Changeset 5682


Ignore:
Timestamp:
Aug 2, 2011, 9:09:56 AM (10 years ago)
Author:
Nicklas Nordborg
Message:

References #1590: Documentation cleanup

FAQ section and removed information related to the Tab2Mage exporter.

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

Legend:

Unmodified
Added
Removed
  • trunk/doc/src/docbook/faq/faqs.xml

    r5110 r5682  
    8585            <simpara>
    8686              The reporter import plug-in can be executed in <emphasis>delete</emphasis>
    87               mode. Run the plug-in again and select the same file you just for the import.
     87              mode. Run the plug-in again and select the same file you used for the import.
    8888              Select the <guilabel>Mode=delete</guilabel> option.
    8989              In the <guilabel>Error handling</guilabel> section select the
     
    338338              button. For more information see
    339339              <xref linkend="biomaterials.samples.create" />.
    340               Pooling can also be applied to extracts and labeled extracts.
    341             </para>
    342           </answer>
    343         </qandaentry>
    344         <qandaentry>
    345           <question>
    346             <para>
    347               I would like to add a software type in BASE but there is no button for
    348               doing so. Is it possible?
    349             </para>
    350           </question>
    351           <answer>
    352             <para>
    353               No, this is not possible, since there is only one place
    354               software is used, namely to register the feature extraction
    355               of a scanned image.
    356             </para>
    357           </answer>
    358         </qandaentry>
    359 
    360         <qandaentry>
    361           <question>
    362             <para>
    363               I need to create a new hardware type but the
     340              Pooling can also be applied to extracts.
     341            </para>
     342          </answer>
     343        </qandaentry>
     344        <qandaentry>
     345          <question>
     346            <para>
     347              I need to create a new item subtype but the
    364348              &gbNew;
    365349              button is grey and does not work. Why?
     
    369353            <para>
    370354              Your privileges are not high enough and you have not been granted
    371               permission to create hardware types. Contact your BASE administrator.
     355              permission to create subtypes. Contact your BASE administrator.
    372356              For more information about permissions, please refer to
    373357              <xref linkend="user_administration" />.
     
    538522    </sect1>
    539523
    540     <sect1 id="faqs.data_repositories">
    541       <title>Data Deposition to Public Repositories related questions with answers</title>
    542       <qandaset defaultlabel='qanda'>
    543         <?dbhtml cellspacing="0px" cellpadding="0px" ?>
    544         <qandaentry>
    545           <question>
    546             <para>
    547               I am asked by reviewers to deposit my microarray data in a public
    548               repository. How can BASE help me?
    549             </para>
    550           </question>
    551           <answer>
    552             <para>
    553               The BASE development team are working on a plug-in
    554               that produces a Tab2Mage file accepted by ArrayExpress.
    555               For the plug-in to work properly, a series of rules need to be
    556               followed, please refer to
    557               <xref linkend="experiments_analysis.magexport" />
    558               for additional information.
    559             </para>
    560             <para>
    561               More information about the Tab2Mage format can be found at
    562               <ulink url="http://tab2mage.sourceforge.net"
    563                 >http://tab2mage.sourceforge.net</ulink>.
    564               To send the submission to array express, use the ArrayExpress FTP site
    565               at <ulink url="ftp://ftp.ebi.ac.uk pwd">ftp://ftp.ebi.ac.uk pwd</ulink>.
    566               Log in with username and password <userinput>aexpress</userinput>.
    567             </para>
    568             <warning>
    569               <para>
    570                 The current export plug-in does not support Tab2Mage normalised and
    571                 transformed files, so some additional work might be required to be
    572                 fully compliant, please refer to Tab2Mage help notes for creating
    573                 these final gene expression files and update the Tab2Mage files.
    574               </para>
    575             </warning>
    576           </answer>
    577         </qandaentry>
    578 
    579         <qandaentry>
    580           <question>
    581             <para>
    582               Repositories want me to be MIAME compliant but how do I know that?
    583             </para>
    584           </question>
    585           <answer>
    586             <itemizedlist>
    587             <listitem>
    588               <para>
    589               Make sure to format your annotation types following the rules
    590               detailed in <xref linkend="experiments_analysis.magexport" />.
    591               </para>
    592             </listitem>
    593             <listitem>
    594               <para>
    595               Before exporting, it is probably a good idea to run the
    596               <guilabel>Experiment Overview</guilabel>
    597               detailed in
    598               <xref linkend="webclient.itemoverview" />.
    599               By selecting stringent criteria from the interface, the tool will
    600               detect all missing information that could be requested by
    601               repositories.
    602               </para>
    603             </listitem>
    604             <listitem>
    605               <para>
    606               If the experiment overview does not report any error any more,
    607               you can run the Tab2Mage export plug-in suitable for ArrayExpress.
    608               </para>
    609             </listitem>
    610             </itemizedlist>
    611           </answer>
    612         </qandaentry>
    613 
    614         <qandaentry>
    615           <question>
    616             <para>
    617               I have exported in Tab2Mage file, does it mean I am MIAME compliant?
    618             </para>
    619           </question>
    620           <answer>
    621             <para>
    622               No, not necessarily! Tab2Mage exporter complies with Tab2Mage
    623               specifications so you will be Tab2Mage compliant. However, MIAME
    624               compliance depends very much on the kind of annotation you have
    625               supplied. Please refer to the previous question for more information
    626               about how to check for MIAME compliance in BASE using the Experiment
    627               overview function.
    628             </para>
    629           </answer>
    630         </qandaentry>
    631 
    632         <qandaentry>
    633           <question>
    634             <para>
    635               I have deleted the data files from BASE file system since I have
    636               imported them in tables. So I do not have data files to send to
    637               ArrayExpress anymore.
    638             </para>
    639           </question>
    640           <answer>
    641             <para>
    642               You can export the data from the tables again. Go to the
    643               <guilabel>Raw data</guilabel> tab for each of the
    644               raw bioassays you need to export. Use the
    645               &gbExport; button to export the data. See
    646               <xref linkend="import_export_data.export.table_export" />.
    647               for more information.
    648             </para>
    649           </answer>
    650         </qandaentry>
    651 
    652         <qandaentry>
    653           <question>
    654             <para>
    655               I have created pooled samples in BASE. Can I export in Tab2Mage format?
    656             </para>
    657           </question>
    658           <answer>
    659             <para>
    660               No, sorry, not for the moment. The
    661               Tab2Mage exporter does not support pooling events. We are working on
    662               adding this features in future version of the plug-in.
    663             </para>
    664           </answer>
    665         </qandaentry>
    666       </qandaset>
    667     </sect1>
    668524
    669525    <sect1 id="faqs.analysis">
     
