Ecology has become a data intensive science over the last decades which often relies on the reuse of data in cross-experimental analyses. However, finding data which qualifies for the reuse in a specific context can be challenging. It requires good quality metadata and annotations as well as efficient search strategies. To date, full text search (often on the metadata only) is the most widely used search strategy although it is known to be inaccurate. Faceted navigation is providing a filter mechanism which is based on fine granular metadata, categorizing search objects along numeric and categorical parameters relevant for their discovery. Selecting from these parameters during a full text search creates a system of filters which allows to refine and improve the results towards more relevance. We developed a framework for the efficient annotation and faceted navigation in ecology. It consists of an XML schema for storing the annotation of search objects and is accompanied by a vocabulary focused on ecology to support the annotation process. The framework consolidates ideas which originate from widely accepted metadata standards, textbooks, scientific literature, and vocabularies as well as from expert knowledge contributed by researchers from ecology and adjacent disciplines.
Extreme climatic events threaten forests and their climate mitigation potential globally. Understanding the drivers promoting ecosystems stability is therefore considered crucial to mitigate adverse climate change effects on forests. Here, we use structural equation models to explain how tree species richness, asynchronous species dynamics and diversity in hydraulic traits affect the stability of forest productivity along an experimentally manipulated biodiversity gradient ranging from 1 to 24 tree species. Tree species richness improved stability by increasing species asynchrony. That is at higher species richness, inter-annual variation in productivity among tree species buffered the community against stress-related productivity declines. This effect was mediated by the diversity of species’ hydraulic traits in relation to drought tolerance and stomatal control, but not the community-weighted means of these traits. Our results demonstrate important mechanisms by which tree species richness stabilizes forest productivity, thus emphasizing the importance of hydraulically diverse, mixed-species forests to adapt to climate change.
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.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.