Curating scientific information in knowledge infrastructures

Interpreting observational data is a fundamental task in the sciences, specifically in earth and environmental science where observational data are increasingly acquired, curated, and published systematically by environmental research infrastructures. Typically subject to substantial processing, observational data are used by research communities, their research groups and individual scientists, who interpret such primary data for their meaning in the context of research investigations. The result of interpretation is information—meaningful secondary or derived data—about the observed environment. Research infrastructures and research communities are thus essential to evolving uninterpreted observational data to information. In digital form, the classical bearer of information are the commonly known “(elaborated) data products,” for instance maps. In such form, meaning is generally implicit e.g., in map colour coding, and thus largely inaccessible to machines. The systematic acquisition, curation, possible publishing and further processing of information gained in observational data interpretation—as machine readable data and their machine readable meaning—is not common practice among environmental research infrastructures. For a use case in aerosol science, we elucidate these problems and present a Jupyter based prototype infrastructure that exploits a machine learning approach to interpretation and could support a research community in interpreting observational data and, more importantly, in curating and further using resulting information about a studied natural phenomenon. © 2018 The Author(s).Peer reviewe

A Geovisual Analytic Approach to Understanding Geo-Social Relationships in the International Trade Network

The world has become a complex set of geo-social systems interconnected by networks, including transportation networks, telecommunications, and the internet. Understanding the interactions between spatial and social relationships within such geo-social systems is a challenge. This research aims to address this challenge through the framework of geovisual analytics. We present the GeoSocialApp which implements traditional network analysis methods in the context of explicitly spatial and social representations. We then apply it to an exploration of international trade networks in terms of the complex interactions between spatial and social relationships. This exploration using the GeoSocialApp helps us develop a two-part hypothesis: international trade network clusters with structural equivalence are strongly ‘balkanized’ (fragmented) according to the geography of trading partners, and the geographical distance weighted by population within each network cluster has a positive relationship with the development level of countries. In addition to demonstrating the potential of visual analytics to provide insight concerning complex geo-social relationships at a global scale, the research also addresses the challenge of validating insights derived through interactive geovisual analytics. We develop two indicators to quantify the observed patterns, and then use a Monte-Carlo approach to support the hypothesis developed above

An introduction to the Minimum Information about a Digital Specimen (MIDS) digitisation standard.

Digitisation is the process of converting analogue data about physical specimens to digital representation that includes electronic text, images and other forms. The term has been used diversely within the natural science collections community, and between different digitisation initiatives, the outputs can be quite different. Digitisation of individual specimens provides explicit and precise details about each object curated in a collection. This digitisation is based on diverse aims, the needs of specific projects and the specific practices and workflows in different institutions, so the digitised output has a wide range of uses. Capturing and presenting such data from future digitisation in standard formats is essential so that data can be more easily understood, compared, analysed and communicated via the Internet. By harmonising a framework that clarifies what is meant by different levels of digitisation (MIDS level), as well as the minimum information to be captured at each level, it becomes easier to consistently measure the extent of digitisation achieved over time and to set priorities for the remaining work. Similarly, ensuring that enough data are captured, curated and published is essential so they are useful for the widest possible range of future research, teaching and learning purposes. The Minimum Information about a Digital Specimen (MIDS) specification aims to address these problems. MIDS is a 'minimum specification', which means that the information specified as necessary at a each MIDS level is the minimum expected to be made digitally available following each major stage of digitisation. More is not precluded. From September 2020, MIDS specification work is now the work topic of an approved TDWG Task Group

MIDS Level 1: Specification, conformance checklist, mapping template and instructions for use

Approved formally as a TDWG Task Group (TG) in September 2020, TG MIDS is working to harmonise a framework for "Minimum Information about a Digital Specimen (MIDS)". MIDS clarifies what is meant by different levels of digitization (MIDS levels) and specifies the minimum information to be captured at each level. Capturing and presenting data in future digitization in standard formats is essential so that data can be more easily understood, compared, analysed and communicated via the Internet. Adopting MIDS and working to achieve specific MIDS levels in digitization ensures that enough data are captured, curated and published such that they are useful for the widest possible range of future research, teaching and learning purposes. Adopting MIDS makes it easier to consistently measure the extent of digitization achieved over time and to set priorities for the remaining work. In the year since MIDS was first introduced at TDWG 2020, the TG has focussed on the details of MIDS level 1, representing the basic minimum level of information to be expected and captured in basic digitization activities such as creating a catalogue record and (optionally) making photographic or other digital images of specimens. To help the community adopt and embed MIDS conformance as a core part of digitization and data publishing/management pipelines, the MIDS specification consists of definitions of the expected information elements, a template for mapping terms/fields in institutional collection management systems and other data management schemas to those information elements, a conformance proforma allowing declaration of how a digitization or data publishing event conforms to MIDs, and instructions for use

