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ISA-RO-Nanopublication Use Case


In this showcase we intend to pass through all steps of an experiment to investigate and demonstrate the combination of study capture models. Because this showcase involves collaboration with GigaScience, a secondary goal for this showcase is to work out a Publishers' scenario for workflow preservation.

We will start with a use case. Metabolomics has been suggested, but Peter Li from GigaScience may have a use case ready-to-go.

The models and their focus

  1. ISA (Investigation, Study, Assay)
    Focus: capture metadata of data-generating steps.
  2. RO (Research Objects)
    Focus: capture metadata of computational data analysis.
  3. Nanopublication
    Focus: add attribution/citation to metadata capture.


Starting data somewhere after the Beyond the PDF meeting. We plan to work on the plan at the Beyond the PDF meeting in March. Another opportunity in March may be when Phillipe (ISA) visits Leiden. 


Summary of initial meeting dd. 14/2/2013

Thanks to Susanna Sansone for the notes.
Jun, Marco, Alejandra and Philippe met today to discuss how to
'encapsulate' ISA information into the Research Object (RO) and create
nanopublications etc.

Given your link to us and to the above activities, we wonder if you are
interested in working together on a use case that also brings the
GigaScience/GigaDB component in.
Marco, Alejandra and Philippe will be at Beyond PDF meeting; you can
have a chat on this there.

In brief, the idea would be pilot all the steps, starting from one/more
ISA-Tab datasets and:
- run an analysis workflow (using Risa, Galaxy and GenomeSpace as
relevant) and publishing the workflow in myExperiment
- (RO)ifying the whole workflow, encapsulating the ISA-OWL representation
- create relevant nano statements
- publish all in GigaDB with DOIs

It this works, we can imagine to write a accompanying article, if you
are interested, for GigaScience.

Just an idea and I leave you to talk more about this with them at the
Beyond PDF meeting.

Response from Scott Edmunds (GigaScience)

Will do. Peter is in the middle of deploying the new look Galaxy server with all of the SOAP tools and workflows, so once that is done we'll look at ISA-Galaxy. We have 3 papers with data + workflows that would all be good examples to trial for this. I can see the Risa page, and I'm not sure bioconductor or R is useful for these examples at the moment, but the ISA-Galaxy stuff certainly will be. Is there any links or info we can look on that yet? 

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