Tomoko Ohta

60 papers A* 3A 2B 3Journal 21Unranked 30
YearRankTypeTitle / Venue / Authors
2024 J jnl
RegulaTome: a corpus of typed, directed, and signed relations between biomedical entities in the scientific literature.
Database J. Biol. Databases Curation
Katerina C. Nastou, Farrokh Mehryary, Tomoko Ohta, Jouni Luoma, Sampo Pyysalo, Lars Juhl Jensen
2024 J jnl
STRING-ing together protein complexes: corpus and methods for extracting physical protein interactions from the biomedical literature.
Bioinform.
Farrokh Mehryary, Katerina C. Nastou, Tomoko Ohta, Lars Juhl Jensen, Sampo Pyysalo
2023 J jnl
S1000: a better taxonomic name corpus for biomedical information extraction.
Bioinform.
Jouni Luoma, Katerina C. Nastou, Tomoko Ohta, Harttu Toivonen, Evangelos Pafilis, Lars Juhl Jensen, Sampo Pyysalo
2016 J jnl
Cell line name recognition in support of the identification of synthetic lethality in cancer from text.
Bioinform.
Suwisa Kaewphan, Sofie Van Landeghem, Tomoko Ohta, Yves Van de Peer, Filip Ginter, Sampo Pyysalo
2016 B conf
Typed Entity and Relation Annotation on Computer Science Papers.
LREC
Yuka Tateisi, Tomoko Ohta, Sampo Pyysalo, Yusuke Miyao, Akiko Aizawa
2015 J jnl
Overview of the Cancer Genetics and Pathway Curation tasks of BioNLP Shared Task 2013.
BMC Bioinform.
Sampo Pyysalo, Tomoko Ohta, Rafal Rak, Andrew Rowley, Hong-Woo Chun, Sung-Jae Jung, Sung-Pil Choi, Jun'ichi Tsujii, Sophia Ananiadou
2013 J jnl
A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text.
Bioinform.
Makoto Miwa, Tomoko Ohta, Rafal Rak, Andrew Rowley, Douglas B. Kell, Sampo Pyysalo, Sophia Ananiadou
2013 J jnl
BioCause: Annotating and analysing causality in the biomedical domain.
BMC Bioinform.
Claudiu Mihaila, Tomoko Ohta, Sampo Pyysalo, Sophia Ananiadou
2013 — conf
Overview of BioNLP Shared Task 2013.
BioNLP@ACL (Shared Task)
Claire Nédellec, Robert Bossy, Jin-Dong Kim, Jung-Jae Kim, Tomoko Ohta, Sampo Pyysalo, Pierre Zweigenbaum
2013 — conf
Overview of the Cancer Genetics (CG) task of BioNLP Shared Task 2013.
BioNLP@ACL (Shared Task)
Sampo Pyysalo, Tomoko Ohta, Sophia Ananiadou
2013 — conf
Overview of the Pathway Curation (PC) task of BioNLP Shared Task 2013.
BioNLP@ACL (Shared Task)
Tomoko Ohta, Sampo Pyysalo, Rafal Rak, Andrew Rowley, Hong-Woo Chun, Sung-Jae Jung, Sung-Pil Choi, Sophia Ananiadou, Jun'ichi Tsujii
2013 — ed.
Proceedings of the BioNLP Shared Task 2013 Workshop, Sofia, Bulgaria, August 9, 2013
BioNLP@ACL (Shared Task)
Claire Nédellec, Robert Bossy, Jin-Dong Kim, Jung-Jae Kim, Tomoko Ohta, Sampo Pyysalo, Pierre Zweigenbaum
2013 J jnl
Wide coverage biomedical event extraction using multiple partially overlapping corpora.
BMC Bioinform.
Makoto Miwa, Sampo Pyysalo, Tomoko Ohta, Sophia Ananiadou
2012 — conf
Bridging the Gap Between Scope-based and Event-based Negation/Speculation Annotations: A Bridge Not Too Far.
ExProM@ACL
Pontus Stenetorp, Sampo Pyysalo, Tomoko Ohta, Sophia Ananiadou, Jun'ichi Tsujii
2012 J jnl
Event extraction across multiple levels of biological organization.
