Changeset 3412
- Timestamp:
- May 30, 2007, 5:35:48 PM (16 years ago)
- Location:
- trunk/doc/src/docbook
- Files:
-
- 1 added
- 2 deleted
- 3 edited
Legend:
- Unmodified
- Added
- Removed
-
trunk/doc/src/docbook/faq/faqs.xml
r3402 r3412 277 277 by marking their checkboxes. Then click on the <guibutton>Pool</guibutton> 278 278 button. For more information see 279 <xref linkend=" sample.manage.createsample.pool" />.279 <xref linkend="biomaterials.samples.create" />. 280 280 Pooling can also be applied to extracts and labeled extracts. 281 281 </para> -
trunk/doc/src/docbook/userdoc/array_lims.xml
r3394 r3412 314 314 <para>Clicking on the <inlinemediaobject> 315 315 <imageobject> 316 <imagedata fileref="figures/add. gif" format="GIF"/>316 <imagedata fileref="figures/add.png" format="PNG"/> 317 317 </imageobject> 318 318 </inlinemediaobject> add Array batch button available from the … … 438 438 <para>Clicking on the <inlinemediaobject> 439 439 <imageobject> 440 <imagedata fileref="figures/add. gif" format="GIF"/>440 <imagedata fileref="figures/add.png" format="PNG"/> 441 441 </imageobject> 442 442 </inlinemediaobject> add Array slides button. </para> -
trunk/doc/src/docbook/userdoc/biomaterials.xml
r3399 r3412 41 41 menu again to insist on this natural progression. 42 42 </para> 43 <para> 44 Biosources correspond to the native biological entity used in an experiment prior to any 45 treatment. 46 </para> 47 <para> 48 Samples are central to BASE2 to describe the sample processing. So samples can be 49 created from other samples if user want to track sample processing event in a finely 50 granular fashion. 51 </para> 52 <para> 53 Extracts correspond to nucleic acid material extracted from a tissue sample or a cell 54 culture sample. 55 </para> 56 <para> 57 Labeled extracts correspond to nucleic acid materials which have undergone a marking 58 procedure using a fluorescent or radioactive compound for detection in a microarray 59 assay. 60 </para> 43 <itemizedlist> 44 <listitem> 45 <simpara> 46 Biosources correspond to the native biological entity used in an experiment 47 prior to any treatment. 48 </simpara> 49 </listitem> 50 <listitem> 51 <simpara> 52 Samples are central to BASE2 to describe the sample processing. So samples can 53 be created from other samples if user want to track sample processing event in a 54 finely granular fashion. 55 </simpara> 56 </listitem> 57 <listitem> 58 <simpara> 59 Extracts correspond to nucleic acid material extracted from a tissue sample or a 60 cell culture sample. 61 </simpara> 62 </listitem> 63 <listitem> 64 <simpara> 65 Labeled extracts correspond to nucleic acid materials which have undergone a 66 marking procedure using a fluorescent or radioactive compound for detection in a 67 microarray assay. 68 </simpara> 69 </listitem> 70 </itemizedlist> 61 71 <para> 62 72 BASE2 allows users to create any of the these entities fairly freely, however it is … … 71 81 </tip> 72 82 </sect1> 73 <sect1 id="biomaterial.biosources"> 74 <title>Biosources</title> 75 <para> 76 Go to 77 <menuchoice> 78 <guimenu>View</guimenu> 79 <guimenuitem>Biosources</guimenuitem> 80 </menuchoice> 81 . 82 </para> 83 <itemizedlist> 84 <listitem> 85 <para> 86 <guilabel>Biosource</guilabel> 87 </para> 88 <helptext external_id="biosources.edit" title="Edit biosources"> 89 <para> 90 This tab allows users to enter essential information about a biosource. 91 </para> 92 <variablelist> 93 <varlistentry> 94 <term> 95 <guilabel>Name</guilabel> 96 </term> 97 <listitem> 98 <para> 99 This is the only mandatory field. BASE2 by default assigns 100 <replaceable>New Biosource</replaceable> 101 as name but it is advised to provide unique sensible names. 102 </para> 103 </listitem> 104 </varlistentry> 105 <varlistentry> 106 <term> 107 <guilabel>External id</guilabel> 108 </term> 109 <listitem> 110 <para> 111 An external reference identifiers (e.g. a patient identification 112 code) can be supplied using this field. 113 </para> 114 </listitem> 115 </varlistentry> 116 <varlistentry> 117 <term> 118 <guilabel>Description</guilabel> 119 </term> 120 <listitem> 121 <para> 122 A free text description can be supplied using this field. 123 </para> 124 </listitem> 125 </varlistentry> 126 </variablelist> 127 <para> 128 Change tab to 129 <guilabel>Annotations</guilabel> 130 if you want annotate the biosource, otherwise close the pop-up window by 131 either clicking on the &gbSave; button to store the information in BASE2 or 132 on the &gbCancel; button to abort. 133 </para> 134 </helptext> 135 <nohelp> 136 <figure id="write_docbook_doc.figures.biosource-tab-1"> 137 <title> 138 The 139 <guilabel>Biosource</guilabel> 140 tab 141 </title> 142 <screenshot> 143 <mediaobject> 144 <imageobject> 145 <imagedata contentwidth="10cm" width="10cm" 146 fileref="figures/biosource-tab-1.png" format="PNG" /> 147 </imageobject> 148 </mediaobject> 149 </screenshot> 150 </figure> 151 </nohelp> 152 </listitem> 153 <listitem> 154 <para> 155 <guilabel>Annotations</guilabel> 156 </para> 157 <para> 158 This tab allows BASE2 users to use annotation types to refine biosource 159 description. 160 </para> 161 <para> 162 A list of annotation types that are owned by or shared to you will be displayed. 163 </para> 164 <important> 165 <para> 166 In order to use this feature, annotation type must be declared and made 167 available. To learn more about annotation types, please refer to 168 <xref linkend="annotations" /> 169 </para> 170 </important> 171 <para> 172 See 83 <sect1 id="biomaterials.biosources"> 84 <title>BioSources</title> 85 86 87 <sect2 id="biomaterials.biosources.properties"> 88 <title>Properties</title> 89 <sect3 id="biomaterials.biosources.properties.biosource"> 90 <title>Biosource</title> 91 <para>This tab allows users to enter essential information about a biosource.</para> 92 <variablelist> 93 <varlistentry> 94 <term> 95 <guilabel>Name</guilabel> 96 </term> 97 <listitem> 98 <para> 99 This is the only mandatory field. BASE2 by default assigns 100 <replaceable>New biosource</replaceable> 101 as name but it is advised to provide unique sensible names. 102 </para> 103 </listitem> 104 </varlistentry> 105 <varlistentry> 106 <term> 107 <guilabel>External ID</guilabel> 108 </term> 109 <listitem> 110 <para> 111 An external reference identifiers (e.g. a patient identification 112 code) can be supplied using this field. 113 </para> 114 </listitem> 115 </varlistentry> 116 <varlistentry> 117 <term> 118 <guilabel>Description</guilabel> 119 </term> 120 <listitem> 121 <para>A free text description can be supplied using this field.</para> 122 </listitem> 123 </varlistentry> 124 </variablelist> 125 <figure id="write_docbook_doc.figures.biosource-tab-1"> 126 <title>Biosource properties</title> 127 <screenshot> 128 <mediaobject> 129 <imageobject> 130 <imagedata contentwidth="10cm" width="10cm" 131 fileref="figures/biosource-tab-1.png" format="PNG" /> 132 </imageobject> 133 </mediaobject> 134 </screenshot> 135 </figure> 136 </sect3> 137 <sect3 id="biomaterials.biosource.properties.annotations"> 138 <title>Annotations</title> 139 <para> 140 This allows BASE2 users to use annotation types to refine biosource description. 141 More about annotating items can be read in 173 142 <xref linkend="annotations.annotating" /> 174 to get more information on how to set annotation types. 175 </para> 176 </listitem> 177 </itemizedlist> 178 <para> 179 Click on the &gbSave; button to store the information in BASE2 or on the &gbCancel; 180 button to abort. 181 </para> 182 183 <sect2 id="biomaterial.biosource.manage.detail_view"> 184 <title>Viewing biosources</title> 185 <para> 186 From the biosource list view, clicking on the biosource 187 <guilabel>Name</guilabel> 188 opens a detailed view for that biosource, showing a summary of all information 189 available in BASE2 about that particular entity. 190 </para> 191 <para> 192 The default behavior opens the detailed view on the 193 <guilabel>Properties</guilabel> 194 tab, which shows a summary information and displays the list of samples derived from 195 a biosource, if any. 196 </para> 197 <figure id="write_docbook_doc.figures.biosource-itemview-prop"> 198 <title>BioSource Item View, properties tab</title> 199 <screenshot> 200 <mediaobject> 201 <imageobject> 202 <imagedata contentwidth="12cm" width="12cm" 203 fileref="figures/biosource-itemview-prop.png" format="PNG" /> 204 </imageobject> 205 </mediaobject> 206 </screenshot> 207 </figure> 208 <para> 209 By clicking on the 210 <guilabel>Annotations</guilabel> 211 tab, users can display the list of Annotation Types used to annotate a Biosource. 212 </para> 213 <figure id="write_docbook_doc.figures.biosource-itemview-annot"> 214 <title>BioSource Item View, annotations tab</title> 215 <screenshot> 216 <mediaobject> 217 <imageobject> 218 <imagedata contentwidth="13cm" width="13cm" 219 fileref="figures/biosource-itemview-annot.png" format="PNG" /> 220 </imageobject> 221 </mediaobject> 222 </screenshot> 223 </figure> 224 <para> 225 Clicking the 226 <inlinemediaobject> 227 <imageobject> 228 <imagedata fileref="figures/edit.gif" format="GIF" /> 229 </imageobject> 230 </inlinemediaobject> 231 <guiicon>edit icon</guiicon> 232 in the 233 <interface>value</interface> 234 for any of the annotations (e.g. 'antibiotic' in our example), opens an Annotate 235 window (which is a BioSource Edit window set on the annotation tab) and highlights 236 the selected Annotation Type, prompting for data entry. 237 </para> 238 <figure id="write_docbook_doc.figures.biosource-itemview-annot-edit"> 239 <title>BioSource annotations edit</title> 240 <screenshot> 241 <mediaobject> 242 <imageobject> 243 <imagedata contentwidth="12cm" width="12cm" 244 fileref="figures/biosource-itemview-annot-edit.png" format="PNG" /> 245 </imageobject> 246 </mediaobject> 247 </screenshot> 248 </figure> 249 <para> 250 The relevant Annotation Type is highlighted and a list of possible values is 251 displayed. 252 </para> 253 <para> 254 Again, all Annotation types marked with a 255 <inlinemediaobject> 256 <imageobject> 257 <imagedata fileref="figures/annotated.gif" format="GIF" /> 258 </imageobject> 259 </inlinemediaobject> 260 symbol have been used to provided information. 261 </para> 262 <para> 263 Click on the &gbSave; button to store the information in BASE2 or on the &gbCancel; 264 button to abort. 265 </para> 143 . 144 </para> 145 </sect3> 266 146 </sect2> 267 147 </sect1> 268 <sect1 id=" sample.manage">269 <title> ManagingSamples</title>148 <sect1 id="biomaterial.samples"> 149 <title>Samples</title> 270 150 <para> 271 Samples result from processing events applied to 272 <guilabel>BioSource</guilabel> 273 material or other 274 <guilabel>Samples</guilabel> 275 before they are turned into an 276 <guilabel>Extract</guilabel> 277 . 151 Samples result from processing events applied to biosource material or other samples 152 before they are turned into an extract. In other words, samples can be created from 153 biosource items or from one or more sample items.When a sample is created from several 154 other samples, a pooling event is performed. 278 155 </para> 279 156 <para> 280 In other words, Samples can be created from BioSource items or from one or more Sample 281 items. 