TEES is available as a stable version or the latest repository version, downloadable from the above icons. To get started, read the Quick Start guide.
For documentation, see the Wiki and the API docs.
New in TEES 2.1
- Using TEES 2.1 in the BioNLP'13 and DDIExtraction 2013 Shared Tasks
- Precalculated TEES analyses for several corpora
Overview
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.
Biomedical event extraction refers to the automatic detection of molecular interactions from research articles. Events can accurately represent complex statements, e.g. the sentence “Protein A causes protein B to bind protein C” produces the event CAUSE(A, BIND(B, C)). Such formal structures can be processed with computational methods, allowing large-scale analysis of the literature, as well as applications such as pathway construction.
TEES has been evaluated in the following Shared Tasks. Models for predicting their targets are provided with TEES and can be used on any unannotated text.
- BioNLP 2009 Shared Task (1st place, PDF)
- BioNLP 2011 Shared Task (1st place in 4/8 tasks, only system to participate in all tasks, PDF)
- DDI 2011 (Drug-drug interactions) Challenge (4th place, at 96% of the performance of the best system, PDF)
For a list of all scientific publications on TEES, see the Publications page. TEES has been used to successfully predict GENIA type events for all PubMed abstracts and PMC full text articles, and the resulting data is available in the EVEX database.