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Licenses
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!
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.
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 |
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 |