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Article
Open AccessOverview of the Cancer Genetics and Pathway Curation tasks of BioNLP Shared Task 2013
Since their introduction in 2009, the BioNLP Shared Task events have been instrumental in advancing the development of methods and resources for the automatic extraction of information from the biomedical lite...
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Article
Grid-based framework for high-performance processing of scientific knowledge
An essential matter in the knowledge-based information society is how to extract useful information quickly from a large volume of literature. Since most existing data mining frameworks deal with structured in...
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Article
Open AccessThe 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies
BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and access...
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Chapter and Conference Paper
Pathway Construction and Extension Using Natural Language Processing
Construction and maintenance of signaling pathway is a time-consuming and labor-intensive task. In addition, integration of various pathways is also ineffective since several markup languages are used to expre...
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Chapter and Conference Paper
Corpus Construction for Extracting Disease-Gene Relations
Many corpus-based statistical methods have been used to tackle issues of extracting disease-gene relations (DGRs) from literature. There are two limitations in the corpus-based approach: One is that available ...
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Article
Open AccessU-Compare bio-event meta-service: compatible BioNLP event extraction services
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Article
Open AccessThe 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications
The interaction between biological researchers and the bioinformatics tools they use is still hampered by incomplete interoperability between such tools. To ensure interoperability initiatives are effectively ...
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Chapter and Conference Paper
Feasibility Study for Procedural Knowledge Extraction in Biomedical Documents
We propose how to extract procedural knowledge rather than declarative knowledge utilizing machine learning method with deep language processing features in scientific documents, as well as how to model it. We...
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Chapter and Conference Paper
Multi-words Terminology Recognition Using Web Search
Terminology recognition system which is a fundamental research for Technology Opportunity Discovery (TOD) has been intensively studied in limited range of domains, especially in bio-medical domain. We propose ...
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Chapter and Conference Paper
Relation Extraction Based on Composite Kernel Combining Pattern Similarity of Predicate-Argument Structure
Lots of valuable textual information is used to extract relations between named entities from literature. Composite kernel approach is proposed in this paper. The composite kernel approach calculates similarit...
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Chapter and Conference Paper
Smart Searching System for Virtual Science Brain
To decide research topics or analyze technical trends, researchers should collect and analyze information from hundreds of thousands of articles, patents, and technical reports. To facilitate the process, info...
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Chapter and Conference Paper
Procedural Knowledge Extraction on MEDLINE Abstracts
Text mining is a popular methodology for building Technology Intelligence which helps companies or organizations to make better decisions by providing knowledge about the state-of-the-art technologies obtained...
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Article
Open AccessThe DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows
Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems ...
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Chapter and Conference Paper
Natural Language Query Processing for Life Science Knowledge
As the progress of life science, human knowledge about life science keeps increased and diversified. To effectively access the diverse and complex knowledge base, people need to cope with complex representatio...
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Chapter and Conference Paper
Extracting Protein Sub-cellular Localizations from Literature
Protein Sub-cellular Localization (PSL) prediction is an important task for predicting protein functions. Because the sequence-based approach used in the most previous work has focused on prediction of locatio...
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Article
Open AccessAutomatic recognition of topic-classified relations between prostate cancer and genes using MEDLINE abstracts
Automatic recognition of relations between a specific disease term and its relevant genes or protein terms is an important practice of bioinformatics. Considering the utility of the results of this approach, w...
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Chapter and Conference Paper
Unsupervised Event Extraction from Biomedical Literature Using Co-occurrence Information and Basic Patterns
In this paper, we propose a new unsupervised method of extracting events from biomedical literature, which uses the score measures of events and patterns having reciprocal effects on each other. We, first, gen...
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Chapter and Conference Paper
Unsupervised Event Extraction from Biomedical Text Based on Event and Pattern Information
In this paper, we proposed a new event extraction method from biomedical texts. It can extend patterns by unsupervised way based on event and pattern information. Evaluation of our system on GENIA corpus achie...
