A Quick Guide to Using the ISA Structure

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A Quick Guide to Using ISA in SEEK

ISA stands for Investigations, Studies and Assays. It is the structure developed by the ISA-TAB community (http://isacommons.org) and adopted by the SEEK to help you describe your data and experiments.
In SEEK, you can upload or link to any data or protocols from your projects, but they don’t normally exist in isolation. ISA provides a framework for expressing how the work in your projects fits together. For example, you may have transcriptomics, proteomics and metabolomics data which was all created to address the same biological problem.
ISA also allows you to associate your data to the SOPs that were used to create them.
The aim of using the ISA structure is to ensure a complete record of the experiment and associated assets is available and accessible to other project members in a standard format.

Investigations, Studies and Assays Defined

  • Investigation: a high level description of the overall area of research.
  • Study: a particular biological hypothesis, which you are planning to test in various ways, using various techniques, which could be experimental, informatics, modelling, or a mixture
  • Assay: specific, individual experiments, measurements, or modelling tasks

Viewing Associations Between SEEK Assets

In SEEK, the ISA structure is displayed graphically, so you can see at a glance what items are associated with one another.

Using ISA when Uploading SEEK Assets

You can link assets to ISA descriptions, or vice versa, so it doesn’t matter which you do first. Many projects prefer to have a higher level structure of Investigations and Studies defined from the beginning, so that new experiments can be linked up with little work for the uploader.

Starting with your Data

When uploading your data, you will be asked wish assay(s) it is associated with. If you have already described the assay in the SEEK, you can find it from the drop-down list and link it, if you have not yet described your assay, you can leave this step out for the time-being.
Once you have uploaded your data, you can create a new assay if necessary and link it back to your data. New assays can be associated with pre-existing Studies and Investigations, or new ones can be created as required.
If you upload data without linking it to the ISA structure, you won’t be able to link it to SOPs.

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