Tomoko Ohta


2016

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Typed Entity and Relation Annotation on Computer Science Papers
Yuka Tateisi | Tomoko Ohta | Sampo Pyysalo | Yusuke Miyao | Akiko Aizawa
Proceedings of the Tenth International Conference on Language Resources and Evaluation (LREC'16)

We describe our ongoing effort to establish an annotation scheme for describing the semantic structures of research articles in the computer science domain, with the intended use of developing search systems that can refine their results by the roles of the entities denoted by the query keys. In our scheme, mentions of entities are annotated with ontology-based types, and the roles of the entities are annotated as relations with other entities described in the text. So far, we have annotated 400 abstracts from the ACL anthology and the ACM digital library. In this paper, the scheme and the annotated dataset are described, along with the problems found in the course of annotation. We also show the results of automatic annotation and evaluate the corpus in a practical setting in application to topic extraction.

2013

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Proceedings of the BioNLP Shared Task 2013 Workshop
Claire Nédellec | Robert Bossy | Jin-Dong Kim | Jung-jae Kim | Tomoko Ohta | Sampo Pyysalo | Pierre Zweigenbaum
Proceedings of the BioNLP Shared Task 2013 Workshop

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Overview of BioNLP Shared Task 2013
Claire Nédellec | Robert Bossy | Jin-Dong Kim | Jung-jae Kim | Tomoko Ohta | Sampo Pyysalo | Pierre Zweigenbaum
Proceedings of the BioNLP Shared Task 2013 Workshop

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Overview of the Cancer Genetics (CG) task of BioNLP Shared Task 2013
Sampo Pyysalo | Tomoko Ohta | Sophia Ananiadou
Proceedings of the BioNLP Shared Task 2013 Workshop

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Overview of the Pathway Curation (PC) task of BioNLP Shared Task 2013
Tomoko Ohta | Sampo Pyysalo | Rafal Rak | Andrew Rowley | Hong-Woo Chun | Sung-Jae Jung | Sung-Pil Choi | Sophia Ananiadou | Jun’ichi Tsujii
Proceedings of the BioNLP Shared Task 2013 Workshop

2012

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brat: a Web-based Tool for NLP-Assisted Text Annotation
Pontus Stenetorp | Sampo Pyysalo | Goran Topić | Tomoko Ohta | Sophia Ananiadou | Jun’ichi Tsujii
Proceedings of the Demonstrations at the 13th Conference of the European Chapter of the Association for Computational Linguistics

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PubMed-Scale Event Extraction for Post-Translational Modifications, Epigenetics and Protein Structural Relations
Jari Björne | Sofie Van Landeghem | Sampo Pyysalo | Tomoko Ohta | Filip Ginter | Yves Van de Peer | Sophia Ananiadou | Tapio Salakoski
BioNLP: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing

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New Resources and Perspectives for Biomedical Event Extraction
Sampo Pyysalo | Pontus Stenetorp | Tomoko Ohta | Jin-Dong Kim | Sophia Ananiadou
BioNLP: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing

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Bridging the Gap Between Scope-based and Event-based Negation/Speculation Annotations: A Bridge Not Too Far
Pontus Stenetorp | Sampo Pyysalo | Tomoko Ohta | Sophia Ananiadou | Jun’ichi Tsujii
Proceedings of the Workshop on Extra-Propositional Aspects of Meaning in Computational Linguistics

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Open-domain Anatomical Entity Mention Detection
Tomoko Ohta | Sampo Pyysalo | Jun’ichi Tsujii | Sophia Ananiadou
Proceedings of the Workshop on Detecting Structure in Scholarly Discourse

2011

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From Pathways to Biomolecular Events: Opportunities and Challenges
Tomoko Ohta | Sampo Pyysalo | Jun’ichi Tsujii
Proceedings of BioNLP 2011 Workshop

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Towards Exhaustive Event Extraction for Protein Modifications
Sampo Pyysalo | Tomoko Ohta | Makoto Miwa | Jun’ichi Tsujii
Proceedings of BioNLP 2011 Workshop

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Overview of BioNLP Shared Task 2011
Jin-Dong Kim | Sampo Pyysalo | Tomoko Ohta | Robert Bossy | Ngan Nguyen | Jun’ichi Tsujii
Proceedings of BioNLP Shared Task 2011 Workshop

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Overview of the Epigenetics and Post-translational Modifications (EPI) task of BioNLP Shared Task 2011
Tomoko Ohta | Sampo Pyysalo | Jun’ichi Tsujii
Proceedings of BioNLP Shared Task 2011 Workshop

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Overview of the Infectious Diseases (ID) task of BioNLP Shared Task 2011
Sampo Pyysalo | Tomoko Ohta | Rafal Rak | Dan Sullivan | Chunhong Mao | Chunxia Wang | Bruno Sobral | Jun’ichi Tsujii | Sophia Ananiadou
Proceedings of BioNLP Shared Task 2011 Workshop

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Overview of the Entity Relations (REL) supporting task of BioNLP Shared Task 2011
Sampo Pyysalo | Tomoko Ohta | Jun’ichi Tsujii
Proceedings of BioNLP Shared Task 2011 Workshop

