养分循环研究数据管理概念模型的构建

近年来,农田生态系统NPK养分循环研究已经积累了大量的数据,迫切需要建立可长期保存数据、并为养分循环研究全局决策服务的数据管理系统,本文描述了用于养分循环数据管理的概念模型的设计,并说明构建模型的过程,最后给出依据该模型建立数据库系统应用实例。结果表明,依据模型建立的数据库系统可提供按照时间、地点、专题查询的功能,能够管理野外观测数据、专题图和研究报告等多种类型数据,并快速提取和分析数据。     

Design and realization of an on-line database for multidimensional microscopic images of biological specimens

The BioImage database is a new scientific database for multidimensional microscopic images of biological specimens, which is available through the World Wide Web (WWW). The development of this database has followed an iterative approach, in which requirements and functionality have been revised and extended. The complexity and innovative use of the data meant that technical and biological expertise has been crucial in the initial design of the data model. A controlled vocabulary was introduced to ensure data consistency. Pointers are used to reference information stored in other databases. The data model was built using InfoModeler as a database design tool. The database management system is the Informix Dynamic Server with Universal Data Option. This object-relational system allows the handling of complex data using features such as collection types, inheritance, and user-defined data types. Informix datablades are used to provide additional functionality: the Web Integration Option enables WWW access to the database; the Video Foundation Blade provides functionality for video handling.     

Design of a data model for developing laboratory information management and analysis systems for protein production

Data management has emerged as one of the central issues in the high-throughput processes of taking a protein target sequence through to a protein sample. To simplify this task, and following extensive consultation with the international structural genomics community, we describe here a model of the data related to protein production. The model is suitable for both large and small facilities for use in tracking samples, experiments, and results through the many procedures involved. The model is described in Unified Modeling Language (UML). In addition, we present relational database schemas derived from the UML. These relational schemas are already in use in a number of data management projects.     

PhD: a web database application for phenotype data management

A database application has been developed for phenotype data management employing the Entity-Attribute-Value (EAV) model. By applying the EAV model, this application allows users to manage arbitrary phenotypes and customize data entry forms; therefore, it is suitable for different and multi-center projects.     

StressDB: a locally installable web-based relational microarray database designed for small user communities

We have built a microarray database, StressDB, for management of microarray data from our studies on stress-modulated genes in Arabidopsis. StressDB provides small user groups with a locally installable web-based relational microarray database. It has a simple and intuitive architecture and has been designed for cDNA microarray technology users. StressDB uses Windows(trade mark) 2000 as the centralized database server with Oracle(trade mark) 8i as the relational database management system. It allows users to manage microarray data and data-related biological information over the Internet using a web browser. The source-code is currently available on request from the authors and will soon be made freely available for downloading from our website athttp://arastressdb.cac.psu.edu.     

HydroServer Lite as an open source solution for archiving and sharing environmental data for independent university labs

Managing, archiving, and sharing large amounts of data are essential tasks in ecological laboratories, and detailed data management plans are now required by major funding agencies. Many independent research labs may lack the technical or financial resources needed to support some of the more comprehensive data management solutions that have become available. In this paper we describe an open-source solution to data management, archiving, and sharing that can be implemented and customized by someone with limited computer programming experience using free software and standardized web services. This software, HydroServer Lite, is a light-weight database and data management web-based application that integrates with and makes data available on a large data sharing network developed by the Consortium of Universities for the Advancement of Hydrologic Sciences, Inc. (CUAHSI). The CUAHSI Hydrologic Information System facilitates data sharing through a network of local HydroServers that are registered with the central registry. Each HydroServer may contain a variety of ecological and climate data, stored in a standardized relational database model. Someone searching for data that are registered in the central registry can query the network by source, location, variable type, and dates. These data can be downloaded from the local HydroServer to a computer in an office or lab where they can be manipulated and analyzed without compromising the data in the archives. We offer this HydroServer Lite case study as a possible solution for independent research laboratories looking for a data management system that requires little technical expertise or initial cost to set up.     

中国生态农业模式管理信息及决策支持系统的建立

根据全国生态农业试点县建设和典型生态农业模式研究的经验,利用Access数据库技术建立了全国首批生态农业县有关自然资源背景、农业生产水平、生态环境与工程技术等各种基础信息数据库和所推广应用的生态农业模式信息数据库,可快速方便地提供各生态农业县相关信息或知识的查询或编辑．在此基础上,采用了面向对象的推理方法建立了生态农业模式区域决策的知识库体系模型,并利用Visual C^++语言初步开发出生态农业模式的区域决策支持系统,基本上实现了区域生态农业模式的决策推荐．     

xtalPiMS: a PiMS-based web application for the management and monitoring of crystallization trials

A major advance in protein structure determination has been the advent of nanolitre-scale crystallization and (in a high-throughput environment) the development of robotic systems for storing and imaging crystallization trials. Most of these trials are carried out in 96-well (or higher density) plates and managing them is a significant information management challenge. We describe xtalPiMS, a web-based application for the management and monitoring of crystallization trials. xtalPiMS has a user-interface layer based on the standards of the Protein Information Management System (PiMS) and a database layer which links the crystallization trial images to the meta-data associated with a particular crystallization trial. The user interface has been optimized for the efficient monitoring of high-throughput environments with three different automated imagers and work to support a fourth imager is in progress, but it can even be of use without robotics. The database can either be a PiMS database or a legacy database for which a suitable mapping layer has been developed.     

