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54. The Third ACGG-DB Meeting Report: Towards an international collaborative infrastructure for glycobioinformatics

Author

Aoki-Kinoshita, Kiyoko F, Sawaki, Hiromichi, An, Hyun Joo, Cho, Jin Won, Hsu, Daniel, Kato, Masaki, Kawano, Shin, Kawasaki, Toshisuke, Khoo, Kay-Hooi, Kim, Jaehan, Kim, Jin-Dong, Li, Xianyu, Lütteke, Thomas, Okuda, Shujiro, Packer, Nicolle H, Paulson, James C, Raman, Rahul, Ranzinger, René, Shen, Huali, Shikanai, Toshihide, Yamada, Issaku, Yang, Pengyuan, Yamaguchi, Yoshiki, Ying, Wantao, Yoo, Jong Shin, Zhang, Yang, and Narimatsu, Hisashi

Published
2013
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55. New challenges for text mining: mapping between text and manually curated pathways

Author

Tateisi Yuka, Matsuzaki Takuya, Okanohara Daisuke, Ohta Tomoko, Kim Jin-Dong, Oda Kanae, and Tsujii Jun'ichi

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background Associating literature with pathways poses new challenges to the Text Mining (TM) community. There are three main challenges to this task: (1) the identification of the mapping position of a specific entity or reaction in a given pathway, (2) the recognition of the causal relationships among multiple reactions, and (3) the formulation and implementation of required inferences based on biological domain knowledge. Results To address these challenges, we constructed new resources to link the text with a model pathway; they are: the GENIA pathway corpus with event annotation and NF-kB pathway. Through their detailed analysis, we address the untapped resource, ‘bio-inference,’ as well as the differences between text and pathway representation. Here, we show the precise comparisons of their representations and the nine classes of ‘bio-inference’ schemes observed in the pathway corpus. Conclusions We believe that the creation of such rich resources and their detailed analysis is the significant first step for accelerating the research of the automatic construction of pathway from text.

Published
2008
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65. BioHackathon 2015: Semantics of data for life sciences and reproducible research

Author

Vos, Rutger A., primary, Katayama, Toshiaki, additional, Mishima, Hiroyuki, additional, Kawano, Shin, additional, Kawashima, Shuichi, additional, Kim, Jin-Dong, additional, Moriya, Yuki, additional, Tokimatsu, Toshiaki, additional, Yamaguchi, Atsuko, additional, Yamamoto, Yasunori, additional, Wu, Hongyan, additional, Amstutz, Peter, additional, Antezana, Erick, additional, Aoki, Nobuyuki P., additional, Arakawa, Kazuharu, additional, Bolleman, Jerven T., additional, Bolton, Evan E., additional, Bonnal, Raoul J. P., additional, Bono, Hidemasa, additional, Burger, Kees, additional, Chiba, Hirokazu, additional, Cohen, Kevin B., additional, Deutsch, Eric W., additional, Fernández-Breis, Jesualdo T., additional, Fu, Gang, additional, Fujisawa, Takatomo, additional, Fukushima, Atsushi, additional, García, Alexander, additional, Goto, Naohisa, additional, Groza, Tudor, additional, Hercus, Colin, additional, Hoehndorf, Robert, additional, Itaya, Kotone, additional, Juty, Nick, additional, Kawashima, Takeshi, additional, Kim, Jee-Hyub, additional, Kinjo, Akira R., additional, Kotera, Masaaki, additional, Kozaki, Kouji, additional, Kumagai, Sadahiro, additional, Kushida, Tatsuya, additional, Lütteke, Thomas, additional, Matsubara, Masaaki, additional, Miyamoto, Joe, additional, Mohsen, Attayeb, additional, Mori, Hiroshi, additional, Naito, Yuki, additional, Nakazato, Takeru, additional, Nguyen-Xuan, Jeremy, additional, Nishida, Kozo, additional, Nishida, Naoki, additional, Nishide, Hiroyo, additional, Ogishima, Soichi, additional, Ohta, Tazro, additional, Okuda, Shujiro, additional, Paten, Benedict, additional, Perret, Jean-Luc, additional, Prathipati, Philip, additional, Prins, Pjotr, additional, Queralt-Rosinach, Núria, additional, Shinmachi, Daisuke, additional, Suzuki, Shinya, additional, Tabata, Tsuyosi, additional, Takatsuki, Terue, additional, Taylor, Kieron, additional, Thompson, Mark, additional, Uchiyama, Ikuo, additional, Vieira, Bruno, additional, Wei, Chih-Hsuan, additional, Wilkinson, Mark, additional, Yamada, Issaku, additional, Yamanaka, Ryota, additional, Yoshitake, Kazutoshi, additional, Yoshizawa, Akiyasu C., additional, Dumontier, Michel, additional, Kosaki, Kenjiro, additional, and Takagi, Toshihisa, additional

Published
2020
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71. Improving protein coreference resolution by simple semantic classification

