Atsuko Yamaguchi

Publication Activity (10 Years)

Years Active: 1997-2023
Publications (10 Years): 23

Top Topics

Semantic Interoperability

Sequence Alignment

Linked Open Data

Top Venues

J. Biomed. Semant.

Publications

Jae-Moon Shin, Toyofumi Fujiwara, Atsuko Yamaguchi
Ontology-based expansion of virtual gene panels to improve diagnostic efficiency for rare genetic diseases. SWAT4HCLS (2023)
Atsuko Yamaguchi, Yasunori Yamamoto
A Comparative Study on Storing and Retrieval of URIs for Life Sciences Databases. IJCKG (Workshop/Poster/Demo) (2023)
Atsuko Yamaguchi, Jae-Moon Shin, Toyofumi Fujiwara
Gene Ranking based on Paths from Phenotypes to Genes on Knowledge Graph. IJCKG (2021)
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
BioHackathon 2015: Semantics of data for life sciences and reproducible research. F1000Research 9 (2020)
Tatsuya Kushida, Kouji Kozaki, Yasunori Yamamoto, Atsuko Yamaguchi, Takahiro Kawamura, Takako Nakagawa, Yuka Tateisi, Toshihisa Takagi
Reconstruction of Hierarchical Structures in a Thesaurus-based Ontology through Curation by Domain Experts. ICBO (2019)
Atsuko Yamaguchi, Hideki Hatanaka, Satoshi Fukuchi, Motonori Ota
Semantic Integration of Intrinsically Disordered Proteins and Existing DBs. SWAT4HCLS (2019)
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
BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services. F1000Research 8 (2019)
Atsuko Yamaguchi, Tatsuya Kushida, Yasunori Yamamoto, Kouji Kozaki
Investigating Schema Definitions Using RDFS and OWL 2 for RDF Databases in Life Sciences. JIST (2) (2019)
Norio Kobayashi, Yasunori Yamamoto, Atsuko Yamaguchi
UmakaData Extension: Toward Realization of a Practical SPARQL Endpoint Discovery Service for Life Sciences. SWAT4HCLS (2019)
Yasunori Yamamoto, Atsuko Yamaguchi
Finding RDF Data you need by Umaka Suite. SWAT4HCLS (2019)
Atsuko Yamaguchi, Hiroyuki Toh
Implementing LOD Surfer as a Search System for the Annotation of Multiple Protein Sequence Alignment. JIST (2018)
Yasunori Yamamoto, Atsuko Yamaguchi, Andrea Splendiani
YummyData: providing high-quality open life science data. Database J. Biol. Databases Curation 2018 (2018)
Atsuko Yamaguchi, Kouji Kozaki, Yasunori Yamamoto, Hiroshi Masuya, Norio Kobayashi
LOD Surfer API: Web API for LOD Surfing Using Class-Class Relationships in Life Sciences. SWAT4LS (2017)
Atsuko Yamaguchi, Kouji Kozaki, Yasunori Yamamoto, Hiroshi Masuya, Norio Kobayashi
Semantic Graph Analysis for Federated LOD Surfing in Life Sciences. JIST (2017)
Yasunori Yamamoto, Atsuko Yamaguchi, Andrea Splendiani
Umaka-Yummy Data: A Place to Facilitate Communication between Data Providers and Consumers. SWAT4LS (2016)
Atsuko Yamaguchi, Kouji Kozaki, Kai Lenz, Yasunori Yamamoto, Hiroshi Masuya, Norio Kobayashi
Semantic Data Acquisition by Traversing Class-Class Relationships Over Linked Open Data. JIST (2016)
Yasunori Yamamoto, Atsuko Yamaguchi, Andrea Splendiani
Umaka-Yummy Data: Where Providers and Consumers in Life Sciences Communicate with Each Other. JIST (Workshops & Posters) (2016)
Atsuko Yamaguchi, Kouji Kozaki, Kai Lenz, Yasunori Yamamoto, Hiroshi Masuya, Norio Kobayashi
SPARQL Builder: Constructing SPARQL Query by Traversing Class-Class Relationships for Life Science Databases. JIST (Workshops & Posters) (2016)
Atsuko Yamaguchi, Kouji Kozaki, Kai Lenz, Yasunori Yamamoto, Hiroshi Masuya, Norio Kobayashi
Data Acquisition by Traversing Class-Class Relationships over the Linked Open Data. ISWC (Posters & Demos) (2016)
Atsuko Yamaguchi, Yasunori Yamamoto, Kouji Kozaki, Kai Lenz, Hiroshi Masuya, Norio Kobayashi
SPARQL Query Construction with Monitoring Service for Endpoints. SWAT4LS (2016)
Atsuko Yamaguchi, Katsuhiko Okubo, Norio Kobayashi, Kouji Kozaki, Sadahiro Kumagai, Kai Lenz, Tomoe Nobusada, Hongyan Wu, Yasunori Yamamoto, Hideki Hatanaka
RDF-Based Integration with SPARQL Building System for Life Science Database Archive. SWAT4LS (2015)
Atsuko Yamaguchi, Kouji Kozaki, Kai Lenz, Hongyan Wu, Yasunori Yamamoto, Norio Kobayashi
Efficiently Finding Paths Between Classes to Build a SPARQL Query for Life-Science Databases. JIST (2015)
Hongyan Wu, Atsuko Yamaguchi, Jin-Dong Kim
