1. Shared Genomics www.nibhi.org.uk/sharedgenomics
Sharing paths of exploration to support collaborative reasoning in genomic data analysis
David Hoyle, Mark Delderfield, Peter Crowther, Lee Kitching, Gareth Smith, Iain Buchan
Typical stages of the iterative data analysis cycle
Implementation of Shared Genomics Workbench
Developed a workbench for genomic medical research that supports the whole analysis cycle and integrates with other solutions:
Stage
Offers genome-wide data analysis that is powered by a High Performance Computer Cluster. 1 2 3 4 5 W o r k b e n c h
Integrates with the Taverna workflow engine for processing and retrieving information from remote sources.
Stores meta-data of each analysis job and provides an ordered view of information to investigator as required.
Database
Implemented an animated, three- dimensional graphical user interface (CoverFlow) using MS Silverlight to enable the replay of viewed annotation images.
Provides investigators with a way to share insights over the web using a CoverFlow representing their exploration of the genetic variations statistically associated with a subject’s phenotype.
Capturing the paths of exploration
Challenges
An exploratory path will consist of reviewing results from many statistical analyses, along with sources of information that might assist in the interpretation of those results.
To assess the biological plausibility of a genetic variation (SNP) being associated with a subject’s phenotype, chains of annotations are viewed e.g. NCBI for lookup of SNP to gene information and KEGG for gene to pathway information.
Each annotation might be structured data or a web page, with further links and active areas to review more detailed content.
The path taken by investigators through annotations (Stage 4 of analysis cycle) is commonly not captured electronically. Rather than rely upon investigator recollections, the annotation visited during a piece of research can automatically be captured and stored.
A visually intuitive way of browsing and commenting on annotation sessions helps the investigator record and remember the chain of evidence that led to their conclusions.
Sharing annotation sessions enables collaborators to exchange ideas around particular patho-physiological conditions more easily.
Opportunities
Tools for annotation retrieval,
capture and visualisation
User-directed capture of importance and comments
‘One click’ annotation of SNPs (genetic markers)
Double clicking on image during review process opens up a ‘live’ copy
CoverFlow tool: a mechanism for reviewing interesting annotation sessions
Review previous comments or add new ones
A smart space for sharing insights with collaborators
Annotations time ordered
A Microsoft funded project from the Northwest Institute for Bio-Health Informatics (NIBHI), in collaboration with: the Manchester Asthma and Allergy Study (A. Custovic & A. Simpson) and NW eHealth (J. New & M. Gibson); and Microsoft Research (C. Bishop, J. Winn & D. Heckerman).