Bioinform.
Sampo Pyysalo, Tomoko Ohta, Makoto Miwa, Han-Cheol Cho, Junichi Tsujii, Sophia Ananiadou
2012 — conf
New Resources and Perspectives for Biomedical Event Extraction.
BioNLP@HLT-NAACL
Sampo Pyysalo, Pontus Stenetorp, Tomoko Ohta, Jin-Dong Kim, Sophia Ananiadou
2012 J jnl
Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011.
BMC Bioinform.
Sampo Pyysalo, Tomoko Ohta, Rafal Rak, Daniel E. Sullivan, Chunhong Mao, Chunxia Wang, Bruno W. S. Sobral, Jun'ichi Tsujii, Sophia Ananiadou
2012 — conf
PubMed-Scale Event Extraction for Post-Translational Modifications, Epigenetics and Protein Structural Relations.
BioNLP@HLT-NAACL
Jari Björne, Sofie Van Landeghem, Sampo Pyysalo, Tomoko Ohta, Filip Ginter, Yves Van de Peer, Sophia Ananiadou, Tapio Salakoski
2012 A conf
brat: a Web-based Tool for NLP-Assisted Text Annotation.
EACL
Pontus Stenetorp, Sampo Pyysalo, Goran Topic, Tomoko Ohta, Sophia Ananiadou, Jun'ichi Tsujii
2011 J jnl
An analysis of gene/protein associations at PubMed scale.
J. Biomed. Semant.
Sampo Pyysalo, Tomoko Ohta, Jun'ichi Tsujii
2011 — conf
BioNLP Shared Task 2011: Supporting Resources.
BioNLP@ACL (Shared Task)
Pontus Stenetorp, Goran Topic, Sampo Pyysalo, Tomoko Ohta, Jin-Dong Kim, Jun'ichi Tsujii
2011 J jnl
Event extraction for DNA methylation.
J. Biomed. Semant.
Tomoko Ohta, Sampo Pyysalo, Makoto Miwa, Jun'ichi Tsujii
2011 J jnl
Extracting Bio-molecular Events from literature - the BioNLP'09 Shared Task.
Comput. Intell.
Jin-Dong Kim, Tomoko Ohta, Sampo Pyysalo, Yoshinobu Kano, Jun'ichi Tsujii
2011 — conf
From Pathways to Biomolecular Events: Opportunities and Challenges.
BioNLP@ACL
Tomoko Ohta, Sampo Pyysalo, Jun'ichi Tsujii
2011 J jnl
Linguistic scope-based and biological event-based speculation and negation annotations in the BioScope and Genia Event corpora.
J. Biomed. Semant.
Veronika Vincze, György Szarvas, György Móra, Tomoko Ohta, Richárd Farkas
2011 J jnl
Ontology design patterns to disambiguate relations between genes and gene products in GENIA.
J. Biomed. Semant.
Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Sampo Pyysalo, Tomoko Ohta, Anika Oellrich, Dietrich Rebholz-Schuhmann
2011 — conf
Overview of BioNLP Shared Task 2011.
BioNLP@ACL (Shared Task)
Jin-Dong Kim, Sampo Pyysalo, Tomoko Ohta, Robert Bossy, Ngan L. T. Nguyen, Jun'ichi Tsujii
2011 — conf
Overview of the Entity Relations (REL) supporting task of BioNLP Shared Task 2011.
BioNLP@ACL (Shared Task)
Sampo Pyysalo, Tomoko Ohta, Jun'ichi Tsujii
2011 — conf
Overview of the Epigenetics and Post-translational Modifications (EPI) task of BioNLP Shared Task 2011.
BioNLP@ACL (Shared Task)
Tomoko Ohta, Sampo Pyysalo, Jun'ichi Tsujii
2011 — conf
Overview of the Infectious Diseases (ID) task of BioNLP Shared Task 2011.
BioNLP@ACL (Shared Task)
Sampo Pyysalo, Tomoko Ohta, Rafal Rak, Daniel E. Sullivan, Chunhong Mao, Chunxia Wang, Bruno W. S. Sobral, Jun'ichi Tsujii, Sophia Ananiadou
2011 — conf
Towards Exhaustive Event Extraction for Protein Modifications.
