Please wait a minute...
New Technology of Library and Information Service  2011, Vol. 27 Issue (9): 21-27    DOI: 10.11925/infotech.1003-3513.2011.09.04
Current Issue | Archive | Adv Search |
Overview of Semantic Relations Extraction Between Biomedical Entities by Key Verbs
Wang Xiuyan, Cui Lei
Department of Information Management and Information System(Medicine),China Medical University, Shenyang 110001, China
Export: BibTeX | EndNote (RIS)      
Abstract  The paper mainly reviews the semantic relation extraction studies used key verbs(i.e.semantic verb),and introduces the methods of biomedical semantic relations extraction. The key verbs used in the present researches are manually selected, so the verb selection method involves more subjective factors, and influences the objectivity, accuracy and comprehensiveness of key verbs selection.Therefore, how to find these verbs automatically may be a key task of relations mining.
Key wordsBiomedical entity      Semantic relation extraction      Information extraction      Key verbs     
Received: 09 June 2011      Published: 02 December 2011



Cite this article:

Wang Xiuyan, Cui Lei. Overview of Semantic Relations Extraction Between Biomedical Entities by Key Verbs. New Technology of Library and Information Service, 2011, 27(9): 21-27.

URL:     OR

[1] Cohen K B,Hunter L.Getting Started in Text Mining[J].PLoS Computational Biology,2008,4(1):l-3.

[2] PubMed [EB/OL].[2011-05-21].

[3] 张智,张正国.蛋白质相互作用的文本挖掘研究进展[J].中国生物医学工程学报,2008,27(5):764-772,782.

[4] 刘迁,焦慧,贾惠波.信息抽取技术的发展现状及构建方法的研究[J].计算机应用研究,2007,24(7):6-9.

[5] [JP2]Skusa A,Ruegg A,Kohler J.Extraction of Biological Interaction Networks from Scientific Literature[J].Briefings in Bioinformatics,2005,6(3):263-276.[JP]

[6] 杨志豪.面向生物医学领域的文本挖掘技术研究[D]. 大连:大连理工大学,2008.

[7] 徐健,张智雄,吴振新.实体关系抽取的技术方法综述[J].现代图书情报技术,2008(8):18-23.

[8] Cohen A M,Hersh W R.A Survey of Current Work in Biomedical Text Mining[J].Briefings in Bioinformatics,2005,6(1):57-71.

[9] Jenssen T K,Laegreid A,Komorowski J,et a1.A Literature Network of Human Genes for High Throughput Analysis of Gene Expression[J].Nature Genetics,2001,28(1):21-28.

[10] Stapley B J, Benoit G.Bibliometrics:Information Retrieval and Visualization from Co-occurernces of Gene Names in Medline Abstracts[C]. In:Proceedings of Pacific Symposium on Biocomputing.2000:529-540.

[11] Wren J D, Garner H R. Shared Relationship Analysis: Ranking Set Cohesion and Commonalities Within a Literature-derived Relationship Network[J]. Bioinformatics, 2004, 20(2): 191-198.

[12] Jelier R,Jenster G, Dorssers L,et al.Co-occurrence Based Meta-analysis of Scientific Texts: Retrieving Biological Relationships Between Genes[J]. Bioinformatics,2005,21(9): 2049-2058.

[13] Adamic L A, Wilkinson D, Huberman B A, et al. A Literature Based Method for Identifying Gene-disease Connections[C]. In:Proceedings of IEEE Computer Society Bioinformatics Conference. 2002:109-117.

[14] Chun H W, Tsuruoka Y, Kim J D,et al.Extraction of Gene-disease Relations from Medline Using Domain Dictionaries and Machine Learning[C]. In:Proceedings of Pacific Symposium on Biocomputing. 2006:4-15.

[15] Marcotte E M, Xenarios I, Eisenberg D.Mining Literature for Protein-protein Interactions [J]. Bioinformatics,2001,17(4):359-363.

[16] Xiao J, Su J, Zhou G D,et a1.Protein-protein Interaction Extraction:A Supervised Learning Approach[C]. In:Proceedings of the 1st International Symposiumon Semantic Mining in Biomedicine.2005:148-156.