Author

Nguyen Ngan, Kim Jin-Dong, Miwa Makoto, Matsuzaki Takuya, and Tsujii Junichi

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background Current research has shown that major difficulties in event extraction for the biomedical domain are traceable to coreference. Therefore, coreference resolution is believed to be useful for improving event extraction. To address coreference resolution in molecular biology literature, the Protein Coreference (COREF) task was arranged in the BioNLP Shared Task (BioNLP-ST, hereafter) 2011, as a supporting task. However, the shared task results indicated that transferring coreference resolution methods developed for other domains to the biological domain was not a straight-forward task, due to the domain differences in the coreference phenomena. Results We analyzed the contribution of domain-specific information, including the information that indicates the protein type, in a rule-based protein coreference resolution system. In particular, the domain-specific information is encoded into semantic classification modules for which the output is used in different components of the coreference resolution. We compared our system with the top four systems in the BioNLP-ST 2011; surprisingly, we found that the minimal configuration had outperformed the best system in the BioNLP-ST 2011. Analysis of the experimental results revealed that semantic classification, using protein information, has contributed to an increase in performance by 2.3% on the test data, and 4.0% on the development data, in F-score. Conclusions The use of domain-specific information in semantic classification is important for effective coreference resolution. Since it is difficult to transfer domain-specific information across different domains, we need to continue seek for methods to utilize such information in coreference resolution.

Published
2012
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73. BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services

Author

Katayama, Toshiaki, primary, Kawashima, Shuichi, additional, Micklem, Gos, additional, Kawano, Shin, additional, Kim, Jin-Dong, additional, Kocbek, Simon, additional, Okamoto, Shinobu, additional, Wang, Yue, additional, Wu, Hongyan, additional, Yamaguchi, Atsuko, additional, Yamamoto, Yasunori, additional, Antezana, Erick, additional, Aoki-Kinoshita, Kiyoko F., additional, Arakawa, Kazuharu, additional, Banno, Masaki, additional, Baran, Joachim, additional, Bolleman, Jerven T., additional, Bonnal, Raoul J. P., additional, Bono, Hidemasa, additional, Fernández-Breis, Jesualdo T., additional, Buels, Robert, additional, Campbell, Matthew P., additional, Chiba, Hirokazu, additional, Cock, Peter J. A., additional, Cohen, Kevin B., additional, Dumontier, Michel, additional, Fujisawa, Takatomo, additional, Fujiwara, Toyofumi, additional, Garcia, Leyla, additional, Gaudet, Pascale, additional, Hattori, Emi, additional, Hoehndorf, Robert, additional, Itaya, Kotone, additional, Ito, Maori, additional, Jamieson, Daniel, additional, Jupp, Simon, additional, Juty, Nick, additional, Kalderimis, Alex, additional, Kato, Fumihiro, additional, Kawaji, Hideya, additional, Kawashima, Takeshi, additional, Kinjo, Akira R., additional, Komiyama, Yusuke, additional, Kotera, Masaaki, additional, Kushida, Tatsuya, additional, Malone, James, additional, Matsubara, Masaaki, additional, Mizuno, Satoshi, additional, Mizutani, Sayaka, additional, Mori, Hiroshi, additional, Moriya, Yuki, additional, Murakami, Katsuhiko, additional, Nakazato, Takeru, additional, Nishide, Hiroyo, additional, Nishimura, Yosuke, additional, Ogishima, Soichi, additional, Ohta, Tazro, additional, Okuda, Shujiro, additional, Ono, Hiromasa, additional, Perez-Riverol, Yasset, additional, Shinmachi, Daisuke, additional, Splendiani, Andrea, additional, Strozzi, Francesco, additional, Suzuki, Shinya, additional, Takehara, Junichi, additional, Thompson, Mark, additional, Tokimatsu, Toshiaki, additional, Uchiyama, Ikuo, additional, Verspoor, Karin, additional, Wilkinson, Mark D., additional, Wimalaratne, Sarala, additional, Yamada, Issaku, additional, Yamamoto, Nozomi, additional, Yarimizu, Masayuki, additional, Kawamoto, Shoko, additional, and Takagi, Toshihisa, additional

Published
2019
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80. U-Compare bio-event meta-service: compatible BioNLP event extraction services

Author

Kano Yoshinobu, Björne Jari, Ginter Filip, Salakoski Tapio, Buyko Ekaterina, Hahn Udo, Cohen K Bretonnel, Verspoor Karin, Roeder Christophe, Hunter Lawrence E, Kilicoglu Halil, Bergler Sabine, Van Landeghem Sofie, Van Parys Thomas, Van de Peer Yves, Miwa Makoto, Ananiadou Sophia, Neves Mariana, Pascual-Montano Alberto, Özgür Arzucan, Radev Dragomir R, Riedel Sebastian, Sætre Rune, Chun Hong-Woo, Kim Jin-Dong, Pyysalo Sampo, Ohta Tomoko, and Tsujii Jun'ichi

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Published
2011
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81. Investigating heterogeneous protein annotations toward cross-corpora utilization

