GTPM: Genome, Transcriptome, Proteome, Metabolome

A software system for handling and analysis of the complete molecular datasets

• Handle all four levels of data in one system
• Database system
• Tool for research groups
• Model the data at the appropriate level (not a data reduction tool)
• Capabilities: browse, search, interface
• Integration with public resources (seq/lit DB, Gene Ontology, ...)
• Data exchange: other groups; publication; deposition
• Open Source (GPL)

Implementation

• Currently ongoing...
• Layered implementation; MySQL (other RDBMS), Python, GUI, API
• Basic DB interaction mechanism done
• Data model development ongoing; focus on genome and transcriptome
• Tests using public data. Gunnar Norstedt, CMM, KI
• Integration of analysis tools; statistics, pathway analysis, ...
• XML data exchange using emerging standards (MAML, ...)

Issues

• How handle species, taxonomy? General/specific/hierarchical?
• How model differences? Mutations, conditions, treatments...
• Representation of pathways (metabolism, signalling)