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 (EACL, 1999)

Building an Annotated Corpus in the Molecular-Biology Domain. - Yuka Tateisi; Tomoko Ohta; Nigel Collier; Chikashi Nobata; Jun'ichi Tsujii (SAIC@COLING, 2000)

Stretching TEI: Converting the Genia Corpus. - Tomaz Erjavec; Jin-Dong Kim; Tomoko Ohta; Yuka Tateisi; Jun'ichi Tsujii (LINC@EACL, 2003)

Encoding Biomedical Resources in TEI: The Case of the GENIA Corpus. - Tomaz Erjavec; Jin-Dong Kim; Tomoko Ohta; Yuka Tateisi; Jun'ichi Tsujii (BioNLP@ACL, 2003)

GENIA corpus - a semantically annotated corpus for bio-textmining. - Jin-Dong Kim; Tomoko Ohta; Yuka Tateisi; Jun'ichi Tsujii (ISMB (Supplement of Bioinformatics), 2003)

A Robust Retrieval Engine for Proximal and Structural Search. - Katsuya Masuda; Takashi Ninomiya; Yusuke Miyao; Tomoko Ohta; Jun'ichi Tsujii (HLT-NAACL, 2003)

Syntax Annotation for the GENIA Corpus. - Yuka Tateisi; Akane Yakushiji; Tomoko Ohta; Jun'ichi Tsujii (IJCNLP (companion), 2005)

Developing a Robust Part-of-Speech Tagger for Biomedical Text. - Yoshimasa Tsuruoka; Yuka Tateishi; Jin-Dong Kim; Tomoko Ohta; John McNaught; Sophia Ananiadou; Jun'ichi Tsujii (Panhellenic Conference on Informatics, 2005)

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 (ACL, 2006)

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 (ACL, 2006)

Automatic Construction of Predicate-argument Structure Patterns for Biomedical Information Extraction. - Akane Yakushiji; Yusuke Miyao; Tomoko Ohta; Yuka Tateisi; Jun'ichi Tsujii (EMNLP, 2006)

Linguistic and Biological Annotations of Biological Interaction Events. - Tomoko Ohta; Yuka Tateisi; Jin-Dong Kim; Akane Yakushiji; Jun'ichi Tsujii (LREC, 2006)

From Text to Pathway: Corpus Annotation for Knowledge Acquisition from Biomedical Literature. - Jin-Dong Kim; Tomoko Ohta; Kanae Oda; Jun'ichi Tsujii (APBC, 2008)

Corpus annotation for mining biomedical events from literature. - Jin-Dong Kim; Tomoko Ohta; Jun'ichi Tsujii (BMC Bioinform., 2008)

New challenges for text mining: mapping between text and manually curated pathways. - Kanae Oda; Jin-Dong Kim; Tomoko Ohta; Daisuke Okanohara; Takuya Matsuzaki; Yuka Tateisi; Jun'ichi Tsujii (BMC Bioinform., 2008)

Overview of BioNLP'09 Shared Task on Event Extraction. - Jin-Dong Kim; Tomoko Ohta; Sampo Pyysalo; Yoshinobu Kano; Jun'ichi Tsujii (BioNLP@HLT-NAACL (Shared Task), 2009)

Incorporating GENETAG-style annotation to GENIA corpus. - Tomoko Ohta; Jin-Dong Kim; Sampo Pyysalo; Yue Wang 040; Jun'ichi Tsujii (BioNLP@HLT-NAACL, 2009)

Static Relations: a Piece in the Biomedical Information Extraction Puzzle. - Sampo Pyysalo; Tomoko Ohta; Jin-Dong Kim; Jun'ichi Tsujii (BioNLP@HLT-NAACL, 2009)

Integration of Static Relations to Enhance Event Extraction from Text. - Sofie Van Landeghem; Sampo Pyysalo; Tomoko Ohta; Yves Van de Peer (BioNLP@ACL, 2010)

Event Extraction for Post-Translational Modifications. - Tomoko Ohta; Sampo Pyysalo; Makoto Miwa; Jin-Dong Kim; Jun'ichi Tsujii (BioNLP@ACL, 2010)

