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Natural language descriptions of organismal phenotypes, a principal object of study in biology, are abundant in the biological literature. Expressing these phenotypes as logical statements using ontologies would enable large-scale analysis on phenotypic information from diverse systems. However, considerable human effort is required to make these phenotype descriptions amenable to machine reasoning. Natural language processing tools have been developed to facilitate this task, and the training and evaluation of these tools depend on the availability of high quality, manually annotated gold standard data sets. We describe the development of an expert-curated gold standard data set of annotated phenotypes for evolutionary biology. The gold standard was developed for the curation of complex comparative phenotypes for the Phenoscape project. It was created by consensus among three curators and consists of entity-quality expressions of varying complexity. We use the gold standard to evaluate annotations created by human curators and those generated by the Semantic CharaParser tool. Using four annotation accuracy metrics that can account for any level of relationship between terms from two phenotype annotations, we found that machine-human consistency, or similarity, was significantly lower than inter-curator (human-human) consistency. Surprisingly, allowing curatorsaccess to external information did not significantly increase the similarity of their annotations to the gold standard or have a significant effect on inter-curator consistency. We found that the similarity of machine annotations to the gold standard increased after new relevant ontology terms had been added. Evaluation by the original authors of the character descriptions indicated that the gold standard annotations came closer to representing their intended meaning than did either the curator or machine annotations. These findings point toward ways to better design software to augment human curators and the use of the gold standard corpus will allow training and assessment of new tools to improve phenotype annotation accuracy at scale.

In recent decades, intensive research on non-avian dinosaurs has strongly suggested that these animals were restricted to terrestrial environments.sup.1. Historical proposals that some groups, such as sauropods and hadrosaurs, lived in aquatic environments.sup.2,3 were abandoned decades ago.sup.4-6. It has recently been argued that at least some of the spinosaurids--an unusual group of large-bodied theropods of the Cretaceous era--were semi-aquatic.sup.7,8, but this idea has been challenged on anatomical, biomechanical and taphonomic grounds, and remains controversial.sup.9-11. Here we present unambiguous evidence for an aquatic propulsive structure in a dinosaur, the giant theropod Spinosaurus aegyptiacus.sup.7,12. This dinosaur has a tail with an unexpected and unique shape that consists of extremely tall neural spines and elongate chevrons, which forms a large, flexible fin-like organ capable of extensive lateral excursion. Using a robotic flapping apparatus to measure undulatory forces in physical models of different tail shapes, we show that the tail shape of Spinosaurus produces greater thrust and efficiency in water than the tail shapes of terrestrial dinosaurs and that these measures of performance are more comparable to those of extant aquatic vertebrates that use vertically expanded tails to generate forward propulsion while swimming. These results are consistent with the suite of adaptations for an aquatic lifestyle and piscivorous diet that have previously been documented for Spinosaurus.sup.7,13,14. Although developed to a lesser degree, aquatic adaptations are also found in other members of the spinosaurid clade.sup.15,16, which had a near-global distribution and a stratigraphic range of more than 50 million years.sup.14, pointing to a substantial invasion of aquatic environments by dinosaurs. Discovery that the giant theropod dinosaur Spinosaurus has a large flexible tail indicates that it was primarily aquatic and swam in a similar manner to extant tail-propelled aquatic vertebrates., Author(s): Nizar Ibrahim [sup.1] , Simone Maganuco [sup.2] [sup.3] , Cristiano Dal Sasso [sup.3] , Matteo Fabbri [sup.4] , Marco Auditore [sup.3] , Gabriele Bindellini [sup.3] [sup.5] , David M. [...]

This study investigates the effect of a mixed composition class in an American University on student interaction and writing over a semester. The class was a freshman academic writing course that consisted of fifteen international and ten American students. Some teachers believe that a mixed composition class enhances cultural understanding, and that cultural diversity presents a good learning environment, contributing to developing student writing and language skills; others believe the contrary because the needs of the ESL and native English speakers (NES) cannot be addressed simultaneously. To investigate this issue, we used student journals, interviewed students and observed the class. This paper describes the change in students' attitudes and interaction, the benefits that students gained from the course, and the teachers'/researchers' approach to teaching the course.