设备功能视点下的海洋生态本体构建及应用研究
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摘要
21世纪被称为海洋的世纪，计算机智能信息处理技术与海洋科学的结合，也即“数字海洋”成为科技发展的趋势，而海洋科技信息的存储、表示和处理技术是“数字海洋”发展的基础。许多国家的能源、生态、环境、地理等众多机构对海洋进行了长期的研究，留下了许多有价值的观测数据、实验结果和文献资料，这些数据为海洋科学研究提供了有力的数据基础。
但是，由于海洋数据来源和表示的多样性，集成利用和共享这些数据资料存在许多问题：如数据格式不统一，数据收集、统计的角度不同，同义词，一词多义，术语分类不明确等问题。本体作为“共享概念模型明确的形式化的规范说明”，用于捕获相关领域的知识，提供对该领域知识的共同理解。本体与其它概念模型的不同在于本体是用严格一致的视点来确定概念、概念之间的等级层次（is-a）或整体部分（part-of）关系，即本体确定了所有组织结构共同认可的语义一致约定，所以本体能够作为一个中间件在这些不同机构之间实现数据共享和合作。
海洋生态系统包含海洋、盐泽、河口、珊瑚礁、深海和海底，对于海洋和陆地环境健康非常重要。生态保护和危机管理正不断地受到全世界海洋科学研究机构、政府、水产养殖和其他机构越来越多的关注。显然，从一个明确的视点进行本体建模对于这些机构之间的协作是至关重要的。
能量流动和物质循环是海洋生态系统的两个基本过程，正是这两个过程使各种生物因子、非生物因子以及它们之间的相互作用组成一个完整的功能单元。本文借鉴工程领域文献中的“功能”概念，把物质循环、能量流动等过程看成功能，物理实体（包含海洋生物和海洋）看成设备，由主动体agent执行这些功能。
本文确定“设备功能”视点，提出海洋生态领域上层本体，指导构建了海洋生态系统的概念模型。扩展了OWL-DL语法、语义，用于海洋生态形式化本体的表示。基于构建的海洋生态形式化OWL本体和SWRL规则，开发了海洋生态知识管理系统，为用户提供一个海洋科学研究与合作的语义支撑平台。本文的研究内容主要包括如下5个方面：
（1）研究本体建模方法和相关理论，提出了基于知识工程的领域本体构建方法，指导构建海洋生态本体概念模型和形式化本体；
（2）针对海洋生态系统的知识特点，提出海洋生态静态结构和动态功能作用过程的知识组织模型；确定“设备功能”视点，构建海洋生态领域上层本体，为海洋生态领域知识表达和海洋生态问题的研究提供了统一明确的视点；
（3）借鉴扩展Kitamura设备功能知识框架理论，构建了海洋生态功能过程模型（包含行为模型、碳循环、营养行为、物质循环等）；基于Mizoguchi提出的HOZO角色理论，构建了海洋生态概念模型（包含海洋生物本体、海洋环境本体、物质代谢原料本体、海洋水文地理本体）。采用HOZO编辑工具，进行建模，生成了图形化、可视化的海洋生态本体；
（4）分析了本体描述语言OWL-DL在角色表达方面的不足，对OWL-DL的语法、语义进行扩展，提出面向过程的OWL-Process模型，对海洋生态功能过程本体和实例进行了OWL-Process形式化语义描述；在Protégé平台下，对海洋生态领域上层本体和海洋生态领域知识本体用OWL-DL形式化编码；针对海洋生态异常现象，构建相应的SWRL规则库；
（5）基于构建的海洋生态本体知识库，研究语义检索和本体规则推理，开发了海洋生态知识管理系统，实现了海洋生态知识导航、语义查询、知识检索和生态危机预警功能。通过不断完善SWRL规则库，加强本体规则推理，尝试为海洋生态危机提供较为准确的预警信息，在海洋生态环境保护和海洋生态危机预警方面发挥积极的作用。
The21st century is said to be the century of ocean. The combination ofintelligent information processing technology and marine science gives rise to a newresearch field, called “digital marine”. Many researches (e.g., those on energy,ecology, environment, and so on) have been carried out by many countries for a longtime. Throughout these researches, there left many valuable documents such asobservational data, experimental results, papers, and patents as well, which provide anabundant data foundation for marine science research.
However, these documents are hardly shared or reused sufficiently amonginstitutes due to the differences both in the format and in teleological or taxonomicalviewpoints. Ontology as “a formal, explicit specification of a sharedconceptualization” captures related domain knowledge, and provides a shared andcommon understanding of a specific domain. The difference between ontology andother concept model is that ontology takes a strictly consistent viewpoint to specifyconcepts, and the hierarchical (is-a) or mereological (part-of) relations betweenconcepts as well. That is, ontology specifies a semantic-consistent agreement to whichall parties should commit, and thus can be used as a middleware to facilitate datasharing and cooperation among these institutes.