Author

Pyysalo Sampo, Sætre Rune, Kim Jin-Dong, Wang Yue, and Tsujii Jun'ichi

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background The number of corpora, collections of structured texts, has been increasing, as a result of the growing interest in the application of natural language processing methods to biological texts. Many named entity recognition (NER) systems have been developed based on these corpora. However, in the biomedical community, there is yet no general consensus regarding named entity annotation; thus, the resources are largely incompatible, and it is difficult to compare the performance of systems developed on resources that were divergently annotated. On the other hand, from a practical application perspective, it is desirable to utilize as many existing annotated resources as possible, because annotation is costly. Thus, it becomes a task of interest to integrate the heterogeneous annotations in these resources. Results We explore the potential sources of incompatibility among gene and protein annotations that were made for three common corpora: GENIA, GENETAG and AIMed. To show the inconsistency in the corpora annotations, we first tackle the incompatibility problem caused by corpus integration, and we quantitatively measure the effect of this incompatibility on protein mention recognition. We find that the F-score performance declines tremendously when training with integrated data, instead of training with pure data; in some cases, the performance drops nearly 12%. This degradation may be caused by the newly added heterogeneous annotations, and cannot be fixed without an understanding of the heterogeneities that exist among the corpora. Motivated by the result of this preliminary experiment, we further qualitatively analyze a number of possible sources for these differences, and investigate the factors that would explain the inconsistencies, by performing a series of well-designed experiments. Our analyses indicate that incompatibilities in the gene/protein annotations exist mainly in the following four areas: the boundary annotation conventions, the scope of the entities of interest, the distribution of annotated entities, and the ratio of overlap between annotated entities. We further suggest that almost all of the incompatibilities can be prevented by properly considering the four aspects aforementioned. Conclusion Our analysis covers the key similarities and dissimilarities that exist among the diverse gene/protein corpora. This paper serves to improve our understanding of the differences in the three studied corpora, which can then lead to a better understanding of the performance of protein recognizers that are based on the corpora.

Published
2009
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82. Corpus annotation for mining biomedical events from literature

Author

Tsujii Jun'ichi, Ohta Tomoko, and Kim Jin-Dong

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background Advanced Text Mining (TM) such as semantic enrichment of papers, event or relation extraction, and intelligent Question Answering have increasingly attracted attention in the bio-medical domain. For such attempts to succeed, text annotation from the biological point of view is indispensable. However, due to the complexity of the task, semantic annotation has never been tried on a large scale, apart from relatively simple term annotation. Results We have completed a new type of semantic annotation, event annotation, which is an addition to the existing annotations in the GENIA corpus. The corpus has already been annotated with POS (Parts of Speech), syntactic trees, terms, etc. The new annotation was made on half of the GENIA corpus, consisting of 1,000 Medline abstracts. It contains 9,372 sentences in which 36,114 events are identified. The major challenges during event annotation were (1) to design a scheme of annotation which meets specific requirements of text annotation, (2) to achieve biology-oriented annotation which reflect biologists' interpretation of text, and (3) to ensure the homogeneity of annotation quality across annotators. To meet these challenges, we introduced new concepts such as Single-facet Annotation and Semantic Typing, which have collectively contributed to successful completion of a large scale annotation. Conclusion The resulting event-annotated corpus is the largest and one of the best in quality among similar annotation efforts. We expect it to become a valuable resource for NLP (Natural Language Processing)-based TM in the bio-medical domain.

Published
2008
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83. Proceedings of the SIGIR 2017 workshop on open knowledge base and question answering (OKBQA2017)

Author

Choi, Key Sun, Mitamura, Teruko, Vossen, Piek, Kim, Jin Dong, Ngomo, Axel Cyrille Ngonga, Network Institute, and Language

Subjects
SDG 17 - Partnerships for the Goals
Abstract

Over the past years, several challenges and calls for research projects have pointed out the dire need for pushing natural language interfaces. In this context, the importance of Semantic Web data as a premier knowledge source is rapidly increasing. But we are still far from having accurate natural language interfaces that allow handling complex information needs in a user-centric and highly performant manner. The development of such interfaces requires collaboration of a range of different fields, including natural language processing, information extraction, knowledge base construction and population, reasoning, and question answering. With the goal to join forces in the collaborative development of natural language QA systems, the second OKBQA workshop is organized within the 40th SIGIR conference.

Published
2017

91. Serum cystatin C level: An excellent predictor of mortality in patients with cirrhotic ascites

Author

Seo, Yeon Seok, primary, Park, Soo Young, additional, Kim, Moon Young, additional, Kim, Sang Gyune, additional, Park, Jun Yong, additional, Yim, Hyung Joon, additional, Jang, Byoung Kuk, additional, Park, Seung Ha, additional, Kim, Ji Hoon, additional, Suk, Ki Tae, additional, Kim, Jin Dong, additional, Kim, Tae Yeob, additional, Cho, Eun Young, additional, Lee, Jun Sung, additional, Jung, Soung Won, additional, Jang, Jae Young, additional, An, Hyonggin, additional, Tak, Won Young, additional, Baik, Soon Koo, additional, Hwang, Jae Seok, additional, Kim, Young Seok, additional, Sohn, Joo Hyun, additional, and Um, Soon Ho, additional

Published
2018
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