    681537          <answer>
    682538            <para>
    683               It is possible to trick the system to filter out <constant>null</constant>
    684               values but not non-<constant>null</constant> values. Use an expression like:
    685               <userinput>ch(1) == 0 || ch(1) != 0</userinput>. This will match
     539              Yes, use an expression like:
     540              <userinput>ch(0) != null</userinput>. This will match
    686541              all values, except <constant>null</constant> values.
    687542            </para>
     
    704559              though even though this might depend on your set-up...)
    705560              The plug-in is not included in a standard BASE installation, but
    706               can be downloaded from the <ulink url="http://lev.thep.lu.se/trac/baseplugins"
     561              can be downloaded from the <ulink url="http://baseplugins.thep.lu.se/wiki/se.lu.thep.affymetrix"
    707562                >BASE plug-ins web site</ulink>.
    708563            </para>
  • trunk/doc/src/docbook/userdoc/annotations.xml

    r5436 r5682  
    163163          <listitem>
    164164            <para>
    165             The name of the annotation type.
    166             <nohelp>
    167             See <xref linkend="experiments_analysis.magexport" />
    168             if you are going to use this annotation type when
    169             exporting Tab2Mage files.
    170             </nohelp>
     165            The name of the annotation type.
    171166            </para>
    172167          </listitem>
     
    604599  </sect1>
    605600
    606   <sect1 id="annotations.bestpractices">
    607     <title>Best Practices and Tab2Mage Export functionality</title>
    608     <para>
    609     See <xref linkend="experiments_analysis.magexport" />.
    610     </para>
    611   </sect1>
    612  
    613601  <sect1 id="annotations.annotating">
    614602    <title>Annotating items</title>
  • trunk/doc/src/docbook/userdoc/experiments.xml