[17] Donaldson I,Martin J,De Bruijn B,et al.PreBIND and Textomy:Mining the Biomedical Literature for Protein-protein Interactions Using a Support Vector Machine[J].BMC Bioinformatics,2003,4:11.

[18] Saetre R, Yoshida K, Miwa M,et al.Extracting Protein Interactions from Text with the Unified AkaneRE Event Extraction System[J].IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2010,7(3): 442-453.

[19] Craven M, Kumlien J. Constructing Biological Knowledge Bases by Extracting Information from Textsources[C]. In:Proceedings of the 7th International Conference on Intelligent Systems for Molecular Biology.1999:77-86.

[20] Stapley B J,Kelley L A,Strenberg M J.Predicting the Subcellular Location of Proteins from Text Using Support Vector Machines[C]. In:Proceedings of Pacific Symposium on Biocomputing.2002:374-385.

[21] Eskin E,Agichtein E.Combining Text Mining and Sequence Analysis to Discover Protein Functional Regions[C]. In:Proceedings of Pacific Symposium on Biocomputing.2004:288-299.

[22] Lee S, Lee K H, Song M,et al.Building the Process-drug-side Effect Network to Discover the Relationship Between Biological Processes and Side Effects[J]. BMC Bioinformatics,2011,12(S2):2.

[23] Garten Y, Altman R B. Pharmspresso: A Text Mining Tool for Extraction of Pharmacogenomic Concepts and Relationships from Full Text[J]. BMC Bioinformatics,2009,10(S2):6.

[24] Li J, Zhu X, Chen J Y. Building Disease-specific Drug-protein Connectivity Maps from Molecular Interaction Networks and PubMed Abstracts[J]. PLoS Computational Biology,2009,5(7).

[25] Bundschus M, Dejori M, Stetter M,et al.Extraction of Semantic Biomedical Relations from Text Using Conditional Random Fields[J].BMC Bioinformatics,2008, 9:207.

[26] Wren J D,Bekeredjian R,Stewart J A.Knowledge Discovery by Automated Identification and Ranking of Implicit Relationships[J].Bioinformaties,2004,20(3):389-398.

[27] Barbosa-Silva A, Soldatos T G, Magalhaes I L F, et al. LAITOR-Literature Assistant for Identification of Terms Co-occurrences and Relationships[J]. BMC Bioinformatics,2010,11: 70.

[28] Zweigenbaum P,Demner-Fushman D,Yu H,et al.Frontiers of Biomedical Text Mining:Current Progress[J]. Briefings in Bioinformatics,2007,8(5):358-375.

[29] Friedman C, Kra P, Yu H. et al. GENIES: A Natural-language Processing System for the Extraction of Molecular Pathways from Journal Articles[J].Bioinformatics,2001,17(S1): 74-82.

[30] Proux D, Rechenmann F, Julliard L. A Pragmatic Information Extraction Strategy for Gathering Data on Genetic Interactions[C].In: Proceedings of International Conference on Intelligent Systems for Molecular Biology.2000, 8:279-285.

[31] Leroy G,Chen H,Martinez J D.A Shallow Parser Based on Closed-class Words to Capture Relations in Biomedical Text[J].Journal of Biomedical Informatics,2003,36(3):145-158.

[32] McDonald D M, Chen H, Su H,et al. Extracting Gene Pathway Relations Using a Hybrid Grammar: The Arizona Relation Parser[J]. Bioinformatics,2004,20(18):3370-3378.

[33] Koike A,Niwa Y,Takagi T. Automatic Extraction of Gene/Protein Biological Functions from Biomedical Text[J]. Bioinformatics,2005,21 (7):1227-1236.

[34] [JP2]Pustejovsky J,Castano,Zhang J.Robust Relational Parsing over Biomedical Literature:Extracting Inhibit Relations [C].In:Proceedings of the 7th Pacific Symposium on Biocomputing.2002:362-373.[JP]

[35] Temkin J M,Gilder M R. Extraction of Protein Interaction Information from Unstructured Text Using a Context-free Grammar[J].Bioinformatics,2003,19(16):2046-2053.

