鲽形目分类检索及分子生物学应用模式研究
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摘要
进入21世纪以来,由于分类学对生物多样性的重要基础作用,渔业、环境保护、生态学和系统学研究等领域的国际组织等对重振分类学研究高度重视,挖掘与分享分类学信息成为生物多样性公约(CBD)框架下全球生物分类倡议(GTI)的热点议题。为实现自然生物资源的可持续利用,GTI不遗余力地解决CDB贯彻执行中的“分类学障碍”问题。分类学信息的数字化和弥合应用进程不断加快,传统知识数字化、信息存储数字化、数据标准统一化和共享网络化成为分类学信息化发展的必然趋势。但自林奈和拉马克以来,分类阶元系统及描述和分类检索表等分类学研究成果大多是以纸质方式保存,其内容丰富、种类繁多、结构复杂、数量庞大,数字化工作难以一蹴而就,大量沉睡在图书馆、博物馆和档案室里分类学资料等待处理;同时少量数字化信息分散在多个不同结构的数据库中。由于缺少有效的数字化工具,尤其是缺乏能弥和传统分类信息和分子序列信息的软件,在物种分类检索和亲缘关系研究过程中,信息集成与关联分析十分不便。
鲽形目鱼类进化历史悠久复杂,形态构造呈特殊的不对称性,许多种类因美味可口而具有重要经济价值,开展分类学研究有典型的生物学代表意义和生产指导意义,但其分类系统至今尚未统一。论文依托前期工作基础,通过设计专项数据库、建立标准化数据索引和开发流程化分类学功能模块,探索将信息要素和分类检索研究方法有机融为一体的技术方法,研究了形态构造特征信息和分子序列信息的弥合模式,设计研制了以分类阶元系统为目录索引,以分类检索表、分子标记、DNA条码分子鉴定、生物学参考信息、参考文献和亲缘关系分析等为主要功能组成和应用方向的《鲽形目分类信息分析系统(Pleuronectiformes Taxonomy Information Analysis System)》(简称《鲽形目分类系统,PTIAS》;著作权登记号2009SR02219),建立了鲽形目分类学信息软件开发模式。
1.基于GTI规划的2008-2020年分类学产出,建立了鲽形目分类学数据源综合模糊评价体系。在对数据源进行初步评估、筛选和归类的基础上,分析了不同数据源内容、结构及其相互间关系,设计了适用于PTIAS系统的元数据、索引体系和数据库模式,为分类检索系统的开发奠定了数据基础。
2.设计了可兼容不同GTI数据库分类目录的数字化分类阶元系统。基于树型数据窗口(Treeview Datawindow),建立了可扩展上下级阶元、可任意组合不同阶元的数字化分类阶元系统模块,为动态应用阶元组合动态整合数据、开展信息比较分析、构建专项数据库等数据操作等奠定了索引目录结构基础。
3、提出了定距式二歧检索表BiosKey算法。建立了以数据过滤模式调取检索表的特征性状并进行组合查询的方法,讨论了传统二歧检索表的树数据结构的同组层无序化特征,及其将之与二叉树结构进行辨分的必要性,为纸质分类检索表的数字化提供了新的工具。同时,基于各种系统的树结构相似性、阶层体系相似性和物种阶元单位的高度一致性,探索了将BiosKey算法应用于建立支序回溯系统,用以集成各类系统信息的可行性。
4.从序列信息检索直观化角度出发,基于mtDNA和nDNA基因组结构和数据窗口(Datawindow, DW),建立了直观的分子标记热键检索模式;设计了通过鼠标控制函数检索DNA条码、分子标记等序列信息,并与分类系统目录进行阶元关联的方法。
5.研究了大尺寸数据库的快速处理技术,同时建立了不同DOS模式的Blast、Clustal、Phylip软件包的Windows平台运行的优化环境。为加速数据检索、提取和数据库重建,设计了将数据存储(Datastore)嵌入内存数据块进行索引化操作的快速算法,为Windows系统中大文件访问与处理中的I/O与内存限制的瓶颈技术问题。
6.研究了以平台模块方式处理不同分类学信息的系统设计与构建方法。按分别设计、系统集成模式,开发了9个数据模块、9个分类学功能模块和3个数据处理辅助模块。各种标准化数据用于有序化伺服系统初始化、数据库和检索索引,或通过程序内建函数转化为分类学专业格式如林奈分类目录、分类检索表、分子序列表和系统发育树等,或为系统的可见与不可见控件如选择列表、数据存储索引等提供初始化参数。
7.针对GTI分类学信息门户,基于微软Web浏览控件建立了物种Web信息浏览与编辑工具,方便于使用者自定制Web信息的采集与管理,并基于复合索引实现了Web信息与系统阶元目录的有效关联。
Since the beginning of the 21st Century, international organizations specializing in fishery, ecology and environmental protection, and systemics studies have been attaching primary importance to taxonomy for its fundamental role in biodiversity studies. Protocols on unearthing and sharing taxonomic information have become a hotspot issue of the Global Taxonomy Initiative (GTI) under the Convention on Biological Diversity (CBD). GTI spares no effort to tackle the“taxonomic impediment”which seriously hinders the taxonomic applications to the sustained exploitation of natural biological resources. Henceforth the digital taxonomic information system has been promoted at such an accelerated speed that it is inevitable to digitalize storage of existing knowledge, share the network and standardize the integrated data. However, following Linnaeus, almost all research results on classification were kept in printed format with abundant contents, rich types, complex structures and plentiful numbers of languages. At present, taxonomic data still scatters in different subject databases with most technical literature slumbering in libraries, museums and archives. The fact that few types of software are designed for exploitation and digitalization of the traditional taxonomic information, especially the lack of a system to bridge the traditional taxonomic data and the molecular sequences, increases the difficulty in connecting various data for comprehensive applications.
Pleuronectiformes(flatfish)is an order with special asymmetric shape and structure, and a long complicated history of evolution. Many species of the order are of great importance to the local economy for their valuable relish. Taxonomy research is meaningful for both biological studies and aquaculture production, but up to now the taxonomic system remains unintegrated.
