Learn More
The Gene Regulation Ontology (GRO) is designed as a novel approach to model complex events that are part of the gene regulatory processes. We introduce the design requirements for such a conceptual model and discuss terminological resources suitable to base its construction on. The ontology defines gene regulation events in terms of ontological classes and(More)
The vast majority of existing approaches to opinion feature extraction rely on mining patterns only from a single review corpus, ignoring the nontrivial disparities in word distributional characteristics of opinion features across different corpora. In this paper, we propose a novel method to identify opinion features from online reviews by exploiting the(More)
MOTIVATION Gene Ontology (GO) has been manually developed to provide a controlled vocabulary for gene product attributes. It continues to evolve with new concepts that are compiled mostly from existing concepts in a compositional way. If we consider the relatively slow growth rate of GO in the face of the fast accumulation of the biological data, it is much(More)
The need for associating, or grounding , protein names in the literature with the entries of proteome databases such as Swiss-Prot is well-recognized. The protein names in the biomedical literature show a high degree of morphological and syntactic variations, and various anaphoric expressions including null anaphors. We present a biomedical anaphora(More)
The need for extracting general biological interactions of arbitrary types from the rapidly growing volume of the biomedical literature is drawing increased attention, while the need for this much diversity also requires both a robust treatment of complex linguistic phenomena and a method to consistently characterize the results. We present a biomedical(More)
Semantic querying over the biomedical literature has gained popularity, where a semantic representation of biomedical documents is required. Previous BioNLP Shared Tasks exercised semantic event extraction with a small number of pre-defined event concepts. The GRO task of the BioNLP'13-ST imposes the challenge of dealing with over 100 GRO concepts. Its(More)
As the importance of automatically extracting and analyzing various natural language assertions about protein-protein interactions in biomedical publications is recognized, many uses of natural language processing techniques are proposed in the literature. However, most proposals to date make rather simplifying assumptions about the syntactic aspects of(More)
Taxonomies are the backbone of many structured, semantic knowledge resources. Recent works for extracting taxonomic relations from text focused on collecting lexical-syntactic patterns to extract the taxonomic relations by matching the patterns to text. These approaches, however, often show low coverage due to the lack of contextual analysis across(More)