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Data Integration & Data Mining Tool
Donald DunbarBHF CoRE Bioinformatics Team
Edinburgh Bioinformatics MeetingApril 2013
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BHF CoRE Bioinformatics
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Data Integration and our Data Mining Tool
Our strategy is to help biologists make the most of their ‘-omics’ data
We analyse array and sequence data using current methods
Biologists mine their results in a custom built, secure web based platform
We help integrate other relevant data from biologist’s lab and the literature
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Data Mining Tool
• Wish list– Web accessible– Secure– Complex queries across datasets– Technology agnostic– Query cross species– Annotation, statistics and graphs– Links to external databases– Include downstream tools
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Data Mining Tool
• Login via EASE or htaccess (+ vpn)• Built in PHP with mySQL back end• Generic database structure for statistics
– counts, intensity, fold change, p-value• Separate annotation tables• Includes experiment details and QC info• Query builder type interface• Output as tables with links• Gene set enrichment, heat-map and literature
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Data Integration
• Across technologies– array, sequencing– gene expression, methylation, proteomics, genetics
• Across species– Human, mouse, rat, fly, fish
• At the gene level– Probe level for within array– Entrez gene within species– orthologous groups across species
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Development• New platform: Drupal
– Some nice features– New look and feel
• Web services– interactions, diseases, TF binding sites, miRNA…
• More use of literature data– Top 10 co-cited on gene detail page– Better visualisation– Better text mining
• Correlation data (expression profiles)– searchable with other stats
• Cross experiment gene sets
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Thanks• Jon Manning• John Mullins• Our collaborators• British Heart Foundation
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[email protected] | www.bioinf.mvm.ed.ac.uk
“Providing bioinformatics services to biology teamsthroughout the research process”