Saccharomyces cerevisiae is one of the best-studied model organisms, yet the three-dimensional structure and molecular function of many yeast proteins remain unknown. Yeast proteins were parsed into 14,934 domains, and those lacking sequence similarity to proteins of known structure were folded using the Rosetta de novo structure prediction method on the World Community Grid. This structural da...

KinetochoreDB is an online resource for the kinetochore and its related proteins. It provides comprehensive annotations on 1554 related protein entries in terms of their amino acid sequence, protein domain context, protein 3D structure, predicted intrinsically disordered region, protein-protein interaction, post-translational modification site, functional domain and key metabolic/signaling path...

Today, with the strong growth of the internet, the search service has been developed rapidly, support web users to easily search for their information. However, with the explosion of information is increasingly enormous, how to return search results satisfy the user remains a difficult problem. Currently, many web-based bookmark systems (such as delicous.com) allows users to easily share and or...

The Internet plays a major role as a source of news. Many publishers offer online versions of their newspapers to paying customers. Online newspapers bear more similarity with traditional print papers than with regular news sites. In a close collaboration with Mediengruppe Madsack publisher of newspapers in several German federal states, we aim at providing a semantically enriched online newspa...

This paper demonstrates a new method for leveraging free-text annotations to infer semantic properties of documents. Free-text annotations are becoming increasingly abundant, due to the recent dramatic growth in semistructured, user-generated online content. An example of such content is product reviews, which are often annotated by their authors with pros/cons keyphrases such as “a real bargai...

MOTIVATION The detection of function-related local 3D-motifs in protein structures can provide insights towards protein function in absence of sequence or fold similarity. Protein loops are known to play important roles in protein function and several loop classifications have been described, but the automated identification of putative functional 3D-motifs in such classifications has not yet b...

Despite sequences being core to NLP, scant work has considered how to handle noisy sequence labels from multiple annotators for the same text. Given such annotations, we consider two complementary tasks: (1) aggregating sequential crowd labels to infer a best single set of consensus annotations; and (2) using crowd annotations as training data for a model that can predict sequences in unannotat...

Numerous databases of alternative splice forms have been generated over the recent years, which – beside of using heterogenous input data – differ substantially in the definition and in the representation of patterns. Motivated by this, we have developed a novel relative position notation system to univocally describe alternative splicing (AS) events, and a parsing and visualization tool (AStaL...

Social relations like power and influence are difficult concepts to define, but are easily recognizable when expressed. In this paper, we describe a multi-layer annotation scheme for social power relations that are recognizable from online written interactions. We introduce a typology of four types of power relations between dialog participants: hierarchical power, situational power, influence ...

This study compared the effects of two annotation modalities on the reading comprehension of Iranian intermediate level EFL learners. The two experimental groups under study received treatment on 10 academic L2 reading passages under one of two conditions: One group received treatment on key words in the reading passages through a multimedia environment providing textual annotations. The second...