[36] Fundel K, Kuffner R, Zimmer R. RelEx——Relation Extraction Using Dependency Parse Trees[J]. Bioinformatics, 2007, 23(3): 365-371.

[37] Rinaldi F, Schneider G, Kaljurand K, et al.Mining of Relations Between Proteins over Biomedical Scientific Literature Using a Deep-linguistic Approach[J]. Artificial Intelligence in Medicine,2007, 39 (2): 127-136.

[38] Jiao D Z,Wild D J.Extraction of CYP Chemical Interactions from Biomedical Literature Using Natural Language Processing Methods[J].Journal of Chemical Information and Modeling,2009,49 (2): 263-269.

[39] Coulet A, Shah N H, Garten Y,et al. Using Text to Build Semantic Networks for Pharmacogenomics[J]. Journal of Biomedical Informatics,2010,43 (6): 1009-1019.

[40] Daraselia N.Extracting Human Protein Interactions from MEDLINE Using a Full-Sentence Parser[J].Bioinformatics,2004,20(5):604-611.

[41] Rindflesch T C,Tanabe L, Weinstein J N,et al.EDGAR: Extraction of Drugs,Genes and Relations from the Biomedical Literature[C].In: Proceedings of Pacific Symposium on Biocomputing.2000,5:517-528.

[42] Jahiruddin, Abulaish M, Dey L.A Concept-driven Biomedical Knowledge Extraction and Visualization Framework for Conceptualization of Text Corpora[J].Journal of Biomedical Informatics, 2010, 43 (6): 1020-1035.

[43] Yang Z H, Lin H F, Wu B D.BioPPIExtractor: A Protein-protein Interaction Extraction System for Biomedical Literature[J].Expert Systems with Applications,2009,36 (2): 2228-2233.

[44] Gaizauskas R, Demetriou G, Artymiuk P J,et al. Protein Structures and Information Extraction from Biological Texts: The PASTA System[J]. Bioinformatics,2003,19(1):135-143.

[45] Hu Z Z, Narayanaswamy M, Ravikumar K E, et al.Literature Mining and Database Annotation of Protein Phosphorylation Using a Rule-based System[J]. Bioinformatics,2005, 21(11):2759-2765.

[46] Saric J,Jensen L J, Ouzounova R,et al. Extraction of Regulatory Gene/Protein Networks from Medline[J]. Bioinformatics,2006,22(6): 645-650.

[47] Tsai R,Lai P T, Dai H,et al.HypertenGene: Extracting Key Hypertension Genes from Biomedical Literature with Position and Automatically-generated Template Features[J]. BMC Bioinformatics, 2009,10: 9.

[48] 杨志豪,洪莉,林鸿飞,等.基于支持向量机的生物医学文献蛋白质关系抽取[J]. 智能系统学报,2008,3(4):361-369.

[49] Bui Q C,Nuallain B O,Boucher C A,et al. Extracting Causal Relations on HIV Drug Resistance from Literature[J]. BMC Bioinformatics,2010,11: 101.

[50] Leroy G, Chen H C. Genescene: An Ontology-enhanced Integration of Linguistic and Co-occurrence Based relations in Biomedical Texts[J].Journal of the American Society for Information Science and Technology,2005,56 (5): 457-468.

[51] Bjorne J, Ginter F, Pyysalo S, et al.Complex Event Extraction at PubMed Scale[J].Bioinformatics, 2010, 26 (12): i382-i390.

[52] Abulaish M, Dey L.An Ontology-based Pattern Mining System for Extracting Information from Biological Texts[C]. In:Proceedings of International conference on Rough Sets, Fuzzy Sets, Data Mining, and Granular Computing.2005,3642: 420-429.

[53] Huang M L,Zhu X Y,Ding S L,et al.ONBIRES:Ontology-based Biological Relation Extraction System [C].In:Proceedings of the 4th Asia Pacific Bioinformatics Conference.London:Imperial College Press. 2006:327-336.

