source: trunk/uk/ac/ebi/Tab2MageExporter/README.txt @ 366

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1Release Note: Tab2Mage Export Current Implementation
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4How do I define and configure the plugin
5-------------------------------------------------------
6Please note, to test the tab2mage plugin, you do not need to define and configure the plugin. It is automatically done for you. Once you have updated or installed Nutribase successfully proceed to the experiment page, select and click on an experiment and on the edit page, click on the export tab and follow subsequent instructions.
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8On the export GUI, you can save the file to be exported on the base2 file system using the browse button for the Save As field. This is a mandatory field.
9
10Important Notice:
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12Exported tab2mage file would be located on the base2 file system (in the location you have specified). This file can be downloaded to your desktop environment.  After 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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14Controls:
15--------------
16Export fails with a message, if:
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18- No bioassay is assigned to an experiment
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20- If the logged in user do not own the experiment or has no read permission on the experiment.
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22- If experimental factors have not been specified for an experiment.
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24- Also, 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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26-Finally, if an array slide has not been provided for Hybridization
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28Tab2Mage Sections
29--------
30Experiment Section
31-----------------------------
32  - Provides information about an experiment.
33- The user must specify the release date for the experiment when initiating the tab2mage export.
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35Protocol Section
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37- This section displays all the protocols used within an experiment. The associated parameters are also displayed if any
38  - Protocol parameters are delimited with a semi colon.
39
40Hybridization Section
41-------------------------------
42Hybridization - Protocol Section
43---------------------------------------------
44  - If  protocol has not been utilized in the experiment then
45    - no protocol id is displayed in the hybridization section.
46
47Hybridization - BiomaterialXteristics
48-------------------------------------------------
49- These are all the xteristics and annotations of a biosource, excluding annotations of deleted annotation types or characteristics.
50- if a biosource exist i.e. has been used in an experiment , there might be biomaterial xteristics.
51- if no biosource is used, then there would be no biomaterial xteristics in the export.
52
53Hybridization - Experimental Factors
54--------------------------------------------------
55- if experimental factors  have been declared for an experiment but has a null value (i.e. it’s value has not been specified).
56-  the default value for the experimental factor would be displayed, if it has been specified during the creation of  the linked annotation type.
57   
58What is not supported
59----------------------------------
60- Inherited annotations are not exported or supported for Protocol parameters in this current version.
61
62- 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 this would then be supported.
63 
64- Pooling of biomaterials - Pooled sample, extract, and labeled extract are not exported with the current Tab2mage release, and this would be supported in another release.
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66- 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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68- Experiment publication’s pages, issues and volume are not supported.
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70
71
72/**
73*This is a release note created for the tab2mage export *developed at the EBI for *Base2 and NutriBase.
74/*
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