BIONDA: a free database for a fast information on published biomarkers

Michael Turewicz; Anika Frericks-Zipper; Markus Stepath; Karin Schork; Spoorti Ramesh; Katrin Marcus; Martin Eisenacher

doi:10.1093/bioadv/vbab015

BIONDA: a free database for a fast information on published biomarkers

Bioinform Adv. 2021 Aug 18;1(1):vbab015. doi: 10.1093/bioadv/vbab015. eCollection 2021.

Authors

Michael Turewicz^{1

2}, Anika Frericks-Zipper^{1

2}, Markus Stepath^{1

2}, Karin Schork^{1

2}, Spoorti Ramesh^{1

2}, Katrin Marcus^{1

2}, Martin Eisenacher^{1

2}

Affiliations

¹ Medizinisches Proteom-Center, Ruhr University Bochum, Bochum 44801, Germany.
² Center for Protein Diagnostics (PRODI), Medical Proteome Analysis, Ruhr University Bochum, Bochum 44801, Germany.

Abstract

Summary: Because of the steadily increasing and already manually unmanageable total number of biomarker-related articles in biomedical research, there is a need for intelligent systems that extract all relevant information from biomedical texts and provide it as structured information to researchers in a user-friendly way. To address this, BIONDA was implemented as a free text mining-based online database for molecular biomarkers including genes, proteins and miRNAs and for all kinds of diseases. The contained structured information on published biomarkers is extracted automatically from Europe PMC publication abstracts and high-quality sources like UniProt and Disease Ontology. This allows frequent content updates.

Availability and implementation: BIONDA is freely accessible via a user-friendly web application at http://bionda.mpc.ruhr-uni-bochum.de. The current BIONDA code is available at GitHub via https://github.com/mpc-bioinformatics/bionda.

Supplementary information: Supplementary data are available at Bioinformatics Advances online.