    r4889 r5682  
    295295  </sect2>
    296296
    297   <sect2 id="experiments_analysis.magexport">
    298     <title>Tab2Mage export</title>
    299     <para>
    300       <ulink url="http://tab2mage.sourceforge.net/"
    301       >Tab2Mage format</ulink> is a tab-delimited format veted by
    302       <ulink url="http://www.ebi.ac.uk/microarray/"
    303       >EBI's ArrayExpress</ulink>
    304       repository for submission microarray data.
    305       Tab2Mage format has been chosen by BASE to provide an
    306       easy way for data deposition to public repository when
    307       submitting a manuscript and publishing experimental
    308       data.
    309     </para>
    310      
    311     <para>
    312       BASE has been engineered to closely map the MIAME
    313       concepts and a number of BASE entities can be mapped
    314       directly to Tab2Mage elements. However, since MIAME is
    315       focused on microarray processing workflow, information
    316       about the biological sample is down to the user. To
    317       accommodate the annotation needs of users, BASE provides
    318       a mechanism that allows annotation customization to meet
    319       user specific requirements. BASE allows to create
    320       annotation type for quantitative annotation and
    321       qualitative annotation
    322     </para>     
    323 
    324     <para>
    325       BASE can export an experiment to Tab2Mage
    326       format thanks to a dedicated export plug-in.
    327       For the plug-in to work, it is important to understand that
    328       information recorded in BASE should be
    329       formatted following a small number of rules. Failing to
    330       do so may impair the possibility of exporting to
    331       ArrayExpress.
    332     </para>
    333    
    334     <note>
    335       <para>
    336       The Tab2Mage export plug-in has not yet been included in the main
    337       distribution. Hopefully, it will appear in the next (2.4) release.
    338       </para>
    339     </note>
    340 
    341     <sect3 id="experiments_analysis.magexport.annotations">
    342       <title>Biomaterial annotations</title>
    343       <para>
    344         Tab2Mage specifications only allow <emphasis>BioSource</emphasis>
    345         items to be annotated with <emphasis>BioMaterialCharacteristics</emphasis>.
    346       </para>
    347       <warning>
    348         <para>
    349           All BASE Annotation Types used to annotate at
    350           the level of <emphasis>Sample</emphasis> and
    351           <emphasis>Extract</emphasis> items will
    352           be lost during the export in Tab2Mage format in
    353           order to comply with the ArrayExpress Tab2Mage
    354           parser.
    355         </para>
    356       </warning>
    357       <note>
    358         <para>
    359           In the context of data exchange between BASE
    360           instances, the export function can be altered to
    361           allow attachment of annotations to items
    362           other than biosources, therefore avoiding loss of
    363           information.
    364         </para>
    365       </note>
    366     </sect3>
    367 
    368     <sect3 id="experiments_analysis.magexport.units">
    369       <title>Annotation units</title>
    370       <para>
    371         To associate units to BASE annotation types and
    372         remain compatible with Tab2Mage specifications,
    373         users need to adhere to the following convention:
    374       </para>
    375       <para>
    376         <userinput>annotation_type_name(unit_name)</userinput> as in
    377         <userinput>body mass(kg)</userinput> or <userinput>concentration(mg/ml)</userinput>
    378       </para>
    379       <warning>
    380         <para>
    381           Only one unit can be specified at any one time
    382           for any given annotation type. In order to
    383           enable Tab2Mage support, it might be necessary
    384           to declare several related Annotation Type in
    385           order to report similar kind of information but
    386           expressed in a different unit. Specifying Age
    387           for instance is a good example on how to deal
    388           with such cases: One should create several
    389           related annotation types e.g. <userinput>Age(week)</userinput>,
    390           <userinput>Age(year)</userinput> or <userinput>Age(month)</userinput>
    391           as those variations maybe be necessary when reporting the age of a
    392           mouse or the age of a human volunteer.
    393         </para>
    394       </warning>
    395     </sect3>
    396     <sect3
    397       id="experiments_analysis.magexport.parameters">
    398       <title>Protocol parameters</title>
    399       <para>
    400         In order to ensure MIAME compliance, Tab2Mage
    401         specifications cater for reporting parameters
    402         attached to protocols and all parameters attached to
    403         a protocol should be declared in the protocol
    404         section of a Tab2Mage file.
    405       </para>
    406      
    407       <para>
    408         In BASE terms, Tab2Mage elements such as
    409         <emphasis>BioMaterialCharacteristics</emphasis>,
    410         <emphasis>Parameter</emphasis> or
    411         <emphasis>FactorValues</emphasis> are all annotation
    412         types. But, it is necessary to flag those annotations types meant to
    413         be used as protocol parameters as such so that they
    414         can identified by the Tab2Mage exporter and handled
    415         appropriately.
    416       </para>
    417 
    418       <warning>
    419         <para>
    420           It is not possible to use the same
    421           annotation type <emphasis>Temperature</emphasis> for reporting a
    422           patient body temperature (which is a
    423           <emphasis>Biomaterial Characteristic</emphasis>) and hybridization
    424           temperature (which is a protocol parameter).
    425           Hence it will be necessary to declare 2 distinct
    426           annotation types:
    427         </para>
    428       </warning>
    429      
    430       <itemizedlist>
    431       <listitem>
    432         <para>
    433         Annotation type to be used as <emphasis>BioSource
    434           characteristics</emphasis>: <userinput>body temperature (degree_C)</userinput>
    435         </para>
    436       </listitem>
    437       <listitem>
    438         <para>
    439         Annotation type to be used as <emphasis>protocol parameter</emphasis>:
    440         <userinput>hybridization temperature (degree_C)</userinput>
    441         </para>
    442       </listitem>
    443       </itemizedlist>
    444     </sect3>
    445          
    446     <sect3 id="experiments_analysis.magexport.factors">
    447       <title>Experimental factors</title>
    448       <para>
    449         It is a MIAME requirement to identify <emphasis>Experimental
    450         Variables</emphasis> when submitting data to ArrayExpress
    451         (provided the study is an intervention study).
    452         Therefore, BASE users willing to use the Tab2Mage
    453         export function will have to declare <emphasis>Experimental
    454         Factors</emphasis> using the the <guilabel>Experimental Factor</guilabel>
    455         tab available when editing experiments. See
    456         <xref linkend="experiments_analysis.experiment.factors" /> for more information.
    457       </para>
    458      
    459       <para>
    460         Values for the experimental factors are take from annotations.
    461         The annotation must exist at the raw bioassay level, which
    462         probably means that you have to inherit the annotation from
    463         some other item, for example, a biosource or a sample.
    464         It is also possible to use a protocol parameter as
    465         experimental factor. See <xref linkend="annotations" /> for
    466         more information about annotations.
    467       </para>
    468     </sect3>
    469   </sect2>
    470297</sect1>
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