Third Party Data Annotation Tools

Introduction

Third party data annotation tools are available that can be used to create spreadsheets containing experiment information (description, protocols, sample information etc) for submission to ArrayExpress through our spreadsheet submission route. The name of the format of the spreadsheets created is MAGE-TAB.

These tools are not supported by EBI and we do not provide help in using them. However, we have listed them here as they may assist you in creating your experiment information spreadsheet.

Alternatively, you can generate a template spreadsheet specific to your experiment by creating an experiment on our spreadsheet submission web site and then selecting the 'generate template' option.

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2. Tools available

2.1 Annotare 

http://code.google.com/p/annotare/

A Mac and PC downloadable annotation tool able to read in and write out MAGE-TAB spreadsheet files for submission to ArrayExpress.

2.2 ISAcreator

http://isatab.sourceforge.net/

A Mac and PC compatible desktop annotation tool. It creates ISA-Tab format files which can be converted - via the ISAconverter tool- to several other formats required by public repositories, including MAGE-TAB for submission to ArrayExpress. .

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3. Submitting data prepared with third party tools

The above tools create spreadsheet files containing information about your experiment. To submit your experiment to us, you need to upload the spreadsheet files along with zipped archives containing your data files through our spreadsheet submission system web page.

1. Create a login account on the spreadsheet submissions web page

2. Create your experiment

   Click 'Create experiment' to start a new experiment submission and enter a name for the experiment.

   You do not need to create a template spreadsheet but can go straight to uploading files.

3. Upload your spreadsheet and data files in one or more zipped archives.

   Click 'Upload files' then upload your completed spreadsheet and all your data files in one or more zipped archives.

4. Submit your experiment.

   Click 'Submit experiment' to send this submission to us for curation.

5. After completing your experiment submission:
   • You'll receive a immediate confirmation email saying that your experiment has been submitted.
   • We will send you an accession number when all the required information has been provided.
   • We will load your experiment into ArrayExpress and provide you with a reviewer login for viewing the data before it is made public.

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