Atsuko Yamaguchi

50 papers B 1Misc 1Journal 17Unranked 29
YearRankTypeTitle / Venue / Authors
2025 J jnl
Ontology-based expansion of virtual gene panels to improve diagnostic efficiency for rare genetic diseases.
BMC Medical Informatics Decis. Mak.
Jae-Moon Shin, Toyofumi Fujiwara, Hirotomo Saitsu, Atsuko Yamaguchi
2024 — conf
A semantic design for the biological processes associated with intrinsically disordered proteins.
SWAT4HCLS
Atsuko Yamaguchi, Yumiko Kado, Shigetaka Sakamoto, Satoshi Fukuchi, Motonori Ota
2024 — conf
Extracting Long COVID Knowledge from LitCovid: A Glossary-Based Approach.
IIAI-AAI
Atsuko Yamaguchi, Reo Takeda, Yuka Tateisi
2024 — ed.
Proceedings of the Workshop, Poster and Demonstration Sessions at IJCKG 2023 co-located with 12th International Joint Conference on Knowledge Graphs (IJCKG 2023), Tokyo, Japan, December 8-9, 2023.
IJCKG (Workshop/Poster/Demo)
Atsuko Yamaguchi, Shusaku Egami, Kouji Kozaki, Takahiro Kawamura, Boris Villazón-Terrazas, Marut Buranarach
2023 — ed.
14th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4HCLS 2023), Basel, Switzerland, February 13-16, 2023.
SWAT4HCLS
Atsuko Yamaguchi, Andrea Splendiani, M. Scott Marshall, Chris Baker, Jerven T. Bolleman, Albert Burger, Leyla Jael Castro, Ole Eigenbrod, Sabine Österle, Martin Romacker, Andra Waagmeester
2023 — conf
A Comparative Study on Storing and Retrieval of URIs for Life Sciences Databases.
IJCKG (Workshop/Poster/Demo)
Atsuko Yamaguchi, Yasunori Yamamoto
2023 — conf
Ontology-based expansion of virtual gene panels to improve diagnostic efficiency for rare genetic diseases.
SWAT4HCLS
Jae-Moon Shin, Toyofumi Fujiwara, Atsuko Yamaguchi
2021 — conf
Gene Ranking based on Paths from Phenotypes to Genes on Knowledge Graph.
IJCKG
Atsuko Yamaguchi, Jae-Moon Shin, Toyofumi Fujiwara
2020 J jnl
BioHackathon 2015: Semantics of data for life sciences and reproducible research.
F1000Research
Rutger A. Vos, Toshiaki Katayama, Hiroyuki Mishima, Shin Kawano, Shuichi Kawashima, Jin-Dong Kim, Yuki Moriya, Toshiaki Tokimatsu, Atsuko Yamaguchi, Yasunori Yamamoto, Hongyan Wu, Peter Amstutz, Erick Antezana, Nobuyuki P. Aoki, Kazuharu Arakawa, Jerven T. Bolleman, Evan E. Bolton, Raoul Jean Pierre Bonnal, Hidemasa Bono, Kees Burger, Hirokazu Chiba, Kevin Bretonnel Cohen, Eric W. Deutsch, Jesualdo Tomás Fernández-Breis, Gang Fu, Takatomo Fujisawa, Atsushi Fukushima, Alexander García Castro, Naohisa Goto, Tudor Groza, Colin Hercus, Robert Hoehndorf, Kotone Itaya, Nick S. Juty, Takeshi Kawashima, Jee-Hyub Kim, Akira R. Kinjo, Masaaki Kotera, Kouji Kozaki, Sadahiro Kumagai, Tatsuya Kushida, Thomas Lütteke, Masaaki Matsubara, Joe Miyamoto, Attayeb Mohsen, Hiroshi Mori, Yuki Naito, Takeru Nakazato, Jeremy NguyenXuan, Kozo Nishida, Naoki Nishida, Hiroyo Nishide, Soichi Ogishima, Tazro Ohta, Shujiro Okuda, Benedict Paten, Jean-Luc Perret, Philip Prathipati, Pjotr Prins, Núria Queralt-Rosinach, Daisuke Shinmachi, Shinya Suzuki, Tsuyosi Tabata, Terue Takatsuki, Kieron R. Taylor, Mark Thompson, Ikuo Uchiyama, Bruno Vieira, Chih-Hsuan Wei, Mark D. Wilkinson, Issaku Yamada, Ryota Yamanaka, Kazutoshi Yoshitake, Akiyasu C. Yoshizawa, Michel Dumontier, Kenjiro Kosaki, Toshihisa Takagi
2019 J jnl
BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services.