282 </para> 283 <para> 284 When a Sample is created from several other Samples, a 'pooling' event is performed. A 285 specific section details how to create pools, refer to 286 <xref linkend="sample.manage.createsample.pool" /> 287 </para> 288 <para> 289 For every step of transformation from BioSource to Sample, it is possible to provide 157 For every step of transformation from biosource to sample, it is possible to provide 290 158 information about the protocol used to perform this task. It is not enforced in BASE2 291 159 but it should serve as guidance when devising the granularity of the sample processing … … 293 161 compliance. 294 162 </para> 295 <sect2 id="sample.manage.createsamplefrombiosource"> 296 <title>Creating Samples</title> 297 <orderedlist> 298 <listitem> 299 <para>Creating Samples from the BioSource page</para> 163 <para> 164 Use 165 <menuchoice> 166 <guimenu>View</guimenu> 167 <guimenuitem>Biosource</guimenuitem> 168 </menuchoice> 169 to get to the list of biosources. 170 </para> 171 <sect2 id="biomaterials.samples.create"> 172 <title>Create sample</title> 173 <para> 174 Beside the common way, using the &gbNew; button, a sample can be created in one of 175 the following ways: 176 <variablelist> 177 <varlistentry> 178 <term>from either biosource list- or single view- page.</term> 179 <listitem> 180 <para> 181 No matter how complex the sample processing phase is, at least one 182 sample has to be anchored to a biosource. Therefore, a natural way 183 to create an sample is to click on 184 <inlinemediaobject> 185 <imageobject> 186 <imagedata fileref="figures/add.png" format="PNG" /> 187 </imageobject> 188 </inlinemediaobject> 189 in the sample column of the biosource list view. There is also a 190 corresponding button, 191 <guibutton>Create sample…</guibutton> 192 in the toolbar when viewing a single biosource. 193 </para> 194 </listitem> 195 </varlistentry> 196 <varlistentry> 197 <term>from the sample list page</term> 198 <listitem> 199 <para> 200 Pooled samples can also be created by first selecting the parents 201 from the list of samples and then press 202 <guibutton>Pool…</guibutton> 203 in the toolbar. 204 </para> 205 </listitem> 206 </varlistentry> 207 </variablelist> 208 </para> 209 </sect2> 210 <sect2 id="biomaterials.samples.properties"> 211 <title>Properties</title> 212 <sect3 id="biomaterials.samples.properties.sample"> 213 <title>Sample</title> 214 <helptext external_id="sample.edit" title="Edit sample"> 215 <variablelist> 216 <varlistentry> 217 <term> 218 <guilabel>Name</guilabel> 219 </term> 220 <listitem> 221 <para> 222 The sample's name(required). BASE2 by default assigns names to 223 samples (by suffixing 224 <replaceable>s#</replaceable> 225 when creating a sample from an existing biosource or 226 <replaceable>New Sample</replaceable> 227 otherwise) but it is possible to edit at will. 228 </para> 229 </listitem> 230 </varlistentry> 231 <varlistentry> 232 <term> 233 <guilabel>External ID</guilabel> 234 </term> 235 <listitem> 236 <para> 237 An identification used to identify the sample outside BASE. 238 </para> 239 </listitem> 240 </varlistentry> 241 <varlistentry> 242 <term> 243 <guilabel>Original quantity</guilabel> 244 </term> 245 <listitem> 246 <para> 247 This is meant to report information about the actual mass of 248 sample created. 249 </para> 250 </listitem> 251 </varlistentry> 252 <varlistentry> 253 <term> 254 <guilabel>Created</guilabel> 255 </term> 256 <listitem> 257 <para> 258 A date when the sample was created. The information can be 259 important when running quality controls on data and account for 260 potential confounding factor (e.g. day effect). 261 </para> 262 </listitem> 263 </varlistentry> 264 <varlistentry> 265 <term> 266 <guilabel>Registered</guilabel> 267 </term> 268 <listitem> 269 <para>The date at which the sample was entered in BASE2.</para> 270 </listitem> 271 </varlistentry> 272 <varlistentry> 273 <term> 274 <guilabel>Protocol</guilabel> 275 </term> 276 <listitem> 277 <para>The protocol used to produce this sample.</para> 278 </listitem> 279 </varlistentry> 280 <varlistentry> 281 <term> 282 <guilabel>Description</guilabel> 283 </term> 284 <listitem> 285 <para> 286 A text field to report any information that not can be captured 287 otherwise. 288 </para> 289 </listitem> 290 </varlistentry> 291 </variablelist> 292 </helptext> 293 </sect3> 294 <sect3 id="biomaterials.samples.properties.parents"> 295 <title>Parents</title> 296 <helptext external_id="sample.parents" title="Sample's parents"> 300 297 <para> 301 No matter how complex the sample processing phase is, at least one Sample 302 has to be anchored to a BioSource. 298 This is meant to keep track of the sample origin. BASE2 distinguished 299 between 2 cases which are controled by the 300 <guilabel>Pooled</guilabel> 301 radio-button in the edit pop-up window. 303 302 </para> 303 <itemizedlist> 304 <listitem> 305 <para> 306 If the parent is a biosource the radio-button is set to 307 <guilabel>No</guilabel> 308 . This will make the biosource select button active, which allows 309 users to point to a biosource from which the sample originates from. 310 </para> 311 </listitem> 312 <listitem> 313 <para> 314 When the parent is one or several other samples the radio-button is 315 set to 316 <guilabel>Yes</guilabel> 317 . Upon selection, the biosource select button is deactivated and the 318 samples box and button are activated. This allows users to specify 319 one or more samples to be selected from a sample list view page. 320 </para> 321 </listitem> 322 </itemizedlist> 323 </helptext> 324 </sect3> 325 <sect3 id="biomaterials.samples.properties.annotation_param"> 326 <title>Annotations & parameters</title> 327 <para> 328 As seen in the biosource section, this tab allows users to further supply 329 information about the sample provided they have defined or shared annotation 330 types to annotate sample items. 331 </para> 332 <para> 333 To learn more about annotation types and how to define a value for a type, 334 please refer to 335 <xref linkend="annotations" /> 336 </para> 337 </sect3> 338 <sect3 id="biomaterials.samples.properties.inherited"> 339 <title>Inherited annotations</title> 340 <para> 341 This tab contains a list of those annotations that are inherited from the 342 sample's parents. Information about working with innherited annotations can be 343 found in 344 <xref linkend="annotations.inheriting" /> 345 . 346 </para> 347 </sect3> 348 </sect2> 349 </sect1> 350 351 <sect1 id="biomaterials.extracts"> 352 <title>Extracts</title> 353 <para> 354 Extract items should be used to describe the events that transform a sample material 355 into an extract material. An extract can be created from one sample item or from one or 356 more extract items. When an extract is created from several other extracts, a pooling 357 event is performed. 358 </para> 359 <para> 360 During the transformation from samples to extracts, it is possible to provide 361 information about the protocol used to perform this task. It is not enforced in BASE2 362 but it should serve as guidance when devising the granularity of the sample processing 363 task. Also, it is good practice to provide protocol information. 364 </para> 365 <sect2 id="biomaterials.extracts.create"> 366 <title>Create extract</title> 367 <para> 368 Beside the common way, using the &gbNew; button, an extract can be created in one of 369 the following ways: 370 <variablelist> 371 <varlistentry> 372 <term>from either sample list- or single view- page.</term> 373 <listitem> 374 <para> 375 No matter how complex the extract processing phase is, at least one 376 extract has to be anchored to a sample. Therefore, a natural way to 377 create an extract is to click on 378 <inlinemediaobject> 379 <imageobject> 380 <imagedata fileref="figures/add.png" format="PNG" /> 381 </imageobject> 382 </inlinemediaobject> 383 in the extracts column for the sample that should be a parent of the 384 extract. 385 </para> 386 <para> 387 There is also a corresponding button, 388 <guibutton>Create extract…</guibutton> 389 in the toolbar when viewing a single sample. 390 </para> 391 </listitem> 392 </varlistentry> 393 <varlistentry> 394 <term>from the extract list page</term> 395 <listitem> 396 <para> 397 Pooled extract can also be created by first selecting the parents 398 from the list of extracts and then press 399 <guibutton>Pool…</guibutton> 400 in the toolbar. The selected extracts will be put into the parent 401 property. 402 </para> 403 </listitem> 404 </varlistentry> 405 </variablelist> 406 </para> 407 </sect2> 408 <sect2 id="biomaterials.extracts.properties"> 409 <title>Properties</title> 410 <sect3 id="biomaterials.extracts.properties.extract"> 411 <title>Extract</title> 412 <helptext external_id="extract.edit" title="Edit extract"> 413 <variablelist> 414 <varlistentry> 415 <term> 416 <guilabel>Name</guilabel> 417 </term> 418 <listitem> 419 <para> 420 A mandatory field for providing the extract's name. BASE2 by 421 default assigns names to extract (by suffixing 422 <replaceable>e#</replaceable> 423 when creating an extract from an existing sample or 424 <replaceable>New extract</replaceable> 425 otherwise) but it is possible to edit it at will. 426 </para> 427 </listitem> 428 </varlistentry> 429 <varlistentry> 430 <term> 431 <guilabel>External ID</guilabel> 432 </term> 433 <listitem> 434 <para>The extracts identification outside BASE</para> 435 </listitem> 436 </varlistentry> 437 <varlistentry> 438 <term> 439 <guilabel>Original quantity</guilabel> 440 </term> 441 <listitem> 442 <para> 443 Holds information about the original mass of the created 444 extract. 445 </para> 446 </listitem> 447 </varlistentry> 448 <varlistentry> 449 <term> 450 <guilabel>Created</guilabel> 451 </term> 452 <listitem> 453 <para> 454 The date when the extract was created. The information can be 455 important when running quality controls on data and account for 456 potential confounding factor (e.g. day effect) 457 </para> 458 </listitem> 459 </varlistentry> 460 <varlistentry> 461 <term> 462 <guilabel>Registered</guilabel> 463 </term> 464 <listitem> 465 <para> 466 This is automatically populated with a date at which the sample 467 was entered in BASE2 system. 468 </para> 469 </listitem> 470 </varlistentry> 471 <varlistentry> 472 <term> 473 <guilabel>Protocol</guilabel> 474 </term> 475 <listitem> 476 <para> 477 The extraction protocol that was used to produce the extract. 478 </para> 479 </listitem> 480 </varlistentry> 481 <varlistentry> 482 <term> 483 <guilabel>Description</guilabel> 484 </term> 485 <listitem> 486 <para> 487 A text field to report any information that not can be captured 488 otherwise. 489 </para> 490 </listitem> 491 </varlistentry> 492 </variablelist> 493 </helptext> 494 <figure id="write_docbook_doc.figures.extract-tab-1"> 495 <title>Extract tab</title> 496 <screenshot> 497 <mediaobject> 498 <imageobject> 499 <imagedata contentwidth="12cm" width="12cm" 500 fileref="figures/extract-tab-1.png" format="PNG" /> 501 </imageobject> 502 </mediaobject> 503 </screenshot> 504 </figure> 505 </sect3> 506 507 <sect3 id="biomaterials.extracts.properties.parents"> 508 <title>Parents</title> 509 <helptext external_id="extract.parents" title="Extract's parents"> 304 510 <para> 305 Therefore, a natural way to create a Sample is to click on the 306 <inlinemediaobject> 511 This important tab allows users to select the extract origin. BASE2 512 distinguished between 2 cases which are controled by the 513 <guilabel>Pooled</guilabel> 514 radio-button. 