Towards Event Extraction from Full Texts on Infectious Diseases. - Sampo Pyysalo; Tomoko Ohta; Han-Cheol Cho; Daniel E. Sullivan; Chunhong Mao; Bruno W. S. Sobral; Jun'ichi Tsujii; Sophia Ananiadou (BioNLP@ACL, 2010)

Applying ontology design patterns to the implementation of relations in GENIA. - Robert Hoehndorf; Axel-Cyrille Ngonga Ngomo; Sampo Pyysalo; Tomoko Ohta; Anika Oellrich; Dietrich Rebholz-Schuhmann (Semantic Mining in Biomedicine, 2010)

Linguistic scope-based and biological event-based speculation and negation annotations in the Genia Event and BioScope corpora. - Veronika Vincze; György Szarvas; György Móra; Tomoko Ohta; Richárd Farkas (Semantic Mining in Biomedicine, 2010)

Medie and Info-pubmed: 2010 update. - Tomoko Ohta; Takuya Matsuzaki; Naoaki Okazaki; Makoto Miwa; Rune Sætre; Sampo Pyysalo; Jun'ichi Tsujii (BMC Bioinform., 2010)

A Re-Evaluation of Biomedical Named Entity-Term Relations. - Tomoko Ohta; Sampo Pyysalo; Jin-Dong Kim; Jun'ichi Tsujii (J. Bioinform. Comput. Biol., 2010)

Improving the Inter-Corpora Compatibility for protein Annotations. - Yue Wang 040; Jin-Dong Kim; Rune Sætre; Sampo Pyysalo; Tomoko Ohta; Jun'ichi Tsujii (J. Bioinform. Comput. Biol., 2010)

Overview of BioNLP Shared Task 2011. - Jin-Dong Kim; Sampo Pyysalo; Tomoko Ohta; Robert Bossy; Ngan L. T. Nguyen; Jun'ichi Tsujii (BioNLP@ACL (Shared Task), 2011)

From Pathways to Biomolecular Events: Opportunities and Challenges. - Tomoko Ohta; Sampo Pyysalo; Jun'ichi Tsujii (BioNLP@ACL, 2011)

Overview of the Epigenetics and Post-translational Modifications (EPI) task of BioNLP Shared Task 2011. - Tomoko Ohta; Sampo Pyysalo; Jun'ichi Tsujii (BioNLP@ACL (Shared Task), 2011)

Towards Exhaustive Event Extraction for Protein Modifications. - Sampo Pyysalo; Tomoko Ohta; Makoto Miwa; Jun'ichi Tsujii (BioNLP@ACL, 2011)

Overview of the Infectious Diseases (ID) task of BioNLP Shared Task 2011. - Sampo Pyysalo; Tomoko Ohta; Rafal Rak; Daniel E. Sullivan; Chunhong Mao; Chunxia Wang; Bruno W. S. Sobral; Jun'ichi Tsujii; Sophia Ananiadou (BioNLP@ACL (Shared Task), 2011)

Overview of the Entity Relations (REL) supporting task of BioNLP Shared Task 2011. - Sampo Pyysalo; Tomoko Ohta; Jun'ichi Tsujii (BioNLP@ACL (Shared Task), 2011)

BioNLP Shared Task 2011: Supporting Resources. - Pontus Stenetorp; Goran Topic; Sampo Pyysalo; Tomoko Ohta; Jin-Dong Kim; Jun'ichi Tsujii (BioNLP@ACL (Shared Task), 2011)

Ontology design patterns to disambiguate relations between genes and gene products in GENIA. - Robert Hoehndorf; Axel-Cyrille Ngonga Ngomo; Sampo Pyysalo; Tomoko Ohta; Anika Oellrich; Dietrich Rebholz-Schuhmann (J. Biomed. Semant., 2011)

Event extraction for DNA methylation. - Tomoko Ohta; Sampo Pyysalo; Makoto Miwa; Jun'ichi Tsujii (J. Biomed. Semant., 2011)

An analysis of gene/protein associations at PubMed scale. - Sampo Pyysalo; Tomoko Ohta; Jun'ichi Tsujii (J. Biomed. Semant., 2011)

