varlistentry> 333 <term><guilabel>Min/max value</guilabel></term> 334 <listitem> 335 <para> 336 Available for numerical annotation types only. 337 Specifies the minimum and maximum allowed value. 338 If left empty, the bound(s) are undefined and any 339 value is allowed. 340 </para> 341 </listitem> 342 </varlistentry> 343 344 <varlistentry> 345 <term><guilabel>Max length</guilabel></term> 346 <listitem> 347 <para> 348 The maximum allowed length of a string annotation value. 349 If empty, 255 is the maximum length. If you need longer 350 values than that, use a <emphasis>text</emphasis> 351 annotation type. 352 </para> 353 </listitem> 354 </varlistentry> 355 356 <varlistentry> 357 <term><guilabel>Input box width/height</guilabel></term> 358 <listitem> 359 <para> 360 A suggested display width and height of the element 361 used for input. These values are ignored in the current 362 implementation. 363 </para> 364 </listitem> 365 </varlistentry> 366 367 <varlistentry> 368 <term><guilabel>Values</guilabel></term> 369 <listitem> 370 <para> 371 A list of predefined values that the user is allowed 372 to select from. This option is only activated if the 373 <guilabel>Interface</guilabel> option is set 374 to <guilabel>selection list</guilabel> or 375 <guilabel>radiobuttons/checkboxes</guilabel>. 376 Actual values can be supplied using one line for each 377 value (a return entry is used as separator). 378 </para> 379 </listitem> 380 </varlistentry> 381 382 </variablelist> 383 384 <seeother> 385 <other external_id="annotationtype.edit">Properties</other> 386 <other external_id="annotationtype.edit.items">Item types</other> 387 <other external_id="annotationtype.edit.categories">Categories</other> 388 </seeother> 389 </helptext> 390 </sect2> 391 392 <sect2 id="annotations.types.items"> 393 <title>Item types</title> 394 395 <figure 396 id="annotations.figures.annotationtype.items"> 397 <title>Annotation type items</title> 398 <screenshot> 399 <mediaobject> 400 <imageobject> 401 <imagedata 402 fileref="figures/annotationtype_items.png" format="PNG" /> 403 </imageobject> 404 </mediaobject> 405 </screenshot> 406 </figure> 407 408 <helptext external_id="annotationtype.edit.items" 409 title="Item types"> 410 411 <para> 412 On this tab you select the item types that you wish to 413 annotate with the annotation type. Simply use 414 left and right buttons to move selection options 415 between the <guilabel>Enabled for</guilabel> 416 and <guilabel>Disabled for</guilabel> lists. 417 </para> 418 419 <note> 420 <para> 421 If the annotation type has been marked as a 422 <guilabel>Protocol</guilabel> parameter, these settings are 423 ignored, with one exception. If you wish to view parameter 424 values in the list view for a specific item type you must select 425 the item type here. Otherwise the parameter will not be present 426 as a displayable column. 427 </para> 428 </note> 429 430 <seeother> 431 <other external_id="annotationtype.edit">Properties</other> 432 <other external_id="annotationtype.edit.options">Options</other> 433 <other external_id="annotationtype.edit.categories">Categories</other> 434 </seeother> 435 </helptext> 436 </sect2> 437 438 <sect2 id="annotations.types.categories"> 439 <title>Categories</title> 440 441 <helptext external_id="annotationtype.edit.categories" 442 title="Categories"> 443 444 <para> 445 Annotation type can be grouped together by 446 placing them in one or more categories. This 447 enhances display by avoid overcrowding the list 448 of annotation types presented to users. It also 449 allows to improve the display of information. 450 </para> 451 452 <para> 453 The <guilabel>Categories</guilabel> list displays 454 the currently associated categories. Use the 455 <guibutton>Add categories</guibutton> button 456 to add more categories, or the <guilabel>Remove</guilabel> 457 button to remove the selected categories. 458 </para> 459 460 <seeother> 461 <other external_id="annotationtype.edit">Properties</other> 462 <other external_id="annotationtype.edit.options">Options</other> 463 <other external_id="annotationtype.edit.items">Item types</other> 464 </seeother> 465 </helptext> 466 </sect2> 467 </sect1> 468 469 <sect1 id="annotations.categories"> 470 <title>Annotation type categories</title> 471 472 <para> 473 <guilabel>Annotation Type Categories</guilabel> 474 allow grouping of related Annotation Types, based on 475 users requirements. 476 </para> 477 478 <para> 479 For managing categories go to 480 <menuchoice> 481 <guimenu>Administrate</guimenu> 482 <guimenuitem>Types</guimenuitem> 483 <guisubmenu>Annotation Type categories</guisubmenu> 484 </menuchoice>. 485 </para> 486 487 <example id="annotation_types.example.atcategory"> 488 <title>Annotation category examples</title> 489 490 <para> 491 <itemizedlist> 492 <listitem> 493 <para> 494 A category <userinput>Hematology Descriptors</userinput> 495 could be created to group together annotation types such as 496 <userinput>Lymphocyte count</userinput> and 497 <userinput>Hematocrite</userinput> 498 </para> 499 </listitem> 500 501 <listitem> 502 <para> 503 A category <userinput>Plasma Clinical Descriptors</userinput> 504 could be created to group together annotation types such as 505 <userinput>ALT activity (UI/mL)</userinput> and 506 <userinput>LDH activity (UI/mL)</userinput> 507 </para> 508 </listitem> 509 </itemizedlist> 510 </para> 511 </example> 512 </sect1> 513 514 <sect1 id="annotations.bestpractices"> 515 <title>Best Practices and Tab2Mage Export functionality</title> 516 <para> 517 See <xref linkend="experiments_analysis.magexport" />. 518 </para> 519 </sect1> 412 520 413 521 </chapter>
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