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：克服在分布式数据库环境中搜索时的命名复杂性：迈向真正的互操作性的一步。摘要随着Web上生物信息内容呈指数级增长，普通公众(就此而言，许多科学家)可能无法访问所有实际可用的和/或他们需要的高质量信息，因为生物体通常由一个以上的科学名称已知(其中许多可能不为用户所知)，不同的信息提供者可能对同一生物使用不同的名称。重要的国际项目，如全球生物多样性信息基金(见www.gbi.org)，已将生物名称确定为将不同领域的数据库(例如，标本数据库与GenBank或生态数据库等)互连的核心手段。因为有机体名称很可能是这两个数据库共有的唯一数据库字段。回答复杂的生物学问题需要数据库之间真正的互操作性。如果没有一种机制使人们能够获得关于某一特定生物体的所有现有信息，就不可能实现这一目标。因此，制定GBIF和相关的国家努力的一个基础组成部分必须是提供一份应对某一特定生物体进行搜索的所有名字清单的手段。GBIF的提出者清楚地认识到对互操作性这一组成部分的需要，但到目前为止，还没有专门针对提供软件工具来使之成为可能的努力。在这个项目中，我们将实施这样的机制。它将允许即使是最天真的网络用户获得生物信息，而不需要了解复杂的命名和相关的奥秘。为此，我们将开发一个任何用户都能理解的查询界面/门户；一套标准和协议，用于表示与平台无关的搜索请求(将作为URL发送)和结果集(将以XML形式使用HTTP返回)；以及一组特定于平台的转换器和搜索例程，用于从参与命名的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.