Ecohydraulic modelling of anabranching rivers

In this paper we provide the first quantitative evidence of the spatial complexity of habitat diversity across the flow regime for locally anabranching channels, and their potential increased biodiversity value in comparison to managed single-thread rivers. Ecohydraulic modelling is used to provide evidence for the potential ecological value of anabranching channels. Hydraulic habitat (biotopes) of an anabranched reach of the River Wear at Wolsingham, UK is compared with an adjacent artificially straightened single-thread reach downstream. 2D hydraulic modelling was undertaken across the flow regime. Simulated depth and velocity data were used to calculate Froude number (Fr) index; known to be closely associated with biotope type, allowing biotope maps to be produced for each flow simulation using published Fr limits. The gross morphology of the anabranched reach appears to be controlling flow hydraulics, creating a complex and diverse biotope distribution at low and intermediate flows. This contrasts markedly with the near uniform biotope pattern modelled for the heavily modified single-thread reach. As discharge increases the pattern of biotopes altered to reflect a generally higher energy system, interestingly, however, a number of low energy biotopes were activated through the anabranched reach as new sub-channels became inundated and this process is creating valuable refugia for macroinvertebrates and fish, during times of flood. In contrast, these low energy areas were not seen in the straightened single thread reach. Model results suggest that anabranched channels have a vital role to play in regulating flood energy on river systems and in creating and maintaining hydraulic habitat diversity

Meridional Survey of the Central Pacific Reveals Iodide Accumulation in Equatorial Surface Waters and Benthic Sources in the Abyssal Plain

The distributions of iodate and iodide were measured along the GEOTRACES GP15 meridional transect at 152°W from the shelf of Alaska to Papeete, Tahiti. The transect included oxygenated waters near the shelf of Alaska, the full water column in the central basin in the North Pacific Basin, the upper water column spanning across seasonally mixed regimes in the north, oligotrophic regimes in the central gyre, and the equatorial upwelling. Iodide concentrations are highest in the permanently stratified tropical mixed layers, which reflect accumulation due to light-dependent biological processes, and decline rapidly below the euphotic zone. Vertical mixing coefficients (Kz), derived from complementary 7Be data, enabled iodide oxidation rates to be estimated at two stations. Iodide half-lives of 3–4 years show the importance of seasonal mixing processes in explaining north-south differences in the transect, and also contribute to the decrease in iodide concentrations with depth below the mixed layer. These estimated half-lives are consistent with a recent global iodine model. No evidence was found for significant inputs of iodine from the Alaskan continental margin, but there is a significant enrichment of iodide in bottom waters overlying deep sea sediments from the interior of the basin

Time preferences and risk aversion: tests on domain differences

The design and evaluation of environmental policy requires the incorporation of time and risk elements as many environmental outcomes extend over long time periods and involve a large degree of uncertainty. Understanding how individuals discount and evaluate risks with respect to environmental outcomes is a prime component in designing effective environmental policy to address issues of environmental sustainability, such as climate change. Our objective in this study is to investigate whether subjects' time preferences and risk aversion across the monetary domain and the environmental domain differ. Crucially, our experimental design is incentivized: in the monetary domain, time preferences and risk aversion are elicited with real monetary payoffs, whereas in the environmental domain, we elicit time preferences and risk aversion using real (bee-friendly) plants. We find that subjects' time preferences are not significantly different across the monetary and environmental domains. In contrast, subjects' risk aversion is significantly different across the two domains. More specifically, subjects (men and women) exhibit a higher degree of risk aversion in the environmental domain relative to the monetary domain. Finally, we corroborate earlier results, which document that women are more risk averse than men in the monetary domain. We show this finding to, also, hold in the environmental domain

Evaluating the fidelity of the cerium paleoredox tracer during variable carbonate diagenesis on the Great Bahamas Bank

Inferring redox conditions for ancient marine environments is critical to our understanding of biogeochemical cycles over Earth history. Because of the redox sensitivity of cerium (Ce) relative to other rare earth elements (REEs) and its uptake in marine carbonates, the Ce anomaly (Ce/Ce*) is widely applied to ancient carbonates as a proxy for local redox conditions in the water column. However, carbonate sediments and rocks are particularly vulnerable to multiple stages and styles of post-depositional diagenetic alteration where the diagenetic redox conditions and fluid compositions can vary widely from overlying seawater. Evaluations of the effects of this post-depositional alteration for the Ce anomaly have mostly been limited to ancient carbonate rocks rather than recent, well-characterized analog facies. Here, we report on analyses of REE plus yttrium concentrations (REY) and Ce anomalies in bulk carbonate samples from drill cores collected in the Bahamas (Clino and Unda) that allow us to track loss or retention of primary signals of initial oxic deposition through a range of subsequent alteration scenarios mostly under anoxic conditions. Specifically, these materials have experienced well-constrained overprints linked to meteoric processes and marine burial diagenesis, including dolomitization. Our results show that, regardless of mineralogy, diagenetic fluid composition, and redox state, the REY patterns in these carbonates, including the Ce anomaly, are similar to those of modern oxic seawater, indicating that they likely record the seawater signatures of primary deposition. As such, the Ce anomaly in shallow marine carbonates has the potential to preserve records of primary deposition even when subject to multiple stages and styles of diagenetic alteration, confirming its utility in studies of ancient marine redox