Biodiversity and Ecosystem Informatics - BDEI - Overcoming nomenclatural complications while searching in a distributed database environment: One step toward true interoperability

EIA-0131928 Lane，Meredith Academy of Natural Sciences - PhiladelphiaBDEI：在分布式数据库环境中搜索时克服命名复杂性：迈向真正互操作性的一步。摘要随着Web上生物信息内容的指数级增长，（就此而言，许多科学家）可能无法访问所有实际可用的高质量信息，或者他们需要的，因为生物体通常有一个以上的科学名称（其中许多可能是用户不知道的），不同的信息提供者可能对同一生物体使用不同的名称。重要的国际项目，如全球生物多样性信息设施（见www.gbif.org），已经确定生物体名称是连接不同领域数据库的核心手段（例如，与GenBank或生态学数据库等的标本数据库）因为微生物名称很可能是两个数据库中唯一的公共数据库字段。要回答复杂的生物学问题，就需要真正的互操作性数据库。如果没有一种机制允许获取关于某一特定生物体的所有可用信息，这一目标就无法实现。因此，GBIF开发的一个基础组成部分和相关的国家努力必须是一种手段，提供一个应搜索某一特定生物体的所有名称的列表。GBIF的提议者清楚地认识到了互操作性这一组成部分的必要性，但到目前为止，还没有专门针对提供软件工具使其成为可能的努力。在本项目中，我们将实施这样的机制。它将允许即使是最幼稚的网络用户获得生物信息，而不需要理解命名和相关奥秘的复杂性。为此，我们将开发一个任何用户都能理解的查询接口/门户网站;一组标准和协议，用于表示搜索请求（将作为URL发送）和结果集（将使用HTTP作为XML返回），这些标准和协议是独立于平台的;以及一组特定于平台的翻译器和搜索例程，用于从参与的命名数据提供者检索数据。

EIA-0131928Lane, Meredith Academy of Natural Sciences - PhiladelphiaBDEI: Overcoming nomenclatural complications while searching in a distributed database environment: One step toward true interoperability.SummaryWith biological information content growing exponentially on the Web, the average member of the public(and for that matter, many scientists) may not be able to access all of the high-quality information actuallyavailable and/or that they need because organisms are often known by more than one scientific name (many of which will perhaps be unknown to the user), and different information providers may use different names for the same organism.Important international projects such as the Global Biodiversity Information Facility (see www.gbif.org)have identified organism names as the core means for interconnecting databases from different domains(e.g., specimen databases with GenBank or ecological databases, etc.) because the organism name ishighly likely to be the only database field common to both databases. True interoperability amongdatabases is required to answer complex biological questions. This goal cannot be reached without amechanism to allow access to all available information on a particular organism.Therefore, a foundation component in the development of the GBIF and associated national effortsmust be a means to provide a list of all the names that should be searched for a given organism. The needfor this component of interoperability was clearly recognized by the proposers of GBIF, but to date therehave been no efforts specifically directed at providing software tools to make it possible. In this project,we will implement such a mechanism. It will allow even the most naive Web user to obtain biologicalinformation without needing to understand the complexities of nomenclature and associated arcana. To dothis, we will develop a query interface/portal understandable to any user; a set of standards and protocols for representing search requests (which will be sent as a URL) and result sets (which will be returned as XML using HTTP) that is platform-independent; and a set of platform-specific translators and search routines for retrieving data from participatingnomenclatural data providers.