For exploring the methods to integrate all of the taxonomic information of the specific taxa under a Windows application, this thesis develops a program named“Pleuronectiformes Taxonomy Information Analysis System (PTIAS)”(National copyright registration number: 2009SR02219) to find out the techniques for bridging and transforming taxa/taxon taxonomic information to specialized corresponding formats,such as taxonomy system, identification keys, molecular markers, DNA barcodes, phylogeny tree, bibliographies and other taxonomic references.
1. Illustrate the method of constructing taxonomic data modules for PTIAS. Based on taxonomy outputs of GTI scheme from 2008 to 2020, the thesis first built a comprehensive evaluation module by fuzzy analysis, then evaluated, selected and categorized data sources with a standpoint of taxonomy, and then analyzed the structure, content and relations among various databases, and finally designed a metadata and index system with a database module for PTIAS.
2. Design a digital taxonomy system module for integrating different taxonomic catalogs from GTI databases to PTIAS. Based on treeview database, the thesis established an extendable stratum module, able to stretch to all taxon levels and compose any taxon or taxa combination to bridge taxonomic information. The module is designed as the basic component for data connection, comparably analysis, database reconstruction and other data processing of certain species group dynamically designated.
3. Devise a BiosKey algorithm for traditional identification keys and Cladistics Trackback System of PTIAS. Based on keys in printed format and attributes of datawindow, the thesis studies a concise tree module, extendable to display pictures of shape characteristics of flatfishes, and able to apply in multi-key searching, forming an index mechanism for deriving terminology words from original keys. The necessity of distinguishing structure of dichotomous key from binary tree is discussed, since there is no sub node with priority of order or comparable values in the same level during the procession of dichotomous grouping. For probing the possibility of integrating necessary information of phylogenetic systems and Linnaean system and even identification keys, a digital Cladistics Traceback System is suggested to be used for integrating various system viewpoints based on the similar tree data structure, the collective taxa strata and the completely unified species taxon of all systems.
4. Present a visual hot-key index module for molecular markers of PTIAS. Based on genome structure of mtDNA and nDNA, the graphic markers are put into datawindow as functional buttons of indexes for retrieving sequence records. Each hot-key is traced by the mousemove function, and is bound to retrieving indexes and data of DNA barcodes, molecular markers and the taxonomic catalog when activated.
5. Study on a rapid processing method for large database and build an optimized the local environment for Blast, Clustal W and Phylip package with different MS-DOS modes under Windows system. For accelerating date retrieving, data extracting and database reconstructing, data-store technique was infixed to file mapping process to lead indexes searching into data blocks of memory. Using a settable small amount of buffer, the rapid method could completely overcome the choke point of I/O and memory when dealing with big files.
