accepted

Harmonizing, annotating, and sharing data in biodiversity-ecosystem functioning research

2013-01-01

2015-05-07

Nadrowski, K. et al. (2013). Harmonizing, annotating and sharing data in biodiversity-ecosystem functioning research. Methods in Ecology and Evolution, 4, 201–205. doi: 10.1111/2041-210x.12009

2013-02-11

1. The new, integrative research field of biodiversity – ecosystem functioning (BEF) depends on close collaboration between researchers from different disciplines working on different scales in time, space, as well as taxon resolution. Data can describe everything from abiotic ecosystem components, to genes and organs of organisms to attributes like element stocks and fluxes at the plot scale. Harmonizing these data is difficult, since the datasets are diverse in structure and often follow diverging naming conventions. Here we argue that a simple way to promote the use of shared naming conventions and data annotation is to provide tools that work in the same environment that scientists are most comfortable with, i.e. spreadsheets. 2. We demonstrate this with BEFdata, our new, open-source Ruby on Rails web application with a PostgreSQL database, for data management in cooperating research projects. We employ a bottom-up approach to adhere to evolving naming conventions by validating data against lists of unique categories that grow as data is uploaded from a formatted workbook of spreadsheets. The web application provides a common platform to access and edit the categories. Metadata can be downloaded from BEFdata in Ecological Metadata Language (EML). BEFdata provides a safe environment during the time of on-going analysis because other project members can access raw data only after acceptance of a detailed data request (‘paper proposal’). 3. BEFdata allows the harmonizing and storing of data in a relational database while data and metadata preparation and editing can be done in a spreadsheet software. Because of the generic database scheme, BEFdata can be used for any research domain. The portal automates the communication with previous knowledge by presenting lists of names aggregated from different datasets, making them at the same time accessible online. BEFdata aims to facilitate the compilation of coherent datasets by cooperating scientists, thereby increasing their ability to answer complex questions and perform meta-analyses. The EML-export tool of BEFdata will also assist in publishing data in global repositories, and thus increase data visibility.

Karin Nadrowski, Sophia Ratcliffe, Christian Wirth