The aim of this project is the representation of liver-specific molecular interactions at the cellular and tissue level in a database that effectively supports and integrates reconstruction and analysis of large biochemical reaction networks.
From our VLN partner groups, we require the following experimental and theoretical input:
- Data model exchange and adaptation
- Data integration between LKB and SABIO-RK
- Joint curation tool & software development
- Open exchange of curated data with SABIO
- Development of annotator support tools
- Format for description of functional sub-models for import into Sycamore
Methods:
- Implement an extensible framework with a postgreSQL database backend and a JSP-based web-interface
- Establish standardized network reconstruction pipeline (effective interplay of curation and functional validation)
- Versatile and user-friendly representation of pathways and meta-data (e.g. evidence type and strength)
- Allow flexible construction of mathematical models from the data source (e.g. biochemical scope and detail, evidence thresholds, flux constraints)
Milestones:
- Population of LKB with hepatocyte metabolic network data and its future extensions
- Systematic representation of gene-transcript-protein-reaction relations
- Development of an interface between LKB and FASIMU enabling direct transfer of database content into flux-balance calculations
This project is part of Virtual Liver, a major national initiative funded by the German Federal Ministry for Education and Research (BMBF) and is connected to WP subproject F2. Further partners in this project are Prof. Ulf Leser, Knowledge Management in Bioinformatics, Humboldt-Universität zu Berlin, Institute for Computer Science and Prof. Ursula Kummer, Modeling of Biological Processes, University of Heidelberg, BIOQUANT.
Researchers
Prof. Hermann-Georg Holzhütter
Christian Bölling
Michael Weidlich