[54] Abulaish M, Dey L.Biological Relation Extraction and Query Answering from MEDLINE Abstracts Using Ontology-based Text Mining[J].Data & Knowledge Engineering, 2007, 61(2):228-262.

[55] Chagoyen M,Carmona-Saez P, Shatkay H, et al. Discovering Semantic Features in the Literature: A Foundation for Building Functional Associations[J].BMC Bioinformatics,2006,7:41.

[56] Rebholz-Schuhmann D,Jimeno-Yepes A,Arregui M,et al. Measuring Prediction Capacity of Individual Verbs for the Identification of Protein Interactions[J]. Journal of Biomedical Informatics,2010, 43(2):200-207.

[57] Albert S, Gaudan S, Knigge H, et al. Computer-assisted Generation of a Protein-interaction Database for Nuclear Receptors[J]. Molecular Endocrinology, 2003, 17(8):1555-1567.

[58] Wattarujeekrit T, Shah P, Collier N. PASBio: Predicate-argument Structures for Event Extraction in Molecular Biology[J]. BMC Bioinformatics,2004,5(1):155.

[59] Tateisi Y, Ohta T, Tsujii J. Annotation of Predicate-argument Structure on Molecular Biology Text[C].In:Proceedings of Workshop on the 1st International Joint Conference on Natural Language Processing.2004.

[60] Yakushiji A,Tateisi Y, Miyao Y,et al.Finding Anchor Verbs for Biomedical IE Using Predicate-Argument Structures[C]. In:Proceedings of the 42nd Annual Meeting of the Association for Computational Linguistics.2004:158-161.

[61] Sekimizu T,Park H.S,Tsujii J.Identifying the Interaction Between Genes and Gene Products Based on Frequently Seen Verbs in Medline Abstracts[J].Genome Informatics,1998,9:62-71.

[62] Rindflesch T C, Rayan J, Hunter L. Extracting Molecular Binding Relationships from Biomedical Text[C].In:Proceedings of the 6th Applied Natural Language Processing Conference, Association for Computational Linguistics.2000:188-195.

[63] Bodenreider O.The Unified Medical Language System (UMLS):Integrating Biomedical Terminology[J]. Nucleic Acids Research,2004,32(S1): 267-270.

[64] Rindflesch T C, Libbus B, Hristovski D, et al. Semantic Relations Asserting the Etiology of Genetic Diseases[C].In: Proceedings of AMIA Annual Symposium.2003:554-558.

[65] Masseroli M,Kilicoglu H,Lang F M,et al.Argument-predicate Distance as a Filter for Enhancing Precision in Extracting Predications on the Genetic Etiology of Disease[J].BMC Bioinformatics,2006,7(1):291.

[66] Hristovski D, Kastrin A, Peterlin B, et al. Semantic Relations for Interpreting DNA Microarray Data[C]. In: Proceedings of AMIA Annual Symposium.2009:255-259.

[67] Park J C,Kim H S,Kim J J.Bidirectional Incremental Parsing for Automatic Pathway Identification with Combinatory Categorical Grammar[C]. In:Proceedings of Pacific Symposium on Biocomputing.2001:396-407.

[68] Sharma A,Swaminathan R,Yang H.A Verb-centric Approach for Relationship Extraction in Biomedical Text[C].In: Proceedings of the IEEE 4th International Conference on Semantic Computing.2010:377-385.

[69] Ahlers C B,Fiszman M,Demner-Fushman D,et al. Extracting Semantic Predications from MEDLINE Citations for Pharmacogenomics[C].In:Proceedings of Pacific Symposium on Biocomputing.2007:205-208.

[70] Ng S K,Wong M.Toward Routine Automatic Pathway Discovery from Online Scientific Text Abstracts[J].Genome Informatics,1999,10:104-112.

[71] Blaschke C,Andrade M A,Ouzounis C,et al.Automatic Extraction of Biological Information from Scientific Text:Protein-protein Interactions[C].In: Proceedings International Conference on Intelligent Systems for Molecular Biology.1999:60-67.

