Research on Semantic Relevance of Medical Text Oriented to Event Ontology
Li Yueyan1,2, Wang Hao1,2, Deng Sanhong1,2, Chen Yan3
1.School of Information Management, Nanjing University, Nanjing 210023 2.Jiangsu Key Laboratory of Data Engineering & Knowledge Service, Nanjing 210023 3.College of Life Sciences, Nanjing University, Nanjing 210023
李跃艳, 王昊, 邓三鸿, 陈艳. 面向事件本体的医学文本语义关联化研究[J]. 情报学报, 2022, 41(5): 497-511.
Li Yueyan, Wang Hao, Deng Sanhong, Chen Yan. Research on Semantic Relevance of Medical Text Oriented to Event Ontology. 情报学报, 2022, 41(5): 497-511.
1 Charon R. Narrative medicine: form, function, and ethics[J]. Annals of Internal Medicine, 2001, 134(1): 83-87. 2 Charon R. Narrative medicine: a model for empathy, reflection, profession, and trust[J]. JAMA, 2001, 286(15): 1897-1902. 3 Gerard G. Narrative discourse: an essay in method[M]. Ithaca: Cornell University Press, 1984: 23-24. 4 Kibbe W A, Arze C, Felix V, et al. Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data[J]. Nucleic Acids Research, 2015, 43(database issue): D1071-D1078. 5 Amberger J S, Bocchini C A, Schiettecatte F, et al. OMIM.org: Online Mendelian Inheritance in Man (OMIM?), an online catalog of human genes and genetic disorders[J]. Nucleic Acids Research, 2015, 43(database issue): D789-D798. 6 Miller N, Lacroix E M, Backus J E B. MEDLINEplus: building and maintaining the National Library of Medicine’s consumer health Web service[J]. Bulletin of the Medical Library Association, 2000, 88(1): 11-17. 7 Babbi G, Martelli P L, Profiti G, et al. eDGAR: a database of Disease-Gene Associations with annotated Relationships among genes[J]. BMC Genomics, 2017, 18(Suppl 5): 554. 8 Cowell L G, Smith B. Infectious disease ontology[M]// Infectious Disease Informatics. New York: Springer, 2010: 373-395. 9 Vasant D, Chanas L, Malone J, et al. ORDO: an ontology connecting rare disease, epidemiology and genetic data[C]// Proceedings of the 22nd Annual International Conference on Intelligent Systems for Molecular Biology, 2014. 10 Sergouniotis P I, Maxime E, Leroux D, et al. An ontological foundation for ocular phenotypes and rare eye diseases[J]. Orphanet Journal of Rare Diseases, 2019, 14(1): 8. 11 Rappaport N, Nativ N, Stelzer G, et al. MalaCards: an integrated compendium for diseases and their annotation[J]. Database: the Journal of Biological Databases and Curation, 2013, 2013: bat018. 12 K?hler S, Doelken S C, Mungall C J, et al. The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data[J]. Nucleic Acids Research, 2013, 42(D1): D966-D974. 13 Babbi G, Martelli P L, Casadio R. PhenPath: a tool for characterizing biological functions underlying different phenotypes[J]. BMC Genomics, 2019, 20(Suppl 8): 548. 14 Symptom ontology[EB/OL]. [2020-06-10]. https://obofoundry.org/ontology/symp.html. 15 Degtyarenko K, de Matos P, Ennis M, et al. ChEBI: a database and ontology for chemical entities of biological interest[J]. Nucleic Acids Research, 2008, 36(database issue): D344-D350. 16 The UniProt Consortium. UniProt: a hub for protein information[J]. Nucleic Acids Research, 2015, 43(D1): D204-D212. 17 Kuhn M, Szklarczyk D, Franceschini A, et al. STITCH 2: an interaction network database for small molecules and proteins[J]. Nucleic Acids Research, 2010, 38(suppl_1): D552-D556. 