基于顶级本体整合的医学领域语义标注研究
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摘要
信息技术高速发展，信息化建设对于医学领域知识的交流促进作用日益显著。医药卫生信息化建设的质量，取决于医学信息资源组织的科学性、有效性，而医学领域是一个庞大的学科门类，其中的知识很多涉及到与其他学科之间的交叉，使得领域知识比较繁杂。当前，医学信息资源的应用呈现出网络化的发展趋势，已经构成了海量信息资源，逐渐形成了无法语义识别的信息孤岛，传统的信息组织方式逐渐难以满足现有医学信息传播的需要。
语义网技术为解决医学信息资源的共享问题提供了新的方案，它作为面向下一代网络信息资源语义应用的支撑技术，可以使数据以机器理解的形式进行处理和查找，通过一系列的语言、工具和技术，实现计算机之间的数据解释交流。在这些技术中，本体作为语义网的核心能够较好的表达出领域知识的语义层次，语义标注则利用本体将普通的信息资源序化为具有知识层次的形式化信息，使庞大的信息资源以语义关联的规范化形式存在。但是，由于领域本体之间的语义异构情况逐渐突出，使得语义标注的语义富集度受到限制，而顶级本体正是揭示领域知识的高层语义关系的通用知识体系。
本文通过本体的创新构建、本体映射及整合、语义标注等工作，探讨具有医学领域顶级本体语义关系结构的本体语义标注工作机制，尝试建立基于顶级本体整合的医学领域本体语义标注系统模型，实证语义标注新思路，探索本体整合对于语义标注效果的促进作用，力求做到从实际出发，研究并解决现实中存在的本体语义应用障碍，进而提高医学信息资源的语义标注水平，推动面向网络医学信息资源的语义应用，促进医学信息资源的共享和知识发现。本文的内容主要围绕以下几个章节展开：
第一章介绍了本研究选题的时代背景与技术背景，说明了与本研究有关的理论和技术的发展现状，指出研究的理论及现实意义，并提出研究的目标、内容、方法，并针对研究思路进行规划和布局。
第二章对本体整合及语义标注的基本理论和原理进行系统描述，论述利用顶级本体进行整合及语义标注所涉及的主要技术，主要包括本体理论及有关的本体构建、本体映射和集成等有关技术，语义标注理论及相关技术方法等。
第三章详细阐述了本体整合及语义标注领域中主流的应用工具、平台，以及近年来出现的新方法、新系统，对其使用的方法、技术进行详细研究，并选取具有代表性的系统进行比较，总结其技术特点与应用方向，为基于顶级本体整合的语义标注系统建设提供依据。
第四章针对医学领域信息资源特点，深入研究医学领域中信息资源的结构形式，从语义模型的建立和标注方式选取的角度，分析基于顶级本体整合的语义标注模式。
第五章以前文分析为依据，详细设计医学信息资源的领域本体建设、领域本体映射、本体整合及语义标注模型，系统讨论基于顶级本体整合的医学领域信息资源语义标注模型要素。
第六章设计并实现了基于顶级本体整合的医学领域信息资源语义标注系统，并引入医学领域顶级本体进行针对医学信息资源的知识本体建设、本体整合、语义标注全过程测试，实证了语义标注方案的可行性，检验了语义标注系统的可用性，并综合探讨了语义标注过程中出现的问题及系统的特性。
第七章总结全文所做的工作并得出结论，展望基于顶级本体整合相关的语义标注研究在未来的发展前景。
本文实现了对医学信息资源进行基于顶级本体整合的语义标注，实证了医学顶级本体用于领域本体整合及语义标注的可行性。研究结果表明，基于顶级本体整合的语义标注系统是可靠的，采用顶级本体属性结构作为领域本体语义关系基础是具有后处理优势的，基于顶级本体的语义映射与本体整合是可行的，采用整合本体进行医学领域信息资源的语义标注是有效的。从实践层面实现了优化了医学领域本体构建过程，为医学领域本体的互操作提供了新的方案，同时拓展了医学信息资源的语义标注思路，为医学信息资源的高级语义应用打下良好基础。
研究所采用的语义标注方法不同于传统以单一本体为模型的标注系统，并区别于当前的多本体整合模式，采用基于医学领域顶级本体语义结构形式的整合本体标注策略，提出了以顶级本体为整合要素的整合本体语义标注模式，并以此为依据建立了医学领域语义标注原型系统，从而探索基于医学本体的语义标注模式新思路，为本体实现高级语义应用提供参考。研究的具体创新点体现为：
第一，顶级本体属性结构应用于领域本体构建。采取顶级本体属性扩展的方式表达领域本体的知识关系，以此方式构建的领域本体具有相对统一的语义表达框架，同时能够与顶级本体之间保持良好的交流，促进本体互操作。研究过程中出现的知识术语来源可靠；内容表达采用可自由转换的中英文双语；所构建本体具有顶级本体属性结构特征。
第二，顶级本体语义关系参与本体整合。以顶级本体属性框架为基础进行属性合并，在本体概念映射的基础上实现领域本体整合，形成合并本体，以此方式构建的合并本体具有清晰的语义框架，由于语义关系表达的一致性，对于后续的本体整合也具有指导意义。
第三，基于顶级本体整合本体的语义标注。相对于传统的单本体语义标注，整合本体具有知识体系更丰富的特性；相对于领域本体间无关联的多本体语义标注，整合本体具有知识关联更密切的特性；相对于单纯映射的多本体语义标注，基于顶级本体整合的语义标注具有知识表达更完整的特性。
With the high-speed development of the information technology, the role that theinformationization construction plays in promoting the exchange of the knowledge in themedical field has become more and more prominent. The quality of medical and healthinformationization construction depends on the scientific and effective medical informationresource organizations, and the medical field involves a great number of disciplines and a lotof knowledge in them are interleaving with other disciplines, making the knowledge in thefield complex. At present, the application of the medical information resources tends to thedevelopment in the network, a great number of information resources have been established.The information isolated islands, which are difficult to be identified semantically have beenestablished, and the traditional information organization mode has gradually become difficultin meeting the demand of transmission of the current medical information.