MDMPR:小鼠发育代谢表型库

小鼠发育代谢表型库(Mouse Developmental and Metabolic Phenotype Repository,MDMPR)是一个致力于小鼠资源和表型数据实时共享的开放性平台,它依托于科技部重点研发计划“发育编程及其代谢调节”专项项目“建立小鼠发育代谢表型库”。该项目预计在5年内完成500个发育代谢相关小鼠敲除模型的建立,并对其表型数据进行标准化的解析、建立表型数据库。MDMPR作为一个资源及数据集成的库,由多个子系统作为支撑,包括ES细胞数据库、项目管理系统、繁育管理系统、精子库管理系统、表型分析系统,信息化管理深入到项目中每个环节,从基因突变ES细胞制备、基因突变小鼠制备、小鼠繁育,精子冻存到最终的表型分析、数据处理及展示,保证了MDMPR产生数据的真实性及实时性。MDMPR除了不断地推进项目进行,增加自身产生的数据外,也在积极的整合其他的资源及数据,如人特异性基因敲除ES细胞库、蛋白相互作用数据库(STRING)、核心转录调节环路(dbCoRc)和Enhancer-Indel数据库,今后还将进一步整合,帮助发育代谢及其他领域的研究人员能够一站式的获取所需资源和数据、加快研究进程,最终服务于全人类的医疗事业。     

The MUSC DNA Microarray Database

SUMMARY: The Medical University of South Carolina (MUSC) DNA Microarray Database is a web-accessible archive of DNA microarray data. The database was developed using the DNA microarray project/data management system, micro ArrayDB. Annotations for each DNA microarray project and associated cRNA target information are stored in a MySQL relational database and linked to array hybridization data (raw and normalized). At the discretion of investigators, data are placed into the public domain where they can be interrogated and downloaded through a web browser. In addition to serving as an online resource of gene expression data, the MUSC DNA Microarray Database is a model for other academic DNA microarray data repositories. AVAILABILITY: Browsing and downloading of MUSC DNA Microarray Database information can be done after registration at http://proteogenomics.musc.edu/pss/home.php.     

Manure management practices in Lombardy (Italy)

The Lombardy Region of Italy has used a specialised software package, GIARA, to implement an integrated environmental management system that assists farmers in the preparation and submission of nutrient management plans. These are submitted on diskette to a central authority in order to build a regional database of manure utilisation linked to a GIS. At present, the database includes plans for more then 5500 farms representing more then one million cattle and 3.5 million pigs. The information contained in the database allows an evaluation of manure management practices in the Region. Some indicators like nitrogen amount per hectare varies from 100 to 300 kg at the same level of crop requirement and therefore do not seem adequate to evaluate the pollution risk at farm level.     

Management of the natural ecosystems of the Cape Peninsula: current status and future prospects

The Cape Peninsula is an area of outstanding natural beauty and exceptional biodiversity, worthy of proclamation as a World Heritage Site. The area is dominated by fynbos vegetation, usually managed by means of prescribed burning, together with various programmes aimed at the control of invasive alien plant species. Effective management of the Peninsula is bedevilled by the fact that the area is controlled by no less than 14 different public bodies, resulting in fragmentation of effort and the lack of a standardized approach to management. Historically, many official and unofficial investigations have called for this problem to be resolved, without success. The lack of coherent, focused, and well funded fire and alien weed control management plans for the entire Peninsula is a serious deficiency. Despite this, considerable progress has been made towards the establishment of a database for the Peninsula, and the development of decision support systems that can utilize this database for rational management. Adoption of such a system would provide a powerful uniting tramework that would standardize and influence the management approaches adopted by the various controlling authorities.     

Data base management system for lymphatic filariasis--a neglected tropical disease

Background

Researchers working in the area of Public Health are being confronted with large volumes of data on various aspects of entomology and epidemiology. To obtain the relevant information out of these data requires particular database management system. In this paper, we have described about the usages of our developed database on lymphatic filariasis.

Methods

This database application is developed using Model View Controller (MVC) architecture, with MySQL as database and a web based interface. We have collected and incorporated the data on filariasis in the database from Karimnagar, Chittoor, East and West Godavari districts of Andhra Pradesh, India.

Conclusion

The importance of this database is to store the collected data, retrieve the information and produce various combinational reports on filarial aspects which in turn will help the public health officials to understand the burden of disease in a particular locality. This information is likely to have an imperative role on decision making for effective control of filarial disease and integrated vector management operations.     

