Link discovery and interactive exploration in biological databases
Biomine Explorer is a web application that enables interactive exploration of selected publicly available biological knowledge. It is based on the results of the Biomine project that develops methods for the analysis of public biological data sources (annotated sequences, proteins, domains, and orthology groups, genes and gene expressions, gene and protein interactions, scientific articles, and ontologies). All information is handled as networks and Biomine provides probabilistic network search algorithms to automatically extract the most relevant subnetworks.
The most prominent feature of Biomine Explorer is interactive exploration of its large probabilistic networks by using an interactive network visualisation interface. Network editing features and private network repositories are also available as well as a repository of publicly available graphs. All links to Biomine graphs are permanent so they can be used in scientific publications or published on the web.
Until 2012, the Biomine project was carried out by the Discovery Group in the HIIT Basic Research Unit at the Department of Computer Science, University of Helsinki. Here is a (possibly incomplete) list of researchers and contributors in the Biomine project: prof. Hannu Toivonen, Lauri Eronen, Petteri Hintsanen, Kimmo Kulovesi, Atte Hinkka, Laura Langohr.
The development of Biomine Explorer started in 2013 by Vid Podpečan at the Department of Knowledge Technologies, Jožef Stefan Institute. From 2014 onwards Biomine Explorer was developed from scratch and the core Biomine system also received numerous updates and fixes. Biomine Explorer and Biomine are active projects and receive regular updates and new features.
If you have a question or comment about Biomine Explorer or Biomine please send an email to vid.podpecan@ijs.si.