[72] Thomas J,Milward D,Ouzounis C,et al. Automatic Extraction of Protein Interactions from Scientificabstract[C].In:Proceedings of Pacific Symposium on Biocomputing.2000:541-552.

[73] Ono T,Hishigaki H,Tanigami A,et al.Automated Extraction of Information on Protein-protein Interactions from the Biological Literature[J].Bioinformatics,2001,17(2):155-161.

[74] Huang M L,Zhu X Y,Hao Y,et al.Discovering Patterns to Extract Protein-protein Interactions from Full Texts[J].Bioinformatics, 2004,20(18): 3604-3612.

[75] Corney D P,Bemard B,Langdon W,et al.BioRAT:Extracting Biological Information from Full-length Papers[J].Bioinformatics,2004,20(17): 3206-3213.
[1] Tan Ying, Tang Yifei. Extracting Citation Contents with Coreference Resolution[J]. 数据分析与知识发现, 2021, 5(8): 25-33.
[2] Wang Yi,Shen Zhe,Yao Yifan,Cheng Ying. Domain-Specific Event Graph Construction Methods:A Review[J]. 数据分析与知识发现, 2020, 4(10): 1-13.
[3] Tao Yue,Yu Li,Zhang Runjie. Active Learning Strategies for Extracting Phrase-Level Topics from Scientific Literature[J]. 数据分析与知识发现, 2020, 4(10): 134-143.
[4] Zhiqiang Liu,Yuncheng Du,Shuicai Shi. Extraction of Key Information in Web News Based on Improved Hidden Markov Model[J]. 数据分析与知识发现, 2019, 3(3): 120-128.
[5] Chengzhi Zhang,Zheng Li. Extracting Sentences of Research Originality from Full Text Academic Articles[J]. 数据分析与知识发现, 2019, 3(10): 12-18.
[6] Mu Dongmei,Jin Shan,Ju Yuanhong. Finding Association Between Diseases and Genes from Literature Abstracts[J]. 数据分析与知识发现, 2018, 2(8): 98-106.
[7] Yufeng Duan,Sisi Huang. Information Extraction from Chinese Plant Species Diversity Description Text[J]. 现代图书情报技术, 2016, 32(1): 87-96.
[8] Liu Wei, Wang Xing, Song Peiyan. A Noise Cleaning Method for Synonym Extraction Results[J]. 现代图书情报技术, 2015, 31(6): 64-70.
[9] Jiang Chuntao. Automatic Annotation of Bibliographical References in Chinese Patent Documents[J]. 现代图书情报技术, 2015, 31(10): 81-87.
[10] Li Xiangdong, Huo Yayong, Huang Li. Study of Book Pages Automatic Identification and Bibliographic Information Extraction[J]. 现代图书情报技术, 2014, 30(4): 71-77.
[11] Liu Yajing, Wang Yanxi, Hao Dan, Zhou Jinhui. Study on the Methods of Institutional Repository Supporting Research Services[J]. 现代图书情报技术, 2014, 30(3): 1-7.
[12] Zhang Han, Liu Shuangmei. Comparative Analysis of Centrality Indices in Extracting Concepts from Semantic Predication Network——Based on Disease Treatment Research[J]. 现代图书情报技术, 2013, (6): 30-35.
[13] Wang Xiuyan, Cui Lei. Extract Semantic Relations Between Biomedical Entities Applied Hybrid Method[J]. 现代图书情报技术, 2013, 29(3): 77-82.
[14] Huang Xun, You Hongliang, Yu Yang. A Review of Relation Extraction[J]. 现代图书情报技术, 2013, 29(11): 30-39.
[15] He Lin, He Juan, Shen Gengyu, Yang Bo, Huang Shuiqing. An Approach to Discovery of Reference Control Gene for qRT-PCR Experiment Based on Texting Mining[J]. 现代图书情报技术, 2012, 28(7): 109-114.
  Copyright © 2016 Data Analysis and Knowledge Discovery   Tel/Fax:(010)82626611-6626,82624938