The Semantic Web technique has provided the new plan for resolving the sharingproblem of medical information resources. As the support technique of semantic applicationoriented to the next-generation network information resources, it can make the data processedand inquired in the form of machine understanding and realize the data interpretation andexchange between the computers via a series of languages, tools and techniques. As one of thecore techniques of the Semantic Web, the ontology can better express the semantic levels ofthe knowledge in such a field, and Semantic Annotation can use the ontology into the hugeinformation resources, make the resource as knowledge which has formal informationarchitecture with semantic relationships. Nonetheless, because the semantic isomerizationbetween the domain ontologies is more prominent, the semantic enrichment of semanticannotation is restricted, and the semantic annotation is just the general knowledge hierarchyfor indicating the upper-level semantic relationships of domain knowledgement.
The ontology semantic annotation mechanism with the semantic relation structure of theupper-level ontology in the medical field is studied via innovation and building of ontology,mapping and integration of ontology and semantic annotation, etc., an attempt is made tobuild semantic annotation system model of the medical field ontology based on theupper-level ontology integration, demonstrate the new thoughts of semantic annotation,explore the role of the ontology integration in promoting the semantic annotation effects, tryto realize the starting from the actual situation, study and resolve the semantic applicationbarriers of ontology existing in the reality so as to improve the semantic annotation level ofmedical information resources, promote the semantic application oriented to the networkmedical information resources and advance the sharing and knowledge discovery of medicalinformation resources. The contents of the thesis are mainly dealt with by focusing on thefollowing chapters:
ChapterⅠintroduces the time background and technical background of the topic of theproject, describes the present situation of development of the theory and technique related tothe project, points out the theoretical and realistic significance of the project, present thetargets, contents and methods of the project and the planning and layout is carried outaccording to the research thoughts.