Dynamic Join Order Optimization for SPARQL Endpoint Federation. SSWS@ISWC (2015)
Norio Kobayashi, Kai Lenz, Hongyan Wu, Kouji Kozaki, Atsuko Yamaguchi
Prototype Implementation of SPARQL Builder for Life-science Databases by Intelligent Schema Analysis on RDF datasets. SWAT4LS (2014)
Hongyan Wu, Toyofumi Fujiwara, Yasunori Yamamoto, Jerven T. Bolleman, Atsuko Yamaguchi
BioBenchmark Toyama 2012: an evaluation of the performance of triple stores on biological data. J. Biomed. Semant. 5 (2014)
Shin Kawano, Tsutomu Watanabe, Sohei Mizuguchi, Norie Araki, Toshiaki Katayama, Atsuko Yamaguchi
TogoTable: cross-database annotation system using the Resource Description Framework (RDF) data model. Nucleic Acids Res. 42 (Webserver-Issue) (2014)
Atsuko Yamaguchi, Kouji Kozaki, Kai Lenz, Hongyan Wu, Norio Kobayashi
An Intelligent SPARQL Query Builder for Exploration of Various Life-science Databases. IESD@ISWC (2014)
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
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. J. Biomed. Semant. 5 (2014)
Yasunori Yamamoto, Atsuko Yamaguchi, Akinori Yonezawa
Building Linked Open Data towards integration of biomedical scientific literature with DBpedia. J. Biomed. Semant. 4 (2013)
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
The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications. J. Biomed. Semant. 2 (2011)
Atsuko Yamaguchi, Yasunori Yamamoto, Jin-Dong Kim, Toshihisa Takagi, Akinori Yonezawa
Discriminative Optimization of String Similarity and Its Application to Biomedical Abbreviation Clustering. ICMLA (2) (2011)
Yasunori Yamamoto, Atsuko Yamaguchi, Hidemasa Bono, Toshihisa Takagi
Allie: a database and a search service of abbreviations and long forms. Database J. Biol. Databases Curation 2011 (2011)
Yasunori Yamamoto, Atsuko Yamaguchi, Akinori Yonezawa
Building linked open data using approximate string matching methods and domain specific resources. SWAT4LS (2011)
Atsuko Yamaguchi, Yasunori Yamamoto, Jin-Dong Kim, Toshihisa Takagi, Akinori Yonezawa
Discriminative Application of String Similarity Methods to Chemical and Non-chemical Names for Biomedical Abbreviation Clustering. BIBM (2011)
Jin-Dong Kim, Yasunori Yamamoto, Atsuko Yamaguchi, Mitsuteru Nakao, Kenta Oouchida, Hong-Woo Chun, Toshihisa Takagi
Natural Language Query Processing for Life Science Knowledge - Position Paper. AMT (2010)
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
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. J. Biomed. Semant. 1 (2010)
Nobuhisa Ueda, Kiyoko F. Aoki-Kinoshita, Atsuko Yamaguchi, Tatsuya Akutsu, Hiroshi Mamitsuka
A Probabilistic Model for Mining Labeled Ordered Trees: Capturing Patterns in Carbohydrate Sugar Chains. IEEE Trans. Knowl. Data Eng. 17 (8) (2005)
Kiyoko F. Aoki, Nobuhisa Ueda, Atsuko Yamaguchi, Minoru Kanehisa, Tatsuya Akutsu, Hiroshi Mamitsuka
Application of a new probabilistic model for recognizing complex patterns in glycans. ISMB/ECCB (Supplement of Bioinformatics) (2004)
Kiyoko F. Aoki, Nobuhisa Ueda, Atsuko Yamaguchi, Tatsuya Akutsu, Minoru Kanehisa, Hiroshi Mamitsuka
Managing and Analyzing Carbohydrate Data. SIGMOD Rec. 33 (2) (2004)
Kiyoko F. Aoki, Atsuko Yamaguchi, Nobuhisa Ueda, Tatsuya Akutsu, Hiroshi Mamitsuka, Susumu Goto, Minoru Kanehisa
KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains. Nucleic Acids Res. 32 (Web-Server-Issue) (2004)
Atsuko Yamaguchi, Kiyoko F. Aoki, Hiroshi Mamitsuka
-tree and a graph with a polynomially bounded number of spanning trees. Inf. Process. Lett. 92 (2) (2004)
Hiroshi Mamitsuka, Yasushi Okuno, Atsuko Yamaguchi
Mining biologically active patterns in metabolic pathways using microarray expression profiles. SIGKDD Explor. 5 (2) (2003)
Atsuko Yamaguchi, Hiroshi Mamitsuka
Finding the Maximum Common Subgraph of a Partial k-Tree and a Graph with a Polynomially Bounded Number of Spanning Trees. ISAAC (2003)
Atsuko Yamaguchi, Akihiro Sugimoto
An Approximation Algorithm for the Two-Layered Graph Drawing Problem. COCOON (1999)
Atsuko Yamaguchi, Koji Nakano, Satoru Miyano
An Approximation Algorithm for the Minimum Common Supertree Problem. Nord. J. Comput. 4 (2) (1997)