Blog from April, 2011

Expected content of a Research Object (Bio)

PhD student Eleni Mina (LUMC) has produced a 'table of contents' for us that conveys what components she would expect to put in a Research Object for her upcoming experiment. She is at the planning stage of the experiment, which means that the references and plans are all real, but she hasn't performed the experiment yet. The file is in the experimental RObox DropBox folder 'BioRO'. Below is a short description.

I expect that Eleni's TOC would eventually map to the RO model and the RObox interface, and that the RO model would provide the structure and interlinking of the components, while the RO model is used to help structure the RObox interface (a consequence of defining the structure of a RO).

Eleni defined component types, and 'attributes' of components:

  • RO component types: Datasets, Scripts, Web Services, Workflows, Documentation; on my request she added Hypothesis as a component too.
  • RO component attributes: Name, Description, Type, Version; on my request Eleni added 'Role in experiment' which otherwise ended up in the Description.


  • Type: Dataset
    • Name: Huntington Disease dataset 1
    • Description: Human brain dataset. 44 HD samples, 36 Controls age and sex matched. Brain areas:caudate nucleus, frontal cortex and cerebellum. Affymetrix platform
    • Datatype: GEO series datafile (NB this also conveys the origin of the datafile).
    • Version: <unknown>
    • Role in experiment: input (as her supervisor, I would ask for more explanation here; how does this data help address the hypothesis?)
  • Type: Script
    • Name: Analyse_data
    • Description:
      • Input: data matrix, tab delimited.
      • rows->genes,
      • columns->samples
      • Output: list of differentially expressed genes
      • R packages needed: Bioconductor, Affy, Limma, GEOquery
    • Script type: R
    • Version: R version 2.10.1
    • Role in experiment: Script file for the process and analysis of the input affymetrix datasets


This dynamic RO will evolve as Eleni is designing and executing her experiment. I expect this to lead to more annotations/notes and more detail.