ISIS database: An evaluation of records essential for captive management

Species databases are essential for the scientific management of species and specimens in captive wildlife populations. Population managers in North America base their decisions on information in two databases:the International Species Information System (ISIS) and American Zoo and Aquarium Association (AZA) approved regional studbooks. Genetic and demographic management of species relies on studbooks, whereas regional collection planning and management by Taxon Advisory Groups (TAGs) may use a combination of studbooks, direct surveys, and data from ISIS. Use of ISIS data as the primary basis for population management and collection planning is increasing, yet there has been no assessment of how ISIS data differ from studbooks. Thus these databases were compared to determine if they are interchangeable for the purposes of regional collection planning or species management. Population sizes of living individuals in 68 SSP^© taxa were compared to assess the magnitude of differences between the databases. Differences in population size were considerable and highly variable; ISIS on average underestimated the number of living animals in SSP^© taxa populations. Ten studbooks were also analyzed in detail to identify specific types of discrepancies between the two databases. On average, 19.2 ± 2.2% of the information in the ISIS database differed from that in the studbook. Most discrepancies derived from data that were either missing from, or incorrect in, the ISIS database. The most common discrepancies involve parents who were either unidentified or misidentified in the ISIS database (x? = 37.5 ± 5.7% of all records). No single type of discrepancy, however, was prevalent across all 10 species; the overall rate of discrepancies per species was attributable to a combination of discrepancies peculiar to each species. Protocols concerning data entry standards, data collection, and the scope of data collected are likely causes of most discrepancies. In its present form, the ISIS database is not appropriate for single species management; if used cautiously, it can be of assistance in the development of regional collection plans. Development of an ISIS database that is suitable for population management will require an increased commitment to data quality by records keepers, zoological institutions, and ISIS. © 1995 Wiley-Liss, Inc.     

A web based relational database management system for filariasis control

The present study describes a RDBMS (relational database management system) for the effective management of Filariasis, a vector borne disease. Filariasis infects 120 million people from 83 countries. The possible re-emergence of the disease and the complexity of existing control programs warrant the development of new strategies. A database containing comprehensive data associated with filariasis finds utility in disease control. We have developed a database containing information on the socio-economic status of patients, mosquito collection procedures, mosquito dissection data, filariasis survey report and mass blood data. The database can be searched using a user friendly web interface.

Availability     

Lessons from morpholino-based screening in zebrafish

Morpholino oligonucleotides (MOs) are an effective, gene-specific antisense knockdown technology used in many model systems. Here we describe the application of MOs in zebrafish (Danio rerio) for in vivo functional characterization of gene activity. We summarize our screening experience beginning with gene target selection. We then discuss screening parameter considerations and data and database management. Finally, we emphasize the importance of off-target effect management and thorough downstream phenotypic validation. We discuss current morpholino limitations, including reduced stability when stored in aqueous solution. Advances in MO technology now provide a measure of spatiotemporal control over MO activity, presenting the opportunity for incorporating more finely tuned analyses into MO-based screening. Therefore, with careful management, MOs remain a valuable tool for discovery screening as well as individual gene knockdown analysis.     

The AQEM/STAR taxalist – a pan-European macro-invertebrate ecological database and taxa inventory

The European list of aquatic macro-invertebrate taxa, and its associated ecological database, originated within the context of the AQEM project and have been extended during the STAR project. The AQEM/STAR taxalist is a product of co-operation between applied freshwater ecologists and scientists from different zoological fields, applied partners and the administration. The basic idea is that a sound understanding of benthic invertebrate ecology is a prerequisite for the implementation of a biological approach to aquatic ecosystem management in Europe. The database has been generated under the management of BOKU (University of Natural Resources and Applied Life Sciences, Vienna) and UDE (University of Duisburg-Essen) and provides an important means of standardisation and unification of ecological classifications in Europe. This paper outlines the aims for setting up the AQEM/STAR macro-invertebrate taxalist and autecological database and provides a current summary of the numbers of aquatic orders, families, species, and species occurrences in 14 European countries. The number of available and applicable assignments of taxa to each ecological parameter is summarised and examples are given for different parameters and taxonomic groups. Gaps in the autecological information are identified and discussed. Besides its ecological relevance, the operational character of this database is underlined by the fact that it provides the associated taxon codes for each of five different European assessment systems for nearly 10,000 European macro-invertebrate taxa.     

ADAMIS: a database for medical information systems

This paper describes the design and implementation of ADAMIS ('A database for medical information systems'). ADAMIS is a relational database management system for a general hospital environment. Apart from the usual database (DB) facilities of data definition and data manipulation, ADAMIS supports a query language called the 'simplified medical query language' (SMQL) which is completely end-user oriented and highly non-procedural. Other features of ADAMIS include provision of facilities for statistics collection and report generation. ADAMIS also provides adequate security and integrity features and has been designed mainly for use on interactive terminals.     

基于Web的基因组序列数据库管理系统的设计与实现

设计一种基于网络的可用来存储和注释海量DNA数据的数据库模型。整个过程分为三部分：首先是构建数据库框架,然后对原始基因组序列数据进行批量注释并输出有效格式导入数据库,最后通过一个友好的用户交互界面,实现对基因组数据的在线读取,查询,注释等操作。设计的数据库用于解决大量产生并有待分析的基因组序列的有效存储和管理问题。