Dataset Information

Interactive exploration of heterogeneous biological networks with Biomine Explorer.

ABSTRACT: SUMMARY:Biomine Explorer is a web application that enables interactive exploration of large heterogeneous biological networks constructed from selected publicly available biological knowledge sources. It is built on top of Biomine, a system which integrates cross-references from several biological databases into a large heterogeneous probabilistic network. Biomine Explorer offers user-friendly interfaces for search, visualization, exploration and manipulation as well as public and private storage of discovered subnetworks with permanent links suitable for inclusion into scientific publications. A JSON-based web API for network search queries is also available for advanced users. AVAILABILITY AND IMPLEMENTATION:Biomine Explorer is implemented as a web application, which is publicly available at https://biomine.ijs.si. Registration is not required but registered users can benefit from additional features such as private network repositories.

SUBMITTER: Podpecan V

PROVIDER: S-EPMC6954666 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature

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Interactive exploration of heterogeneous biological networks with Biomine Explorer.

Podpečan Vid V Ramšak Živa Ž Gruden Kristina K Toivonen Hannu H Lavrač Nada N

Bioinformatics (Oxford, England) 20191201 24

<h4>Summary</h4>Biomine Explorer is a web application that enables interactive exploration of large heterogeneous biological networks constructed from selected publicly available biological knowledge sources. It is built on top of Biomine, a system which integrates cross-references from several biological databases into a large heterogeneous probabilistic network. Biomine Explorer offers user-friendly interfaces for search, visualization, exploration and manipulation as well as public and privat ...[more]

PMID: 31233141

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Project description:BackgroundLinking high-throughput experimental data with biological networks is a key step for understanding complex biological systems. Currently, visualization tools for large metabolic networks often result in a dense web of connections that is difficult to interpret biologically. The MetNetGE application organizes and visualizes biological networks in a meaningful way to improve performance and biological interpretability.ResultsMetNetGE is an interactive visualization tool based on the Google Earth platform. MetNetGE features novel visualization techniques for pathway and ontology information display. Instead of simply showing hundreds of pathways in a complex graph, MetNetGE gives an overview of the network using the hierarchical pathway ontology using a novel layout, called the Enhanced Radial Space-Filling (ERSF) approach that allows the network to be summarized compactly. The non-tree edges in the pathway or gene ontology, which represent pathways or genes that belong to multiple categories, are linked using orbital connections in a third dimension. Biologists can easily identify highly activated pathways or gene ontology categories by mapping of summary experiment statistics such as coefficient of variation and overrepresentation values onto the visualization. After identifying such pathways, biologists can focus on the corresponding region to explore detailed pathway structure and experimental data in an aligned 3D tiered layout. In this paper, the use of MetNetGE is illustrated with pathway diagrams and data from E. coli and Arabidopsis.ConclusionsMetNetGE is a visualization tool that organizes biological networks according to a hierarchical ontology structure. The ERSF technique assigns attributes in 3D space, such as color, height, and transparency, to any ontological structure. For hierarchical data, the novel ERSF layout enables the user to identify pathways or categories that are differentially regulated in particular experiments. MetNetGE also displays complex biological pathway in an aligned 3D tiered layout for exploration.

Dataset Information

Interactive exploration of heterogeneous biological networks with Biomine Explorer.

Publications

Interactive exploration of heterogeneous biological networks with Biomine Explorer.

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