Overview of the gene regulation network and the bacteria biotope tasks in BioNLP'13 shared task

Robert Bossy, Wiktoria Golik, Zorana Ratkovic, Dialekti Valsamou, Philippe Bessières, Claire Nédellec BMC Bioinformatics 2015, 16(Suppl 10):S1 (13 July 2015)

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We present the two Bacteria Track tasks of BioNLP 2013 Shared Task (ST): Gene Regulation Network (GRN) and Bacteria Biotope(BB). These tasks were previously introduced in the 2011 BioNLP-ST Bacteria Track as Bacteria Gene Interaction (BI) andBacteria Biotope (BB). The Bacteria Track was motivated by a need to develop specific BioNLP tools for fine-grained event extraction in bacteria biology. The 2013 tasks expand on the 2011 version by better addressing the biological knowledge modeling needs. New evaluation metrics were designed for the new goals. Moving beyond a list of gene interactions, the goal of the GRN task is to build a gene regulation network from the extracted gene interactions. BB'13 is dedicated to the extraction of bacteria biotopes, i.e. bacterial environmental information, as was BB'11. BB'13 extends the typology of BB'11 to a large diversity of biotopes, as defined by the OntoBiotope ontology. The detection of entities and events is tackled by distinct subtasks in order to measure the progress achieved by the participant systems since 2011.


This paper details the corpus preparations and the evaluation metrics, as well as summarizing and discussing the participant results. Five groups participated in each of the two tasks. The high diversity of the participant methods reflects the dynamism of the BioNLP research community.

The highest scores for the GRN and BB'13 tasks are similar to those obtained by the participants in 2011, despite of the increase in difficulty. The high density of events in short text segments (multi-event extraction) was a difficult issue for the participating systems for both tasks. The analysis of the BB'13 results also shows that co-reference resolution and entity boundary detection remain major hindrances.


The evaluation results suggest new research directions for the improvement and development of Information Extraction for molecular and environmental biology. The Bacteria Track tasks remain publicly open; the BioNLP-ST website provides an online evaluation service, the reference corpora and the evaluation tools.