6. Research on the method of designing a system and the construction of using platform modules for different taxonomic information. The 9 data modules, 9 taxonomic functional modules and 3 data processing service modules are separately designed and integrated in PTIAS. All of the standardized data functions orderly for platform initialization, databases, indexes, and the taxonomic formats automatically transformed by the built-in program functions such as Linnaean system, identification key, molecular sequence table and phylogenetic tree, as well as initialization parameters for visible or invisible controls like datawindows, dropdown lists and dynamic datastores, etc..
7. Scheme an online data retrieving, editing and extracting method for GTI taxonomic databases. Microsoft web browse active control is employed to develop the component of taxonomic reference information module, and indexes for GTI portals are used to bridge taxonomy catalog and bind information.
鲽形目鱼类进化历史悠久复杂,形态构造呈特殊的不对称性,许多种类因美味可口而具有重要经济价值,开展分类学研究有典型的生物学代表意义和生产指导意义,但其分类系统至今尚未统一。论文依托前期工作基础,通过设计专项数据库、建立标准化数据索引和开发流程化分类学功能模块,探索将信息要素和分类检索研究方法有机融为一体的技术方法,研究了形态构造特征信息和分子序列信息的弥合模式,设计研制了以分类阶元系统为目录索引,以分类检索表、分子标记、DNA条码分子鉴定、生物学参考信息、参考文献和亲缘关系分析等为主要功能组成和应用方向的《鲽形目分类信息分析系统(Pleuronectiformes Taxonomy Information Analysis System)》(简称《鲽形目分类系统,PTIAS》;著作权登记号2009SR02219),建立了鲽形目分类学信息软件开发模式。
1.基于GTI规划的2008-2020年分类学产出,建立了鲽形目分类学数据源综合模糊评价体系。在对数据源进行初步评估、筛选和归类的基础上,分析了不同数据源内容、结构及其相互间关系,设计了适用于PTIAS系统的元数据、索引体系和数据库模式,为分类检索系统的开发奠定了数据基础。
2.设计了可兼容不同GTI数据库分类目录的数字化分类阶元系统。基于树型数据窗口(Treeview Datawindow),建立了可扩展上下级阶元、可任意组合不同阶元的数字化分类阶元系统模块,为动态应用阶元组合动态整合数据、开展信息比较分析、构建专项数据库等数据操作等奠定了索引目录结构基础。
3、提出了定距式二歧检索表BiosKey算法。建立了以数据过滤模式调取检索表的特征性状并进行组合查询的方法,讨论了传统二歧检索表的树数据结构的同组层无序化特征,及其将之与二叉树结构进行辨分的必要性,为纸质分类检索表的数字化提供了新的工具。同时,基于各种系统的树结构相似性、阶层体系相似性和物种阶元单位的高度一致性,探索了将BiosKey算法应用于建立支序回溯系统,用以集成各类系统信息的可行性。
4.从序列信息检索直观化角度出发,基于mtDNA和nDNA基因组结构和数据窗口(Datawindow, DW),建立了直观的分子标记热键检索模式;设计了通过鼠标控制函数检索DNA条码、分子标记等序列信息,并与分类系统目录进行阶元关联的方法。
5.研究了大尺寸数据库的快速处理技术,同时建立了不同DOS模式的Blast、Clustal、Phylip软件包的Windows平台运行的优化环境。为加速数据检索、提取和数据库重建,设计了将数据存储(Datastore)嵌入内存数据块进行索引化操作的快速算法,为Windows系统中大文件访问与处理中的I/O与内存限制的瓶颈技术问题。
6.研究了以平台模块方式处理不同分类学信息的系统设计与构建方法。按分别设计、系统集成模式,开发了9个数据模块、9个分类学功能模块和3个数据处理辅助模块。各种标准化数据用于有序化伺服系统初始化、数据库和检索索引,或通过程序内建函数转化为分类学专业格式如林奈分类目录、分类检索表、分子序列表和系统发育树等,或为系统的可见与不可见控件如选择列表、数据存储索引等提供初始化参数。
7.针对GTI分类学信息门户,基于微软Web浏览控件建立了物种Web信息浏览与编辑工具,方便于使用者自定制Web信息的采集与管理,并基于复合索引实现了Web信息与系统阶元目录的有效关联。
Since the beginning of the 21st Century, international organizations specializing in fishery, ecology and environmental protection, and systemics studies have been attaching primary importance to taxonomy for its fundamental role in biodiversity studies. Protocols on unearthing and sharing taxonomic information have become a hotspot issue of the Global Taxonomy Initiative (GTI) under the Convention on Biological Diversity (CBD). GTI spares no effort to tackle the“taxonomic impediment”which seriously hinders the taxonomic applications to the sustained exploitation of natural biological resources. Henceforth the digital taxonomic information system has been promoted at such an accelerated speed that it is inevitable to digitalize storage of existing knowledge, share the network and standardize the integrated data. However, following Linnaeus, almost all research results on classification were kept in printed format with abundant contents, rich types, complex structures and plentiful numbers of languages. At present, taxonomic data still scatters in different subject databases with most technical literature slumbering in libraries, museums and archives. The fact that few types of software are designed for exploitation and digitalization of the traditional taxonomic information, especially the lack of a system to bridge the traditional taxonomic data and the molecular sequences, increases the difficulty in connecting various data for comprehensive applications.
