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Jari Björne edited this page May 26, 2015 · 12 revisions

TEES is a free and open source program licensed under the GNU General Public License. TEES integrates also a small number of external libraries, compatible with GPL terms, mostly included at Utils/Libraries. Information on their authors and licenses is in their Python source code files. If TEES is used in a publication, the following book should be cited.

@phdthesis{bjorne2014biomedical,
  title={Biomedical Event Extraction with Machine Learning},
  author={Bj{\"o}rne, Jari},
  year={2014},
  school={University of Turku},
  publisher={TUCS Dissertations}
}

TEES uses several external components, and when using TEES their licensing terms need to be also considered. This page gives some guidelines on the conditions on using these external programs, but you should always check their authors' pages for the detailed terms!

Corpora

The BioNLP'11, BioNLP'09 and DDI'11 corpora are generally free for scientific use, but both their source text and annotations have certain specific terms. The BioNLP corpus licenses are included in the data directory where TEES installs the corpora. For more information on using these corpora, the relevant shared task pages should be consulted. It is also important to cite the relevant papers when using these corpora.

Shared Task Home Page
BioNLP'11 https://sites.google.com/site/bionlpst/
BioNLP'09 http://www.nactem.ac.uk/tsujii/GENIA/SharedTask/
DDI'11 http://labda.inf.uc3m.es/DDIExtraction2011/

External Programs

The external programs TEES uses are generally free for scientific use, provided they are properly cited.

Program TEES Usage License
SVM-multiclass classification and training Non-commercial use only. Cannot be redistributed
GENIA Sentence Splitter preprocessing Non-commercial use only
BANNER  preprocessing Common Public License 1.0 
BLLIP Parser and David McClosky's biomodel  preprocessing See readme 
Stanford Parser preprocessing  GNU General Public License (v2 or later). Commercial licensing available
NLTK  WordNet for BB task Apache License, Version 2.0

Resources

On some tasks TEES uses datasets providing contextual information on the biological domain as additional training data. Some of these datasets, or resources derived from them, are downloaded and used as machine learning features when training models for these tasks. If working on these tasks, more information about these resources can be found on their webpages.

Resource TEES task License
 DrugBank XML DDI Non-commercial use only
WordNet BB WordNet 3.0 license
LPSN List of Prokaryotic names with Standing in Nomenclature  BB non-commercial use 
UniProt bacsu REN Creative Commons Attribution-NoDerivs
SubtiWiki REN Community Wiki

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