What is the OSAGE project?

The OSAGE project addresses data modelling and management challenges for gene expression data. The challenges are clear: more data (both text and images), newly identified complex gene-tissue relationships, and the need for reliable, extensible data services. To address such requirements, the OSAGE project uses DB2® Database Management System (DBMS) and Java Technology (J2EE, EJB) to develop a grid data service for gene expression research.

Who is involved?

This project is a collaborative effort with the Edinburgh Mouse Atlas Project (EMAP) at the Human Genetic Unit, Medical Research Council (HGU-MRC), University of Edinburgh. MRC Human Genetics Unit, University of Edinburgh

Project background

The Edinburgh Mouse Atlas is an ongoing project initiated in 1995. The project has
• developed pioneering image processing techniques to reconstruct 3D images from 2D slice images, and
• established a digital atlas and database of spatially mapped data for gene expression and tissue lineage in mouse embryos.

The client and server software providing internet-based access to the digital atlas were developed using ObjectStore® (a commercial, Object-Oriented DBMS).
The ObjectStore-based system supports two data services: EMAP for Anatomy and EMAGE for Gene Expression.
The EMAP database stores nomenclature, tissue lineage, and complex relationships over anatomical components and images. The EMAGE database stores gene expression annotations and painted images identifying regions in which a gene is expressed. The Anatomy database is used as a baseline for nomenclature and images, and is referenced by the EMAGE database.

Science Goals

To further scientific research in gene expression, the EMAP team aspires to expand their systems as follows:
• Support a larger user community, particularly contributing researchers and students working in a grid-based environment
• Store new data and image types, incorporating new knowledge in new forms
• Ensure data and systems longevity
• Support other species, such as human, quail, chicken or rat, using the same or similar technologies
• Support an atlas of adult gene expression

OSAGE Project Goals

The goal of the OSAGE project is to assist the EMAP team in moving towards these goals. A four prong strategy was developed:
1. Design an extensible client-server architecture supporting grid and web access
2. Define generic database schemas to support new species and new data types
3. Re-host the databases on a commercial Relational Data Base Management System
4. Design and implement the re-hosted system to support current and likely future client services

OSAGE Design

An extensible architecture has been defined as shown in the diagram below: