AI Article Synopsis
- The BioNLP 2013 Shared Task introduced two Bacteria Track tasks: Gene Regulation Network (GRN) and Bacteria Biotope (BB), which aim to improve event extraction in bacterial biology compared to the 2011 tasks.
- New evaluation metrics were created to support the tasks' goals, such as building a comprehensive gene regulation network and expanding the types of bacterial environments categorized by the OntoBiotope ontology.
- The study highlights the varied methods used by five participant groups, indicating ongoing active development in the BioNLP field and suggesting future research avenues for improving information extraction in molecular and environmental biology.
Article Abstract
Background: 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) and Bacteria 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.
Results: 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.
Conclusion: 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.
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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4511173 | PMC |
| http://dx.doi.org/10.1186/1471-2105-16-S10-S1 | DOI Listing |
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