F1000Research
Toshiaki Katayama, Shuichi Kawashima, Gos Micklem, Shin Kawano, Jin-Dong Kim, Simon Kocbek, Shinobu Okamoto, Yue Wang, Hongyan Wu, Atsuko Yamaguchi, Yasunori Yamamoto, Erick Antezana, Kiyoko F. Aoki-Kinoshita, Kazuharu Arakawa, Masaki Banno, Joachim Baran, Jerven T. Bolleman, Raoul Jean Pierre Bonnal, Hidemasa Bono, Jesualdo Tomás Fernández-Breis, Robert M. Buels, Matthew P. Campbell, Hirokazu Chiba, Peter J. A. Cock, Kevin Bretonnel Cohen, Michel Dumontier, Takatomo Fujisawa, Toyofumi Fujiwara, Leyla J. García, Pascale Gaudet, Emi Hattori, Robert Hoehndorf, Kotone Itaya, Maori Ito, Daniel Jamieson, Simon Jupp, Nick S. Juty, Alex Kalderimis, Fumihiro Kato, Hideya Kawaji, Takeshi Kawashima, Akira R. Kinjo, Yusuke Komiyama, Masaaki Kotera, Tatsuya Kushida, James Malone, Masaaki Matsubara, Satoshi Mizuno, Sayaka Mizutani, Hiroshi Mori, Yuki Moriya, Katsuhiko Murakami, Takeru Nakazato, Hiroyo Nishide, Yosuke Nishimura, Soichi Ogishima, Tazro Ohta, Shujiro Okuda, Hiromasa Ono, Yasset Pérez-Riverol, Daisuke Shinmachi, Andrea Splendiani, Francesco Strozzi, Shinya Suzuki, Junichi Takehara, Mark Thompson, Toshiaki Tokimatsu, Ikuo Uchiyama, Karin Verspoor, Mark D. Wilkinson, Sarala M. Wimalaratne, Issaku Yamada, Nozomi Yamamoto, Masayuki Yarimizu, Shoko Kawamoto, Toshihisa Takagi
2019 — conf
Finding RDF Data you need by Umaka Suite.
SWAT4HCLS
Yasunori Yamamoto, Atsuko Yamaguchi
2019 — conf
Investigating Schema Definitions Using RDFS and OWL 2 for RDF Databases in Life Sciences.
JIST (2)
Atsuko Yamaguchi, Tatsuya Kushida, Yasunori Yamamoto, Kouji Kozaki
2019 — conf
Reconstruction of Hierarchical Structures in a Thesaurus-based Ontology through Curation by Domain Experts.
ICBO
Tatsuya Kushida, Kouji Kozaki, Yasunori Yamamoto, Atsuko Yamaguchi, Takahiro Kawamura, Takako Nakagawa, Yuka Tateisi, Toshihisa Takagi
2019 — conf
Semantic Integration of Intrinsically Disordered Proteins and Existing DBs.
SWAT4HCLS
Atsuko Yamaguchi, Hideki Hatanaka, Satoshi Fukuchi, Motonori Ota
2019 — conf
UmakaData Extension: Toward Realization of a Practical SPARQL Endpoint Discovery Service for Life Sciences.
SWAT4HCLS
Norio Kobayashi, Yasunori Yamamoto, Atsuko Yamaguchi
2018 — conf
Implementing LOD Surfer as a Search System for the Annotation of Multiple Protein Sequence Alignment.
JIST
Atsuko Yamaguchi, Hiroyuki Toh
2018 J jnl
YummyData: providing high-quality open life science data.
