Tomoko Ohta

Publication Activity (10 Years)

Years Active: 1999-2016
Publications (10 Years): 2

Top Topics

Computer Science

Partially Overlapping

Event Extraction

Named Entity Recognition

Top Venues

BioNLP@ACL (Shared Task)

Publications

Suwisa Kaewphan, Sofie Van Landeghem, Tomoko Ohta, Yves Van de Peer, Filip Ginter, Sampo Pyysalo
Cell line name recognition in support of the identification of synthetic lethality in cancer from text. Bioinform. 32 (2) (2016)
Yuka Tateisi, Tomoko Ohta, Sampo Pyysalo, Yusuke Miyao, Akiko Aizawa
Typed Entity and Relation Annotation on Computer Science Papers. LREC (2016)
Sampo Pyysalo, Tomoko Ohta, Rafal Rak, Andrew Rowley, Hong-Woo Chun, Sung-Jae Jung, Sung-Pil Choi, Jun'ichi Tsujii, Sophia Ananiadou
Overview of the Cancer Genetics and Pathway Curation tasks of BioNLP Shared Task 2013. BMC Bioinform. 16 (S10) (2015)
Tomoko Ohta, Sampo Pyysalo, Rafal Rak, Andrew Rowley, Hong-Woo Chun, Sung-Jae Jung, Sung-Pil Choi, Sophia Ananiadou, Jun'ichi Tsujii
Overview of the Pathway Curation (PC) task of BioNLP Shared Task 2013. BioNLP@ACL (Shared Task) (2013)
Claire Nédellec, Robert Bossy, Jin-Dong Kim, Jung-Jae Kim, Tomoko Ohta, Sampo Pyysalo, Pierre Zweigenbaum
Overview of BioNLP Shared Task 2013. BioNLP@ACL (Shared Task) (2013)
Makoto Miwa, Tomoko Ohta, Rafal Rak, Andrew Rowley, Douglas B. Kell, Sampo Pyysalo, Sophia Ananiadou
A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text. Bioinform. 29 (13) (2013)
Makoto Miwa, Sampo Pyysalo, Tomoko Ohta, Sophia Ananiadou
Wide coverage biomedical event extraction using multiple partially overlapping corpora. BMC Bioinform. 14 (2013)
Sampo Pyysalo, Tomoko Ohta, Sophia Ananiadou
Overview of the Cancer Genetics (CG) task of BioNLP Shared Task 2013. BioNLP@ACL (Shared Task) (2013)
Claudiu Mihaila, Tomoko Ohta, Sampo Pyysalo, Sophia Ananiadou
BioCause: Annotating and analysing causality in the biomedical domain. BMC Bioinform. 14 (2013)
Sampo Pyysalo, Pontus Stenetorp, Tomoko Ohta, Jin-Dong Kim, Sophia Ananiadou
New Resources and Perspectives for Biomedical Event Extraction. BioNLP@HLT-NAACL (2012)
Sampo Pyysalo, Tomoko Ohta, Makoto Miwa, Han-Cheol Cho, Junichi Tsujii, Sophia Ananiadou
Event extraction across multiple levels of biological organization. Bioinform. 28 (18) (2012)
Pontus Stenetorp, Sampo Pyysalo, Tomoko Ohta, Sophia Ananiadou, Jun'ichi Tsujii
Bridging the Gap Between Scope-based and Event-based Negation/Speculation Annotations: A Bridge Not Too Far. ExProM@ACL (2012)
Pontus Stenetorp, Sampo Pyysalo, Goran Topic, Tomoko Ohta, Sophia Ananiadou, Jun'ichi Tsujii
brat: a Web-based Tool for NLP-Assisted Text Annotation. EACL (2012)
Jari Björne, Sofie Van Landeghem, Sampo Pyysalo, Tomoko Ohta, Filip Ginter, Yves Van de Peer, Sophia Ananiadou, Tapio Salakoski
PubMed-Scale Event Extraction for Post-Translational Modifications, Epigenetics and Protein Structural Relations. BioNLP@HLT-NAACL (2012)
Sampo Pyysalo, Tomoko Ohta, Rafal Rak, Daniel E. Sullivan, Chunhong Mao, Chunxia Wang, Bruno W. S. Sobral, Jun'ichi Tsujii, Sophia Ananiadou
Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011. BMC Bioinform. 13 (S-11) (2012)
Pontus Stenetorp, Goran Topic, Sampo Pyysalo, Tomoko Ohta, Jin-Dong Kim, Jun'ichi Tsujii
BioNLP Shared Task 2011: Supporting Resources. BioNLP@ACL (Shared Task) (2011)
Jin-Dong Kim, Tomoko Ohta, Sampo Pyysalo, Yoshinobu Kano, Jun'ichi Tsujii
