BackgroundSince their introduction in 2009, the BioNLP Shared Task events have been instrumental in advancing the development of methods and resources for the automatic extraction of information from the biomedical literature. In this paper, we present the Cancer Genetics (CG) and Pathway Curation (PC) tasks, two event extraction tasks introduced in the BioNLP Shared Task 2013. The CG task focuses on cancer, emphasizing the extraction of physiological and pathological processes at various levels of biological organization, and the PC task targets reactions relevant to the development of biomolecular pathway models, defining its extraction targets on the basis of established pathway representations and ontologies.ResultsSix groups participated in the CG task and two groups in the PC task, together applying a wide range of extraction approaches including both established state-of-the-art systems and newly introduced extraction methods. The best-performing systems achieved F-scores of 55% on the CG task and 53% on the PC task, demonstrating a level of performance comparable to the best results achieved in similar previously proposed tasks.ConclusionsThe results indicate that existing event extraction technology can generalize to meet the novel challenges represented by the CG and PC task settings, suggesting that extraction methods are capable of supporting the construction of knowledge bases on the molecular mechanisms of cancer and the curation of biomolecular pathway models. The CG and PC tasks continue as open challenges for all interested parties, with data, tools and resources available from the shared task homepage.

Although metabolic acid load has been associated with many well-known risk factors for mortality, its clinical implications are not yet clear. To evaluate the association between biomarkers of metabolic acid load, such as serum bicarbonate, serum anion gap and urine pH and mortality, we analyzed the health records of 31,590 adults who underwent a health screening between January 2001 and December 2010 and had an estimated glomerular filtration rate ⩾60 ml min(-1) per 1.73 m2. Urine pH was measured by a dipstick test performed on fast morning urine sample and categorized as acidic (urine pH ⩽5.5), neutral and alkaline (urine pH ⩾8.0). Using the Cox proportional hazard model, the adjusted hazard ratio (aHR) of all-cause mortality of the lowest quartile of serum bicarbonate was 1.460 (95% confidence interval (CI) 1.068-1.995) compared with the highest quartile, after a median follow-up of 93 months. The aHRs of cardiovascular and cancer mortality of the lowest quartile of serum bicarbonate were 2.647 (95% CI 1.148-6.103) and 1.604 (95% CI 1.024-2.513), respectively, compared with the highest quartile. Acidic and neutral urine pH were significantly associated with a higher all-cause mortality (aHR 2.550, 95% CI 1.316-4.935; aHR 2.376 95% CI 1.254-4.501, respectively), compared with an alkaline urine pH. In conclusion, higher metabolic acid load was associated with an increased all-cause and cardiovascular mortality in a healthy population. The association between metabolic acid load and mortality and the causality of the relationship need to be confirmed.

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