515 </para> 516 <itemizedlist> 517 <listitem> 518 <para> 519 If the parent is a sample the radio-button is set to 520 <guilabel>No</guilabel> 521 . The Sample select button is active and allows users to point to 522 the sample from which the sample originates. 523 </para> 524 </listitem> 525 <listitem> 526 <para> 527 The parent is another extract and the radio-button is set to 528 <guilabel>Yes</guilabel> 529 . Upon selection, the samples select button is deactivated and the 530 extracts box and button are activated. This allows users to specify 531 one or more extracts to be selected from an extract list view page. 532 </para> 533 </listitem> 534 </itemizedlist> 535 </helptext> 536 <figure id="write_docbook_doc.figures.extract-tab-2-select-sample"> 537 <title>Parent tab</title> 538 <screenshot> 539 <mediaobject> 307 540 <imageobject> 308 <imagedata fileref="figures/add.gif" format="GIF" /> 541 <imagedata contentwidth="12cm" width="12cm" 542 fileref="figures/extract-tab-2-select-extract.png" format="PNG" /> 309 543 </imageobject> 310 </inlinemediaobject> 311 <guibutton>Create new Sample</guibutton> 312 from the Sample column of the BioSource list view. 313 </para> 314 <figure id="write_docbook_doc.figures.biosource-create-sample"> 315 <title>Creating a Sample from the BioSource list view</title> 316 <screenshot> 317 <mediaobject> 544 </mediaobject> 545 </screenshot> 546 </figure> 547 </sect3> 548 <sect3 id="biomaterials.extracts.properties.annotations_param"> 549 <title>Annotations & parameters</title> 550 <para> 551 As seen in the biosource and sample sections, this tab allows users to supply 552 further information about the extract, provided they have defined annotation 553 types to annotation extract items or have such elements shared to them. 554 </para> 555 <para> 556 To learn more about annotation types, please refer to 557 <xref linkend="annotations" /> 558 </para> 559 </sect3> 560 <sect3 id="biomaterials.extracts.properties.inherited"> 561 <title>Inherited Annotations</title> 562 <para> 563 This tab contains a list of those annotations that are inherited from the 564 extract's parents. Information about working with innherited annotations can be 565 found in 566 <xref linkend="annotations.inheriting" /> 567 . 568 </para> 569 </sect3> 570 </sect2> 571 </sect1> 572 573 <sect1 id="biomaterials.labels"> 574 <title>Labels</title> 575 <para> 576 Before attempting to create labeled extracts, users should make sure that the 577 appropriate label object is present in BASE2. To browse the list of labels, go to 578 <menuchoice> 579 <guimenu>View</guimenu> 580 <guimenuitem>Labels</guimenuitem> 581 </menuchoice> 582 </para> 583 <sect2 id="biomaterials.labels.properties"> 584 <title>Properties</title> 585 <helptext external_id="label.edit" title="Edit label"> 586 <para> 587 The label item is very simple and doesn't need much explanation. There are only 588 two properties for a label 589 <variablelist> 590 <varlistentry> 591 <term> 592 <guilabel>Name</guilabel> 593 </term> 594 <listitem> 595 <para>The name of the label(required).</para> 596 </listitem> 597 </varlistentry> 598 <varlistentry> 599 <term> 600 <guilabel>Description</guilabel> 601 </term> 602 <listitem> 603 <para> 604 An explaining text or other information associated with the 605 label. 606 </para> 607 </listitem> 608 </varlistentry> 609 </variablelist> 610 . 611 </para> 612 </helptext> 613 </sect2> 614 615 </sect1> 616 <sect1 id="biomaterials.labeledextracts"> 617 <title>Labeled extracts</title> 618 <para> 619 Labeled extract items should be used to describe the event that transformed an extract 620 material in a labeled extract material. Labeled extracts can be created from extract 621 items or from one or more labeled extract items. When a labeled extract is created from 622 several other labeled extracts, a pooling event is performed. 623 </para> 624 <para> 625 During the transformation from extracts to labeled extracts, it is possible to provide 626 information about the protocol used to perform this task. It is not enforced in BASE2 627 but it should serve as guidance when devising the granularity of the extract processing 628 task. Also, it is good practice to provide protocol information. 629 </para> 630 <sect2 id="biomaterials.labeledextracts.create"> 631 <title>Creating labeled extracts</title> 632 <para> 633 Beside the regular way of using the &gbNew; button in 634 <menuchoice> 635 <guimenu>View</guimenu> 636 <guimenuitem>Labeled extracts</guimenuitem> 637 </menuchoice> 638 , a labeled extract can be created in one of following ways. 639 </para> 640 <variablelist> 641 <varlistentry> 642 <term>pooling selected labeled extracts</term> 643 <listitem> 644 <para> 645 The toolbar at the list page of labeled extracts contains an addition 646 &gbPool; button. This button allows users to create pooled labeled 647 extracts by selecting the list of labeled extracts used to derived a new 648 labeled extract and then click on the button. 649 </para> 650 <para> 651 This provides an easy and simple way to create pooled labeled extracts. 652 The result of such process is the creation of a new labeled extract, in 653 which, when navigating to the parent tab, shows that all the labeled 654 extracts involved are already set and listed in the Labeled Extract box 655 of the tab. 656 </para> 657 </listitem> 658 </varlistentry> 659 <varlistentry> 660 <term>from the extract pages.</term> 661 <listitem> 662 <para> 663 Following the laboratory workflow, a natural way to create a labeled 664 extract from an extract is to click on the 665 <inlinemediaobject> 318 666 <imageobject> 319 <imagedata contentwidth="13cm" width="13cm" 320 fileref="figures/biosource-create-sample.png" format="PNG" /> 667 <imagedata fileref="figures/add.png" format="PNG" /> 321 668 </imageobject> 322 </mediaobject> 323 </screenshot> 324 </figure> 325 </listitem> 326 <listitem> 327 <para>Creating Samples from the Sample List view page</para> 669 </inlinemediaobject> 670 from the labeled extract column of the extract list view. Corresponding 671 button, 672 <guibutton>New labeled extract</guibutton> 673 is located on the single item view page for each extract. By creating a 674 labeled extract from an extract page will automatically set the extract 675 as a parent. 676 </para> 677 </listitem> 678 </varlistentry> 679 <varlistentry> 680 <term>from single item view of a label</term> 681 <listitem> 682 <para> 683 Click on the 684 <guibutton>New labeled extract…</guibutton> 685 to use the current label and create a new labeled extract with it 686 pre-selected as 687 <guilabel>Label</guilabel> 688 . 689 </para> 690 </listitem> 691 </varlistentry> 692 </variablelist> 693 </sect2> 694 <sect2 id="biomaterials.labeledextracts.properties"> 695 <title>Properties</title> 696 <sect3 id="biomaterials.labeledextracts.properties.labeledextract"> 697 <title>Labeled extract</title> 698 <variablelist> 699 <varlistentry> 700 <term> 701 <guilabel>Name</guilabel> 702 </term> 703 <listitem> 704 <para> 705 The name of the labeled extract (required). BASE2 by default assigns 706 names to labeled extract(by suffixing 707 <replaceable>lbe#</replaceable> 708 when creating a labeled extract from an existing extract or 709 <replaceable>New labeled extract</replaceable> 710 otherwise) but it is possible to edit it at will 711 </para> 712 </listitem> 713 </varlistentry> 714 <varlistentry> 715 <term> 716 <guilabel>Label</guilabel> 717 </term> 718 <listitem> 719 <para> 720 Used to specify which dye or marker was used in the labeling 721 reaction (required). 722 </para> 723 </listitem> 724 </varlistentry> 725 <varlistentry> 726 <term> 727 <guilabel>External ID</guilabel> 728 </term> 729 <listitem> 730 <para>An id used to recognize the labeled extract outside BASE.</para> 731 </listitem> 732 </varlistentry> 733 <varlistentry> 734 <term> 735 <guilabel>Original quantity</guilabel> 736 </term> 737 <listitem> 738 <para>The mass of labeled extract that was created.</para> 739 </listitem> 740 </varlistentry> 741 <varlistentry> 742 <term> 743 <guilabel>Created</guilabel> 744 </term> 745 <listitem> 746 <para> 747 A date should be provided. The information can be important when 748 running quality controls on data and account for potential 749 confounding factor (e.g. day effect). 750 </para> 751 </listitem> 752 </varlistentry> 753 <varlistentry> 754 <term> 755 <guilabel>Registred</guilabel> 756 </term> 757 <listitem> 758 <para> 759 This is automatically populated with a date at which the labeled 760 extract was actually entered in BASE2 system. 761 </para> 762 </listitem> 763 </varlistentry> 764 <varlistentry> 765 <term> 766 <guilabel>Protocol</guilabel> 767 </term> 768 <listitem> 769 <para> 770 The labeling protocol that was used to produce the labeled extract. 771 </para> 772 </listitem> 773 </varlistentry> 774 <varlistentry> 775 <term> 776 <guilabel>Description</guilabel> 777 </term> 778 <listitem> 779 <para> 780 A free text field to report any information that can not be captured 781 otherwise. 782 </para> 783 </listitem> 784 </varlistentry> 785 </variablelist> 786 </sect3> 787 <sect3 id="biomaterials.labeledextracts.properties.parents"> 788 <title>Parents</title> 789 <para> 790 This important tab allows users to select the labeled extract origin. BASE2 791 distinguished between 2 cases which are controled by the 792 <guilabel>Pooled</guilabel> 793 radio-button. 794 </para> 795 <itemizedlist> 796 <listitem> 797 <para>The parent is an extract</para> 798 <para> 799 The radio-button is set to 800 <guilabel>No</guilabel> 801 . The Extract select button is active and allows users to point to one 802 and only one extract from which the labeled extract originates from. 803 </para> 804 </listitem> 805 <listitem> 806 <para>The parent is another labeled extract</para> 807 <para> 808 The radio-button has to be set to 809 <guilabel>Yes</guilabel> 810 . Upon selection, the extract select button is deactivated and the 811 labeled extracts box and button are activated. This allows users to 812 specify one or more extracts to be selected from the labeled extract 813 list view page. 814 </para> 815 </listitem> 816 </itemizedlist> 817 </sect3> 818 <sect3 id="biomaterials.labeledextracts.properties.annotations_param"> 819 <title>Annotations & parameters</title> 820 <para> 821 As seen in the biosource and sample sections, this tab allows users to further 822 supply information about the labeled extract provided they have defined 823 annotation types to annotate labeled extract items or have such elements shared 824 to them. 825 </para> 826 <important> 328 827 <para> 329 This is the alternative for creating Sample from the BioSource. To do so, go 330 to 331 <menuchoice> 332 <guimenu>View</guimenu> 333 <guimenuitem>BioSamples</guimenuitem> 334 </menuchoice> 335 , Click on &gbNew; button 336 </para> 337 <para> 338 A 'Create' pop-up window opens, it contains 4 tabs: 339 <guilabel>Sample</guilabel> 340 , 341 <guilabel>Parents</guilabel> 342 , 343 <guilabel>Annotations & parameters</guilabel> 344 and 345 <guilabel>Inherited Annotations</guilabel> 828 In order to use this feature, annotation type must be declared and made 829 available. To learn more about annotation types and how these are set, 830 please refer to 831 <xref linkend="annotations" /> 346 832 . 