Proposer: J Douglas Armstrong 504492 jda@inf.ed.ac.uk
Self-Proposed: No
Supervisor: J Douglas Armstrong
Subject Areas: Bioinformatics, Databases, Neuroinformatics, WWW Tools and Programming,
Suitable for the following degrees: MSc in Informatics, MSc in Computer Science,
Principal goal of the project: Investigate options and implement an anotation and query tool using a structured ontology for a gene exression database.
Description of the project:
The Fly-trap gene expression database system has been used by researchers in the field of Drosophila neurogenetics since 1996. The gradual move in recent years towards digital recording of patterns of gene expression has stimulated renewed interest from the academic community. Since the initial development phase of the database system there is now a controlled and hierarchical vocabulary (or ontology) of the anatomical terms (e.g. simple example: head>brain>protocerebum>mushroom body>alpha lobe where alpha lobe is part of the mushroom body with is in turn part of the protocerebrum and so on).
Fly-trap contains currently contains free text descriptions of the images and moves contained. This project will allow the same images and movies to be annotated using the controlled vocabulary. This project is to investigate methods for storing this information in a relational database system and providing both query and annotation interfaces.
Several existing solutions will be explored for suitability and if possible directly re-used or modified for use in Flytrap. These include the data structures used by the XSPAN database system and the Java based query interfaces used by the MRC Mouse Atlas.
Resources Required: None
Degree of Difficulty: Moderate
Background Needed: Core database skills are essential.
References: