BioNLP Shared Task 2011: bacteria gene interactions and renaming

Authors:
Julien Jourde;Alain-Pierre Manine;Philippe Veber;Karën Fort;Robert Bossy;Erick Alphonse;Philippe Bessières
Affiliations:
Informatique et Génome -- Institut National de la Recherche Agronomique, MIG INRA, Jouy-en-Josas, France;PredictiveDB, rue Alexandre Parodi, Paris, France;Informatique et Génome -- Institut National de la Recherche Agronomique, MIG INRA, Jouy-en-Josas, France;LIPN -- Université Paris-Nord/CNRS and INIST CNRS, Vandæuvre-lès-Nancy, France;Informatique et Génome -- Institut National de la Recherche Agronomique, MIG INRA, Jouy-en-Josas, France;PredictiveDB, rue Alexandre Parodi, Paris, France;Informatique et Génome -- Institut National de la Recherche Agronomique, MIG INRA, Jouy-en-Josas, France
Venue:
BioNLP Shared Task '11 Proceedings of the BioNLP Shared Task 2011 Workshop
Year:
2011

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Abstract

We present two related tasks of the BioNLP Shared Tasks 2011: Bacteria Gene Renaming (Rename) and Bacteria Gene Interactions (GI). We detail the objectives, the corpus specification, the evaluation metrics, and we summarize the participants' results. Both issued from PubMed scientific literature abstracts, the Rename task aims at extracting gene name synonyms, and the GI task aims at extracting genic interaction events, mainly about gene transcriptional regulations in bacteria.