347 833 </para> 348 <itemizedlist> 349 <listitem> 350 <para>The Sample Tab</para> 351 <para> 352 This tab contains 1 mandatory field for providing the Sample 353 <guilabel>Name</guilabel> 354 . BASE2 by default assigns names to Samples (by suffixing 's#' when 355 creating a Sample from an existing Biosource or 'New Sample' 356 otherwise) but it is possible to edit at will. 357 </para> 358 <para> 359 There are 5 optional fields to provide more detailed information 360 </para> 361 <itemizedlist> 362 <listitem> 363 <para> 364 <guilabel>External ID</guilabel> 365 : for instance to report a barcode attached to a Sample 366 </para> 367 </listitem> 368 <listitem> 369 <para> 370 <guilabel>Original Quantity (ug)</guilabel> 371 : this is meant to report information about the actual mass 372 of biomaterial created 373 </para> 374 </listitem> 375 <listitem> 376 <para> 377 <guilabel>Created</guilabel> 378 : a date should be provided. The information can be 379 important when running quality controls on data and account 380 for potential confounding factor (e.g. day effect) 381 </para> 382 </listitem> 383 <listitem> 384 <para> 385 <guilabel>Protocol</guilabel> 386 : this a controled field. A select-list displays protocols 387 whose type is 388 <guilabel>sampling</guilabel> 389 and which are shared to or owned by the logged-in user. 390 </para> 391 <important> 392 <para> 393 It is not mandatory to supply protocol in BASE2 394 Reporting protocols is a MIAME requirement 395 </para> 396 </important> 397 </listitem> 398 <listitem> 399 <para> 400 <guilabel>Description</guilabel> 401 : a free text field to report any information that not can 402 be captured otherwise 403 </para> 404 </listitem> 405 </itemizedlist> 406 <para> 407 Finally, a 7th field, 408 <guilabel>Registered</guilabel> 409 is automatically populated with a date at which the Sample was 410 entered in BASE2 system. 411 </para> 412 <figure id="write_docbook_doc.figures.biosample-tab-1"> 413 <title>Sample tab</title> 414 <screenshot> 415 <mediaobject> 416 <imageobject> 417 <imagedata contentwidth="10cm" width="10cm" 418 fileref="figures/biosample-tab-1.png" format="PNG" /> 419 </imageobject> 420 </mediaobject> 421 </screenshot> 422 </figure> 423 </listitem> 424 <listitem> 425 <para>The Parents Tab</para> 426 <para> 427 This important tab does what it says on the tin: It is meant to keep 428 track of the Sample origin. BASE2 distinguished between 2 cases 429 which are controled by the 430 <guibutton>pooled</guibutton> 431 radio-button 432 </para> 433 <orderedlist> 434 <listitem> 435 <para>The Parent is a BioSource</para> 436 <para> 437 The 438 <guibutton>Pooled</guibutton> 439 radio-button is set to 440 <guilabel>No</guilabel> 441 </para> 442 <para> 443 The BioSource select button is active and allows users to 444 point to one and only one BioSource from which the Sample 445 originates from. 446 </para> 447 <figure 448 id="write_docbook_doc.figures.biosample-tab-2-select-biosource"> 449 <title> 450 Parent tab and interaction when pooled button is set to 451 No 452 </title> 453 <screenshot> 454 <mediaobject> 455 <imageobject> 456 <imagedata contentwidth="12cm" width="12cm" 457 fileref="figures/biosample-tab-2-select-biosource.png" format="PNG" /> 458 </imageobject> 459 </mediaobject> 460 </screenshot> 461 </figure> 462 </listitem> 463 <listitem> 464 <para>The Parent is another Sample</para> 465 <para> 466 The 467 <guibutton>Pooled</guibutton> 468 radio-button has to be set to 469 <guilabel>Yes</guilabel> 470 </para> 471 <para> 472 Upon selection, the BioSource select button is deactivated 473 and the Samples box and button are activated. 474 </para> 475 <para> 476 This allows users to specify one or more Samples to be 477 selected from the Sample List View page. 478 </para> 479 <figure 480 id="write_docbook_doc.figures.biosample-tab-2-select-sample"> 481 <title> 482 Parent tab and interaction when pooled button is set to 483 Yes 484 </title> 485 <screenshot> 486 <mediaobject> 487 <imageobject> 488 <imagedata contentwidth="12cm" width="12cm" 489 fileref="figures/biosample-tab-2-select-sample.png" format="PNG" /> 490 </imageobject> 491 </mediaobject> 492 </screenshot> 493 </figure> 494 </listitem> 495 </orderedlist> 496 </listitem> 497 <listitem> 498 <para>Annotations & parameters</para> 499 <para> 500 As seen in the BioSource section, this tab allows users to further 501 supply information about the Sample provided they have defined or 502 shared annotation types to annotate Sample items. 503 </para> 504 <para> 505 The display of Annotation Type can be filtered based on the 506 Annotation Type Category they belong to. 507 </para> 508 <important> 509 <para> 510 In order to use this feature, Annotation Type must be declared 511 and made available. To learn more about Annotation Types, please 512 refer to 513 <xref linkend="annotations" /> 514 </para> 515 </important> 516 <para> 517 To provide a value for a given annotation type, simply click on it 518 an use the input field or select a value from the drop-down lists or 519 radio buttons. 520 </para> 521 <figure id="write_docbook_doc.figures.biosample-tab-3"> 522 <title>Annotations & parameters</title> 523 <screenshot> 524 <mediaobject> 525 <imageobject> 526 <imagedata contentwidth="12cm" width="12cm" 527 fileref="figures/biosample-tab-3.png" format="PNG" /> 528 </imageobject> 529 </mediaobject> 530 </screenshot> 531 </figure> 532 </listitem> 533 <listitem> 534 <para>Inherited Annotations case1</para> 535 <para>The next picture shows</para> 536 <figure id="write_docbook_doc.figures.biosample-tab-4"> 537 <title>Inherited Annotations</title> 538 <screenshot> 539 <mediaobject> 540 <imageobject> 541 <imagedata contentwidth="12cm" width="12cm" 542 fileref="figures/biosample-tab-4.png" format="PNG" /> 543 </imageobject> 544 </mediaobject> 545 </screenshot> 546 </figure> 547 <para>Inherited Annotations case2</para> 548 <figure id="write_docbook_doc.figures.biosample-tab-4bis"> 549 <title>Inherited Annotations</title> 550 <screenshot> 551 <mediaobject> 552 <imageobject> 553 <imagedata contentwidth="12cm" width="12cm" 554 fileref="figures/biosample-tab-4bis.png" format="PNG" /> 555 </imageobject> 556 </mediaobject> 557 </screenshot> 558 </figure> 559 </listitem> 560 </itemizedlist> 561 </listitem> 562 </orderedlist> 563 </sect2> 564 <sect2 id="sample.manage.createsample.pool"> 565 <title>Creating Pooled Samples</title> 566 <para> 567 It is common practice when biological material is scarce to pool Samples from 568 equivalent sources. BASE2 provides mechanisms to report on such practice. 569 </para> 570 <para>This section details how.</para> 571 <para>There are 2 ways to create Pooled Samples in BASE2</para> 572 <orderedlist> 573 <listitem> 574 <para> 575 Using the Pooled radio button option from the Sample Create page, and this 576 has been shown already 577 </para> 578 </listitem> 579 <listitem> 580 <para>Using the Pool button in the Menu bar</para> 581 <para> 582 The Sample List View page menu bar contains an additionnal button the usage 583 of which is detailed now. 584 </para> 585 <para> 586 The &gbPool; button 587 <inlinemediaobject> 588 <imageobject> 589 <imagedata fileref="figures/new_pooled.gif" format="GIF" /> 590 </imageobject> 591 </inlinemediaobject> 592 allows users to create Pooled Samples by selecting the list of Samples used 593 to produce that new Sample. 594 </para> 595 <para> 596 Users simply need to tick the select-boxes in front of each relevant Sample 597 and click the 598 <inlinemediaobject> 599 <imageobject> 600 <imagedata fileref="figures/new_pooled.gif" format="GIF" /> 601 </imageobject> 602 </inlinemediaobject> 603 button. 604 </para> 605 <para> 606 This provides an easy and simple way to create Pooled Samples. The result of 607 such process is the creation of a New Sample, which Parent Samples are 608 listing and preset in the Parent tab 609 </para> 610 <figure id="write_docbook_doc.figures.biosample-tab-2-pool-sample"> 611 <title>Pooling of Samples</title> 612 <screenshot> 613 <mediaobject> 614 <imageobject> 615 <imagedata contentwidth="12cm" width="12cm" 616 fileref="figures/biosample-tab-2-pool-sample.png" format="PNG" /> 617 </imageobject> 618 </mediaobject> 619 </screenshot> 620 </figure> 621 </listitem> 622 </orderedlist> 623 </sect2> 624 <sect2 id="sample.manage.delete"> 625 <title>Deleting/Restoring Samples</title> 626 <para> 627 As for other items in BASE2, Samples can be removed. For a generic overview on how 628 to delete and restore items, refer to section 629 <xref linkend="webclient.items.delete" /> 630 </para> 631 <para>To delete, do the following</para> 632 <itemizedlist> 633 <listitem> 634 <para> 635 Select one or more Samples and click &gbDelete; button in the menu bar. 636 </para> 637 <para> 638 All the selected Samples have been marked as deleted and are no longer 639 available from the interface. 640 </para> 641 <para> 642 From the 643 <guilabel>view/preset…</guilabel> 644 select box, ticking the 645 <guilabel>Removed</guilabel> 646 option allows to display those Samples earmarked for deletion. They will be 647 shown with a symbol 648 <guiicon>D</guiicon> 649 in front of them. 650 </para> 651 </listitem> 652 <listitem> 653 <para> 654 Alternately, navigating to the Sample Item View, one can hit the &gbDelete; 655 to performed the task. As showen in the next picture, the Sample is then 656 flagged with the 657 <guiicon>This item has been flagged for deletion</guiicon> 658 </para> 659 <figure id="write_docbook_doc.figures.sample-delete"> 660 <title>Deleting Samples from the Item View</title> 661 <screenshot> 662 <mediaobject> 663 <imageobject> 664 <imagedata contentwidth="12cm" width="12cm" 665 fileref="figures/sample-delete.png" format="PNG" /> 666 </imageobject> 667 </mediaobject> 668 </screenshot> 669 </figure> 670 </listitem> 671 <listitem> 672 <para> 673 Deletion errors can be easily recovered. Select the item to recover from the 674 List View (be sure to check the 675 <guilabel>removed</guilabel> 676 option in the View/preset.. filter) and hit the &gbRestore; to performed the 677 task. 678 </para> 679 </listitem> 680 </itemizedlist> 681 <important> 682 <para> 683 To really delete an item from the database you must use the trashcan. Items 684 deleted from the Trashcan can not be recovered. To learn more about the trashcan 685 function, please refer to 686 <xref linkend="trashcan" /> 687 </para> 688 </important> 834 </important> 835 </sect3> 836 <sect3 id="biomaterials.labeledextracts.properties.inherited"> 837 <title>Inherited annotations</title> 838 <para> 839 This tab contains a list of those annotations that are inherited from the 840 parents of the labeled extract. Information about dealing with innherited 841 annotations can be found in 842 <xref linkend="annotations.inheriting" /> 843 . 844 </para> 845 </sect3> 689 846 </sect2> 690 847 </sect1> 691 848 692 <sect1 id="extract.manage"> 693 <title>Managing Extracts</title> 694 <para> 695 Extract items should be used to describe the events that transform a Sample material in 696 an Extract material. 697 </para> 698 <para>Extracts can be created from Sample items or from one or more Extract items.</para> 699 <para> 700 When an Extract is created from several other Extracts, a Pooling event is performed. A 701 specific section details how to create pooled Extracts 702 </para> 703 <para> 704 During the transformation from Samples to Extracts, it is possible to provide 705 information about the protocol used to perform this task. 706 </para> 707 <para> 708 It is not enforced in BASE2 but it should serve as guidance when devising the 709 granularity of the sample processing task. Also, it is good practice to provide protocol 710 information. 