Please wait a minute...
Advanced Search
现代图书情报技术  2011, Vol. 27 Issue (9): 21-27    DOI: 10.11925/infotech.1003-3513.2011.09.04
  知识组织与知识管理 本期目录 | 过刊浏览 | 高级检索 |
王秀艳, 崔雷
中国医科大学信息管理与信息系统(医学)系 沈阳110001
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
全文: PDF(409 KB)   HTML  
输出: BibTeX | EndNote (RIS)      
摘要 对利用关键动词(即语义关系动词)进行关系抽取的研究进行回顾,并对生物医学语义关系抽取的常用方法进行详细介绍。认为目前关系抽取研究中所利用的关键动词主要是人工选取的,涉及的主观因素较多,影响关键动词选取的客观性、准确性和全面性。因此,如何自动化地找到这些动词可能会成为今后关系挖掘的一项关键任务。
E-mail Alert
关键词 生物医学实体语义关系抽取信息抽取关键动词    
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
收稿日期: 2011-06-09     


王秀艳, 崔雷. 应用关键动词抽取生物医学实体间语义关系研究综述[J]. 现代图书情报技术, 2011, 27(9): 21-27.
Wang Xiuyan, Cui Lei. Overview of Semantic Relations Extraction Between Biomedical Entities by Key Verbs. New Technology of Library and Information Service, DOI:10.11925/infotech.1003-3513.2011.09.04.
[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] 刘志强,都云程,施水才. 基于改进的隐马尔科夫模型的网页新闻关键信息抽取*[J]. 数据分析与知识发现, 2019, 3(3): 120-128.
[2] 牟冬梅,金姗,琚沅红. 基于文献数据的疾病与基因关联关系研究*[J]. 数据分析与知识发现, 2018, 2(8): 98-106.
[3] 段宇锋,黄思思. 中文植物物种多样性描述文本的信息抽取研究*[J]. 现代图书情报技术, 2016, 32(1): 87-96.
[4] 刘伟, 王星, 宋培彦. 同义词抽取结果的噪音清洗方法研究[J]. 现代图书情报技术, 2015, 31(6): 64-70.
[5] 李湘东, 霍亚勇, 黄莉. 图书网页的自动识别及书目信息抽取研究[J]. 现代图书情报技术, 2014, 30(4): 71-77.
[6] 刘雅静, 王衍喜, 郝丹, 周津慧. 机构知识库支撑科研服务方法研究[J]. 现代图书情报技术, 2014, 30(3): 1-7.
[7] 翟东升, 张欣琦, 张杰, 康宁. 分布式专利信息抽取系统设计与构建[J]. 现代图书情报技术, 2013, 29(7/8): 114-121.
[8] 张晗, 刘双梅. 中心度指标对语义述谓网络概念抽取的比较分析——以疾病治疗学研究为例[J]. 现代图书情报技术, 2013, (6): 30-35.
[9] 王秀艳, 崔雷. 采用混合方法抽取生物医学实体间语义关系[J]. 现代图书情报技术, 2013, 29(3): 77-82.
[10] 黄勋, 游宏梁, 于洋. 关系抽取技术研究综述[J]. 现代图书情报技术, 2013, 29(11): 30-39.
[11] 何琳, 何娟, 沈耕宇, 杨波, 黄水清. 一种通过文本挖掘发现实时定量聚合酶链式反应实验内参基因的方法研究[J]. 现代图书情报技术, 2012, 28(7): 109-114.
[12] 高强, 游宏梁. 基于层叠模型的国防领域命名实体识别研究[J]. 现代图书情报技术, 2012, (11): 47-52.
[13] 周虹, 张蓓, 姜爱蓉, 张成昱. 馆藏书目信息自助短信推送服务的设计与实现[J]. 现代图书情报技术, 2011, 27(7/8): 127-131.
[14] 王志超, 翁楠, 王宇. 基于主题句相似度的标题党新闻鉴别技术研究[J]. 现代图书情报技术, 2011, (11): 48-53.
[15] 逯万辉, 马建霞. 基于条件随机场模型的复杂时间信息抽取研究[J]. 现代图书情报技术, 2011, 27(10): 29-33.
Full text



版权所有 © 2015 《数据分析与知识发现》编辑部
地址:北京市海淀区中关村北四环西路33号 邮编:100190