18 Berman H M, Westbrook J, Feng Z, et al. The protein data bank[J]. Nucleic Acids Research, 2000, 28(1): 235-242. 19 Breitkreutz B J, Stark C, Reguly T, et al. The BioGRID interaction database: 2008 update[J]. Nucleic Acids Research, 2008, 36(database issue): D637-D640. 20 Ashburner M, Ball C A, Blake J A, et al. Gene Ontology: tool for the unification of biology[J]. Nature Genetics, 2000, 25(1): 25-29. 21 Binns D, Dimmer E, Huntley R, et al. QuickGO: a web-based tool for Gene Ontology searching[J]. Bioinformatics, 2009, 25(22): 3045-3046. 22 Povey S, Lovering R, Bruford E, et al. The HUGO Gene Nomenclature Committee (HGNC)[J]. Human Genetics, 2001, 109(6): 678-680. 23 Bairoch A. The cellosaurus, a cell-line knowledge resource[J]. Journal of Biomolecular Techniques, 2018, 29(2): 25-38. 24 Xue R C, Fang Z, Zhang M X, et al. TCMID: traditional Chinese medicine integrative database for herb molecular mechanism analysis[J]. Nucleic Acids Research, 2013, 41(D1): D1089-D1095. 25 Ye H, Ye L, Kang H, et al. HIT: linking herbal active ingredients to targets[J]. Nucleic Acids Research, 2011, 39(suppl_1): D1055-D1059. 26 Wishart D S, Feunang Y D, Guo A C, et al. DrugBank 5.0: a major update to the DrugBank database for 2018[J]. Nucleic Acids Research, 2018, 46(D1): D1074-D1082. 27 He Y Q, Cowell L, Diehl A, et al. VO: vaccine ontology[J/OL]. Nature Precedings, (2009-08-05). https://doi.org/10.1038/npre.2009.3553.1. 28 Smith B, Ashburner M, Rosse C, et al. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration[J]. Nature Biotechnology, 2007, 25(11): 1251-1255. 29 He Y Q, Xiang Z S, Zheng J, et al. The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability[J]. Journal of Biomedical Semantics, 2018, 9: Article No.3. 30 Malone J, Stevens R, Jupp S, et al. Ten simple rules for selecting a bio-ontology[J]. PLoS Computational Biology, 2016, 12(2): e1004743. 31 Aranguren M E, Antezana E, Kuiper M, et al. Ontology design patterns for bio-ontologies: a case study on the cell cycle ontology[J]. BMC Bioinformatics, 2008, 9(Suppl 5): S1. 32 Hoehndorf R, Ngonga Ngomo A C, Pyysalo S, et al. Ontology design patterns to disambiguate relations between genes and gene products in GENIA[J]. Journal of Biomedical Semantics, 2011, 2(Suppl 5): S1. 33 Halu A, de Domenico M, Arenas A, et al. The multiplex network of human diseases[J]. npj Systems Biology and Applications, 2019, 5: 15. 34 Choi W, Choi C H, Kim Y R, et al. HerDing: herb recommendation system to treat diseases using genes and chemicals[J]. Database, 2016, 2016: baw011. 35 Deng L, Ye D Y, Zhao J M, et al. MultiSourcDSim: an integrated approach for exploring disease similarity[J]. BMC Medical Informatics and Decision Making, 2019, 19(Suppl 6): Article No.269. 36 Choi W, Lee H. Inference of biomedical relations among chemicals, genes, diseases, and symptoms using knowledge representation learning[J]. IEEE Access, 2019, 7: 179373-179384. 37 OpenKG[EB/OL]. [2020-08-10]. http://www.openkg.cn/. 38 EpiK[EB/OL]. [2020-08-10]. https://epik-protocol.io/#mission. 39 千言中文开源数据集[EB/OL]. [2020-08-10]. https://www.luge.ai/#/. 40 中国疾病知识总库(China Disease Knowledge Total Database)[EB/OL]. (2017-12-26) [2020-08-10]. https://www.baidu.com/link?url=aiR5xn87tCEAwQvCSChrvFzHA_jLTTwE20fmwOUbmHQiQv4XGaSp2WY0gNmHHVXmPrw7qf9o_C1AWezdMNHBQa& wd=&eqid=92adf67f00021bba00000006627ce94c. 41 阮彤, 孙程琳, 王昊奋, 等. 