Database J. Biol. Databases Curation
Yasunori Yamamoto, Atsuko Yamaguchi, Andrea Splendiani
2017 — conf
LOD Surfer API: Web API for LOD Surfing Using Class-Class Relationships in Life Sciences.
SWAT4LS
Atsuko Yamaguchi, Kouji Kozaki, Yasunori Yamamoto, Hiroshi Masuya, Norio Kobayashi
2017 — conf
Semantic Graph Analysis for Federated LOD Surfing in Life Sciences.
JIST
Atsuko Yamaguchi, Kouji Kozaki, Yasunori Yamamoto, Hiroshi Masuya, Norio Kobayashi
2016 — conf
Data Acquisition by Traversing Class-Class Relationships over the Linked Open Data.
ISWC (Posters & Demos)
Atsuko Yamaguchi, Kouji Kozaki, Kai Lenz, Yasunori Yamamoto, Hiroshi Masuya, Norio Kobayashi
2016 — conf
SPARQL Builder: Constructing SPARQL Query by Traversing Class-Class Relationships for Life Science Databases.
JIST (Workshops & Posters)
Atsuko Yamaguchi, Kouji Kozaki, Kai Lenz, Yasunori Yamamoto, Hiroshi Masuya, Norio Kobayashi
2016 — conf
SPARQL Query Construction with Monitoring Service for Endpoints.
SWAT4LS
Atsuko Yamaguchi, Yasunori Yamamoto, Kouji Kozaki, Kai Lenz, Hiroshi Masuya, Norio Kobayashi
2016 — conf
Semantic Data Acquisition by Traversing Class-Class Relationships Over Linked Open Data.
JIST
Atsuko Yamaguchi, Kouji Kozaki, Kai Lenz, Yasunori Yamamoto, Hiroshi Masuya, Norio Kobayashi
2016 — conf
Umaka-Yummy Data: A Place to Facilitate Communication between Data Providers and Consumers.
SWAT4LS
Yasunori Yamamoto, Atsuko Yamaguchi, Andrea Splendiani
2016 — conf
Umaka-Yummy Data: Where Providers and Consumers in Life Sciences Communicate with Each Other.
JIST (Workshops & Posters)
Yasunori Yamamoto, Atsuko Yamaguchi, Andrea Splendiani
2015 — conf
Dynamic Join Order Optimization for SPARQL Endpoint Federation.
SSWS@ISWC
Hongyan Wu, Atsuko Yamaguchi, Jin-Dong Kim
2015 — conf
Efficiently Finding Paths Between Classes to Build a SPARQL Query for Life-Science Databases.
JIST
Atsuko Yamaguchi, Kouji Kozaki, Kai Lenz, Hongyan Wu, Yasunori Yamamoto, Norio Kobayashi
2015 — conf
RDF-Based Integration with SPARQL Building System for Life Science Database Archive.
SWAT4LS
Atsuko Yamaguchi, Katsuhiko Okubo, Norio Kobayashi, Kouji Kozaki, Sadahiro Kumagai, Kai Lenz, Tomoe Nobusada, Hongyan Wu, Yasunori Yamamoto, Hideki Hatanaka
2014 — conf
An Intelligent SPARQL Query Builder for Exploration of Various Life-science Databases.
IESD@ISWC
Atsuko Yamaguchi, Kouji Kozaki, Kai Lenz, Hongyan Wu, Norio Kobayashi
2014 J jnl
BioBenchmark Toyama 2012: an evaluation of the performance of triple stores on biological data.
J. Biomed. Semant.
Hongyan Wu, Toyofumi Fujiwara, Yasunori Yamamoto, Jerven T. Bolleman, Atsuko Yamaguchi
2014 J jnl
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.