Chapter Ⅱ systematically describes the basic theory and principles of mutual operationand semantic annotation with ontology. Discourse upon the main application techniques of thesemantic annotation based on upper-level ontology integration, mainly including somerelevant techniques such as ontology theory and relevant building of ontology, mapping andintegration of ontology, etc., semantic annotation theory and relevant technical methods, etc.
Chapter Ⅲ deals with the relevant mainstream tools and platforms of mapping andsemantic annotation of ontology in the relevant fields and the new methods and systemsoccurring in recent years in details and syudies the methods and techniques use by thesystems in details, compares the representative systems and summarizes the technicalcharacteristics and application directions for construction of the Semantic Annotation Basedon Upper-level Ontology Integration System.
Chapter Ⅳ studies the structure characteristics of information resource in the medicalfield, and analyzes the pattern of semantic annotation based on upper-level ontologyintegration.
Chapter Ⅴ design the domain ontology construction, domain ontology mapping,ontology integration and semantic annotation mode of medical information resources indetails basing on the analysis above, systematically discusses the semantic annotation methodelements of medical field information resources based on the upper-level ontologyintegration.
Chapter Ⅵ designs and realizes the semantic annotation system of medical fieldinformation resources based on the upper-level ontology integration, introduces theupper-level ontology in the medical field to carry out the knowledge ontology construction,ontology integration and whole process test of semantic annotation for the medicalinformation resources, demonstrates the feasibility of the semantic annotation plan, tests theusability of the semantic annotation system, summarizes and discusses the problems occurringin the semantic annotation and characteristics of the system.
Chapter Ⅶ summarizes the work done in the whole thesis and draws the conclusion andgives an outlook to the development prospect of the relevant semantic annotation researchbased on the upper-level ontology integration in the future.
The thesis realizes the semantic annotation of the medical information resources based onthe upper-level ontology integration and demonstrates the feasibility of the medicalupper-level ontology used for the domain ontology integration and semantic annotation. Theresearch results show that the semantic annotation system based on the upper-level ontologyintegration is reliable, it has the post-treatment advantage to take the upper-level ontologyattribute structure as the semantic relation basis of the domain ontology, the semanticmapping and ontology integration based on the upper-level ontology is feasible and it iseffective to take the integration ontology to carry out the semantic annotation of medical fieldinformation resources. The ontology building process in the medical field is realized and optimized from the level of practice, which provides the new plans for the mutual operation ofontology in the medical field, expands the semantic annotation thoughts of medicalinformation resources and lays a good foundation for the advanced semantic application ofmedical information resources.
The semantic annotation method taken in the project is different from that of theannotation system with the single traditional ontology as the model and different from thecurrent multi-ontology integration mode, the integration ontology annotation strategy basedon the semantic structure of the upper-level ontology in the medical field is taken, thesemantic annotation mode of integration ontology with the upper-level ontology as theintegration element is presented, based on which, the prototype system of semantic annotationin the medical field is built so as to explore the new thoughts of semantic annotation modebased n the medical ontology and provide the reference for the ontology to realize theadvanced semantic application. The detailed innovative points of the project are representedas follows:
First, the upper-level ontology attribute structure is applied in the building of domainontology. The method of upper-level ontology attribute expansion is taken to express theknowledge relation of domain ontology. The domain ontology built in such a mode has therelatively uniform semantic expression framework, and it is able to keep the good exchangewith the upper-level ontology and promote the mutual operation of ontology. The knowledgeterms occurring in the research have the reliable sources; both Chinese and English that canbe freely transformed are taken in the expression of the contents; the ontology built has thecharacteristics of the upper-level ontology attribute structure.
Second, the semantic relation of the upper-level ontology attends the ontology integration.The attribute integration is carried out on the basis of the upper-level ontology attributeframework, the domain ontology integration is realized and the integration ontology isestablished on the basis of the ontology concept mapping. The integration ontology built insuch a mode has the clear semantic framework. Because of the consistence of semanticrelation expressions, it is of importance of guiding the subsequent ontology integration.
