Although a large amount of experimentally derived information about RNA editing sites currently exists, this information has remained scattered in a variety of sources and in diverse data formats. Availability of standard collections for high-quality experimental data will be by of great help for systematic studying of RNA editing, especially for developing computational algorithm to predict RN...

We address the problem of evaluating textual, task-oriented dialogues between the customer and the helpdesk, such as those that take the form of online chats. As an initial step towards evaluating automatic helpdesk dialogue systems, we have constructed a test collection comprising 3,700 real Customer-Helpdesk multiturn dialogues by mining Weibo, a major Chinese social media. We have annotated ...

MOTIVATION Since protein domains are the units of evolution, databases of domain signatures such as ProDom or Pfam enable both a sensitive and selective sequence analysis. However, manually curated databases have a low coverage and automatically generated ones often miss relationships which have not yet been discovered between domains or cannot display similarities between domains which have dr...

Model repositories like BioModels.net or JWS online provide a large number of biochemical pathway models in the data format SBML (Systems Biology Markup Language). We have developed semanticSBML, an interactive model merging tool that helps users build, annotate, check, and combine SBML models. It supports the current standard for biological annotations within SBML and uses a large collection o...

For understanding humorous dialogue, a collection of humorous expressions is needed. In addition to humorous expressions, their annotations are important to be used as language resources. In this paper, we analyzed how human assessors annotate humorous expressions extracted from an online community-based questionanswering (CQA) corpus, which contains many interesting examples of humorous commun...

MOTIVATION Protein-protein interaction (PPI) extraction from published biological articles has attracted much attention because of the importance of protein interactions in biological processes. Despite significant progress, mining PPIs from literatures still rely heavily on time- and resource-consuming manual annotations. RESULTS In this study, we developed a novel methodology based on Bayes...

Unsupervised vector-based approaches to semantics can model rich lexical meanings, but they largely fail to capture sentiment information that is central to many word meanings and important for a wide range of NLP tasks. We present a model that uses a mix of unsupervised and supervised techniques to learn word vectors capturing semantic term–document information as well as rich sentiment conten...

SUMMARY Accurate annotations of genomic variants are necessary to achieve full-genome clinical interpretations that are scientifically sound and medically relevant. Many disease associations, especially those reported before the completion of the HGP, are limited in applicability because of potential inconsistencies with our current standards for genomic coordinates, nomenclature and gene struc...

In this paper we introduce the TTCS system, so named after Terms To Conceptual Spaces, that exploits a resource-driven approach relying on BabelNet, NASARI and ConceptNet. TTCS takes in input a term and its context of usage and produces as output a specific type of vector-based semantic representation, where conceptual information is encoded through the Conceptual Spaces (a geometric framework ...

SUMMARY NGS-SNP is a collection of command-line scripts for providing rich annotations for SNPs identified by the sequencing of whole genomes from any organism with reference sequences in Ensembl. Included among the annotations, several of which are not available from any existing SNP annotation tools, are the results of detailed comparisons with orthologous sequences. These comparisons can, fo...