Semantic classification and dependency parsing enabled automated bio-molecular event extraction from text

Syed Toufeeq Ahmed; Radhika Nair; Chintan Patel; Sheela P. Kanwar; Jörg Hakenberg; Hasan Davulcu

doi:10.1145/1854776.1854832

Semantic classification and dependency parsing enabled automated bio-molecular event extraction from text

Syed Toufeeq Ahmed, Radhika Nair, Chintan Patel, Sheela P. Kanwar, Jörg Hakenberg, Hasan Davulcu

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

1 Scopus citations

Abstract

The last two decades of invigorating research in the area of human genome sequencing marked the beginning of large-scale data collection. Much of the valuable knowledge gained is found in published articles, and thus in un-structured textual form. To aid in searching and extracting knowledge from textual sources, we present BioEve, a fully automated system to extract bio-molecular events from Medline abstracts. BioEve first semantically classifies each sentence to the class type of the event mentioned in the sentence, and then using high coverage, class-specific, hand-crafted rules, it extracts the participants of that event.

Original language	English (US)
Title of host publication	2010 ACM International Conference on Bioinformatics and Computational Biology, ACM-BCB 2010
Pages	370-373
Number of pages	4
DOIs	https://doi.org/10.1145/1854776.1854832
State	Published - 2010
Event	2010 ACM International Conference on Bioinformatics and Computational Biology, ACM-BCB 2010 - Niagara Falls, NY, United States Duration: Aug 2 2010 → Aug 4 2010

Publication series

Name	2010 ACM International Conference on Bioinformatics and Computational Biology, ACM-BCB 2010

Other

Other	2010 ACM International Conference on Bioinformatics and Computational Biology, ACM-BCB 2010
Country/Territory	United States
City	Niagara Falls, NY
Period	8/2/10 → 8/4/10

Keywords

Bio-molecular event extraction
Dependency parsing
Information extraction
Semantic classification

ASJC Scopus subject areas

Biomedical Engineering
Health Information Management

Access to Document

10.1145/1854776.1854832

Cite this

Ahmed, S. T., Nair, R., Patel, C., Kanwar, S. P., Hakenberg, J., & Davulcu, H. (2010). Semantic classification and dependency parsing enabled automated bio-molecular event extraction from text. In 2010 ACM International Conference on Bioinformatics and Computational Biology, ACM-BCB 2010 (pp. 370-373). (2010 ACM International Conference on Bioinformatics and Computational Biology, ACM-BCB 2010). https://doi.org/10.1145/1854776.1854832

Semantic classification and dependency parsing enabled automated bio-molecular event extraction from text. / Ahmed, Syed Toufeeq; Nair, Radhika; Patel, Chintan et al.
2010 ACM International Conference on Bioinformatics and Computational Biology, ACM-BCB 2010. 2010. p. 370-373 (2010 ACM International Conference on Bioinformatics and Computational Biology, ACM-BCB 2010).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Ahmed, ST, Nair, R, Patel, C, Kanwar, SP, Hakenberg, J & Davulcu, H 2010, Semantic classification and dependency parsing enabled automated bio-molecular event extraction from text. in 2010 ACM International Conference on Bioinformatics and Computational Biology, ACM-BCB 2010. 2010 ACM International Conference on Bioinformatics and Computational Biology, ACM-BCB 2010, pp. 370-373, 2010 ACM International Conference on Bioinformatics and Computational Biology, ACM-BCB 2010, Niagara Falls, NY, United States, 8/2/10. https://doi.org/10.1145/1854776.1854832

Ahmed ST, Nair R, Patel C, Kanwar SP, Hakenberg J, Davulcu H. Semantic classification and dependency parsing enabled automated bio-molecular event extraction from text. In 2010 ACM International Conference on Bioinformatics and Computational Biology, ACM-BCB 2010. 2010. p. 370-373. (2010 ACM International Conference on Bioinformatics and Computational Biology, ACM-BCB 2010). doi: 10.1145/1854776.1854832

Ahmed, Syed Toufeeq ; Nair, Radhika ; Patel, Chintan et al. / Semantic classification and dependency parsing enabled automated bio-molecular event extraction from text. 2010 ACM International Conference on Bioinformatics and Computational Biology, ACM-BCB 2010. 2010. pp. 370-373 (2010 ACM International Conference on Bioinformatics and Computational Biology, ACM-BCB 2010).

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abstract = "The last two decades of invigorating research in the area of human genome sequencing marked the beginning of large-scale data collection. Much of the valuable knowledge gained is found in published articles, and thus in un-structured textual form. To aid in searching and extracting knowledge from textual sources, we present BioEve, a fully automated system to extract bio-molecular events from Medline abstracts. BioEve first semantically classifies each sentence to the class type of the event mentioned in the sentence, and then using high coverage, class-specific, hand-crafted rules, it extracts the participants of that event.",

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Semantic classification and dependency parsing enabled automated bio-molecular event extraction from text

Abstract

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Keywords

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