J. Biomed. Semant.
Toshiaki Katayama, Mark D. Wilkinson, Kiyoko F. Aoki-Kinoshita, Shuichi Kawashima, Yasunori Yamamoto, Atsuko Yamaguchi, Shinobu Okamoto, Shin Kawano, Jin-Dong Kim, Yue Wang, Hongyan Wu, Yoshinobu Kano, Hiromasa Ono, Hidemasa Bono, Simon Kocbek, Jan Aerts, Yukie Akune, Erick Antezana, Kazuharu Arakawa, Bruno Aranda, Joachim Baran, Jerven T. Bolleman, Raoul Jean Pierre Bonnal, Pier Luigi Buttigieg, Matthew P. Campbell, Yi-An Chen, Hirokazu Chiba, Peter J. A. Cock, Kevin Bretonnel Cohen, Alexandru Constantin
2014 — conf
Prototype Implementation of SPARQL Builder for Life-science Databases by Intelligent Schema Analysis on RDF datasets.
SWAT4LS
Norio Kobayashi, Kai Lenz, Hongyan Wu, Kouji Kozaki, Atsuko Yamaguchi
2014 J jnl
TogoTable: cross-database annotation system using the Resource Description Framework (RDF) data model.
Nucleic Acids Res.
Shin Kawano, Tsutomu Watanabe, Sohei Mizuguchi, Norie Araki, Toshiaki Katayama, Atsuko Yamaguchi
2013 J jnl
Building Linked Open Data towards integration of biomedical scientific literature with DBpedia.
J. Biomed. Semant.
Yasunori Yamamoto, Atsuko Yamaguchi, Akinori Yonezawa
2011 J jnl
Allie: a database and a search service of abbreviations and long forms.
Database J. Biol. Databases Curation
Yasunori Yamamoto, Atsuko Yamaguchi, Hidemasa Bono, Toshihisa Takagi
2011 — conf
Building linked open data using approximate string matching methods and domain specific resources.
SWAT4LS
Yasunori Yamamoto, Atsuko Yamaguchi, Akinori Yonezawa
2011 — conf
Discriminative Application of String Similarity Methods to Chemical and Non-chemical Names for Biomedical Abbreviation Clustering.
BIBM
Atsuko Yamaguchi, Yasunori Yamamoto, Jin-Dong Kim, Toshihisa Takagi, Akinori Yonezawa
2011 — conf
Discriminative Optimization of String Similarity and Its Application to Biomedical Abbreviation Clustering.
ICMLA (2)
Atsuko Yamaguchi, Yasunori Yamamoto, Jin-Dong Kim, Toshihisa Takagi, Akinori Yonezawa
2011 J jnl
The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications.
J. Biomed. Semant.
Toshiaki Katayama, Mark D. Wilkinson, Rutger A. Vos, Takeshi Kawashima, Shuichi Kawashima, Mitsuteru Nakao, Yasunori Yamamoto, Hong-Woo Chun, Atsuko Yamaguchi, Shin Kawano, Jan Aerts, Kiyoko F. Aoki-Kinoshita, Kazuharu Arakawa, Bruno Aranda, Raoul Jean Pierre Bonnal, José María Fernández, Takatomo Fujisawa, Paul M. K. Gordon, Naohisa Goto, Syed Haider, Todd W. Harris, Takashi Hatakeyama, Isaac Ho, Masumi Itoh, Arek Kasprzyk, Nobuhiro Kido, Young-Joo Kim, Akira R. Kinjo, Fumikazu Konishi, Yulia Kovarskaya, Gregory Von Kuster, Alberto Labarga, Vachiranee Limviphuvadh, E. Luke McCarthy, Yasukazu Nakamura, Yunsun Nam, Kozo Nishida, Kunihiro Nishimura, Tatsuya Nishizawa, Soichi Ogishima, Tom Oinn, Shinobu Okamoto, Shujiro Okuda, Keiichiro Ono, Kazuki Oshita, Keun-Joon Park, Nicholas H. Putnam, Martin Senger, Jessica Severin, Yasumasa Shigemoto, Hideaki Sugawara, James Taylor, Oswaldo Trelles, Chisato Yamasaki, Riu Yamashita, Noriyuki Satoh, Toshihisa Takagi
2010 — conf
Natural Language Query Processing for Life Science Knowledge - Position Paper.