711 </para> 712 <sect2 id="extract.manage.createextractfromsample"> 713 <title>Creating Extracts</title> 714 <orderedlist> 715 <listitem> 716 <para>Creating Extracts from the Sample page</para> 717 <para> 718 Following the laboratory workflow, a natural way to create a new Extract is 719 to click on the 720 <guibutton>New extract</guibutton> 721 from the Extract column of the Sample List View. 722 </para> 723 <figure id="write_docbook_doc.figures.sample-create-extract"> 724 <title>Creating an Extract from the Sample list view</title> 725 <screenshot> 726 <mediaobject> 727 <imageobject> 728 <imagedata contentwidth="12cm" width="12cm" 729 fileref="figures/sample-create-extract.png" format="PNG" /> 730 </imageobject> 731 </mediaobject> 732 </screenshot> 733 </figure> 734 </listitem> 735 <listitem> 736 <para>Creating Extracts from the Sample List view page</para> 737 <para> 738 Alternately, Extracts can be created directly ysing the Extract create page. 739 To do so, go to 740 <menuchoice> 741 <guimenu>View</guimenu> 742 <guimenuitem>Extracts</guimenuitem> 743 </menuchoice> 744 , Click on &gbNew; button 745 </para> 746 <para> 747 A 'Create' pop-up window opens, it contains 4 tabs: 748 <guilabel>Extract</guilabel> 749 , 750 <guilabel>Parents</guilabel> 751 , 752 <guilabel>Annotations & parameters</guilabel> 753 and 754 <guilabel>Inherited Annotations</guilabel> 755 . 756 </para> 757 <itemizedlist> 758 <listitem> 759 <para>The Extract Tab</para> 760 <para> 761 This tab contains 1 mandatory field for providing the extract name. 762 </para> 763 <para> 764 BASE2 by default assigns names to Extract (by suffixing 'e#' when 765 creating an Extract from an existing Sample or 'New Extract' 766 otherwise) but it is possible to edit it at will 767 </para> 768 <para> 769 There 5 optional fields to provide more detailed information 770 </para> 771 <itemizedlist> 772 <listitem> 773 <para> 774 <guilabel>External ID</guilabel> 775 : for instance to report a barcode attached to an extract 776 </para> 777 </listitem> 778 <listitem> 779 <para> 780 <guilabel>Original Quantity (ug)</guilabel> 781 : this is meant to report information about the actual mass 782 of biomaterial created 783 </para> 784 </listitem> 785 <listitem> 786 <para> 787 <guilabel>Created</guilabel> 788 : a date should be provided. The information can be 789 important when running quality controls on data and account 790 for potential confounding factor (e.g. day effect) 791 </para> 792 </listitem> 793 <listitem> 794 <para> 795 <guilabel>Protocol</guilabel> 796 : this a controled field. A select-list displays protocol 797 whose type is ' 798 <guilabel>extraction</guilabel> 799 ' and which are shared to or owned by the logged-in user. 800 Reporting Protocol should be viewed as a MIAME requirement 801 </para> 802 </listitem> 803 <listitem> 804 <para> 805 <guilabel>Description</guilabel> 806 : a free text field to report any information that not can 807 be captured otherwise 808 </para> 809 </listitem> 810 </itemizedlist> 811 <para> 812 Finally, a 7th field 813 <guilabel>Registered</guilabel> 814 is automatically populated with a date at which the sample was 815 entered in BASE2 system. 816 </para> 817 <figure id="write_docbook_doc.figures.extract-tab-1"> 818 <title>Extract tab</title> 819 <screenshot> 820 <mediaobject> 821 <imageobject> 822 <imagedata contentwidth="12cm" width="12cm" 823 fileref="figures/extract-tab-1.png" format="PNG" /> 824 </imageobject> 825 </mediaobject> 826 </screenshot> 827 </figure> 828 </listitem> 829 <listitem> 830 <para>The Parents Tab</para> 831 <para> 832 This important tab allows users to select the Extract origin. BASE2 833 distinguished between 2 cases which are controled by the 834 <guibutton>'pooled'</guibutton> 835 radio-button 836 </para> 837 <orderedlist> 838 <listitem> 839 <para>The Parent is a Sample</para> 840 <para> 841 The 842 <guibutton>pooled</guibutton> 843 radio-button is set to 844 <guilabel>No</guilabel> 845 </para> 846 <para> 847 The Sample select button is active and allows users to point 848 to one and only one Sample from which the sample originates 849 from. 850 </para> 851 <figure 852 id="write_docbook_doc.figures.extract-tab-2-select-sample"> 853 <title> 854 Parent tab and interaction when pooled button is set to 855 No 856 </title> 857 <screenshot> 858 <mediaobject> 859 <imageobject> 860 <imagedata contentwidth="12cm" width="12cm" 861 fileref="figures/extract-tab-2-select-sample.png" format="PNG" /> 862 </imageobject> 863 </mediaobject> 864 </screenshot> 865 </figure> 866 </listitem> 867 <listitem> 868 <para>The Parent is another Extract</para> 869 <para> 870 The 871 <guibutton>pooled</guibutton> 872 radio-button has to be set to 873 <guilabel>Yes</guilabel> 874 </para> 875 <para> 876 Upon selection, the Samples select button is deactivated and 877 the Extracts box and button are activated. 878 </para> 879 <para> 880 This allows users to specify one or more extracts to be 881 selected from the Extract list View page. 882 </para> 883 <figure 884 id="write_docbook_doc.figures.extract-tab-2-select-extract"> 885 <title> 886 Parent tab and interaction when pooled button is set to 887 Yes 888 </title> 889 <screenshot> 890 <mediaobject> 891 <imageobject> 892 <imagedata contentwidth="12cm" width="12cm" 893 fileref="figures/extract-tab-2-select-extract.png" format="PNG" /> 894 </imageobject> 895 </mediaobject> 896 </screenshot> 897 </figure> 898 </listitem> 899 </orderedlist> 900 </listitem> 901 <listitem> 902 <para>Annotations & parameters</para> 903 <para> 904 As seen in the BioSource and Sample sections, this tab allows users 905 to supply further information about the Extract, provided they have 906 defined Annotation Types to annotation Extract items or have such 907 elements shared to them. 908 </para> 909 <para> 910 The display of Annotation Type can be filtered based on the 911 Annotation Type Category they belong to. 912 </para> 913 <important> 914 <para> 915 In order to use this feature, Annotation Type must be declared 916 and made available. To learn more about Annotation Types, please 917 refer to 918 <xref linkend="annotations" /> 919 </para> 920 </important> 921 <para> 922 To provide a value for a given annotation type, simply click on it 923 an use the input field or select a value from the drop-down lists or 924 radio buttons. 925 </para> 926 <figure id="write_docbook_doc.figures.extract-tab-3"> 927 <title>Annotations & parameters</title> 928 <screenshot> 929 <mediaobject> 930 <imageobject> 931 <imagedata contentwidth="12cm" width="12cm" 932 fileref="figures/extract-tab-3.png" format="PNG" /> 933 </imageobject> 934 </mediaobject> 935 </screenshot> 936 </figure> 937 </listitem> 938 <listitem> 939 <para>Inherited Annotations case1</para> 940 <para>The next picture shows</para> 941 <figure id="write_docbook_doc.figures.extract-tab-4"> 942 <title>Inherited Annotations</title> 943 <screenshot> 944 <mediaobject> 945 <imageobject> 946 <imagedata contentwidth="12cm" width="12cm" 947 fileref="figures/extract-tab-4.png" format="PNG" /> 948 </imageobject> 949 </mediaobject> 950 </screenshot> 951 </figure> 952 </listitem> 953 </itemizedlist> 954 </listitem> 955 </orderedlist> 956 </sect2> 957 <sect2 id="extract.manage.createextractpool"> 958 <title>Creating Pooled Extracts</title> 959 <para> 960 It is common practice when biological material is scarce to pool extracts from 961 equivalent sources. BASE2 provides mechanisms to report on such practice. This 962 section details how. 963 </para> 964 <para>There are 2 ways to create pooled samples in BASE2:</para> 965 <orderedlist> 966 <listitem> 967 <para> 968 Using the Pooled radio button option from the Extract Create page, and this 969 has been shown already. 970 </para> 971 </listitem> 972 <listitem> 973 <para>Using the Pool button in the Menu bar</para> 974 <para> 975 The Sample List View page menu bar contains an addition &gbPool; 976 <inlinemediaobject> 977 <imageobject> 978 <imagedata fileref="figures/new_pooled.gif" format="GIF" /> 979 </imageobject> 980 </inlinemediaobject> 981 button, the usage of which is detailed now. 982 </para> 983 <para> 984 The &gbPool; 985 <inlinemediaobject> 986 <imageobject> 987 <imagedata fileref="figures/new_pooled.gif" format="GIF" /> 988 </imageobject> 989 </inlinemediaobject> 990 button allows users to create Pooled Extracts by selecting the list of 991 Extracts used to derived a new Extract. Users simply to tick to boxes in 992 front of each relevant Extract and click the 993 <guibutton>Pool...</guibutton> 994 </para> 995 <para> 996 This provides an easy and simple way to create pooled Extracts. The result 997 of such process is the creation of a New Extract, in which, when navigating 998 to the Parent tab, shows that all the Extracts involved are already set and 999 listed in the Extract box of the tab. 1000 </para> 1001 <figure id="write_docbook_doc.figures.biosample-tab-2-pool-extract"> 1002 <title>Pooling of Extracts</title> 1003 <screenshot> 1004 <mediaobject> 1005 <imageobject> 1006 <imagedata contentwidth="12cm" width="12cm" 1007 fileref="figures/extract-tab-2-pool-extract.png" format="PNG" /> 1008 </imageobject> 1009 </mediaobject> 1010 </screenshot> 1011 </figure> 1012 </listitem> 1013 </orderedlist> 1014 </sect2> 1015 <sect2 id="extract.manage.delete"> 1016 <title>Deleting/Restoring Extracts</title> 1017 <para> 1018 As for other items in BASE2, Extracts can be removed. For a generic overview on how 1019 to delete and restore items, refer to section 1020 <xref linkend="webclient.items.delete" /> 1021 </para> 1022 <para>To delete, do the following</para> 1023 <itemizedlist> 1024 <listitem> 1025 <para> 1026 Select one or more Extract and click &gbDelete; button in the menu bar. 1027 </para> 1028 <para> 1029 All the selected Extracts have been marked as deleted and are no longer 1030 available from the interface. 