Extracting Bio-molecular Events from literature - the BioNLP'09 Shared Task. Comput. Intell. 27 (4) (2011)
Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Sampo Pyysalo, Tomoko Ohta, Anika Oellrich, Dietrich Rebholz-Schuhmann
Ontology design patterns to disambiguate relations between genes and gene products in GENIA. J. Biomed. Semant. 2 (S-5) (2011)
Sampo Pyysalo, Tomoko Ohta, Makoto Miwa, Jun'ichi Tsujii
Towards Exhaustive Event Extraction for Protein Modifications. BioNLP@ACL (2011)
Tomoko Ohta, Sampo Pyysalo, Makoto Miwa, Jun'ichi Tsujii
Event extraction for DNA methylation. J. Biomed. Semant. 2 (S-5) (2011)
Jin-Dong Kim, Sampo Pyysalo, Tomoko Ohta, Robert Bossy, Ngan L. T. Nguyen, Jun'ichi Tsujii
Overview of BioNLP Shared Task 2011. BioNLP@ACL (Shared Task) (2011)
Tomoko Ohta, Sampo Pyysalo, Jun'ichi Tsujii
Overview of the Epigenetics and Post-translational Modifications (EPI) task of BioNLP Shared Task 2011. BioNLP@ACL (Shared Task) (2011)
Sampo Pyysalo, Tomoko Ohta, Jun'ichi Tsujii
Overview of the Entity Relations (REL) supporting task of BioNLP Shared Task 2011. BioNLP@ACL (Shared Task) (2011)
Tomoko Ohta, Sampo Pyysalo, Jun'ichi Tsujii
From Pathways to Biomolecular Events: Opportunities and Challenges. BioNLP@ACL (2011)
Veronika Vincze, György Szarvas, György Móra, Tomoko Ohta, Richárd Farkas
Linguistic scope-based and biological event-based speculation and negation annotations in the BioScope and Genia Event corpora. J. Biomed. Semant. 2 (S-5) (2011)
Sampo Pyysalo, Tomoko Ohta, Jun'ichi Tsujii
An analysis of gene/protein associations at PubMed scale. J. Biomed. Semant. 2 (S-5) (2011)
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
U-Compare bio-event meta-service: compatible BioNLP event extraction services. BMC Bioinform. 12 (2011)
Sampo Pyysalo, Tomoko Ohta, Rafal Rak, Daniel E. Sullivan, Chunhong Mao, Chunxia Wang, Bruno W. S. Sobral, Jun'ichi Tsujii, Sophia Ananiadou
Overview of the Infectious Diseases (ID) task of BioNLP Shared Task 2011. BioNLP@ACL (Shared Task) (2011)
Tomoko Ohta, Sampo Pyysalo, Makoto Miwa, Jin-Dong Kim, Jun'ichi Tsujii
Event Extraction for Post-Translational Modifications. BioNLP@ACL (2010)
Tomoko Ohta, Sampo Pyysalo, Makoto Miwa, Jun'ichi Tsujii
Event extraction for DNA methylation. Semantic Mining in Biomedicine (2010)
Yue Wang, Jin-Dong Kim, Rune Sætre, Sampo Pyysalo, Tomoko Ohta, Jun'ichi Tsujii
Improving the Inter-Corpora Compatibility for protein Annotations. J. Bioinform. Comput. Biol. 8 (5) (2010)
Tomoko Ohta, Sampo Pyysalo, Jin-Dong Kim, Jun'ichi Tsujii
A Re-Evaluation of Biomedical Named Entity-Term Relations. J. Bioinform. Comput. Biol. 8 (5) (2010)
Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Sampo Pyysalo, Tomoko Ohta, Anika Oellrich, Dietrich Rebholz-Schuhmann
Applying ontology design patterns to the implementation of relations in GENIA. Semantic Mining in Biomedicine (2010)
Sofie Van Landeghem, Sampo Pyysalo, Tomoko Ohta, Yves Van de Peer
Integration of Static Relations to Enhance Event Extraction from Text. BioNLP@ACL (2010)
Sampo Pyysalo, Tomoko Ohta, Han-Cheol Cho, Daniel E. Sullivan, Chunhong Mao, Bruno W. S. Sobral, Jun'ichi Tsujii, Sophia Ananiadou
Towards Event Extraction from Full Texts on Infectious Diseases. BioNLP@ACL (2010)
Veronika Vincze, György Szarvas, György Móra, Tomoko Ohta, Richárd Farkas
Linguistic scope-based and biological event-based speculation and negation annotations in the Genia Event and BioScope corpora. Semantic Mining in Biomedicine (2010)