AMT
Jin-Dong Kim, Yasunori Yamamoto, Atsuko Yamaguchi, Mitsuteru Nakao, Kenta Oouchida, Hong-Woo Chun, Toshihisa Takagi
2010 J jnl
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows.
J. Biomed. Semant.
Toshiaki Katayama, Kazuharu Arakawa, Mitsuteru Nakao, Keiichiro Ono, Kiyoko F. Aoki-Kinoshita, Yasunori Yamamoto, Atsuko Yamaguchi, Shuichi Kawashima, Hong-Woo Chun, Jan Aerts, Bruno Aranda, Lord H. Barboza, Raoul Jean Pierre Bonnal, Richard M. Bruskiewich, Jan Christian Bryne, José María Fernández, Akira Funahashi, Paul M. K. Gordon, Naohisa Goto, Andreas Groscurth, Alex Gutteridge, Richard C. G. Holland, Yoshinobu Kano, Edward A. Kawas, Arnaud Kerhornou, Eri Kibukawa, Akira R. Kinjo, Michael Kuhn, Hilmar Lapp, Heikki Lehväslaiho, Hiroyuki Nakamura, Yasukazu Nakamura, Tatsuya Nishizawa, Chikashi Nobata, Tamotsu Noguchi, Thomas M. Oinn, Shinobu Okamoto, Stuart Owen, Evangelos Pafilis, Matthew R. Pocock, Pjotr Prins, René Ranzinger, Florian Reisinger, Lukasz Salwínski, Mark J. Schreiber, Martin Senger, Yasumasa Shigemoto, Daron M. Standley, Hideaki Sugawara, Toshiyuki Tashiro, Oswaldo Trelles, Rutger A. Vos, Mark D. Wilkinson, William S. York, Christian M. Zmasek, Kiyoshi Asai, Toshihisa Takagi
2005 J jnl
A Probabilistic Model for Mining Labeled Ordered Trees: Capturing Patterns in Carbohydrate Sugar Chains.
IEEE Trans. Knowl. Data Eng.
Nobuhisa Ueda, Kiyoko F. Aoki-Kinoshita, Atsuko Yamaguchi, Tatsuya Akutsu, Hiroshi Mamitsuka
2004 — conf
Application of a new probabilistic model for recognizing complex patterns in glycans.
ISMB/ECCB (Supplement of Bioinformatics)
Kiyoko F. Aoki, Nobuhisa Ueda, Atsuko Yamaguchi, Minoru Kanehisa, Tatsuya Akutsu, Hiroshi Mamitsuka
2004 J jnl
Finding the maximum common subgraph of a partial
Inf. Process. Lett.
Atsuko Yamaguchi, Kiyoko F. Aoki, Hiroshi Mamitsuka
2004 J jnl
KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains.
Nucleic Acids Res.
Kiyoko F. Aoki, Atsuko Yamaguchi, Nobuhisa Ueda, Tatsuya Akutsu, Hiroshi Mamitsuka, Susumu Goto, Minoru Kanehisa
2004 J jnl
Managing and Analyzing Carbohydrate Data.
SIGMOD Rec.
Kiyoko F. Aoki, Nobuhisa Ueda, Atsuko Yamaguchi, Tatsuya Akutsu, Minoru Kanehisa, Hiroshi Mamitsuka
2003 B conf
Finding the Maximum Common Subgraph of a Partial k-Tree and a Graph with a Polynomially Bounded Number of Spanning Trees.
ISAAC
Atsuko Yamaguchi, Hiroshi Mamitsuka
2003 J jnl
Mining biologically active patterns in metabolic pathways using microarray expression profiles.
SIGKDD Explor.
Hiroshi Mamitsuka, Yasushi Okuno, Atsuko Yamaguchi
1999 Misc conf
An Approximation Algorithm for the Two-Layered Graph Drawing Problem.
COCOON
Atsuko Yamaguchi, Akihiro Sugimoto
1997 J jnl
An Approximation Algorithm for the Minimum Common Supertree Problem.
Nord. J. Comput.
Atsuko Yamaguchi, Koji Nakano, Satoru Miyano