中医药知识图谱构建与应用[J]. 医学信息学杂志, 2016, 37(4): 8-13. 42 Nelson K. Event knowledge: structure and function in development[M]. Lawrence Erlbaum Associates, 1986. 43 Langacker R W. Foundations of cognitive grammar, vol. II, descriptive application[M]. Stanford: Stanford University Press, 1991. 44 Filatova E, Hatzivassiloglou V. Domain-independent detection, extraction, and labeling of atomic events[C]// Proceedings of RANLP, Borovetz, Bulgaria, 2003: 145-152. 45 王寅. 事件域认知模型及其解释力[J]. 现代外语, 2005, 28(1): 17-26, 108. 46 Zhou W, Liu Z T, Zhao Y, et al. A semi-automatic ontology learning based on WordNet and event-based natural language processing[C]// Proceedings of the 2006 International Conference on Information and Automation. IEEE, 2006: 240-244. 47 刘宗田, 黄美丽, 周文, 等. 面向事件的本体研究[J]. 计算机科学, 2009, 36(11): 189-192, 199. 48 陈康, 武港山. 基于Ontology的信息检索技术研究[J]. 中文信息学报, 2005, 19(2): 51-57. 49 Tanev H, Piskorski J, Atkinson M. Real-time news event extraction for global crisis monitoring[C]// Proceedings of the International Conference on Application of Natural Language to Information Systems. Heidelberg: Springer, 2008: 207-218. 50 Liu M F, Li W J, Wu M L, et al. Event-based extractive summarization using event semantic relevance from external linguistic resource[C]// Proceedings of the Sixth International Conference on Advanced Language Processing and Web Information Technology. IEEE, 2007: 117-122. 51 汤庸, 林鹭贤, 罗烨敏, 等. 基于自动问答系统的信息检索技术研究进展[J]. 计算机应用, 2008, 28(11): 2745-2748. 52 Raimond Y, Abdallah S. The event ontology[EB/OL]. (2007-10-25) [2020-10-17]. http://motools.sourceforge.net/event/event.html. 53 Lagoze C, Hunter J. The ABC ontology and model[C]// Proceedings of the International Conference on Dublin Core and Metadata Applications. Tokyo: National Institute of Informatics, 2001: 160-176. 54 Scherp A, Franz T, Saathoff C, et al. F—a model of events based on the foundational ontology dolce+DnS ultralight[C]// Proceedings of the Fifth International Conference on Knowledge Capture. New York: ACM Press, 2009: 137-144. 55 van Hage W, Malaisé V, Segers R, et al. The simple event model ontology[EB/OL]. (2009-11-01) [2020-09-25]. http://semanticweb.cs.vu.nl/2009/11/sem/. 56 徐雷, 王晓光. 叙事型图像语义标注模型研究[J]. 中国图书馆学报, 2017, 43(5): 70-83. 57 What is the CIDOC CRM?[EB/OL]. [2020-09-26]. http://www.cidoc-crm.org/. 58 Event in schema.org[EB/OL]. [2020-09-26]. https://schema.org.cn/Event. 59 朱文跃, 刘宗田. 基于事件本体的突发事件领域知识建模[J]. 计算机工程与应用, 2018, 54(21): 148-155. 60 宋宁远, 王晓光. 基于情节本体的叙事性文本语义结构化表示方法研究[J]. 中国图书馆学报, 2020, 46(2): 96-113. 61 Xu J, Kim S, Song M, et al. Building a PubMed knowledge graph[J]. Scientific Data, 2020, 7: 205. 62 He Y Q, Yu H, Ong E, et al. CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis[J]. Scientific Data, 2020, 7: 181. 63 Speer N K, Zacks J M, Reynolds J R. Human brain activity time-locked to narrative event boundaries[J]. Psychological Science, 2007, 18(5): 449-455. 64 Mann W C, Thompson S A. Rhetorical structure theory: description and construction of text structures[M]// Natural Language Generation. Dordrecht: Springer, 1987: 85-95. 65 仲兆满, 刘宗田, 李存华. 事件本体模型及事件类排序[J]. 北京大学学报(自然科学版), 2013, 49(2): 234-240. 66 杨璐, 王辉强, 李玉环. COVID-19治疗药物的研究进展[J]. 药学学报, 2020, 55(6): 1081-1090. 67 滕俊, 姜云宁, 柴欣楼, 等. 中西医结合治疗新型冠状病毒肺炎研究进展[J]. 中医学报, 2020, 35(4): 720-725.