The GBIF integrated publishing toolkit: facilitating the efficient publishing of biodiversity data on the internet.

David Bloom,Peter Desmet,Laura Russell,Javier Otegui,Robert Guralnick,Kyle Braak,Tim Robertson,Markus Döring,Damon P Little,John Wieczorek

doi:10.1371/journal.pone.0102623

Abstract

The planet is experiencing an ongoing global biodiversity crisis. Measuring the magnitude and rate of change more effectively requires access to organized, easily discoverable, and digitally-formatted biodiversity data, both legacy and new, from across the globe. Assembling this coherent digital representation of biodiversity requires the integration of data that have historically been analog, dispersed, and heterogeneous. The Integrated Publishing Toolkit (IPT) is a software package developed to support biodiversity dataset publication in a common format. The IPT’s two primary functions are to 1) encode existing species occurrence datasets and checklists, such as records from natural history collections or observations, in the Darwin Core standard to enhance interoperability of data, and 2) publish and archive data and metadata for broad use in a Darwin Core Archive, a set of files following a standard format. Here we discuss the key need for the IPT, how it has developed in response to community input, and how it continues to evolve to streamline and enhance the interoperability, discoverability, and mobilization of new data types beyond basic Darwin Core records. We close with a discussion how IPT has impacted the biodiversity research community, how it enhances data publishing in more traditional journal venues, along with new features implemented in the latest version of the IPT, and future plans for more enhancements.

Highlights

Natural history collection records and data collected in citizen science efforts represent irreplaceable information about our biosphere
We describe a tool essential to the publication of biodiversity data: the Global Biodiversity Information Facility (GBIF) Integrated Publishing Toolkit (IPT, http://www.gbif.org/ ipt/), a Java-based software package that provides the biodiversity community with a simple means to perform many necessary functions to publish biodiversity datasets on the web
The IPT simplifies these processes, but still requires some specialized skills and knowledge to properly go from local databases to published Darwin Core Archives

Summary

Introduction

Natural history collection records and data collected in citizen science efforts represent irreplaceable information about our biosphere. The value of these legacy data sources will increase as landscape and climate change accelerates and species-environment steady-state conditions decline [1]. Integration can, in part, be achieved through the utilization of community-developed metadata standards such as Darwin Core [5]. Darwin Core is a vocabulary, or set of terms, that describe biodiversity data. These terms, comprising the Darwin Core standard (http://rs.tdwg.org/ dwc/), have been vetted rigorously for utility by the biodiversity research community and are maintained through a well-defined governance process (http://www.tdwg.org/about-tdwg/process/)

Methods

Results

Conclusion