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BioNLP Shared Task 2011: Supporting Resources
Pontus Stenetorp | Goran Topić | Sampo Pyysalo | Tomoko Ohta | Jin-Dong Kim | Jun’ichi Tsujii
Proceedings of BioNLP Shared Task 2011 Workshop

2010

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Event Extraction for Post-Translational Modifications
Tomoko Ohta | Sampo Pyysalo | Makoto Miwa | Jin-Dong Kim | Jun’ichi Tsujii
Proceedings of the 2010 Workshop on Biomedical Natural Language Processing

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Towards Event Extraction from Full Texts on Infectious Diseases
Sampo Pyysalo | Tomoko Ohta | Han-Cheol Cho | Dan Sullivan | Chunhong Mao | Bruno Sobral | Jun’ichi Tsujii | Sophia Ananiadou
Proceedings of the 2010 Workshop on Biomedical Natural Language Processing

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Integration of Static Relations to Enhance Event Extraction from Text
Sofie Van Landeghem | Sampo Pyysalo | Tomoko Ohta | Yves Van de Peer
Proceedings of the 2010 Workshop on Biomedical Natural Language Processing

2009

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Static Relations: a Piece in the Biomedical Information Extraction Puzzle
Sampo Pyysalo | Tomoko Ohta | Jin-Dong Kim | Jun’ichi Tsujii
Proceedings of the BioNLP 2009 Workshop

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Incorporating GENETAG-style annotation to GENIA corpus
Tomoko Ohta | Jin-Dong Kim | Sampo Pyysalo | Yue Wang | Jun’ichi Tsujii
Proceedings of the BioNLP 2009 Workshop

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Overview of BioNLP’09 Shared Task on Event Extraction
Jin-Dong Kim | Tomoko Ohta | Sampo Pyysalo | Yoshinobu Kano | Jun’ichi Tsujii
Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task

2006

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Semantic Retrieval for the Accurate Identification of Relational Concepts in Massive Textbases
Yusuke Miyao | Tomoko Ohta | Katsuya Masuda | Yoshimasa Tsuruoka | Kazuhiro Yoshida | Takashi Ninomiya | Jun’ichi Tsujii
Proceedings of the 21st International Conference on Computational Linguistics and 44th Annual Meeting of the Association for Computational Linguistics

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An Intelligent Search Engine and GUI-based Efficient MEDLINE Search Tool Based on Deep Syntactic Parsing
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
Proceedings of the COLING/ACL 2006 Interactive Presentation Sessions

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Linguistic and Biological Annotations of Biological Interaction Events
Tomoko Ohta | Yuka Tateisi | Jin-Dong Kim | Akane Yakushiji | Jun-ichi Tsujii
Proceedings of the Fifth International Conference on Language Resources and Evaluation (LREC’06)

This paper discusses an augmentation of a corpus ofresearch abstracts in biomedical domain (the GENIA corpus) with two kinds of annotations: tree annotation and event annotation. The tree annotation identifies the linguistic structure that encodes the relations among entities. The event annotation reveals the semantic structure of the biological interaction events encoded in the text. With these annotations we aim to provide a link between the clue and the target of biological event information extraction.

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Automatic Construction of Predicate-argument Structure Patterns for Biomedical Information Extraction
Akane Yakushiji | Yusuke Miyao | Tomoko Ohta | Yuka Tateisi | Jun’ichi Tsujii
Proceedings of the 2006 Conference on Empirical Methods in Natural Language Processing

2005

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Syntax Annotation for the GENIA Corpus
Yuka Tateisi | Akane Yakushiji | Tomoko Ohta | Jun’ichi Tsujii
Companion Volume to the Proceedings of Conference including Posters/Demos and tutorial abstracts

2003

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Encoding Biomedical Resources in TEI: The Case of the GENIA Corpus
Tomaz Erjavec | Jin-Dong Kim | Tomoko Ohta | Yuka Tateisi | Jun’ichi Tsujii
Proceedings of the ACL 2003 Workshop on Natural Language Processing in Biomedicine

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Stretching TEI: Converting the Genia Corpus
Tomaz Erjavec | Jin-Dong Kim | Tomoko Ohta | Yuka Tateisi | Jun-ichi Tsujii
Proceedings of 4th International Workshop on Linguistically Interpreted Corpora (LINC-03) at EACL 2003

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A Robust Retrieval Engine for Proximal and Structural Search
Katsuya Masuda | Takashi Ninomiya | Yusuke Miyao | Tomoko Ohta | Jun’ichi Tsujii
Companion Volume of the Proceedings of HLT-NAACL 2003 - Short Papers

2000

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Building an Annotated Corpus in the Molecular-Biology Domain
Yuka Tateisi | Tomoko Ohta | Nigel Collier | Chikashi Nobata | Jun-ichi Tsujii
Proceedings of the COLING-2000 Workshop on Semantic Annotation and Intelligent Content

1999

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The GENIA project: corpus-based knowledge acquisition and information extraction from genome research papers
Nigel Collier | Hyun Seok Park | Norihiro Ogata | Yuka Tateishi | Chikashi Nobata | Tomoko Ohta | Tateshi Sekimizu | Hisao Imai | Katsutoshi Ibushi | Jun-ichi Tsujii
Ninth Conference of the European Chapter of the Association for Computational Linguistics