The EcoData retriever: improving access to existing ecological data.

Benjamin D Morris,Ethan P White

doi:10.1371/journal.pone.0065848

Abstract

Ecological research relies increasingly on the use of previously collected data. Use of existing datasets allows questions to be addressed more quickly, more generally, and at larger scales than would otherwise be possible. As a result of large-scale data collection efforts, and an increasing emphasis on data publication by journals and funding agencies, a large and ever-increasing amount of ecological data is now publicly available via the internet. Most ecological datasets do not adhere to any agreed-upon standards in format, data structure or method of access. Some may be broken up across multiple files, stored in compressed archives, and violate basic principles of data structure. As a result acquiring and utilizing available datasets can be a time consuming and error prone process. The EcoData Retriever is an extensible software framework which automates the tasks of discovering, downloading, and reformatting ecological data files for storage in a local data file or relational database. The automation of these tasks saves significant time for researchers and substantially reduces the likelihood of errors resulting from manual data manipulation and unfamiliarity with the complexities of individual datasets.

Highlights

Research in many areas of ecology increasingly relies on the use of data that has already been collected
While not all areas of ecology are well suited to the use of existing data, those that are have become increasingly limited by the quality and quantity of relevant data that can be acquired [1]
Ecologists have seen an enormous increase in the amount of data that is publicly available, including: 1) broad scale coordinated data collection efforts such as the North American Breeding Bird Survey [2], the Forest Inventory and Analysis Program [3], and the new National Ecological Observatory Network, which are designed to conduct widespread monitoring of continental-scale processes relevant to biodiversity, climate change, and other ecological concerns; 2)

Summary

Introduction

Research in many areas of ecology increasingly relies on the use of data that has already been collected. To assist ecologists in quickly and accessing and utilizing available data, we have developed the EcoData Retriever (http:// ecodataretriever.org), a software package that automatically downloads ecological datasets, performs any necessary preprocessing, creates appropriate database structures, and imports the data into the user’s choice of database management systems or text files.

Results

Conclusion