The Image Data Resource

Simon Li

GRE seminar, 6 December 2016

Overview

• Why did we build this?
• How did we create it?
• What can you do with it?

The Image Data Resource

https://idr-demo.openmicroscopy.org

Why did we build this?

Open science: Open access + Open data

Open science: Open access + Open data

• Reproducibility
• Re-use / re-analysis
• Combine with other data sources

Open science: Open access + Open data

Problems with imaging data

• Storage and management
• Discoverability

Contextual metadata is critical

How did we create it?

The Image Data Resource: in numbers

• 25 published studies
• 42 TB data
• 14 million files
• 1 million experiments
• Computational resources:
  • 32 CPUs
  • 128 GB memory

The Image Data Resource: data management

• All studies are curated
• Data is arranged in a common layout
• Cross referenced with:
  • External resources
  • Other IDR studies

What can you do with it?

IDR: A curated collection of diverse cross-referenced studies

• Compare genes and phenotypes across different studies/experiments using MAPR, a new OMERO.web application.
  
  • Genes (19,598)
  • Phenotypes (151)
  • siRNAs
  • Compounds
  • Organisms

The Image Data Resource: in numbers

• 25 published studies
• 42 TB data
• 14 million files
• 1 million experiments
• 19,598 genes
• 151 Phenotypes

Next steps

• Open infrastructure: Build your own IDR
• https://idr-demo.openmicroscopy.org/about/deployment.html

The IDR team

Jason Swedlow

Josh Moore

Simon Li

Eleanor Williams

Gabriella Rustici

Aleksandra Tarkowska

Richard Ferguson

Simone Leo

Alvis Brazma

Ugis Sarkans

Simon Jupp

Tony Burdett

Rafael Carazo-salas

Bálint Antal

Anatole Chessel