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We request that articles making use of the corpus data and tools cite the following paper in BMC Bioinformatics:

BioInfer: A corpus for information extraction in the biomedical domain. Sampo Pyysalo, Filip Ginter, Juho Heimonen, Jari Björne, Jorma Boberg, Jouni Järvinen and Tapio Salakoski. BMC Bioinformatics 2007, 8:50.

The following publications pertain to the BioInfer corpus per se:

  • Pyysalo S, Ginter F, Laippala V, Haverinen K, Heimonen J, Salakoski T: On the unification of syntactic annotations under the Stanford dependency scheme: A case study on BioInfer and GENIA. In Proceedings of the ACL BioNLP'07 Workshop. Prague, Czech Republic. 2007. [PDF]
  • Pyysalo S, Ginter F, Heimonen J, Björne J, Boberg J, Järvinen J, Salakoski T: BioInfer: A corpus for information extraction in the biomedical domain. BMC Bioinformatics 2007, 8:50. [PDF]

The following publications use the BioInfer corpus or earlier versions of the corpus data:

  • Pyysalo S, Ginter F, Pahikkala T, Boberg J, Jäarvinen J, Salakoski T, Koivula J: Analysis of link grammar on biomedical dependency corpus targeted at protein-protein interactions. In Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications (JNLPBA), Geneva, Switzerland. Edited by Collier N, Ruch P, Nazarenko A, 2004:15-21.
  • Tsivtsivadze E, Pahikkala T, Pyysalo S, Boberg J, Mylläri A, Salakoski T: Regularized least-squares for parse ranking. In Proceedings of the Symposium on Intelligent Data Analysis (IDA 05), Madrid, Spain. Edited by Famili AF, Kok JN, Peña JM, Siebes A, Feelders AJ, 2005:464-474.
  • Tsivtsivadze E, Pahikkala T, Boberg J, Salakoski T: Locality-convolution kernel and its application to dependency parse ranking. Proceedings of The 19th International Conference on Industrial, Engineering & Other Applications of Applied Intelligent Systems (IEA/AIE06), Annecy, France 2006.
  • Pyysalo S, Ginter F, Pahikkala T, Boberg J, Jäarvinen J, Salakoski T: Evaluation of Two Dependency Parsers on Biomedical Corpus Targeted at Protein-Protein Interactions. Recent Advances in Natural Language Processing for Biomedical Applications, special issue of the International Journal of Medical Informatics 2006, 75(6):430-442.
  • Pahikkala T, Tsivtsivadze E, Boberg J, Salakoski T: Graph kernels versus graph representations: a case study in parse ranking. In Proceedings of the ECML/PKDD'06 workshop on Mining and Learning with Graphs (MLG'06). Edited by Gärtner T, Garriga GC, Meinl T, 2006.
  • Pahikkala T, Boberg J and Salakoski T: Fast n-fold cross-validation for regularized least-squares., In Proceedings of the Ninth Scandinavian Conference on Artificial Intelligence (SCAI 2006). Edited by Honkela T, Raiko T, Kortela J and Valpola H, 2006:83-90.
  • Pyysalo S, Salakoski T, Aubin S, Nazarenko A: Lexical adaptation of link grammar to the biomedical sublanguage: a comparative evaluation of three approaches. BMC Bioinformatics 2006, 7(Suppl 3).