Linguistic scope-based and biological event-based speculation and negation annotations in the BioScope and Genia Event corpora. - Veronika Vincze; György Szarvas; György Móra; Tomoko Ohta; Richárd Farkas (J. Biomed. Semant., 2011)

U-Compare bio-event meta-service: compatible BioNLP event extraction services. - 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; et al. (BMC Bioinform., 2011)

Extracting Bio-molecular Events from literature - the BioNLP'09 Shared Task. - Jin-Dong Kim; Tomoko Ohta; Sampo Pyysalo; Yoshinobu Kano; Jun'ichi Tsujii (Comput. Intell., 2011)

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 (ExProM@ACL, 2012)

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@HLT-NAACL, 2012)

New Resources and Perspectives for Biomedical Event Extraction. - Sampo Pyysalo; Pontus Stenetorp; Tomoko Ohta; Jin-Dong Kim; Sophia Ananiadou (BioNLP@HLT-NAACL, 2012)

brat: a Web-based Tool for NLP-Assisted Text Annotation. - Pontus Stenetorp; Sampo Pyysalo; Goran Topic; Tomoko Ohta; Sophia Ananiadou; Jun'ichi Tsujii (EACL, 2012)

Event extraction across multiple levels of biological organization. - Sampo Pyysalo; Tomoko Ohta; Makoto Miwa; Han-Cheol Cho; Junichi Tsujii; Sophia Ananiadou (Bioinform., 2012)

Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011. - Sampo Pyysalo; Tomoko Ohta; Rafal Rak; Daniel E. Sullivan; Chunhong Mao; Chunxia Wang; Bruno W. S. Sobral; Jun'ichi Tsujii; Sophia Ananiadou (BMC Bioinform., 2012)

Overview of BioNLP Shared Task 2013. - Claire Nédellec; Robert Bossy; Jin-Dong Kim; Jung-Jae Kim 001; Tomoko Ohta; Sampo Pyysalo; Pierre Zweigenbaum (BioNLP@ACL (Shared Task), 2013)

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 (BioNLP@ACL (Shared Task), 2013)

Overview of the Cancer Genetics (CG) task of BioNLP Shared Task 2013. - Sampo Pyysalo; Tomoko Ohta; Sophia Ananiadou (BioNLP@ACL (Shared Task), 2013)

A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text. - Makoto Miwa; Tomoko Ohta; Rafal Rak; Andrew Rowley; Douglas B. Kell; Sampo Pyysalo; Sophia Ananiadou (Bioinform., 2013)

BioCause: Annotating and analysing causality in the biomedical domain. - Claudiu Mihaila; Tomoko Ohta; Sampo Pyysalo; Sophia Ananiadou (BMC Bioinform., 2013)

Wide coverage biomedical event extraction using multiple partially overlapping corpora. - Makoto Miwa; Sampo Pyysalo; Tomoko Ohta; Sophia Ananiadou (BMC Bioinform., 2013)

Overview of the Cancer Genetics and Pathway Curation tasks of BioNLP Shared Task 2013. - Sampo Pyysalo; Tomoko Ohta; Rafal Rak; Andrew Rowley; Hong-Woo Chun; Sung-Jae Jung; Sung-Pil Choi; Jun'ichi Tsujii; Sophia Ananiadou (BMC Bioinform., 2015)

Typed Entity and Relation Annotation on Computer Science Papers. - Yuka Tateisi; Tomoko Ohta; Sampo Pyysalo; Yusuke Miyao; Akiko Aizawa (LREC, 2016)

Cell line name recognition in support of the identification of synthetic lethality in cancer from text. - Suwisa Kaewphan; Sofie Van Landeghem; Tomoko Ohta; Yves Van de Peer; Filip Ginter; Sampo Pyysalo (Bioinform., 2016)

RegulaTome: a corpus of typed, directed, and signed relations between biomedical entities in the scientific literature. - Katerina C. Nastou; Farrokh Mehryary; Tomoko Ohta; Jouni Luoma; Sampo Pyysalo; Lars Juhl Jensen (Database J. Biol. Databases Curation, 2024)