rBEFdata: documenting data exchange and analysis for a collaborative data management platform

Ecology and Evolution

Claas-Thido Pfaff²  Birgitta König-Ries¹  Anne C. Lang²  Sophia Ratcliffe²  Christian Wirth²  Xingxing Man² 

[1] Department of Mathematics and Computer Science, Friedrich Schiller University of Jena, Jena, Germany;Department of Special Botany and Functional Biodiversity, University of Leipzig, Leipzig, Germany

关键词: Biodiversity ecosystem functioning;    data postprocessing;    data sharing;    ecological metadata language;    metadata;    open science;    open source;    paper proposals;    R;    reproducible science;    semantic integration;    workflow;   

DOI  :  10.1002/ece3.1547

来源: Wiley

【 摘 要 】

Abstract

We are witnessing a growing gap separating primary research data from derived data products presented as knowledge in publications. Although journals today more often require the underlying data products used to derive the results as a prerequisite for a publication, the important link to the primary data is lost. However, documenting the postprocessing steps of data linking, the primary data with derived data products has the potential to increase the accuracy and the reproducibility of scientific findings significantly. Here, we introduce the rBEFdata R package as companion to the collaborative data management platform BEFdata. The R package provides programmatic access to features of the platform. It allows to search for data and integrates the search with external thesauri to improve the data discovery. It allows to download and import data and metadata into R for analysis. A batched download is available as well which works along a paper proposal mechanism implemented by BEFdata. This feature of BEFdata allows to group primary data and metadata and streamlines discussions and collaborations revolving around a certain research idea. The upload functionality of the R package in combination with the paper proposal mechanism of the portal allows to attach derived data products and scripts directly from R, thus addressing major aspects of documenting data postprocessing. We present the core features of the rBEFdata R package along an ecological analysis example and further discuss the potential of postprocessing documentation for data, linking primary data with derived data products and knowledge.

【 授权许可】

CC BY   
© 2015 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.

Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.