EVEX

EVEX is a text mining resource built on top of PubMed abstracts and PubMed Central full texts. It contains over 40 million bio-molecular events among more than 76 million automatically extracted gene/protein name mentions.

The EVEX dataset is the result of running the Turku Event Extraction System together with BANNER and the McClosky-Charniak Parser on a PubMed scale.

Online interface: http://www.evexdb.org/

Main references: S. Van Landeghem; K. Hakala; S. Rönnqvist; T. Salakoski; Y. Van de Peer; F. Ginter. Exploring Biomolecular Literature with EVEX: Connecting Genes through Events, Homology and Indirect Associations. Advances in Bioinformatics, special issue Literature-Mining Solutions for Life Science Research. 2012

Contact: Filip Ginter (ginter@cs.utu.fi), Kai Hakala (kahaka@utu.fi)

Turku Event Extraction System (TEES)

Turku Event Extraction System (TEES) is a free and open source natural language processing system developed for the extraction of events and relations from biomedical text. It is written mostly in Python, and should work in generic Unix/Linux environments.

More information on the TEES’ project page: http://jbjorne.github.io/TEES/

Main references: J. Björne; T. Salakoski. TEES 2.2: Biomedical Event Extraction for Diverse Corpora. BMC bioinformatics. 2015

Contact: Jari Björne (jakrbj@utu.fi)