Third, the semantic annotations of ontology are integrated on the basis of the upper-levelontology. Relative to the semantic annotation of the single traditional ontology, the integrationontology is characterized as the richer knowledge system; relative to the unrelatedmulti-ontology semantic annotations between the pieces of domain ontology, the integrationontology is characterized as closer knowledge relevance; relative to the pure mappedmulti-ontology semantic annotations, the semantic annotations based on the upper-levelontology integration are characterized as more complete knowledge expression.
语义网技术为解决医学信息资源的共享问题提供了新的方案，它作为面向下一代网络信息资源语义应用的支撑技术，可以使数据以机器理解的形式进行处理和查找，通过一系列的语言、工具和技术，实现计算机之间的数据解释交流。在这些技术中，本体作为语义网的核心能够较好的表达出领域知识的语义层次，语义标注则利用本体将普通的信息资源序化为具有知识层次的形式化信息，使庞大的信息资源以语义关联的规范化形式存在。但是，由于领域本体之间的语义异构情况逐渐突出，使得语义标注的语义富集度受到限制，而顶级本体正是揭示领域知识的高层语义关系的通用知识体系。
本文通过本体的创新构建、本体映射及整合、语义标注等工作，探讨具有医学领域顶级本体语义关系结构的本体语义标注工作机制，尝试建立基于顶级本体整合的医学领域本体语义标注系统模型，实证语义标注新思路，探索本体整合对于语义标注效果的促进作用，力求做到从实际出发，研究并解决现实中存在的本体语义应用障碍，进而提高医学信息资源的语义标注水平，推动面向网络医学信息资源的语义应用，促进医学信息资源的共享和知识发现。本文的内容主要围绕以下几个章节展开：
第一章介绍了本研究选题的时代背景与技术背景，说明了与本研究有关的理论和技术的发展现状，指出研究的理论及现实意义，并提出研究的目标、内容、方法，并针对研究思路进行规划和布局。
第二章对本体整合及语义标注的基本理论和原理进行系统描述，论述利用顶级本体进行整合及语义标注所涉及的主要技术，主要包括本体理论及有关的本体构建、本体映射和集成等有关技术，语义标注理论及相关技术方法等。
第三章详细阐述了本体整合及语义标注领域中主流的应用工具、平台，以及近年来出现的新方法、新系统，对其使用的方法、技术进行详细研究，并选取具有代表性的系统进行比较，总结其技术特点与应用方向，为基于顶级本体整合的语义标注系统建设提供依据。
第四章针对医学领域信息资源特点，深入研究医学领域中信息资源的结构形式，从语义模型的建立和标注方式选取的角度，分析基于顶级本体整合的语义标注模式。
第五章以前文分析为依据，详细设计医学信息资源的领域本体建设、领域本体映射、本体整合及语义标注模型，系统讨论基于顶级本体整合的医学领域信息资源语义标注模型要素。
第六章设计并实现了基于顶级本体整合的医学领域信息资源语义标注系统，并引入医学领域顶级本体进行针对医学信息资源的知识本体建设、本体整合、语义标注全过程测试，实证了语义标注方案的可行性，检验了语义标注系统的可用性，并综合探讨了语义标注过程中出现的问题及系统的特性。
第七章总结全文所做的工作并得出结论，展望基于顶级本体整合相关的语义标注研究在未来的发展前景。
本文实现了对医学信息资源进行基于顶级本体整合的语义标注，实证了医学顶级本体用于领域本体整合及语义标注的可行性。研究结果表明，基于顶级本体整合的语义标注系统是可靠的，采用顶级本体属性结构作为领域本体语义关系基础是具有后处理优势的，基于顶级本体的语义映射与本体整合是可行的，采用整合本体进行医学领域信息资源的语义标注是有效的。从实践层面实现了优化了医学领域本体构建过程，为医学领域本体的互操作提供了新的方案，同时拓展了医学信息资源的语义标注思路，为医学信息资源的高级语义应用打下良好基础。
研究所采用的语义标注方法不同于传统以单一本体为模型的标注系统，并区别于当前的多本体整合模式，采用基于医学领域顶级本体语义结构形式的整合本体标注策略，提出了以顶级本体为整合要素的整合本体语义标注模式，并以此为依据建立了医学领域语义标注原型系统，从而探索基于医学本体的语义标注模式新思路，为本体实现高级语义应用提供参考。研究的具体创新点体现为：
第一，顶级本体属性结构应用于领域本体构建。采取顶级本体属性扩展的方式表达领域本体的知识关系，以此方式构建的领域本体具有相对统一的语义表达框架，同时能够与顶级本体之间保持良好的交流，促进本体互操作。研究过程中出现的知识术语来源可靠；内容表达采用可自由转换的中英文双语；所构建本体具有顶级本体属性结构特征。
第二，顶级本体语义关系参与本体整合。以顶级本体属性框架为基础进行属性合并，在本体概念映射的基础上实现领域本体整合，形成合并本体，以此方式构建的合并本体具有清晰的语义框架，由于语义关系表达的一致性，对于后续的本体整合也具有指导意义。
第三，基于顶级本体整合本体的语义标注。相对于传统的单本体语义标注，整合本体具有知识体系更丰富的特性；相对于领域本体间无关联的多本体语义标注，整合本体具有知识关联更密切的特性；相对于单纯映射的多本体语义标注，基于顶级本体整合的语义标注具有知识表达更完整的特性。
With the high-speed development of the information technology, the role that theinformationization construction plays in promoting the exchange of the knowledge in themedical field has become more and more prominent. The quality of medical and healthinformationization construction depends on the scientific and effective medical informationresource organizations, and the medical field involves a great number of disciplines and a lotof knowledge in them are interleaving with other disciplines, making the knowledge in thefield complex. At present, the application of the medical information resources tends to thedevelopment in the network, a great number of information resources have been established.The information isolated islands, which are difficult to be identified semantically have beenestablished, and the traditional information organization mode has gradually become difficultin meeting the demand of transmission of the current medical information.
