Affiliations: Rothamsted Research, BAB division, Harpenden,
UK | University of Bielefeld, Technical Faculty,
Germany | University of Koblenz, Department of Computer Science,
Germany
Abstract: The structure of a closely integrated data warehouse is described
that is designed to link different types and varying numbers of biological
networks, sequence analysis methods and experimental results such as those
coming from microarrays. The data schema is inspired by a combination of graph
based methods and generalised data structures and makes use of ontologies and
meta-data. The core idea is to consider and store biological networks as
graphs, and to use generalised data structures (GDS) for the storage of further
relevant information. This is possible because many biological networks can be
stored as graphs: protein interactions, signal transduction networks, metabolic
pathways, gene regulatory networks etc. Nodes in biological graphs represent
entities such as promoters, proteins, genes and transcripts whereas the edges
of such graphs specify how the nodes are related. The semantics of the nodes
and edges are defined using ontologies of node and relation types. Besides
generic attributes that most biological entities possess (name, attribute
description), further information is stored using generalised data structures.
By directly linking to underlying sequences (exons, introns, promoters, amino
acid sequences) in a systematic way, close interoperability to sequence
analysis methods can be achieved. This approach allows us to store, query and
update a wide variety of biological information in a way that is semantically
compact without requiring changes at the database schema level when new kinds
of biological information is added. We describe how this datawarehouse is being implemented by extending
the text-mining framework ONDEX to link, support and complement different
bioinformatics applications and research activities such as microarray
analysis, sequence analysis and modelling/simulation of biological systems. The
system is developed under the GPL license and can be downloaded from
http://sourceforge.net/projects/ondex/
Keywords: graph database, ontology, Generalised Data Structures, semantic data integration
