| 1 | Release Note: Tab2Mage Export Current Implementation |
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| 2 | ============================================== |
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| 3 | General Information |
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| 4 | ---------------------------------------------------------------------------------------- |
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| 5 | The Tab2Mage export plugin exports an experiment meta - data and annotations in tab2mage specification from BASE. The tab2mage specification is provided by the microarray informatics team at the EBI, Cambridge. The exported experiments along with the raw data and image files can later be exported by the corresponding tab2mage import plugin. (link). |
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| 6 | |
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| 7 | The entry point for this plugin in base is the detail view page of an experiment. Hence, the user needs to create an experiment and all the annotations and parameters first. select and click on an experiment and on the edit page, click on the export tab and follow subsequent instructions. |
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| 8 | |
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| 9 | |
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| 10 | Installation |
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| 11 | ----------------- |
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| 12 | |
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| 13 | - Place Tab2MageExporter.jar into the $BASE2_HOME/www/plugins/ directory on your BASE2 server. |
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| 14 | - Place ebi-plugins-utils.jar in your base installation class path : $BASE2_HOME/web-inf/lib |
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| 15 | - Install as new plugins uk.ac.ebi.nugo.plugins.Tab2MageExporter contained in $BASE_HOME/www/plugins/Tab2MageExporter.jar. |
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| 16 | |
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| 17 | 1. In the BASE web client, go to Administrate -> Plugins -> Definitions. |
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| 18 | 2. Click New. |
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| 19 | 3. In the dialog that opens, |
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| 20 | for class enter " uk.ac.ebi.nugo.plugins.Tab2MageExporter". |
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| 21 | for path enter the path to the plugin jar file, i.e. <BASE_HOME>/www/plugins/ Tab2MageExporter.jar |
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| 22 | 4. Click Save. |
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| 23 | The new plugins appears under the name "Tab2Mage Exporter" in the plugins list and is now ready for use. |
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| 24 | |
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| 25 | For other users to use the plugin as detailed in the next section, please share it to the appropriate users by manually setting the permissions on the item. |
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| 26 | |
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| 27 | |
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| 28 | General Installation instruction is available at: http://base.thep.lu.se/chrome/site/doc/html/admindoc/plugin_installation/plugins.installation.html#plugins.installation |
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| 29 | ========================================================================================== |
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| 30 | Use |
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| 31 | ------- |
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| 32 | Important Notice/ Warning: |
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| 33 | ----------------------------------- |
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| 34 | To use the tab2mage export plugin, you do not need to configure the plugin as it requires no configuration. |
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| 35 | |
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| 36 | The exported tab2mage file would be located on the base2 file system (in the location you have specified). This file can thereafter be downloaded to your desktop environment. After the download, please create an archive including the tab2mage export file and the associated raw data files, for onward submission to a repository like Array Express. |
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| 37 | |
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| 38 | It is advisable to verify that your experiment has all the required annotations and that it is Miame Complaint before running the exporter. To do this go to the Experiment detail view page and click on the overview tab. |
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| 39 | |
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| 40 | The Tab2Mage export fails with a message, if: |
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| 41 | - No bioassay is assigned to an experiment |
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| 42 | - If the logged in user do not own the experiment or has no read permission on the experiment. |
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| 43 | - If experimental factors have not been specified for an experiment. |
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| 44 | - Also, note that if experimental factors (annotation type) for an experiment have been specified, and the annotation types are shared to Project. Do set the Project active before exporting in Tab2mage otherwise export fails. |
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| 45 | -Finally, if an array slide or array design has not been provided for Hybridization. |
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| 46 | |
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| 47 | Besides, using the experiment overview functionality would help to prevent most of these failure points. |
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| 48 | |
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| 49 | |
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| 50 | 1. In the BASE web client, go to View -> Experiment |
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| 51 | 2. Go to the experiment detail view page. |
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| 52 | 3. Verify your experiment with the BASE experiment overview functionality as mentioned above |
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| 53 | 4. Click on the export tab and on the export GUI thats appears, the experiment has been configured as indicated by the black x. |
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| 54 | 5. The overwrite field has also been configured and set to false by default. Do change this to true if you want to overwrite an exisiting file. |
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| 55 | 6. Set the file path where the export file and it's name: (e.g. tab2mage.txt) should be saved on the base2 file system using the browse button for the Save As field. This is a mandatory field. |
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| 56 | 7. Specify the date you would like the experiment to be made public or released by a public respository e.g. Array Express. and click Next |
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| 57 | 8. On the next screen click Finish and wait for the job to complete. You will be shown the progress of the Tab2mage export in the dialog, with the page refreshing itself regularly. |
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| 58 | |
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| 59 | ================================================================================================== |
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| 60 | Dependencies: |
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| 61 | -------------------- |
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| 62 | |
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| 63 | ebi-plugin.utils.jar - this should be in the base intstallation class path. |
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| 64 | |
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| 65 | |
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| 66 | ==================================================================================================== |
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| 67 | Tab2Mage Sections |
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| 68 | ---------------------------- |
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| 69 | Experiment Section |
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| 70 | ----------------------------- |
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| 71 | - Provides information about an experiment. |
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| 72 | - The user must specify the release date for the experiment when initiating the tab2mage export. |
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| 73 | |
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| 74 | Protocol Section |
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| 75 | ------------------------ |
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| 76 | - This section displays all the protocols used within an experiment. The associated parameters are also displayed if any |
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| 77 | - Protocol parameters are delimited with a semi colon. |
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| 78 | |
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| 79 | Hybridization Section |
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| 80 | ------------------------------- |
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| 81 | Hybridization - Protocol Section |
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| 82 | --------------------------------------------- |
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| 83 | - If protocol has not been utilized in the experiment then |
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| 84 | - no protocol id is displayed in the hybridization section. |
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| 85 | |
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| 86 | Hybridization - BiomaterialXteristics |
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| 87 | ------------------------------------------------- |
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| 88 | - These are all the xteristics and annotations of a biosource, excluding annotations of deleted annotation types or characteristics. |
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| 89 | - if a biosource exist i.e. has been used in an experiment , there might be biomaterial xteristics. |
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| 90 | - if no biosource is used, then there would be no biomaterial xteristics in the export. |
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| 91 | |
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| 92 | Hybridization - Experimental Factors |
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| 93 | -------------------------------------------------- |
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| 94 | - if experimental factors have been declared for an experiment but has a null value (i.e. its value has not been specified). |
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| 95 | - the default value for the experimental factor would be displayed, if it has been specified during the creation of the linked annotation type. |
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| 96 | |
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| 97 | ================================================================================== |
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| 98 | |
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| 99 | What is not supported |
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| 100 | ---------------------------------- |
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| 101 | - Inherited annotations are not exported or supported for Protocol parameters in this current version. |
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| 102 | |
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| 103 | - Material Characteristics - not available in the current base2 release and therefore cannot be exported. This requires MGED entries. Ontologies and control vocabularies would be distributed with base2 in the nearest future and can then be supported. |
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| 104 | |
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| 105 | - Pooling of biomaterials - Pooled sample, extract, and labeled extract are not exported with the current Tab2mage release, and would be supported in another release. |
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| 106 | |
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| 107 | - Experiment Quality control - is not supported in base2, hence this will be missing in the tab2mage export at the experiment section |
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| 108 | |
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| 109 | - Experiment publications pages, issues and volume are not supported. |
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| 110 | |
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| 111 | |
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| 112 | |
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| 113 | /** |
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| 114 | *This is a release note created for the tab2mage export developed at the EBI for Base2 and NutriBase. |
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| 115 | /* |
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