Interactive exploration of heterogeneous biological networks with Biomine Explorer

• DOI: 10.1093/bioinformatics/btz509
• Publication Date: 2019-06-19T19:13:03Z
• Authors: Vid Podpečan; Živa Ramšak; Kristina Gruden; Hannu Toivonen; Nada Lavrač
• Keywords: Internet; 0303 health sciences; Computer and information sciences; bioinformatic; Databases, Factual; Bioinformatics; Biodatabases; Applications Notes; info:eu-repo/classification/udc/004.9; biological networks; biological networks, bioinformatic; 03 medical and health sciences; Genetics, developmental biology, physiology; Networks; Software

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.