1031 </para> 1032 <para> 1033 Only by selecting from the 1034 <guilabel>view/preset…</guilabel> 1035 select box the 1036 <guilabel>Removed</guilabel> 1037 option, one can see those of the Extracts earmarked for deletion. They will 1038 be shown with a symbol in front of them. 1039 </para> 1040 </listitem> 1041 <listitem> 1042 <para> 1043 Alternately, navigating to the Extract Item View, one can hit the &gbDelete; 1044 to performed the task. 1045 </para> 1046 <para> 1047 As shown in the next picture, the Extract is then marked with the 1048 <guilabel>This item has been flagged for deletion</guilabel> 1049 </para> 1050 <figure id="write_docbook_doc.figures.extract-delete"> 1051 <title>Deleting Extracts from the Item View</title> 1052 <screenshot> 1053 <mediaobject> 1054 <imageobject> 1055 <imagedata contentwidth="12cm" width="12cm" 1056 fileref="figures/extract-delete.png" format="PNG" /> 1057 </imageobject> 1058 </mediaobject> 1059 </screenshot> 1060 </figure> 1061 </listitem> 1062 <listitem> 1063 <para> 1064 Deletion errors at this stage can be easily recovered. Select the item to 1065 recover from the List View (be sure to check the 1066 <guilabel>removed</guilabel> 1067 option in the View/preset.. filter) and hit the &gbRestore; to performed the 1068 task. 1069 </para> 1070 </listitem> 1071 </itemizedlist> 1072 <important> 1073 <para> 1074 To really delete an item from the database you must use the trashcan. Items 1075 deleted from the Trashcan can not be recovered. To learn more about the trashcan 1076 function, please refer to 1077 <xref linkend="trashcan" /> 1078 </para> 1079 </important> 1080 </sect2> 1081 </sect1> 1082 1083 1084 1085 <sect1 id="label"> 1086 <title>Managing Labels</title> 1087 1088 <sect2 id="label.browse"> 1089 <title>Browsing Labels</title> 1090 <para> 1091 Before attempting to create Labeled Extracts, users should make sure that the 1092 appropriate Label object is present in BASE2 1093 </para> 1094 <para> 1095 To browse the list of Labels, go to 1096 <menuchoice> 1097 <guimenu>View</guimenu> 1098 <guimenuitem>Labels</guimenuitem> 1099 </menuchoice> 1100 It is wise to select the clear filter option or select the 1101 <guilabel>shared to me</guilabel> 1102 option from the view/preset select box in order to view all different dyes. 1103 </para> 1104 <para>Clicking on any of item opens an item view page</para> 1105 <figure id="write_docbook_doc.figures.label-itemview"> 1106 <title>The Label Item View Page</title> 1107 <screenshot> 1108 <mediaobject> 1109 <imageobject> 1110 <imagedata contentwidth="12cm" width="12cm" 1111 fileref="figures/label-itemview.png" format="PNG" /> 1112 </imageobject> 1113 </mediaobject> 1114 </screenshot> 1115 </figure> 1116 <para> 1117 Note the 1118 <guibutton>New labeled extract…</guibutton> 1119 button available from this page. For more detailed about creating Labeled extracts, 1120 see 1121 <xref linkend="labeledextract.manage" /> 1122 </para> 1123 1124 </sect2> 1125 <sect2 id="label.create"> 1126 <title>Creating Labels</title> 1127 <para> 1128 Click on &gbNew; button, a pop-up window opens. Fill in Name and description if 1129 required. Label item are very simple object and do not bear association to 1130 Annotation Type. 1131 </para> 1132 </sect2> 1133 </sect1> 1134 <sect1 id="labeledextract.manage"> 1135 <title>Managing Labeled Extracts</title> 1136 <para> 1137 Labeled Extract items should be used to describe the event that transformed a Extract 1138 material in a Labeled Extract material. 1139 </para> 1140 <para> 1141 Labeled extracts can be created from Extract items or from one or more Labeled extract 1142 items. 1143 </para> 1144 <para> 1145 When a Labeled Extract is created from several other Labeled Extracts, a Pooling event 1146 is performed. A specific section details how to create pooled Labeled Extracts 1147 </para> 1148 <para> 1149 During the transformation from Extracts to Labeled Extracts, it is possible to provide 1150 information about the protocol used to perform this task. 1151 </para> 1152 <para> 1153 It is not enforced in BASE2 but it should serve as guidance when devising the 1154 granularity of the extract processing task. Also, it is good practice to provide 1155 protocol information. 1156 </para> 1157 <sect2 id="labeledextract.manage.createlabeledextractfromextract"> 1158 <title>Creating Labeled Extracts</title> 1159 <orderedlist> 1160 <listitem> 1161 <para>Creating Labeled Extracts from the Extract page</para> 1162 <para> 1163 Following the laboratory workflow, a natural way to create a Labeled Extract 1164 is to click on the 1165 <guibutton>New labeled extract</guibutton> 1166 from the Labeled Extract column of the Extract List View. 1167 </para> 1168 <figure id="write_docbook_doc.figures.sample-create-labeledextract"> 1169 <title>Creating a Labeled Extract from the Extract List View</title> 1170 <screenshot> 1171 <mediaobject> 1172 <imageobject> 1173 <imagedata contentwidth="12cm" width="12cm" 1174 fileref="figures/sample-create-labeledextract.png" format="PNG" /> 1175 </imageobject> 1176 </mediaobject> 1177 </screenshot> 1178 </figure> 1179 </listitem> 1180 <listitem> 1181 <para>Creating Labeled Extracts from the Extract Item View page</para> 1182 <para> 1183 Alternately, Labeled Extracts can be created directly using the Labeled 1184 Extract create page. To do so, go to 1185 <menuchoice> 1186 <guimenu>View</guimenu> 1187 <guimenuitem>Labeled Extracts</guimenuitem> 1188 </menuchoice> 1189 , Click on &gbNew; button 1190 </para> 1191 <para> 1192 A 'Create' pop-up window opens, it contains 4 tabs: 1193 <guilabel>Labeled Extract</guilabel> 1194 , 1195 <guilabel>Parents</guilabel> 1196 , 1197 <guilabel>Annotations & parameters</guilabel> 1198 and 1199 <guilabel>Inherited Annotations</guilabel> 1200 . 1201 </para> 1202 <itemizedlist> 1203 <listitem> 1204 <para>The Labeled Extract Tab</para> 1205 <para> 1206 This tab contains 2 mandatory fields, one for providing the Labeled 1207 Extract 1208 <guilabel>Name</guilabel> 1209 , the other one 1210 <guilabel>Label</guilabel> 1211 to specify which dye or marker was used in the labeling reaction. 1212 </para> 1213 <para> 1214 BASE2 by default assigns names to Labeled Extract(by suffixing 1215 'lbe#' when creating a Labeled Extract from an existing Extract or 1216 'New labeled extract' otherwise) but it is possible to edit it at 1217 will 1218 </para> 1219 <para> 1220 There 5 optional fields to provide more detailed information 1221 </para> 1222 <itemizedlist> 1223 <listitem> 1224 <para> 1225 <guilabel>External ID</guilabel> 1226 : for instance to report a barcode attached to an extract 1227 </para> 1228 </listitem> 1229 <listitem> 1230 <para> 1231 <guilabel>Original Quantity (ug)</guilabel> 1232 : this is meant to report information about the actual mass 1233 of biomaterial created 1234 </para> 1235 </listitem> 1236 <listitem> 1237 <para> 1238 <guilabel>Created</guilabel> 1239 : a date should be provided. The information can be 1240 important when running quality controls on data and account 1241 for potential confounding factor (e.g. day effect) 1242 </para> 1243 </listitem> 1244 <listitem> 1245 <para> 1246 <guilabel>Protocol</guilabel> 1247 : this a controled field. A select-list displays protocol 1248 whose type is ' 1249 <guilabel>labeling</guilabel> 1250 ' and which are shared to or owned by the logged-in user. 1251 Reporting Protocol should be viewed as a MIAME requirement 1252 </para> 1253 </listitem> 1254 <listitem> 1255 <para> 1256 <guilabel>Description</guilabel> 1257 : a free text field to report any information that can not 1258 be captured otherwise 1259 </para> 1260 </listitem> 1261 </itemizedlist> 1262 <para> 1263 Finally, a 7th field 1264 <guilabel>Created</guilabel> 1265 is automatically populated with a date at which the Labeled Extract 1266 was actually entered in BASE2 system. 1267 </para> 1268 <figure id="write_docbook_doc.figures.labeledextract-tab-1"> 1269 <title>Labeled Extract tab</title> 1270 <screenshot> 1271 <mediaobject> 1272 <imageobject> 1273 <imagedata contentwidth="12cm" width="12cm" 1274 fileref="figures/labeledextract-tab-1.png" format="PNG" /> 1275 </imageobject> 1276 </mediaobject> 1277 </screenshot> 1278 </figure> 1279 </listitem> 1280 <listitem> 1281 <para>The Parents Tab</para> 1282 <para> 1283 This important tab allows users to select the Labeled Extract 1284 origin. BASE2 distinguished between 2 cases which are controled by 1285 the 1286 <guibutton>'pooled'</guibutton> 1287 radio-button 1288 </para> 1289 <orderedlist> 1290 <listitem> 1291 <para>The Parent is an Extract</para> 1292 <para> 1293 The 1294 <guibutton>pooled</guibutton> 1295 radio-button is set to 1296 <guilabel>No</guilabel> 1297 </para> 1298 <para> 1299 The Extract select button is active and allows users to 1300 point to one and only one Extract from which the Labeled 1301 Extract originates from. 1302 </para> 1303 <figure 1304 id="write_docbook_doc.figures.labeledextract-tab-2-select-extract"> 1305 <title> 1306 Parent tab and interaction when pooled button is set to 1307 No 1308 </title> 1309 <screenshot> 1310 <mediaobject> 1311 <imageobject> 1312 <imagedata contentwidth="12cm" width="12cm" 1313 fileref="figures/labeledextract-tab-2-select-extract.png" format="PNG" /> 1314 </imageobject> 1315 </mediaobject> 1316 </screenshot> 1317 </figure> 1318 </listitem> 1319 <listitem> 1320 <para>The Parent is another Labeled Extract</para> 1321 <para> 1322 The 1323 <guibutton>pooled</guibutton> 1324 radio-button has to be set to 1325 <guilabel>Yes</guilabel> 1326 </para> 1327 <para> 1328 Upon selection, the Extract select button is deactivated and 1329 the Labeled Extracts box and button are activated. 1330 </para> 1331 <para> 1332 This allows users to specify one or more extracts to be 1333 selected from the Labeled Extract list View page. 1334 </para> 1335 <figure 1336 id="write_docbook_doc.figures.labeledextract-tab-2-select-labeledextract"> 1337 <title> 1338 Parent tab and interaction when pooled button is set to 1339 Yes 1340 </title> 1341 <screenshot> 1342 <mediaobject> 1343 <imageobject> 1344 <imagedata contentwidth="12cm" width="12cm" 1345 fileref="figures/labeledextract-tab-2-select-labeledextract.png" format="PNG" /> 1346 </imageobject> 1347 </mediaobject> 1348 </screenshot> 1349 </figure> 1350 </listitem> 1351 </orderedlist> 1352 </listitem> 1353 <listitem> 1354 <para>Annotations & parameters</para> 1355 <para> 1356 As seen in the BioSource and Sample sections, this tab allows users 1357 to further supply information about the labeled extract provided 1358 they have defined annotation types to annotate Labeled Extract items 1359 or have such elements shared to them. 1360 </para> 1361 <para> 1362 The display of Annotation Types can be filtered based on the 1363 Annotation Type Categories they belong to. 1364 </para> 1365 <important> 1366 <para> 1367 In order to use this feature, Annotation Type must be declared 1368 and made available. To learn more about Annotation Types, please 1369 refer to 1370 <xref linkend="annotations" /> 1371 </para> 1372 </important> 1373 <para> 1374 To provide a value for a given annotation type, simply click on it 1375 an use the input field or select a value from the drop-down lists or 1376 radio buttons. 1377 </para> 1378 <figure id="write_docbook_doc.figures.labeledextract-tab-3"> 1379 <title>Annotations & parameters</title> 1380 <screenshot> 1381 <mediaobject> 1382 <imageobject> 1383 <imagedata contentwidth="12cm" width="12cm" 1384 fileref="figures/labeledextract-tab-3.png" format="PNG" /> 1385 </imageobject> 1386 </mediaobject> 1387 </screenshot> 1388 </figure> 1389 </listitem> 1390 <listitem> 1391 <para>Inherited Annotations case1</para> 1392 <para>The next picture shows</para> 1393 <figure id="write_docbook_doc.figures.labeledextract-tab-4"> 1394 <title>Inherited Annotations</title> 1395 <screenshot> 1396 <mediaobject> 1397 <imageobject> 1398 <imagedata contentwidth="12cm" width="12cm" 1399 fileref="figures/labeledextract-tab-4.png" format="PNG" /> 1400 </imageobject> 1401 </mediaobject> 1402 </screenshot> 1403 </figure> 1404 </listitem> 1405 </itemizedlist> 1406 </listitem> 1407 </orderedlist> 1408 </sect2> 1409 <sect2 id="labeledextract.manage.createelabeledxtract.pool"> 1410 <title>Creating Pooled Labeled Extracts</title> 1411 <para> 1412 It is common practice when biological material is scarce to pool extracts from 1413 equivalent sources. BASE2 provides mechanisms to report on such practice. 1414 </para> 1415 <para>This section details how.