Amadoz Alicia, González-Candelas Fernando
Institut Cavanilles de Biodiversitat i Biologia Evolutiva and Departament de Genètica, Universitat de València, Spain.
BMC Infect Dis. 2007 Apr 20;7:32. doi: 10.1186/1471-2334-7-32.
Most research scientists working in the fields of molecular epidemiology, population and evolutionary genetics are confronted with the management of large volumes of data. Moreover, the data used in studies of infectious diseases are complex and usually derive from different institutions such as hospitals or laboratories. Since no public database scheme incorporating clinical and epidemiological information about patients and molecular information about pathogens is currently available, we have developed an information system, composed by a main database and a web-based interface, which integrates both types of data and satisfies requirements of good organization, simple accessibility, data security and multi-user support.
From the moment a patient arrives to a hospital or health centre until the processing and analysis of molecular sequences obtained from infectious pathogens in the laboratory, lots of information is collected from different sources. We have divided the most relevant data into 12 conceptual modules around which we have organized the database schema. Our schema is very complete and it covers many aspects of sample sources, samples, laboratory processes, molecular sequences, phylogenetics results, clinical tests and results, clinical information, treatments, pathogens, transmissions, outbreaks and bibliographic information. Communication between end-users and the selected Relational Database Management System (RDMS) is carried out by default through a command-line window or through a user-friendly, web-based interface which provides access and management tools for the data.
epiPATH is an information system for managing clinical and molecular information from infectious diseases. It facilitates daily work related to infectious pathogens and sequences obtained from them. This software is intended for local installation in order to safeguard private data and provides advanced SQL-users the flexibility to adapt it to their needs. The database schema, tool scripts and web-based interface are free software but data stored in our database server are not publicly available. epiPATH is distributed under the terms of GNU General Public License. More details about epiPATH can be found at http://genevo.uv.es/epipath.
大多数从事分子流行病学、群体与进化遗传学领域研究的科学家都面临着大量数据的管理问题。此外，传染病研究中使用的数据复杂，通常来自不同机构，如医院或实验室。由于目前尚无整合患者临床和流行病学信息以及病原体分子信息的公共数据库方案，我们开发了一个信息系统，该系统由一个主数据库和一个基于网络的界面组成，可整合这两类数据，并满足良好组织、易于访问、数据安全和多用户支持的要求。
从患者抵达医院或健康中心，到实验室对感染性病原体获得的分子序列进行处理和分析，期间会从不同来源收集大量信息。我们将最相关的数据划分为12个概念模块，并围绕这些模块组织了数据库架构。我们的架构非常完整，涵盖了样本来源、样本、实验室流程、分子序列、系统发育结果、临床检测与结果、临床信息、治疗、病原体、传播、疫情爆发和文献信息等多个方面。最终用户与选定的关系数据库管理系统（RDMS）之间的通信默认通过命令行窗口或通过一个用户友好的基于网络的界面进行，该界面提供数据访问和管理工具。
epiPATH是一个用于管理传染病临床和分子信息的信息系统。它便于处理与感染性病原体及其获得的序列相关的日常工作。该软件旨在进行本地安装以保护私人数据，并为高级SQL用户提供根据自身需求进行调整的灵活性。数据库架构、工具脚本和基于网络的界面是免费软件，但存储在我们数据库服务器中的数据不公开提供。epiPATH根据GNU通用公共许可证的条款进行分发。有关epiPATH的更多详细信息可在http://genevo.uv.es/epipath上找到。