Pleuronectiformes(flatfish)is an order with special asymmetric shape and structure, and a long complicated history of evolution. Many species of the order are of great importance to the local economy for their valuable relish. Taxonomy research is meaningful for both biological studies and aquaculture production, but up to now the taxonomic system remains unintegrated.
For exploring the methods to integrate all of the taxonomic information of the specific taxa under a Windows application, this thesis develops a program named“Pleuronectiformes Taxonomy Information Analysis System (PTIAS)”(National copyright registration number: 2009SR02219) to find out the techniques for bridging and transforming taxa/taxon taxonomic information to specialized corresponding formats,such as taxonomy system, identification keys, molecular markers, DNA barcodes, phylogeny tree, bibliographies and other taxonomic references.
1. Illustrate the method of constructing taxonomic data modules for PTIAS. Based on taxonomy outputs of GTI scheme from 2008 to 2020, the thesis first built a comprehensive evaluation module by fuzzy analysis, then evaluated, selected and categorized data sources with a standpoint of taxonomy, and then analyzed the structure, content and relations among various databases, and finally designed a metadata and index system with a database module for PTIAS.
2. Design a digital taxonomy system module for integrating different taxonomic catalogs from GTI databases to PTIAS. Based on treeview database, the thesis established an extendable stratum module, able to stretch to all taxon levels and compose any taxon or taxa combination to bridge taxonomic information. The module is designed as the basic component for data connection, comparably analysis, database reconstruction and other data processing of certain species group dynamically designated.
3. Devise a BiosKey algorithm for traditional identification keys and Cladistics Trackback System of PTIAS. Based on keys in printed format and attributes of datawindow, the thesis studies a concise tree module, extendable to display pictures of shape characteristics of flatfishes, and able to apply in multi-key searching, forming an index mechanism for deriving terminology words from original keys. The necessity of distinguishing structure of dichotomous key from binary tree is discussed, since there is no sub node with priority of order or comparable values in the same level during the procession of dichotomous grouping. For probing the possibility of integrating necessary information of phylogenetic systems and Linnaean system and even identification keys, a digital Cladistics Traceback System is suggested to be used for integrating various system viewpoints based on the similar tree data structure, the collective taxa strata and the completely unified species taxon of all systems.
4. Present a visual hot-key index module for molecular markers of PTIAS. Based on genome structure of mtDNA and nDNA, the graphic markers are put into datawindow as functional buttons of indexes for retrieving sequence records. Each hot-key is traced by the mousemove function, and is bound to retrieving indexes and data of DNA barcodes, molecular markers and the taxonomic catalog when activated.
5. Study on a rapid processing method for large database and build an optimized the local environment for Blast, Clustal W and Phylip package with different MS-DOS modes under Windows system. For accelerating date retrieving, data extracting and database reconstructing, data-store technique was infixed to file mapping process to lead indexes searching into data blocks of memory. Using a settable small amount of buffer, the rapid method could completely overcome the choke point of I/O and memory when dealing with big files.
6. Research on the method of designing a system and the construction of using platform modules for different taxonomic information. The 9 data modules, 9 taxonomic functional modules and 3 data processing service modules are separately designed and integrated in PTIAS. All of the standardized data functions orderly for platform initialization, databases, indexes, and the taxonomic formats automatically transformed by the built-in program functions such as Linnaean system, identification key, molecular sequence table and phylogenetic tree, as well as initialization parameters for visible or invisible controls like datawindows, dropdown lists and dynamic datastores, etc..
7. Scheme an online data retrieving, editing and extracting method for GTI taxonomic databases. Microsoft web browse active control is employed to develop the component of taxonomic reference information module, and indexes for GTI portals are used to bridge taxonomy catalog and bind information.
引文
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