BioNLP@ACL
Sampo Pyysalo, Tomoko Ohta, Makoto Miwa, Jun'ichi Tsujii
2011 J jnl
U-Compare bio-event meta-service: compatible BioNLP event extraction services.
BMC Bioinform.
Yoshinobu Kano, Jari Björne, Filip Ginter, Tapio Salakoski, Ekaterina Buyko, Udo Hahn, K. Bretonnel Cohen, Karin Verspoor, Christophe Roeder, Lawrence E. Hunter, Halil Kilicoglu, Sabine Bergler, Sofie Van Landeghem, Thomas Van Parys, Yves Van de Peer, Makoto Miwa, Sophia Ananiadou, Mariana L. Neves, Alberto D. Pascual-Montano, Arzucan Özgür, Dragomir R. Radev, Sebastian Riedel, Rune Sætre, Hong-Woo Chun, Jin-Dong Kim, Sampo Pyysalo, Tomoko Ohta, Jun'ichi Tsujii
2010 J jnl
A Re-Evaluation of Biomedical Named Entity-Term Relations.
J. Bioinform. Comput. Biol.
Tomoko Ohta, Sampo Pyysalo, Jin-Dong Kim, Jun'ichi Tsujii
2010 — conf
An Analysis of gene/protein associations at PubMed scale.
Semantic Mining in Biomedicine
Sampo Pyysalo, Tomoko Ohta, Jun'ichi Tsujii
2010 — conf
Applying ontology design patterns to the implementation of relations in GENIA.
Semantic Mining in Biomedicine
Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Sampo Pyysalo, Tomoko Ohta, Anika Oellrich, Dietrich Rebholz-Schuhmann
2010 — conf
Event Extraction for Post-Translational Modifications.
BioNLP@ACL
Tomoko Ohta, Sampo Pyysalo, Makoto Miwa, Jin-Dong Kim, Jun'ichi Tsujii
2010 — conf
Event extraction for DNA methylation.
Semantic Mining in Biomedicine
Tomoko Ohta, Sampo Pyysalo, Makoto Miwa, Jun'ichi Tsujii
2010 J jnl
Improving the Inter-Corpora Compatibility for protein Annotations.
J. Bioinform. Comput. Biol.
Yue Wang, Jin-Dong Kim, Rune Sætre, Sampo Pyysalo, Tomoko Ohta, Jun'ichi Tsujii
2010 — conf
Integration of Static Relations to Enhance Event Extraction from Text.
BioNLP@ACL
Sofie Van Landeghem, Sampo Pyysalo, Tomoko Ohta, Yves Van de Peer
2010 — conf
Linguistic scope-based and biological event-based speculation and negation annotations in the Genia Event and BioScope corpora.
Semantic Mining in Biomedicine
Veronika Vincze, György Szarvas, György Móra, Tomoko Ohta, Richárd Farkas
2010 J jnl
Medie and Info-pubmed: 2010 update.
BMC Bioinform.
Tomoko Ohta, Takuya Matsuzaki, Naoaki Okazaki, Makoto Miwa, Rune Sætre, Sampo Pyysalo, Jun'ichi Tsujii
2010 — conf
Towards Event Extraction from Full Texts on Infectious Diseases.
BioNLP@ACL
Sampo Pyysalo, Tomoko Ohta, Han-Cheol Cho, Daniel E. Sullivan, Chunhong Mao, Bruno W. S. Sobral, Jun'ichi Tsujii, Sophia Ananiadou
2009 — conf
Incorporating GENETAG-style annotation to GENIA corpus.
BioNLP@HLT-NAACL
Tomoko Ohta, Jin-Dong Kim, Sampo Pyysalo, Yue Wang, Jun'ichi Tsujii
2009 — conf
Overview of BioNLP'09 Shared Task on Event Extraction.
BioNLP@HLT-NAACL (Shared Task)
Jin-Dong Kim, Tomoko Ohta, Sampo Pyysalo, Yoshinobu Kano, Jun'ichi Tsujii
2009 — conf
Static Relations: a Piece in the Biomedical Information Extraction Puzzle.
