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Supporting Resources - backup

The goal of the supporting resources for the BioNLP Shared Task 2016 is to provide the task participants with annotations from state-of-the-art automated tools in order to minimise the time-investment necessary to participate in the shared task and to allow for participants to experiment on how to leverage automated analyses provided by existing Natural Language Processing systems. [responsibility...]

Resources and Formats

In the following, are listed resources that are available for the shared task. Each resource is a file to be downloaded, it is the result of a tool (tools are presented) on the train and dev datasets.

POS Tagging

Genia Tagger is tool for part-of-speech tagging, shallow parsing, and named entity recognition for biomedical text.


Stanford Parser is a statistical parser...

Enju Parser parses sentences with the ENJU dependency parser.

CCG Parser provides syntax parsing with CCG Parser.

Term Extraction

BioYatea extracts terms from the corpus using the YaTeA term extractor...

Named Entity Recognition

Stanford NER [synopsis...]

LINNAEUS  is a software for species name recognition and normalization...

OrganismTagger is a hybrid rule-based/machine-learning system that extracts organism mentions from the biomedical literature, normalizes them to their scientific name, and provides grounding to the NCBI Taxonomy database...

SR4GN is a software that provides a species recognition for gene normalization...
[ ! moved from bb3_supporting-resources
SPECIES identifies taxonomic mentions in documents and maps them to corresponding NCBI Taxonomy entries. If you make use of the SPECIES annotations, please cite: Pafilis, E., Frankild, S.P., Fanini, L., Faulwetter, S., Pavloudi, C., Vasileiadou, A., Arvanitidis, C. and Jensen, L.J. (2013). The SPECIES and ORGANISMS resources for fast and accurate identification of taxonomic names in text. PLoS One, 8(6), p.e65390.

Sentence Splitting & Tokenization

Segmentation is an internal alvisnlp plan that generates...

Data Visualization

Brat is a tool for visualization of annotations...