Abstract
BackgroundA significant problem in the study of mechanisms of an organism's development is the elucidation of interrelated factors which are making an impact on the different levels of the organism, such as genes, biological molecules, cells, and cell systems. Numerous sources of heterogeneous data which exist for these subsystems are still not integrated sufficiently enough to give researchers a straightforward opportunity to analyze them together in the same frame of study. Systematic application of data integration methods is also hampered by a multitude of such factors as the orthogonal nature of the integrated data and naming problems.ResultsHere we report on a new version of BiologicalNetworks, a research environment for the integral visualization and analysis of heterogeneous biological data. BiologicalNetworks can be queried for properties of thousands of different types of biological entities (genes/proteins, promoters, COGs, pathways, binding sites, and other) and their relations (interactions, co-expression, co-citations, and other). The system includes the build-pathways infrastructure for molecular interactions/relations and module discovery in high-throughput experiments. Also implemented in BiologicalNetworks are the Integrated Genome Viewer and Comparative Genomics Browser applications, which allow for the search and analysis of gene regulatory regions and their conservation in multiple species in conjunction with molecular pathways/networks, experimental data and functional annotations.ConclusionsThe new release of BiologicalNetworks together with its back-end database introduces extensive functionality for a more efficient integrated multi-level analysis of microarray, sequence, regulatory, and other data. BiologicalNetworks is freely available at http://www.biologicalnetworks.org.
Highlights
A significant problem in the study of mechanisms of an organism’s development is the elucidation of interrelated factors which are making an impact on the different levels of the organism, such as genes, biological molecules, cells, and cell systems
The homology information is imported from the COGs database [32]; we extend the COG groups to cover all organisms available in the IntegromeDB database of BiologicalNetworks
The BiologicalNetworks database has a general purpose graph architecture and is data-type neutral, there is the prospect of further data integration for more complete systems biology studies
Summary
A significant problem in the study of mechanisms of an organism’s development is the elucidation of interrelated factors which are making an impact on the different levels of the organism, such as genes, biological molecules, cells, and cell systems. Systematic application of data integration methods is hampered by a multitude of such factors as the orthogonal nature of the integrated data and naming problems. To analyze and visually integrate publicly available data on the systems level, several web-based tools have been developed: Genomatix [1,2], GeneGO [3], STRING [4], Cytoscape [5], VisANT [6], Ingenuity [7], Pathway Studio [8], PipelinePilot [9], and BiologicalNetworks [10]. Like Taverna [11], GenePattern [12] and Galaxy [13], have been designed for the automatic application of the computational methods and data provenance management rather than visual integration, representation, querying and analysis of the data which are addressed in BiologicalNetworks. Each of the mentioned tools has a distinct set of features, which are highlighted in Table 1, Features/Tools
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