Jung-jae Kim

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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)
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)
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 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)
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)
UNLABELLED Search engines running on MEDLINE abstracts have been widely used by biologists to find publications that are related to their research. The existing search engines such as PubMed, however, have limitations when applied for the task of seeking textual evidence of relations between given concepts. The limitations are mainly due to the problem that(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)
The third edition of the BioNLP Shared Task was held with the grand theme "knowledge base construction (KB)". The Genia Event (GE) task was re-designed and implemented in light of this theme. For its final report, the participating systems were evaluated from a perspective of annotation. To further explore the grand theme, we extended the evaluation from a(More)
UNLABELLED Gene ontology (GO) annotation is a common task among model organism databases (MODs) for capturing gene function data from journal articles. It is a time-consuming and labor-intensive task, and is thus often considered as one of the bottlenecks in literature curation. There is a growing need for semiautomated or fully automated GO curation(More)