source: trunk/uk/ac/ebi/Tab2MageExporter/README.txt @ 360

Last change on this file since 360 was 360, checked in by dominic, 15 years ago

Repackaged Tab2Mage Exporter as a separate plugin from base2 core plugins

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1Release Note: Tab2Mage Export Current Implementation
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3----------------------------------------------------------------------------------------
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.
7
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: Exported 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.
11
12Experiment Section
13-----------------------------
14  - Provides information about an experiment.
15- The user must specify the release date for the experiment when initiating the tab2mage export.
16
17Protocol Section
18------------------------
19- This section displays all the protocols used within an experiment. The associated parameters are also displayed if any
20  - Protocol parameters are delimited with a semi colon.
21
22Hybridization Section
23-------------------------------
24Hybridization - Protocol Section
25---------------------------------------------
26  - If  protocol has not been utilized in the experiment then
27    - no protocol id is displayed in the hybridization section.
28
29Hybridization - BiomaterialXteristics
30-------------------------------------------------
31- These are all the xteristics and annotations of a biosource, excluding annotations of deleted annotation types or characteristics.
32- if a biosource exist i.e. has been used in an experiment , there might be biomaterial xteristics.
33- if no biosource is used, then there would be no biomaterial xteristics in the export.
34
35Hybridization - Experimental Factors
36--------------------------------------------------
37- if experimental factors  have been declared for an experiment but has a null value (i.e. it’s value has not been specified).
38-  the default value for the experimental factor would be displayed, if it has been specified during the creation of  the linked annotation type.
39   
40What is not supported
41----------------------------------
42- Inherited annotations are not exported or supported for Protocol parameters in this current version.
43
44- 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.
45 
46- 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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48- Experiment Quality control - is not supported in base2, hence this will be missing in the tab2mage export at the experiment section
49
50- Experiment publication’s pages, issues and volume are not supported.
51
52Controls:
53--------------------
54Export fails with a message, if:
55  - No bioassay is assigned to an experiment
56
57- If the logged in user do not own the experiment or has no read permission on the experiment.
58
59- If experimental factors have not been specified for an experiment.
60
61- 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.
62
63- Finally, if an array slide has not been provided for Hybridization
64
65
66/**
67*This is a release note created for the tab2mage export *developed at the EBI for *Base2 and NutriBase.
68/*
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