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

Academy Of Natural Sciences Philadelphia, Philadelphia PA

Investigators

Abstract

EIA-0131928 Lane, Meredith Academy of Natural Sciences - Philadelphia BDEI: Overcoming nomenclatural complications while searching in a distributed database environment: One step toward true interoperability. Summary With 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 actually available 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 is highly likely to be the only database field common to both databases. True interoperability among databases is required to answer complex biological questions. This goal cannot be reached without a mechanism to allow access to all available information on a particular organism. Therefore, a foundation component in the development of the GBIF and associated national efforts must be a means to provide a list of all the names that should be searched for a given organism. The need for this component of interoperability was clearly recognized by the proposers of GBIF, but to date there have 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 biological information without needing to understand the complexities of nomenclature and associated arcana. To do this, 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 participating nomenclatural data providers.