Biomine: a network-structured resource of biological entities for link prediction

Authors:
Lauri Eronen;Petteri Hintsanen;Hannu Toivonen
Affiliations:
Department of Computer Science and HIIT, University of Helsinki, Finland;Department of Computer Science and HIIT, University of Helsinki, Finland;Department of Computer Science and HIIT, University of Helsinki, Finland
Venue:
Bisociative Knowledge Discovery
Year:
2012

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Abstract

Biomine is a biological graph database constructed from public databases. Its entities (vertices) include biological concepts (such as genes, proteins, tissues, processes and phenotypes, as well as scientific articles) and relations (edges) between these entities correspond to real-world phenomena such as "a gene codes for a protein" or "an article refers to a phenotype". Biomine also provides tools for querying the graph for connections and visualizing them interactively. We describe the Biomine graph database. We also discuss link discovery in such biological graphs and review possible link prediction measures. Biomine currently contains over 1 million entities and over 8 million relations between them, with focus on human genetics. It is available on-line and can be queried for connecting subgraphs between biological entities.