Marine ecosystems, including oceans, salt marsh, estuaries, coral reefs, the deepsea and the sea floor, are very important for the overall health of both marine andterrestrial environments. Ecological protection and crisis management arecontinuously receiving increased attention in the worldwide marine communityincluding researchers, governments, aqua culturists and other agencies. Certainly,ontology modeling from a fixed viewpoint is crucial for the cooperation among allthese parties.
Energy flow and matter cycle are two basic processes in marine ecosystem.Involved in these two processes are various biological factors, non-biological factors, and the interactions among all these factors. Referring to engineering field literaturethat the “function” concept is used to describe these processes, this paper fixes aviewpoint of device-function, which looks processes in matter cycle as functions, andphysical entities (including marine lives and ocean itself) as devices, the agent whichcarries out such functions.
By fixing such a viewpoint, this paper presents an upper ontology for marineecology, and then constructs a conceptual model for marine ecosystem. An extensionto OWL is also made for formal representation of the ontology. Based on the formalrepresentation and SWRL rules, a marine ecological knowledge management systemis developed, which provides users a semantic support platform for marine scientificresearch and cooperation. This paper focuses on the following five topics.
(1) By studying ontology modeling theory and methodology, a knowledge engineeringapproach is proposed to construct marine ecological concept model and formalontology.
(2) According to marine ecological knowledge characteristics, a marine ecologicalknowledge organization model which includes static structure and dynamic functionknowledge is proposed. This paper fixes a viewpoint of device-function, andconstructs a marine ecological upper ontology, and thus provides a unified viewpointfor the systematization of marine ecological knowledge and corresponding researches.
(3) By extending the functional knowledge representing framework proposed byKitamura, a functional model of marine ecosystem is built, and then based on the roletheory proposed by Mizoguchi, a marine ecosystem conceptual model (includingmarine biology ontology, marine environment ontology, physical metabolic materialontology, marine hydrological ontology) is constructed.
(4) Due to OWL lacks of enough role expressive ability, it is difficult to expresscomplicated dynamic functional knowledge by using the standard OWL. Byextending OWL syntax and semantic, this paper proposes OWL-Process model, andthen constructs marine ecological function ontology and its instances; In Protégéplatform, marine ecological upper ontology and marine ecological knowledgeontology are formally coded in OWL-Process; According to marine ecological abnormal phenomenon principle, this paper constructs the corresponding SWRL rulesets.
(5) Based on marine ecological ontology knowledge base, this paper researchessemantic retrieval and ontology rule reasoning, and develops a marine ecologicalknowledge management system, which implements marine ecological knowledgenavigation, semantic query, knowledge retrieval and ecological crisis warningfunction. Through enriching SWRL rule sets, strengthening ontology rule reasoning,this research tries to provide marine ecological crisis warning more accurately, and toplay positive role in marine ecological environmental protection and marineecological crisis warning.
但是，由于海洋数据来源和表示的多样性，集成利用和共享这些数据资料存在许多问题：如数据格式不统一，数据收集、统计的角度不同，同义词，一词多义，术语分类不明确等问题。本体作为“共享概念模型明确的形式化的规范说明”，用于捕获相关领域的知识，提供对该领域知识的共同理解。本体与其它概念模型的不同在于本体是用严格一致的视点来确定概念、概念之间的等级层次（is-a）或整体部分（part-of）关系，即本体确定了所有组织结构共同认可的语义一致约定，所以本体能够作为一个中间件在这些不同机构之间实现数据共享和合作。
海洋生态系统包含海洋、盐泽、河口、珊瑚礁、深海和海底，对于海洋和陆地环境健康非常重要。生态保护和危机管理正不断地受到全世界海洋科学研究机构、政府、水产养殖和其他机构越来越多的关注。显然，从一个明确的视点进行本体建模对于这些机构之间的协作是至关重要的。
能量流动和物质循环是海洋生态系统的两个基本过程，正是这两个过程使各种生物因子、非生物因子以及它们之间的相互作用组成一个完整的功能单元。本文借鉴工程领域文献中的“功能”概念，把物质循环、能量流动等过程看成功能，物理实体（包含海洋生物和海洋）看成设备，由主动体agent执行这些功能。
本文确定“设备功能”视点，提出海洋生态领域上层本体，指导构建了海洋生态系统的概念模型。扩展了OWL-DL语法、语义，用于海洋生态形式化本体的表示。基于构建的海洋生态形式化OWL本体和SWRL规则，开发了海洋生态知识管理系统，为用户提供一个海洋科学研究与合作的语义支撑平台。本文的研究内容主要包括如下5个方面：
（1）研究本体建模方法和相关理论，提出了基于知识工程的领域本体构建方法，指导构建海洋生态本体概念模型和形式化本体；
（2）针对海洋生态系统的知识特点，提出海洋生态静态结构和动态功能作用过程的知识组织模型；确定“设备功能”视点，构建海洋生态领域上层本体，为海洋生态领域知识表达和海洋生态问题的研究提供了统一明确的视点；
（3）借鉴扩展Kitamura设备功能知识框架理论，构建了海洋生态功能过程模型（包含行为模型、碳循环、营养行为、物质循环等）；基于Mizoguchi提出的HOZO角色理论，构建了海洋生态概念模型（包含海洋生物本体、海洋环境本体、物质代谢原料本体、海洋水文地理本体）。采用HOZO编辑工具，进行建模，生成了图形化、可视化的海洋生态本体；
（4）分析了本体描述语言OWL-DL在角色表达方面的不足，对OWL-DL的语法、语义进行扩展，提出面向过程的OWL-Process模型，对海洋生态功能过程本体和实例进行了OWL-Process形式化语义描述；在Protégé平台下，对海洋生态领域上层本体和海洋生态领域知识本体用OWL-DL形式化编码；针对海洋生态异常现象，构建相应的SWRL规则库；
（5）基于构建的海洋生态本体知识库，研究语义检索和本体规则推理，开发了海洋生态知识管理系统，实现了海洋生态知识导航、语义查询、知识检索和生态危机预警功能。通过不断完善SWRL规则库，加强本体规则推理，尝试为海洋生态危机提供较为准确的预警信息，在海洋生态环境保护和海洋生态危机预警方面发挥积极的作用。