The Semantic Web technique has provided the new plan for resolving the sharingproblem of medical information resources. As the support technique of semantic applicationoriented to the next-generation network information resources, it can make the data processedand inquired in the form of machine understanding and realize the data interpretation andexchange between the computers via a series of languages, tools and techniques. As one of thecore techniques of the Semantic Web, the ontology can better express the semantic levels ofthe knowledge in such a field, and Semantic Annotation can use the ontology into the hugeinformation resources, make the resource as knowledge which has formal informationarchitecture with semantic relationships. Nonetheless, because the semantic isomerizationbetween the domain ontologies is more prominent, the semantic enrichment of semanticannotation is restricted, and the semantic annotation is just the general knowledge hierarchyfor indicating the upper-level semantic relationships of domain knowledgement.
The ontology semantic annotation mechanism with the semantic relation structure of theupper-level ontology in the medical field is studied via innovation and building of ontology,mapping and integration of ontology and semantic annotation, etc., an attempt is made tobuild semantic annotation system model of the medical field ontology based on theupper-level ontology integration, demonstrate the new thoughts of semantic annotation,explore the role of the ontology integration in promoting the semantic annotation effects, tryto realize the starting from the actual situation, study and resolve the semantic applicationbarriers of ontology existing in the reality so as to improve the semantic annotation level ofmedical information resources, promote the semantic application oriented to the networkmedical information resources and advance the sharing and knowledge discovery of medicalinformation resources. The contents of the thesis are mainly dealt with by focusing on thefollowing chapters:
ChapterⅠintroduces the time background and technical background of the topic of theproject, describes the present situation of development of the theory and technique related tothe project, points out the theoretical and realistic significance of the project, present thetargets, contents and methods of the project and the planning and layout is carried outaccording to the research thoughts.
Chapter Ⅱ systematically describes the basic theory and principles of mutual operationand semantic annotation with ontology. Discourse upon the main application techniques of thesemantic annotation based on upper-level ontology integration, mainly including somerelevant techniques such as ontology theory and relevant building of ontology, mapping andintegration of ontology, etc., semantic annotation theory and relevant technical methods, etc.
