Success of the NaCTeM team in the BioCreAtIvE challenge for 2010


Team NaCTeM participated in the most recent BioCreAtIvE III protein-protein interaction (PPI) challenge and achieved the best performance, in what was considered the most challenging task, the Interaction Method Task (IMT). This involves automatically detecting experimental techniques used in research articles that support given PPIs. Such detection is crucial not only for the correct annotation of experimentally determined protein interactions but also for other annotations, such as evidence codes in Gene Ontology, and assigning other controlled vocabulary terms to an article.

Among systems submitted by 8 international teams, NaCTeM's yielded the best overall performance as measured by a range of evaluation metrics.

BioCreAtIvE (Critical Assessment of Information Extraction in Biology) is a series of established international events devoted to the evaluation of biomedical information extraction (IE) systems. Past BioCreAtIvE events were held in 2004 (I), 2006 (II), 2009 (II.5). Before a BioCreAtIvE event, the organisers announce a number of text mining challenges, ranging from the recognition of named (biological) entities, entity disambiguation and normalisation, to the extraction of relations between entities. They then provide gold standard data and invite research groups to test their text mining systems by running them against the gold standard. A workshop is held at the end of each BioCreAtIvE, where participants are invited to present and discuss their systems and results.

BioCreAtIvE events provide an excellent forum for computer scientists, bioinformaticians and biomedical researchers to share research experiences in IE, in the context of real-world challenges. Work presented in BioCreAtIvE is published as special issues in prestigious journals (e.g., BMC Bioinformatics (2006), Genome Biology (2008) and IEEE Transactions on Computational Biology and Bioinformatics (2010)) and is frequently cited: on average, each BioCreAtIvE I paper was cited 64.3 times, each BioCreAtIvE II paper 29.4 times (results obtained by searching BioCreAtIvE journal papers (i.e., excluding the proceedings papers) in Google Scholar on 14 Sep 2010). The BioCreAtIvE II.5 special issue has only recently been published.

The NaCTeM BioCreAtIvE team consisted of S.Ananiadou, R.T. Batista-Navarro, R. Nawaz, C. Nobata, R. Rak, A. Restificar, C.J. Rupp and X. Wang.

This work was supported mainly by BBSRC (BB/G013160/1 Automated Biological Event Extraction from the Literature for Drug Discovery) as well as UK PubMed Central funders (Arthritis Research Campaign, BBSRC, British Heart Foundation, Cancer Research UK, Chief Scientist Office, Department of Health - National Institute of Health Research, Medical Research Council, Wellcome Trust).

Team NaCTeM (Left to right): C.J. Rupp, Riza T. Batista-Navarro, Xinglong Wang, Sophia Ananiadou, Chikashi Nobata, Angelo Restificar, Rafal Rak.

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