publication . Article . Other literature type . 2013

Negated bio-events: analysis and identification.

Raheel Nawaz; Sophia Ananiadou; Paul Thompson;
Open Access English
  • Published: 16 Jan 2013 Journal: BMC Bioinformatics, volume 14, issue 1, page 14 (issn: 1471-2105, Copyright policy)
  • Publisher: Springer Nature
  • Country: United Kingdom
Abstract
<p>Abstract</p> <p>Background</p> <p>Negation occurs frequently in scientific literature, especially in biomedical literature. It has previously been reported that around 13% of sentences found in biomedical research articles contain negation. Historically, the main motivation for identifying negated events has been to ensure their exclusion from lists of extracted interactions. However, recently, there has been a growing interest in negative results, which has resulted in negation detection being identified as a key challenge in biomedical relation extraction. In this article, we focus on the problem of identifying negated bio-events, given gold standard event ...
Subjects
free text keywords: Biochemistry, Molecular Biology, Computer Science Applications, Research Article, Applied Mathematics, Structural Biology, Information retrieval, Feature engineering, Relationship extraction, Negation, Metaknowledge, Biomedical text mining, Computer science, Scientific literature, lcsh:Computer applications to medicine. Medical informatics, lcsh:R858-859.7, lcsh:Biology (General), lcsh:QH301-705.5
Related Organizations
75 references, page 1 of 5

Ananiadou, S, Kell, DB, Tsujii, J. Text mining and its potential applications in systems biology. Trends Biotechnol. 2006; 24 (12): 571-579 [PubMed]

Hull, D, Pettifer, S, Kell, D. Defrosting the digital library: bibliographic tools for the next generation web. PLoS Comput Biol. 2008; 4 (10): e1000204 [OpenAIRE] [PubMed]

Text Mining for Biology and Biomedicine. 2006

Cohen, KB, Hunter, L, Troyanskaya, O. Getting started in text mining. PLoS Comput Biol. 2008; 4 (1): e20 [OpenAIRE] [PubMed]

Zweigenbaum, P, Demner-Fushman, D, Yu, H, Cohen, KB. Frontiers of biomedical text mining: current progress. Brief Bioinform. 2007; 8 (5): 358-375 [OpenAIRE] [PubMed]

Rzhetsky, A, Iossifov, I, Koike, T, Krauthammer, M, Kra, P, Morris, M, Yu, H, Duboué, PA, Weng, W, Wilbur, WJ. GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data. J Biomed Inform. 2004; 37 (1): 43-53 [PubMed]

Miyao, Y, Ohta, T, Masuda, K, Tsuruoka, Y, Yoshida, K, Ninomiya, T, Tsujii, J. Semantic Retrieval for the Accurate Identification of Relational Concepts in Massive Textbases. ACL '06: Proceedings of the 21st International Conference on Computational Linguistics and the 44th annual meeting of the ACL. 2006: 1017-1024

Ananiadou, S, Thompson, P, Nawaz, R. Improving Search Through Event-based Biomedical Text Mining. First International Workshop on Automated Motif Discovery in Cultural Heritage and Scientific Communication Texts (AMICUS 2010), CLARIN/DARIAH 2010. 2010 [OpenAIRE]

Kim, J-D, Ohta, T, Tsujii, J. Corpus annotation for mining biomedical events from literature. BMC Bioinformatics. 2008; 9 (10) [OpenAIRE]

MEDLINE.

Nawaz, R, Thompson, P, Ananiadou, S. Event Interpretation: A Step towards Event-Centred Text Mining. 2010

Universals of Human Language. 1978

Tottie, G. Negation in English Speech and Writing: A Study in Variation. 1991

Horn, LR. A Natural History of Negation. 2001

Mutalik, PG, Deshpande, A, Nadkarni, PM. Use of general-purpose negation detection to augment concept indexing of medical documents: a quantitative study using the UMLS. J Am Med Inform Assoc. 2001; 8 (6): 598-609 [OpenAIRE] [PubMed]

75 references, page 1 of 5
Abstract
<p>Abstract</p> <p>Background</p> <p>Negation occurs frequently in scientific literature, especially in biomedical literature. It has previously been reported that around 13% of sentences found in biomedical research articles contain negation. Historically, the main motivation for identifying negated events has been to ensure their exclusion from lists of extracted interactions. However, recently, there has been a growing interest in negative results, which has resulted in negation detection being identified as a key challenge in biomedical relation extraction. In this article, we focus on the problem of identifying negated bio-events, given gold standard event ...
Subjects
free text keywords: Biochemistry, Molecular Biology, Computer Science Applications, Research Article, Applied Mathematics, Structural Biology, Information retrieval, Feature engineering, Relationship extraction, Negation, Metaknowledge, Biomedical text mining, Computer science, Scientific literature, lcsh:Computer applications to medicine. Medical informatics, lcsh:R858-859.7, lcsh:Biology (General), lcsh:QH301-705.5
Related Organizations
75 references, page 1 of 5

Ananiadou, S, Kell, DB, Tsujii, J. Text mining and its potential applications in systems biology. Trends Biotechnol. 2006; 24 (12): 571-579 [PubMed]

Hull, D, Pettifer, S, Kell, D. Defrosting the digital library: bibliographic tools for the next generation web. PLoS Comput Biol. 2008; 4 (10): e1000204 [OpenAIRE] [PubMed]

Text Mining for Biology and Biomedicine. 2006

Cohen, KB, Hunter, L, Troyanskaya, O. Getting started in text mining. PLoS Comput Biol. 2008; 4 (1): e20 [OpenAIRE] [PubMed]

Zweigenbaum, P, Demner-Fushman, D, Yu, H, Cohen, KB. Frontiers of biomedical text mining: current progress. Brief Bioinform. 2007; 8 (5): 358-375 [OpenAIRE] [PubMed]

Rzhetsky, A, Iossifov, I, Koike, T, Krauthammer, M, Kra, P, Morris, M, Yu, H, Duboué, PA, Weng, W, Wilbur, WJ. GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data. J Biomed Inform. 2004; 37 (1): 43-53 [PubMed]

Miyao, Y, Ohta, T, Masuda, K, Tsuruoka, Y, Yoshida, K, Ninomiya, T, Tsujii, J. Semantic Retrieval for the Accurate Identification of Relational Concepts in Massive Textbases. ACL '06: Proceedings of the 21st International Conference on Computational Linguistics and the 44th annual meeting of the ACL. 2006: 1017-1024

Ananiadou, S, Thompson, P, Nawaz, R. Improving Search Through Event-based Biomedical Text Mining. First International Workshop on Automated Motif Discovery in Cultural Heritage and Scientific Communication Texts (AMICUS 2010), CLARIN/DARIAH 2010. 2010 [OpenAIRE]

Kim, J-D, Ohta, T, Tsujii, J. Corpus annotation for mining biomedical events from literature. BMC Bioinformatics. 2008; 9 (10) [OpenAIRE]

MEDLINE.

Nawaz, R, Thompson, P, Ananiadou, S. Event Interpretation: A Step towards Event-Centred Text Mining. 2010

Universals of Human Language. 1978

Tottie, G. Negation in English Speech and Writing: A Study in Variation. 1991

Horn, LR. A Natural History of Negation. 2001

Mutalik, PG, Deshpande, A, Nadkarni, PM. Use of general-purpose negation detection to augment concept indexing of medical documents: a quantitative study using the UMLS. J Am Med Inform Assoc. 2001; 8 (6): 598-609 [OpenAIRE] [PubMed]

75 references, page 1 of 5
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