Hunflair corpora

This repository re-hosts biomedical Named Entity Recognition corpora for HunFlair which are no longer available at their original location. If you use one of these corpora to produce results for publication, please cite the original publications (see list below):

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Data sets and references

• CLL

@article{kaewphan2016cell,
  title={Cell line name recognition in support of the identification of synthetic lethality in cancer from text},
  author={Kaewphan, Suwisa and Van Landeghem, Sofie and Ohta, Tomoko and Van de Peer, Yves and Ginter, Filip and Pyysalo, Sampo},
  journal={Bioinformatics},
  volume={32},
  number={2},
  pages={276--282},
  year={2016},
  publisher={Oxford University Press}
}

Website: https://turkunlp.org/Cell-line-recognition/
Paper: https://doi.org/10.1093/bioinformatics/btv570

• Gellus

@article{kaewphan2016cell,
  title={Cell line name recognition in support of the identification of synthetic lethality in cancer from text},
  author={Kaewphan, Suwisa and Van Landeghem, Sofie and Ohta, Tomoko and Van de Peer, Yves and Ginter, Filip and Pyysalo, Sampo},
  journal={Bioinformatics},
  volume={32},
  number={2},
  pages={276--282},
  year={2016},
  publisher={Oxford University Press}
}

Website: https://turkunlp.org/Cell-line-recognition/
Paper: https://doi.org/10.1093/bioinformatics/btv570

• OSIRIS (v0.2)

@article{furlong2008osirisv1,
  title={OSIRISv1. 2: a named entity recognition system for sequence variants of genes in biomedical literature},
  author={Furlong, Laura I and Dach, Holger and Hofmann-Apitius, Martin and Sanz, Ferran},
  journal={BMC bioinformatics},
  volume={9},
  number={1},
  pages={1--16},
  year={2008},
  publisher={Springer}
}

Paper: https://doi.org/10.1186/1471-2105-9-84

• Variome

@article{verspoor2013annotating,
  title={Annotating the biomedical literature for the human variome},
  author={Verspoor, Karin and Jimeno Yepes, Antonio and Cavedon, Lawrence and McIntosh, Tara and Herten-Crabb, Asha and Thomas, Zo{\"e} and Plazzer, John-Paul},
  journal={Database},
  volume={2013},
  year={2013},
  publisher={Oxford Academic}
}

Paper: https://doi.org/10.1093%2Fdatabase%2Fbat019