The21st century is said to be the century of ocean. The combination ofintelligent information processing technology and marine science gives rise to a newresearch field, called “digital marine”. Many researches (e.g., those on energy,ecology, environment, and so on) have been carried out by many countries for a longtime. Throughout these researches, there left many valuable documents such asobservational data, experimental results, papers, and patents as well, which provide anabundant data foundation for marine science research.
However, these documents are hardly shared or reused sufficiently amonginstitutes due to the differences both in the format and in teleological or taxonomicalviewpoints. Ontology as “a formal, explicit specification of a sharedconceptualization” captures related domain knowledge, and provides a shared andcommon understanding of a specific domain. The difference between ontology andother concept model is that ontology takes a strictly consistent viewpoint to specifyconcepts, and the hierarchical (is-a) or mereological (part-of) relations betweenconcepts as well. That is, ontology specifies a semantic-consistent agreement to whichall parties should commit, and thus can be used as a middleware to facilitate datasharing and cooperation among these institutes.
Marine ecosystems, including oceans, salt marsh, estuaries, coral reefs, the deepsea and the sea floor, are very important for the overall health of both marine andterrestrial environments. Ecological protection and crisis management arecontinuously receiving increased attention in the worldwide marine communityincluding researchers, governments, aqua culturists and other agencies. Certainly,ontology modeling from a fixed viewpoint is crucial for the cooperation among allthese parties.
Energy flow and matter cycle are two basic processes in marine ecosystem.Involved in these two processes are various biological factors, non-biological factors, and the interactions among all these factors. Referring to engineering field literaturethat the “function” concept is used to describe these processes, this paper fixes aviewpoint of device-function, which looks processes in matter cycle as functions, andphysical entities (including marine lives and ocean itself) as devices, the agent whichcarries out such functions.
By fixing such a viewpoint, this paper presents an upper ontology for marineecology, and then constructs a conceptual model for marine ecosystem. An extensionto OWL is also made for formal representation of the ontology. Based on the formalrepresentation and SWRL rules, a marine ecological knowledge management systemis developed, which provides users a semantic support platform for marine scientificresearch and cooperation. This paper focuses on the following five topics.
(1) By studying ontology modeling theory and methodology, a knowledge engineeringapproach is proposed to construct marine ecological concept model and formalontology.
(2) According to marine ecological knowledge characteristics, a marine ecologicalknowledge organization model which includes static structure and dynamic functionknowledge is proposed. This paper fixes a viewpoint of device-function, andconstructs a marine ecological upper ontology, and thus provides a unified viewpointfor the systematization of marine ecological knowledge and corresponding researches.
(3) By extending the functional knowledge representing framework proposed byKitamura, a functional model of marine ecosystem is built, and then based on the roletheory proposed by Mizoguchi, a marine ecosystem conceptual model (includingmarine biology ontology, marine environment ontology, physical metabolic materialontology, marine hydrological ontology) is constructed.
(4) Due to OWL lacks of enough role expressive ability, it is difficult to expresscomplicated dynamic functional knowledge by using the standard OWL. Byextending OWL syntax and semantic, this paper proposes OWL-Process model, andthen constructs marine ecological function ontology and its instances; In Protégéplatform, marine ecological upper ontology and marine ecological knowledgeontology are formally coded in OWL-Process; According to marine ecological abnormal phenomenon principle, this paper constructs the corresponding SWRL rulesets.
(5) Based on marine ecological ontology knowledge base, this paper researchessemantic retrieval and ontology rule reasoning, and develops a marine ecologicalknowledge management system, which implements marine ecological knowledgenavigation, semantic query, knowledge retrieval and ecological crisis warningfunction. Through enriching SWRL rule sets, strengthening ontology rule reasoning,this research tries to provide marine ecological crisis warning more accurately, and toplay positive role in marine ecological environmental protection and marineecological crisis warning.
引文
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