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ICYMI: Check out the latest developer news, including features in WordPress 6.6 and a sneak peek at enhancements already underway for 6.7:…
ICYMI: Check out the latest developer news, including features in WordPress 6.6 and a sneak peek at enhancements already underway for 6.7:…
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📣 Excited to announce my new monthly column, "Building WordPress". In my first article, I explore the fascinating evolution of #WordPress design…
📣 Excited to announce my new monthly column, "Building WordPress". In my first article, I explore the fascinating evolution of #WordPress design…
Liked by Brian Kemper
Experience & Education
Licenses & Certifications
Publications
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PathText: A text mining integrator for biological pathway visualizations
Bioinformatics
Motivation: Metabolic and signaling pathways are an increasingly important part of organizing knowledge in systems biology. They serve to integrate collective interpretations of facts scattered throughout literature. Biologists construct a pathway by reading a large number of articles and interpreting them as a consistent network, but most of the models constructed currently lack direct links to those articles. Biologists who want to check the original articles have to spend substantial amounts…
Motivation: Metabolic and signaling pathways are an increasingly important part of organizing knowledge in systems biology. They serve to integrate collective interpretations of facts scattered throughout literature. Biologists construct a pathway by reading a large number of articles and interpreting them as a consistent network, but most of the models constructed currently lack direct links to those articles. Biologists who want to check the original articles have to spend substantial amounts of time to collect relevant articles and identify the sections relevant to the pathway. Furthermore, with the scientific literature expanding by several thousand papers per week, keeping a model relevant requires a continuous curation effort. In this article, we present a system designed to integrate a pathway visualizer, text mining systems and annotation tools into a seamless environment. This will enable biologists to freely move between parts of a pathway and relevant sections of articles, as well as identify relevant papers from large text bases. The system, PathText, is developed by Systems Biology Institute, Okinawa Institute of Science and Technology, National Centre for Text Mining (University of Manchester) and the University of Tokyo, and is being used by groups of biologists from these locations.
Other authorsSee publication -
Community Platform for Pathway Model Building
10th International Conference on Systems Biology
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Connecting Text Mining and Pathways using the PathText Resource
International Conference on Language Resources and Evaluation
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PathText: Text Mining Tools Integrated with Biological Pathway
Genomes to Systems Conference
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EKOSS: A Knowledge-User Centered Approach to Knowledge Sharing, Discovery, and Integration on the Semantic Web
International Semantic Web Conference
Languages
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Japanese
Elementary proficiency
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English
Native or bilingual proficiency
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