BioNLP@HLT-NAACL
Sampo Pyysalo, Tomoko Ohta, Jin-Dong Kim, Jun'ichi Tsujii
2008 J jnl
Corpus annotation for mining biomedical events from literature.
BMC Bioinform.
Jin-Dong Kim, Tomoko Ohta, Jun'ichi Tsujii
2008 B conf
From Text to Pathway: Corpus Annotation for Knowledge Acquisition from Biomedical Literature.
APBC
Jin-Dong Kim, Tomoko Ohta, Kanae Oda, Jun'ichi Tsujii
2008 J jnl
New challenges for text mining: mapping between text and manually curated pathways.
BMC Bioinform.
Kanae Oda, Jin-Dong Kim, Tomoko Ohta, Daisuke Okanohara, Takuya Matsuzaki, Yuka Tateisi, Jun'ichi Tsujii
2006 A* conf
An Intelligent Search Engine and GUI-based Efficient MEDLINE Search Tool Based on Deep Syntactic Parsing.
ACL
Tomoko Ohta, Yusuke Miyao, Takashi Ninomiya, Yoshimasa Tsuruoka, Akane Yakushiji, Katsuya Masuda, Jumpei Takeuchi, Kazuhiro Yoshida, Tadayoshi Hara, Jin-Dong Kim, Yuka Tateisi, Jun'ichi Tsujii
2006 A* conf
Automatic Construction of Predicate-argument Structure Patterns for Biomedical Information Extraction.
EMNLP
Akane Yakushiji, Yusuke Miyao, Tomoko Ohta, Yuka Tateisi, Jun'ichi Tsujii
2006 B conf
Linguistic and Biological Annotations of Biological Interaction Events.
LREC
Tomoko Ohta, Yuka Tateisi, Jin-Dong Kim, Akane Yakushiji, Jun'ichi Tsujii
2006 A* conf
Semantic Retrieval for the Accurate Identification of Relational Concepts in Massive Textbases.
ACL
Yusuke Miyao, Tomoko Ohta, Katsuya Masuda, Yoshimasa Tsuruoka, Kazuhiro Yoshida, Takashi Ninomiya, Jun'ichi Tsujii
2005 — conf
Developing a Robust Part-of-Speech Tagger for Biomedical Text.
Panhellenic Conference on Informatics
Yoshimasa Tsuruoka, Yuka Tateishi, Jin-Dong Kim, Tomoko Ohta, John McNaught, Sophia Ananiadou, Jun'ichi Tsujii
2005 — conf
Syntax Annotation for the GENIA Corpus.
IJCNLP (companion)
Yuka Tateisi, Akane Yakushiji, Tomoko Ohta, Jun'ichi Tsujii
2003 — conf
A Robust Retrieval Engine for Proximal and Structural Search.
HLT-NAACL
Katsuya Masuda, Takashi Ninomiya, Yusuke Miyao, Tomoko Ohta, Jun'ichi Tsujii
2003 — conf
Encoding Biomedical Resources in TEI: The Case of the GENIA Corpus.
BioNLP@ACL
Tomaz Erjavec, Jin-Dong Kim, Tomoko Ohta, Yuka Tateisi, Jun'ichi Tsujii
2003 — conf
GENIA corpus - a semantically annotated corpus for bio-textmining.
ISMB (Supplement of Bioinformatics)
Jin-Dong Kim, Tomoko Ohta, Yuka Tateisi, Jun'ichi Tsujii
2003 — conf
Stretching TEI: Converting the Genia Corpus.
LINC@EACL
Tomaz Erjavec, Jin-Dong Kim, Tomoko Ohta, Yuka Tateisi, Jun'ichi Tsujii
2000 — conf
Building an Annotated Corpus in the Molecular-Biology Domain.
SAIC@COLING
Yuka Tateisi, Tomoko Ohta, Nigel Collier, Chikashi Nobata, Jun'ichi Tsujii
1999 A conf
The GENIA project: corpus-based knowledge acquisition and information extraction from genome research papers.
EACL
Nigel Collier, Hyun Seok Park, Norihiro Ogata, Yuka Tateishi, Chikashi Nobata, Tomoko Ohta, Tateshi Sekimizu, Hisao Imai, Katsutoshi Ibushi, Jun'ichi Tsujii