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Review
. 2014:2014:298473.
doi: 10.1155/2014/298473. Epub 2014 Aug 19.

Biomedical relation extraction: from binary to complex

Deyu Zhou  1 , Dayou Zhong  1 , Yulan He  2
Affiliations
Review

Biomedical relation extraction: from binary to complex

Deyu Zhou et al. Comput Math Methods Med. 2014.

Abstract

Biomedical relation extraction aims to uncover high-quality relations from life science literature with high accuracy and efficiency. Early biomedical relation extraction tasks focused on capturing binary relations, such as protein-protein interactions, which are crucial for virtually every process in a living cell. Information about these interactions provides the foundations for new therapeutic approaches. In recent years, more interests have been shifted to the extraction of complex relations such as biomolecular events. While complex relations go beyond binary relations and involve more than two arguments, they might also take another relation as an argument. In the paper, we conduct a thorough survey on the research in biomedical relation extraction. We first present a general framework for biomedical relation extraction and then discuss the approaches proposed for binary and complex relation extraction with focus on the latter since it is a much more difficult task compared to binary relation extraction. Finally, we discuss challenges that we are facing with complex relation extraction and outline possible solutions and future directions.

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Figures

Figure 1
Figure 1
Total bibliographical data in MEDLINE since 1995 and the two stages of biomedical relation extraction research.
Figure 2
Figure 2
The general framework of a relation extraction system.
Figure 3
Figure 3
General procedure of a PPI extraction system employing different methodologies.
Figure 4
Figure 4
An example of identifying trigger words based on the predefined pattern.
Figure 5
Figure 5
Event extraction rules employed in [58].
Figure 6
Figure 6
An example of a sentence with target event edge to be extracted.
Figure 7
Figure 7
The dependency path for the sentence “The binding of I kappa B/MAD-3 to NF-kappa B p65 is sufficient to retarget NF-kappa B p65 from the nucleus to the cytoplasm.”
See this image and copyright information in PMC

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Publication types