Chapter Ⅲ deals with the relevant mainstream tools and platforms of mapping andsemantic annotation of ontology in the relevant fields and the new methods and systemsoccurring in recent years in details and syudies the methods and techniques use by thesystems in details, compares the representative systems and summarizes the technicalcharacteristics and application directions for construction of the Semantic Annotation Basedon Upper-level Ontology Integration System.
Chapter Ⅳ studies the structure characteristics of information resource in the medicalfield, and analyzes the pattern of semantic annotation based on upper-level ontologyintegration.
Chapter Ⅴ design the domain ontology construction, domain ontology mapping,ontology integration and semantic annotation mode of medical information resources indetails basing on the analysis above, systematically discusses the semantic annotation methodelements of medical field information resources based on the upper-level ontologyintegration.
Chapter Ⅵ designs and realizes the semantic annotation system of medical fieldinformation resources based on the upper-level ontology integration, introduces theupper-level ontology in the medical field to carry out the knowledge ontology construction,ontology integration and whole process test of semantic annotation for the medicalinformation resources, demonstrates the feasibility of the semantic annotation plan, tests theusability of the semantic annotation system, summarizes and discusses the problems occurringin the semantic annotation and characteristics of the system.
Chapter Ⅶ summarizes the work done in the whole thesis and draws the conclusion andgives an outlook to the development prospect of the relevant semantic annotation researchbased on the upper-level ontology integration in the future.
The thesis realizes the semantic annotation of the medical information resources based onthe upper-level ontology integration and demonstrates the feasibility of the medicalupper-level ontology used for the domain ontology integration and semantic annotation. Theresearch results show that the semantic annotation system based on the upper-level ontologyintegration is reliable, it has the post-treatment advantage to take the upper-level ontologyattribute structure as the semantic relation basis of the domain ontology, the semanticmapping and ontology integration based on the upper-level ontology is feasible and it iseffective to take the integration ontology to carry out the semantic annotation of medical fieldinformation resources. The ontology building process in the medical field is realized and optimized from the level of practice, which provides the new plans for the mutual operation ofontology in the medical field, expands the semantic annotation thoughts of medicalinformation resources and lays a good foundation for the advanced semantic application ofmedical information resources.
The semantic annotation method taken in the project is different from that of theannotation system with the single traditional ontology as the model and different from thecurrent multi-ontology integration mode, the integration ontology annotation strategy basedon the semantic structure of the upper-level ontology in the medical field is taken, thesemantic annotation mode of integration ontology with the upper-level ontology as theintegration element is presented, based on which, the prototype system of semantic annotationin the medical field is built so as to explore the new thoughts of semantic annotation modebased n the medical ontology and provide the reference for the ontology to realize theadvanced semantic application. The detailed innovative points of the project are representedas follows:
First, the upper-level ontology attribute structure is applied in the building of domainontology. The method of upper-level ontology attribute expansion is taken to express theknowledge relation of domain ontology. The domain ontology built in such a mode has therelatively uniform semantic expression framework, and it is able to keep the good exchangewith the upper-level ontology and promote the mutual operation of ontology. The knowledgeterms occurring in the research have the reliable sources; both Chinese and English that canbe freely transformed are taken in the expression of the contents; the ontology built has thecharacteristics of the upper-level ontology attribute structure.
Second, the semantic relation of the upper-level ontology attends the ontology integration.The attribute integration is carried out on the basis of the upper-level ontology attributeframework, the domain ontology integration is realized and the integration ontology isestablished on the basis of the ontology concept mapping. The integration ontology built insuch a mode has the clear semantic framework. Because of the consistence of semanticrelation expressions, it is of importance of guiding the subsequent ontology integration.
Third, the semantic annotations of ontology are integrated on the basis of the upper-levelontology. Relative to the semantic annotation of the single traditional ontology, the integrationontology is characterized as the richer knowledge system; relative to the unrelatedmulti-ontology semantic annotations between the pieces of domain ontology, the integrationontology is characterized as closer knowledge relevance; relative to the pure mappedmulti-ontology semantic annotations, the semantic annotations based on the upper-levelontology integration are characterized as more complete knowledge expression.
引文
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