</para> 1416 <para>There are 2 ways to create pooled Labeled Extracts in BASE2</para> 1417 <orderedlist> 1418 <listitem> 1419 <para> 1420 Using the Pooled radio button option from the Labeled Extract Create page, 1421 and this has been shown already 1422 </para> 1423 </listitem> 1424 <listitem> 1425 <para>Using the Pool button in the Menu bar</para> 1426 <para> 1427 The Labeled Extracts List View page menu bar contains an addition &gbPool; 1428 button, the usage of which is detailed now. 1429 </para> 1430 <para> 1431 The &gbPool; button 1432 <inlinemediaobject> 1433 <imageobject> 1434 <imagedata fileref="figures/new_pooled.gif" format="GIF" /> 1435 </imageobject> 1436 </inlinemediaobject> 1437 allows users to create Pooled Labeled Extracts by selecting the list of 1438 Labeled Extracts used to derived a new Labeled Extract. Users simply have to 1439 tick to boxes in front of each relevant Labeled Extract and click the 1440 <guibutton>Pool...</guibutton> 1441 </para> 1442 <para> 1443 This provides an easy and simple way to create pooled Labeled Extracts. The 1444 result of such process is the creation of a New Labeled Extract, in which, 1445 when navigating to the Parent tab, shows that all the Labeled Extracts 1446 involved are already set and listed in the Labeled Extract box of the tab. 1447 </para> 1448 <figure 1449 id="write_docbook_doc.figures.labeledextract-tab-2-pool-labeledextract"> 1450 <title>Pooling of Labeled Extracts:</title> 1451 <screenshot> 1452 <mediaobject> 1453 <imageobject> 1454 <imagedata contentwidth="12cm" width="12cm" 1455 fileref="figures/labeledextract-tab-2-pool-labeledextract.png" format="PNG" /> 1456 </imageobject> 1457 </mediaobject> 1458 </screenshot> 1459 </figure> 1460 </listitem> 1461 </orderedlist> 1462 </sect2> 1463 <sect2 id="labeledextract.manage.delete"> 1464 <title>Deleting/Restoring Labeled Extracts</title> 1465 <para> 1466 As for other items in BASE2, Labeled Extracts can be deleted. For a generic overview 1467 on how to delete and restore items, refer to section 1468 <xref linkend="webclient.items.delete" /> 1469 </para> 1470 <para>To delete, do the following</para> 1471 <itemizedlist> 1472 <listitem> 1473 <para> 1474 Select one or more Labeled Extract and click &gbDelete; button in the menu 1475 bar. 1476 </para> 1477 <para> 1478 All the selected Labeled Extracts have been marked as deleted and are no 1479 longer available from the interface. 1480 </para> 1481 <para> 1482 Only by selecting from the 1483 <guilabel>view/preset…</guilabel> 1484 select box the 1485 <guilabel>Removed</guilabel> 1486 option, one can see those of the Labeled Extracts earmarked for deletion. 1487 They will be shown with a symbol in front of them. 1488 </para> 1489 </listitem> 1490 <listitem> 1491 <para> 1492 Alternately, navigating to the Labeled Extract Item View, one can hit the 1493 &gbDelete; to performed the task. As showed in the next picture, the Labeled 1494 Extract is then marked with the 1495 <inlinemediaobject> 1496 <imageobject> 1497 <imagedata fileref="figures/deleted.gif" format="GIF" /> 1498 </imageobject> 1499 </inlinemediaobject> 1500 <guiicon>This item has been flagged for deletion</guiicon> 1501 </para> 1502 <figure id="write_docbook_doc.figures.labeledextract-delete"> 1503 <title>Deleting Labeled Extracts from the Item View</title> 1504 <screenshot> 1505 <mediaobject> 1506 <imageobject> 1507 <imagedata contentwidth="12cm" width="12cm" 1508 fileref="figures/labeledextract-delete.png" format="PNG" /> 1509 </imageobject> 1510 </mediaobject> 1511 </screenshot> 1512 </figure> 1513 </listitem> 1514 <listitem> 1515 <para> 1516 Deletion errors at this stage can be easily recovered. Select the item to 1517 recover from the List View (be sure to check the 1518 <guilabel>Removed</guilabel> 1519 option in the View/preset.. filter) and hit the &gbRestore; to performed the 1520 task. 1521 </para> 1522 </listitem> 1523 </itemizedlist> 1524 <important> 1525 <para> 1526 To really delete an item from the database you must use the trashcan. Items 1527 deleted from the Trashcan can not be recovered. To learn more about the trashcan 1528 function, please refer to 1529 <xref linkend="trashcan" /> 1530 </para> 1531 </important> 1532 </sect2> 1533 </sect1> 1534 <sect1 id="hybridization.manage"> 1535 <title>Managing Hybridizations</title> 849 <sect1 id="biomaterials.hybridizations"> 850 <title>Hybridizations</title> 1536 851 <para> 1537 852 An hybridization event corresponds to the application of one or more labeled extracts 1538 853 materials to a microarray slide under conditions detailed in hybridization protocols. 854 Use 855 <menuchoice> 856 <guimenu>View</guimenu> 857 <guimenuitem>Hybridizatons</guimenuitem> 858 </menuchoice> 859 to get to the hybridizations. 1539 860 </para> 1540 <para>In BASE2, there are 3 possible routes to create an hybridization object.</para> 1541 <sect2 id="hybridization.manage.create"> 1542 <title>Creating Hybridizations</title> 1543 <orderedlist> 1544 <listitem> 1545 <para>Creating Hybridization from the Labeled Extract List View page</para> 861 <sect2 id="biomaterials.hybridizations.create"> 862 <title>Creating hybridizations</title> 863 <para> 864 In BASE2, there are 2 possible routes to create an hybridization object except the 865 common way with the &gbNew; button at hybridization list page. 866 </para> 867 <variablelist> 868 <varlistentry> 869 <term>from the labeled extract list view page</term> 870 <listitem> 871 <para> 872 Select at least one labeled extract, to create a hybridization from, by 873 ticking the selection boxes before the name field. 874 </para> 875 <para> 876 Click on the 877 <guibutton>New hybridzation…</guibutton> 878 from the toolbar of labeled extract list view. 879 </para> 880 </listitem> 881 </varlistentry> 882 <varlistentry> 883 <term>from a labeled extract single item page</term> 884 <listitem> 885 <para> 886 When viewing a label extract in single item view, click on the 887 <guibutton>New hybridization…</guibutton> 888 button from the toolbar of the labeled extract item view. 889 </para> 890 </listitem> 891 </varlistentry> 892 </variablelist> 893 </sect2> 894 <sect2 id="biomaterials.hybridizations.properties"> 895 <title>Properties</title> 896 897 <sect3 id="biomaterials.hybridizations.hybridization"> 898 <title>Hybridization</title> 899 <variablelist> 900 <varlistentry> 901 <term> 902 <guilabel>Name</guilabel> 903 </term> 904 <listitem> 905 <para> 906 <replaceable>New hybridization</replaceable> 907 is BASE2 default name but it is strongly advise to provide a 908 meaningful and unique name (required). 909 </para> 910 </listitem> 911 </varlistentry> 912 913 <varlistentry> 914 <term> 915 <guilabel>Created</guilabel> 916 </term> 917 <listitem> 918 <para> 919 A date should be provided. The information can be important when 920 running quality controls on data and account for potential 921 confounding factor (e.g. to account for a day effect) 922 </para> 923 </listitem> 924 </varlistentry> 925 926 <varlistentry> 927 <term> 928 <guilabel>Registered</guilabel> 929 </term> 930 <listitem> 931 <para> 932 This field is automatically populated with a date at which the 933 hybridization was entered in BASE2 system. 934 </para> 935 </listitem> 936 </varlistentry> 937 938 <varlistentry> 939 <term> 940 <guilabel>Protocol</guilabel> 941 </term> 942 <listitem> 943 <para> 944 The hybridization protocol that was used to do the hybridization. 945 </para> 946 </listitem> 947 </varlistentry> 948 949 <varlistentry> 950 <term> 951 <guilabel>Hardware</guilabel> 952 </term> 953 <listitem> 954 <para> 955 The hybridization-station that was used during the hybridization. 956 </para> 957 </listitem> 958 </varlistentry> 959 960 <varlistentry> 961 <term> 962 <guilabel>Array slide</guilabel> 963 </term> 964 <listitem> 965 <para>The array slide that was used in the hybridization.</para> 966 <note> 967 <para> 968 Ideally, The Array Slides should have been created but for those 969 users with permission to do, Array Slides could be generated at 970 that point. 971 </para> 972 </note> 973 </listitem> 974 </varlistentry> 975 976 <varlistentry> 977 <term> 978 <guilabel>Description</guilabel> 979 </term> 980 <listitem> 981 <para> 982 A free text field to report any information that can not be captured 983 otherwise 984 </para> 985 </listitem> 986 </varlistentry> 987 </variablelist> 988 <figure id="write_docbook_doc.figures.hybridization-tab-1"> 989 <title>Hybridization tab</title> 990 <screenshot> 991 <mediaobject> 992 <imageobject> 993 <imagedata contentwidth="12cm" width="12cm" 994 fileref="figures/hybridization-tab-1.png" format="PNG" /> 995 </imageobject> 996 </mediaobject> 997 </screenshot> 998 </figure> 999 </sect3> 1000 <sect3 id="biomaterials.hybridizations.properties.labeledextracts"> 1001 <title>Labeled extracts</title> 1002 <figure id="write_docbook_doc.figures.hybridization-tab-2"> 1003 <title>Labeled Extract tab</title> 1004 <screenshot> 1005 <mediaobject> 1006 <imageobject> 1007 <imagedata contentwidth="12cm" width="12cm" 1008 fileref="figures/hybridization-tab-2.png" format="PNG" /> 1009 </imageobject> 1010 </mediaobject> 1011 </screenshot> 1012 </figure> 1013 <para> 1014 This important tab allows users to select the labeled extracts applied to an 1015 array slide, and specify the amount of material used, expressed in microgram. 1016 </para> 1017 <para> 1018 Use the buttons to the right for adding and removing the items in the list. 1019 Select one or several labeled extracts in the list and write the used mass in 1020 the field below. 1021 </para> 1022 </sect3> 1023 <sect3 id="biomaterials.hybridizations.properties.annotations_param"> 1024 <title>Annotations & parameters</title> 1025 <para> 1026 As seen in the biosource and sample sections, this tab allows users to supply 1027 further information about the hybridization provided annotation types have been 1028 defined or shared to annotate hybridization items. 1029 </para> 1030 <important> 1546 1031 <para> 1547 Select at least one Labeled Extract by ticking to selection boxes before the 1548 name field. 1032 In order to use this feature, annotation type must be declared and made 1033 available. To learn more about annotation types and how these are set, 1034 please refer to 1035 <xref linkend="annotations" /> 1549 1036 </para> 1550 <para> 1551 Click on the 1552 <guibutton>New hybridzation (to be changed)</guibutton> 1553 from the menu bar of Labeled Extract list view. 1554 </para> 1555 <figure id="write_docbook_doc.figures.hyb-create-labeledlistview"> 1556 <title>Creating a Hybridization from the Labeled Extract List View</title> 1557 <screenshot> 1558 <mediaobject> 1559 <imageobject> 1560 <imagedata contentwidth="12cm" width="12cm" 1561 fileref="figures/hyb-create-labeledlistview.png" format="PNG" /> 1562 </imageobject> 1563 </mediaobject> 1564 </screenshot> 1565 </figure> 1566 </listitem> 1567 <listitem> 1568 <para>Creating Hybridization from the Labeled Extract Item View page</para> 1569 <para> 1570 After having selected a Labeled Extract and displayed it in the Item View, 1571 Click on the 1572 <guibutton>New hybridization</guibutton> 1573 button from the Menu bar of the Labeled Extract Item View. 1574 </para> 1575 <figure id="write_docbook_doc.figures.hyb-create-labeleditemview"> 1576 <title>Creating a Hybridization from the Labeled Extract Item View</title> 1577 <screenshot> 1578 <mediaobject> 1579 <imageobject> 1580 <imagedata contentwidth="12cm" width="12cm" 1581 fileref="figures/hyb-create-labeleditemview.png" format="PNG" /> 1582 </imageobject> 1583 </mediaobject> 1584 </screenshot> 1585 </figure> 1586 </listitem> 1587 <listitem> 1588 <para>Creating Hybridizations from the Hybridization List View page</para> 1589 <para> 1590 Hybridizations can be created directly using the Hybridization create page. 1591 To do so, go to 1592 <menuchoice> 1593 <guimenu>View</guimenu> 1594 <guimenuitem>Hybridizations</guimenuitem> 1595 </menuchoice> 1596 , Click on &gbNew; 1597 </para> 1598 <figure id="write_docbook_doc.figures.hyb-create"> 1599 <title>Creating Hybridizations from the Hybridization List View</title> 1600 <screenshot> 1601 <mediaobject> 1602 <imageobject> 1603 <imagedata contentwidth="12cm" width="12cm" 1604 fileref="figures/hyb-create.png" format="PNG" /> 1605 </imageobject> 1606 </mediaobject> 1607 </screenshot> 1608 </figure> 1609 <para> 1610 Irrespective of the methods chosen to create the Hybridization item, A 1611 'Create' pop-up window will open. It contains 4 distinct tabs: 1612 <guilabel>Hybridization</guilabel> 1613 , 1614 <guilabel>Parents</guilabel> 1615 , 1616 <guilabel>Annotations & parameters</guilabel> 1617 and 1618 <guilabel>Inherited Annotations</guilabel> 1619 . 