Sampo Pyysalo, Tomoko Ohta, Jun'ichi Tsujii
An Analysis of gene/protein associations at PubMed scale. Semantic Mining in Biomedicine (2010)
Tomoko Ohta, Takuya Matsuzaki, Naoaki Okazaki, Makoto Miwa, Rune Sætre, Sampo Pyysalo, Jun'ichi Tsujii
Medie and Info-pubmed: 2010 update. BMC Bioinform. 11 (S-5) (2010)
Sampo Pyysalo, Tomoko Ohta, Jin-Dong Kim, Jun'ichi Tsujii
Static Relations: a Piece in the Biomedical Information Extraction Puzzle. BioNLP@HLT-NAACL (2009)
Jin-Dong Kim, Tomoko Ohta, Sampo Pyysalo, Yoshinobu Kano, Jun'ichi Tsujii
Overview of BioNLP'09 Shared Task on Event Extraction. BioNLP@HLT-NAACL (Shared Task) (2009)
Tomoko Ohta, Jin-Dong Kim, Sampo Pyysalo, Yue Wang, Jun'ichi Tsujii
Incorporating GENETAG-style annotation to GENIA corpus. BioNLP@HLT-NAACL (2009)
Jin-Dong Kim, Tomoko Ohta, Jun'ichi Tsujii
Corpus annotation for mining biomedical events from literature. BMC Bioinform. 9 (2008)
Jin-Dong Kim, Tomoko Ohta, Kanae Oda, Jun'ichi Tsujii
From Text to Pathway: Corpus Annotation for Knowledge Acquisition from Biomedical Literature. APBC (2008)
Kanae Oda, Jin-Dong Kim, Tomoko Ohta, Daisuke Okanohara, Takuya Matsuzaki, Yuka Tateisi, Jun'ichi Tsujii
New challenges for text mining: mapping between text and manually curated pathways. BMC Bioinform. 9 (S-3) (2008)
Akane Yakushiji, Yusuke Miyao, Tomoko Ohta, Yuka Tateisi, Jun'ichi Tsujii
Automatic Construction of Predicate-argument Structure Patterns for Biomedical Information Extraction. EMNLP (2006)
Tomoko Ohta, Yuka Tateisi, Jin-Dong Kim, Akane Yakushiji, Jun'ichi Tsujii
Linguistic and Biological Annotations of Biological Interaction Events. LREC (2006)
Yusuke Miyao, Tomoko Ohta, Katsuya Masuda, Yoshimasa Tsuruoka, Kazuhiro Yoshida, Takashi Ninomiya, Jun'ichi Tsujii
Semantic Retrieval for the Accurate Identification of Relational Concepts in Massive Textbases. ACL (2006)
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
An Intelligent Search Engine and GUI-based Efficient MEDLINE Search Tool Based on Deep Syntactic Parsing. ACL (2006)
Yuka Tateisi, Akane Yakushiji, Tomoko Ohta, Jun'ichi Tsujii
Syntax Annotation for the GENIA Corpus. IJCNLP (companion) (2005)
Yoshimasa Tsuruoka, Yuka Tateishi, Jin-Dong Kim, Tomoko Ohta, John McNaught, Sophia Ananiadou, Jun'ichi Tsujii
Developing a Robust Part-of-Speech Tagger for Biomedical Text. Panhellenic Conference on Informatics (2005)
Tomaz Erjavec, Jin-Dong Kim, Tomoko Ohta, Yuka Tateisi, Jun'ichi Tsujii
Encoding Biomedical Resources in TEI: The Case of the GENIA Corpus. BioNLP@ACL (2003)
Katsuya Masuda, Takashi Ninomiya, Yusuke Miyao, Tomoko Ohta, Jun'ichi Tsujii
A Robust Retrieval Engine for Proximal and Structural Search. HLT-NAACL (2003)
Tomaz Erjavec, Jin-Dong Kim, Tomoko Ohta, Yuka Tateisi, Jun'ichi Tsujii
Stretching TEI: Converting the Genia Corpus. LINC@EACL (2003)
Jin-Dong Kim, Tomoko Ohta, Yuka Tateisi, Jun'ichi Tsujii
GENIA corpus - a semantically annotated corpus for bio-textmining. ISMB (Supplement of Bioinformatics) (2003)
Yuka Tateisi, Tomoko Ohta, Nigel Collier, Chikashi Nobata, Jun'ichi Tsujii
Building an Annotated Corpus in the Molecular-Biology Domain. SAIC@COLING (2000)
Nigel Collier, Hyun Seok Park, Norihiro Ogata, Yuka Tateishi, Chikashi Nobata, Tomoko Ohta, Tateshi Sekimizu, Hisao Imai, Katsutoshi Ibushi, Jun'ichi Tsujii
The GENIA project: corpus-based knowledge acquisition and information extraction from genome research papers. EACL (1999)