Interactive exploration of heterogeneous biological networks with Biomine Explorer

Vid Podpečan; Živa Ramšak; Kristina Gruden; Hannu Toivonen; Nada Lavrač

doi:10.1093/bioinformatics/btz509

Interactive exploration of heterogeneous biological networks with Biomine Explorer

Bioinformatics. 2019 Dec 15;35(24):5385-5388. doi: 10.1093/bioinformatics/btz509.

Authors

Vid Podpečan¹, Živa Ramšak², Kristina Gruden², Hannu Toivonen³, Nada Lavrač^{1

4}

Affiliations

¹ Department of Knowledge Technologies, Jožef Stefan Institute, Ljubljana, Slovenia.
² Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.
³ Department of Computer Science, University of Helsinki, Helsinki, Finland.
⁴ Centre for Information Technologies and Applied Mathematics, University of Nova Gorica, Nova Gorica, Slovenia.

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Databases, Factual
Internet
Software*