1620 </para> 1621 <itemizedlist> 1622 <listitem> 1623 <para>The Hybridization Tab</para> 1624 1625 <variablelist> 1626 <varlistentry> 1627 <term> 1628 <interface>Name</interface> 1629 </term> 1630 <listitem> 1631 <para> 1632 New Hybridization is BASE2 default name but it is 1633 strongly advise to provide a meaningful and unique name 1634 as it matters for tab2mage export to function properly. 1635 </para> 1636 <para> 1637 There are 5 optional fields to provide more detailed 1638 information 1639 </para> 1640 1641 </listitem> 1642 </varlistentry> 1643 1644 <varlistentry> 1645 <term> 1646 <guilabel>Created</guilabel> 1647 </term> 1648 <listitem> 1649 <para> 1650 A date should be provided. The information can be 1651 important when running quality controls on data and 1652 account for potential confounding factor (e.g. to 1653 account for a day effect) 1654 </para> 1655 </listitem> 1656 </varlistentry> 1657 1658 <varlistentry> 1659 <term> 1660 <guilabel>Protocol</guilabel> 1661 </term> 1662 <listitem> 1663 <para> 1664 This is a controled field. A select-list displays 1665 protocol whose type is ' 1666 <guilabel>hybridization</guilabel> 1667 ' and which are shared to or owned by the logged-in 1668 user. 1669 </para> 1670 <important> 1671 <para> 1672 Reporting Protocols should be viewed as a MIAME 1673 requirement 1674 </para> 1675 </important> 1676 </listitem> 1677 </varlistentry> 1678 1679 <varlistentry> 1680 <term> 1681 <guilabel>Hardware</guilabel> 1682 </term> 1683 <listitem> 1684 <para> 1685 This is a controled field. A select-list displays 1686 Hardware whose type is ' 1687 <guilabel>Hybridization station</guilabel> 1688 ' and which are shared to or owned by the logged-in 1689 user. 1690 </para> 1691 </listitem> 1692 </varlistentry> 1693 1694 <varlistentry> 1695 <term> 1696 <guilabel>Array Slide</guilabel> 1697 </term> 1698 <listitem> 1699 <para> 1700 This is meant to specify the actual microarray slide. 1701 </para> 1702 <note> 1703 <para> 1704 Ideally, The Array Slides should have been created 1705 but for those users with permission to do, Array 1706 Slides could be generated at that point. 1707 </para> 1708 </note> 1709 </listitem> 1710 </varlistentry> 1711 1712 <varlistentry> 1713 <term> 1714 <guilabel>Description</guilabel> 1715 </term> 1716 <listitem> 1717 <para> 1718 A free text field to report any information that can not 1719 be captured otherwise 1720 </para> 1721 </listitem> 1722 </varlistentry> 1723 1724 <varlistentry> 1725 <term> 1726 <guilabel>Registered</guilabel> 1727 </term> 1728 <listitem> 1729 <para> 1730 This 7th field is automatically populated with a date at 1731 which the sample was entered in BASE2 system. 1732 </para> 1733 </listitem> 1734 </varlistentry> 1735 </variablelist> 1736 1737 <figure id="write_docbook_doc.figures.hybridization-tab-1"> 1738 <title>Hybridization tab</title> 1739 <screenshot> 1740 <mediaobject> 1741 <imageobject> 1742 <imagedata contentwidth="12cm" width="12cm" 1743 fileref="figures/hybridization-tab-1.png" format="PNG" /> 1744 </imageobject> 1745 </mediaobject> 1746 </screenshot> 1747 </figure> 1748 </listitem> 1749 <listitem> 1750 <para>The Labeled Extract Tab</para> 1751 <para> 1752 This important tab allows users to select the Labeled Extracts 1753 applied to an Array Slide, and specify the amount of material used, 1754 expressed in microgram. 1755 </para> 1756 <figure id="write_docbook_doc.figures.hybridization-tab-2"> 1757 <title>Labeled Extract tab</title> 1758 <screenshot> 1759 <mediaobject> 1760 <imageobject> 1761 <imagedata contentwidth="12cm" width="12cm" 1762 fileref="figures/hybridization-tab-2.png" format="PNG" /> 1763 </imageobject> 1764 </mediaobject> 1765 </screenshot> 1766 </figure> 1767 </listitem> 1768 <listitem> 1769 <para>Annotations & parameters</para> 1770 <para> 1771 As seen in the BioSource and Sample sections, this tab allows users 1772 to supply further information about the hybridization provided 1773 annotation types have been defined or shared to annotate 1774 Hybridization items. The display of Annotation Types can be filtered 1775 based on the Annotation Type Category they belong to. 1776 </para> 1777 <important> 1778 <para> 1779 In order to use this feature, Annotation Type must be declared 1780 and made available. To learn more about Annotation Types, please 1781 refer to 1782 <xref linkend="annotations" /> 1783 </para> 1784 </important> 1785 <para> 1786 To provide a value for a given annotation type, simply click on it 1787 and use the input field or select a value from the drop-down lists 1788 or radio buttons. 1789 </para> 1790 <para> 1791 A caption also reminds users if Annotation Types are parameters 1792 <inlinemediaobject> 1793 <imageobject> 1794 <imagedata fileref="figures/parameter.gif" format="GIF" /> 1795 </imageobject> 1796 </inlinemediaobject> 1797 and if annotation values have already been supplied, marked by the 1798 <inlinemediaobject> 1799 <imageobject> 1800 <imagedata fileref="figures/annotated.gif" format="GIF" /> 1801 </imageobject> 1802 </inlinemediaobject> 1803 logo. 1804 </para> 1805 <figure id="write_docbook_doc.figures.hybridization-tab-3"> 1806 <title>Annotations & parameters</title> 1807 <screenshot> 1808 <mediaobject> 1809 <imageobject> 1810 <imagedata contentwidth="12cm" width="12cm" 1811 fileref="figures/hybridization-tab-3.png" format="PNG" /> 1812 </imageobject> 1813 </mediaobject> 1814 </screenshot> 1815 </figure> 1816 </listitem> 1817 <listitem> 1818 <para>Inherited Annotations</para> 1819 <para> 1820 The next screenshot shows a typical view of the functionality. 1821 </para> 1822 <figure id="write_docbook_doc.figures.hybridization-tab-4"> 1823 <title>Inherited Annotations</title> 1824 <screenshot> 1825 <mediaobject> 1826 <imageobject> 1827 <imagedata contentwidth="12cm" width="12cm" 1828 fileref="figures/hybridization-tab-4.png" format="PNG" /> 1829 </imageobject> 1830 </mediaobject> 1831 </screenshot> 1832 </figure> 1833 <para> 1834 Note the tags used to distinguish between Annotation Types which are 1835 parameters noted 1836 <inlinemediaobject> 1837 <imageobject> 1838 <imagedata fileref="figures/parameter.gif" format="GIF" /> 1839 </imageobject> 1840 </inlinemediaobject> 1841 and those which are Biomaterial Characteristics,noted 1842 <inlinemediaobject> 1843 <imageobject> 1844 <imagedata fileref="figures/annotation.gif" format="GIF" /> 1845 </imageobject> 1846 </inlinemediaobject> 1847 </para> 1848 </listitem> 1849 </itemizedlist> 1850 </listitem> 1851 </orderedlist> 1852 </sect2> 1853 <sect2 id="hybridization.manage.viewedit"> 1854 <title>Viewing/Editing Hybridizations</title> 1855 <para> 1856 As for other items in BASE2, Hybridizations can be edited. To do so, do the 1857 following 1858 </para> 1859 <itemizedlist> 1860 <listitem> 1861 <para> 1862 Press and hold one of the 1863 <keycap>CTRL</keycap> 1864 , 1865 <keycap>ALT</keycap> 1866 or 1867 <keycap>SHIFT</keycap> 1868 keys while clicking on the name of an Hybridization Item, which is a live 1869 link. 1870 </para> 1871 </listitem> 1872 <listitem> 1873 <para> 1874 Alternately, navigating to the Hybridization Item View, one can hit the 1875 <guibutton>Edit</guibutton> 1876 to performed the task. 1877 </para> 1878 </listitem> 1879 1880 <listitem> 1881 <para> 1882 The Hybridization item View summarizes key information such as the list of 1883 <guilabel>Labeled Extracts</guilabel> 1884 , and the list of associated 1885 <guilabel>Scans</guilabel> 1886 . Both are available as hyperlinks to allow quick and easy navigation. 1887 </para> 1888 <figure id="write_docbook_doc.figures.hybridization-itemview"> 1889 <title>Hardware Item View</title> 1890 <screenshot> 1891 <mediaobject> 1892 <imageobject> 1893 <imagedata contentwidth="10cm" width="10cm" 1894 fileref="figures/hybridization-itemview.png" format="PNG" /> 1895 </imageobject> 1896 </mediaobject> 1897 </screenshot> 1898 </figure> 1899 </listitem> 1900 </itemizedlist> 1901 1902 </sect2> 1903 1904 <sect2 id="hybridization.manage.delete"> 1905 <title>Deleting/Restoring Hybridizations</title> 1906 <para> 1907 As for other items in BASE2, Hybridizations can be deleted. For a generic overview 1908 on how to delete and restore items, refer to section 1909 <xref linkend="webclient.items.delete" /> 1910 </para> 1911 1912 <para>To delete, do the following</para> 1913 <itemizedlist> 1914 <listitem> 1915 <para> 1916 Select one or more Hybridization Items and click on the &gbDelete; button in 1917 the menu bar. 1918 </para> 1919 <para> 1920 All the selected Hybridizations have been marked as deleted and are no 1921 longer available from the interface. 1922 </para> 1923 <para> 1924 Only by selecting from the 1925 <guilabel>view/preset…</guilabel> 1926 select box the 1927 <guilabel>Removed</guilabel> 1928 option, one can see those of the Hybridizations earmarked for deletion. They 1929 will be shown with a symbol in front of them. 1930 </para> 1931 </listitem> 1932 <listitem> 1933 <para> 1934 Alternately, navigating to the Hybridization Item View, one can hit the 1935 &gbDelete; to performed the task. As shown in the next picture, the 1936 Hybridization is then marked with the 1937 <inlinemediaobject> 1938 <imageobject> 1939 <imagedata fileref="figures/deleted.gif" format="GIF" /> 1940 </imageobject> 1941 </inlinemediaobject> 1942 <guilabel>This item has been flagged for deletion</guilabel> 1943 </para> 1944 <figure id="write_docbook_doc.figures.hybridization-delete"> 1945 <title>Deleting Hybridizations from the Hybridization Item View</title> 1946 <screenshot> 1947 <mediaobject> 1948 <imageobject> 1949 <imagedata contentwidth="10cm" width="10cm" 1950 fileref="figures/hybridization-delete.png" format="PNG" /> 1951 </imageobject> 1952 </mediaobject> 1953 </screenshot> 1954 </figure> 1955 </listitem> 1956 </itemizedlist> 1957 <important> 1958 <para> 1959 To really delete an item from the database you must use the trashcan. Items 1960 deleted from the Trashcan can not be recovered. To learn more about the trashcan 1961 function, please refer to 1962 <xref linkend="trashcan" /> 1963 </para> 1964 </important> 1037 </important> 1038 </sect3> 1039 <sect3 id="biomaterials.hybridizations.properties.inherited"> 1040 <title>Inherited annotations</title> 1041 <para> 1042 This tab contains a list of those annotations that are inherited from the 1043 labeled extracts. Information about dealing with innherited annotations can be 1044 found in 1045 <xref linkend="annotations.inheriting" /> 1046 . 1047 </para> 1048 </sect3> 1965 1049 </sect2> 1966 1050 </sect1>
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