Discriminative application of string similarity methods to chemical and non-chemical names for biomedical abbreviation clustering

BACKGROUND: Various computational methods are presently available to classify whether a protein variation is disease-associated or not. However data derived from recent technological advancements make it feasible to extend the annotation of disease-associated variations in order to include specific phenotypes. Here we tackle the problem of distinguishing between genetic variations associated to cancer and variations associated to other genetic diseases. RESULTS: We implement a new method based on Support Vector Machines that takes as input the protein variant and the protein function, as described by its associated Gene Ontology terms. Our approach succeeds in discriminating between germline variants that are likely to be cancer-associated from those that are related to other genetic disorders. The method performs with values of 90% accuracy and 0.61 Matthews correlation coefficient on a set comprising 6478 germline variations (16% are cancer-associated) in 592 proteins. The sensitivity and the specificity on the cancer class are 69% and 66%, respectively. Furthermore the method is capable of correctly excluding some 96% of 3392 somatic cancer-associated variations in 1983 proteins not included in the training/testing set. CONCLUSIONS: Here we prove feasible that a large set of cancer associated germline protein variations can be successfully discriminated from those associated to other genetic disorders. This is a step further in the process of protein variant annotation. Scoring largely improves when protein function as encoded by Gene Ontology terms is considered, corroborating the role of protein function as a key feature for a correct annotation of its variations

Reproductive Biology and Embryonic Diapause as a Survival Strategy for the East Asian Endemic Eagle Ray Aetobatus narutobiei

Batoids comprise five of the seven most threatened families of sharks and rays. The East Asian endemic Naru eagle ray Aetobatus narutobiei is a large bodied ray whose estuarine habitat overlaps with an economically valuable bivalve fishery. In response to decreased bivalve yields, the government initiated a predator control program and as a result, Naru eagle rays have faced intense and targeted fishing pressure during the last two decades. The long-term impacts of the predator control program on the population of rays and bivalves and their balance in the ecosystem are unknown because the life history of the Naru eagle ray has not been characterized. To begin to fill these critical knowledge gaps, the reproductive life history of the Naru eagle was described. Females mature at a larger size than males and require nearly twice as many years to reach maturity (DW50, 952.0 mm vs. 764.2 mm; Age50, 6.0 years vs. 3.5 years). Both males and females reproduce annually and their reproductive cycles are synchronized and seasonal. Females have a single ovary and paired uteri, are viviparous, and reproduce via matrotrophic histotrophy. Mating occurs in August and September and gestation lasts approximately 12 months including a 9.5-month diapause that begins soon after mating and ends in June of the following year, leaving 2.5 months for embryos to complete development. Fecundity ranged from 1 to 7 embryos per brood (n = 158, mean ± SD = 3.36 ± 1.26) and was positively correlated with female disc width (linear regression; F = 105.73, d.f. = 151, P < 0.05). Naru eagle rays are vulnerable to overfishing because of their low fecundity, long reproductive cycle and long time to reach sexual maturity. Obligate embryonic diapause during overwintering and seasonal migrations is a survival strategy that benefits the adults and neonates. This research is a valuable resource to help guide science-based management, conservation and protection of the endemic Asian A. narutobiei and its nursery areas