Implementation of a workflow for publishing citeable environmental data: successes, challenges and opportunities from a data centre perspective

In recent years, the development and implementation of a robust way to cite data have encouraged many previously sceptical environmental researchers to publish the data they create, thus ensuring that more data than ever are now open and available for re-use within and between research communities. Here, we describe a workflow for publishing citeable data in the context of the environmental sciences—an area spanning many domains and generating a vast array of heterogeneous data products. The processes and tools we have developed have enabled rapid publication of quality data products including datasets, models and model outputs which can be accessed, re-used and subsequently cited. However, there are still many challenges that need to be addressed before researchers in the environmental sciences fully accept the notion that datasets are valued outputs and time should be spent in properly describing, storing and citing them. Here, we identify current challenges such as citation of dynamic datasets and issues of recording and presenting citation metrics. In conclusion, whilst data centres may have the infrastructure, tools, resources and processes available to publish citeable datasets, further work is required before large-scale uptake of the services offered is achieved. We believe that once current challenges are met, data resources will be viewed similarly to journal publications as valued outputs in a researcher’s portfolio, and therefore both the quality and quantity of data published will increase

Meeting the challenge of environmental data publication: an operational infrastructure and workflow for publishing data

Here we describe the defined workflow and its supporting infrastructure, which are used by the Natural Environment Research Council’s (NERC) Environmental Information Data Centre (EIDC) (http://​eidc.​ceh.​ac.​uk/​) to enable publication of environmental data in the fields of ecology and hydrology. The methods employed and issues discussed are also relevant to publication in other domains. By utilising a clearly defined workflow for data publication, we operate a fully auditable, quality controlled series of steps permitting publication of environmental data. The described methodology meets the needs of both data producers and data users, whose requirements are not always aligned. A stable, logically created infrastructure supporting data publication allows the process to occur in a well-managed and secure fashion, while remaining flexible enough to deal with a range of data types and user requirements. We discuss the primary issues arising from data publication, and describe how many of them have been resolved by the methods we have employed, with demonstrable results. In conclusion, we expand on future directions we wish to develop to aid data publication by both solving problems for data generators and improving the end-user experience

Report: community workshop on environmental model code of long-term value

Software is increasingly essential to research activities, from data collection to its processing and storage, and its publication and use. It underpins other scholarly research output and can be used, reused, re-examined, and further developed (Katz and Chue Hong 2024). Recognising the role of research software in environmental science, this report covers a workshop on environmental model code of long-term value run by The UK Centre for Ecology & Hydrology (UKCEH) on 21st November 2023

Natural capital metrics. Phase 1 final report: central components

This is a condensed version of the Natural Capital Metrics (NCMet) project Phase 1 report. It focuses on three key components: i) the conceptual framework, ii) development of six example evidence-chains and their associated data and model inventories, and iii) early development work towards a Natural Capital Portal to provide access to relevant data, models and maps of natural capital. All outputs are preliminary and are undergoing considerable refinement in the second phase of the project. Phase 2 outputs will be available in 2018

The correlation between reading and mathematics ability at age twelve has a substantial genetic component

Dissecting how genetic and environmental influences impact on learning is helpful for maximizing numeracy and literacy. Here we show, using twin and genome-wide analysis, that there is a substantial genetic component to children’s ability in reading and mathematics, and estimate that around one half of the observed correlation in these traits is due to shared genetic effects (so-called Generalist Genes). Thus, our results highlight the potential role of the learning environment in contributing to differences in a child’s cognitive abilities at age twelve

Review of methods for assessing deposition of reactive nitrogen pollutants across complex terrain with focus on the UK

This review is a summary of the most up-to-date knowledge regarding assessment of atmospheric deposition of reactive nitrogen (Nr) pollutants across complex terrain in the UK. Progress in the understanding of the mechanisms and quantification of Nr deposition in areas of complex topography is slow, as no concerted attempts to measure the components of Nr in complex terrain have been made in the last decade. This is likely due to the inherent complexity of the atmospheric processes and chemical interactions which contribute to deposition in these areas. More than 300 studies have been reviewed, and we have consulted with a panel of international experts which we assembled for that purpose. We report here on key findings and knowledge gaps identified regarding measurement and modelling techniques used to quantify deposition of Nr across complex terrain in the UK, which depending on definition, may represent up to 60% of land coverage across Great Britain. The large body of peer reviewed papers, reports and other items reviewed in this study has highlighted both the strengths and weaknesses in the tools available to scientists, regulators and policy makers. This review highlights that there is no coherent global research effort to constrain the uncertainties in Nr deposition over complex terrain, despite the clearly identified risk of N deposition to ecosystems and water quality. All evidence identified that enhanced Nr deposition across complex terrain occurs, and magnitude of the enhancement is not known; however, there are major uncertainties particularly in the differences between modelled and measured wet deposition in complex terrain and representing accurate surface interactions in models. Using simplified estimates for Nr deposition, based on current understanding of current measurement and model approaches, an enhancement across UK complex terrain in the range of a factor of 1.4–2.5 (i.e. 40–150% larger than current estimates) is likely over complex upland terrain. If at the upper limits of this, then significantly more ecosystems in the UK would be at a direct risk of degradation, and the potential for long-term non-remediable water quality issues increased

Large scale meta-analysis characterizes genetic architecture for common psoriasis associated variants

Psoriasis is a complex disease of skin with a prevalence of about 2%. We conducted the largest meta-analysis of genome-wide association studies (GWAS) for psoriasis to date, including data from eight different Caucasian cohorts, with a combined effective sample size amp;gt;39,000 individuals. We identified 16 additional psoriasis susceptibility loci achieving genome-wide significance, increasing the number of identified loci to 63 for European-origin individuals. Functional analysis highlighted the roles of interferon signalling and the NFkB cascade, and we showed that the psoriasis signals are enriched in regulatory elements from different T cells (CD8(+) T-cells and CD4(+) T-cells including T(H)0, T(H)1 and T(H)17). The identified loci explain similar to 28% of the genetic heritability and generate a discriminatory genetic risk score (AUC = 0.76 in our sample) that is significantly correlated with age at onset (p = 2 x 10(-89)). This study provides a comprehensive layout for the genetic architecture of common variants for psoriasis.Funding Agencies|National Institutes of Health [R01AR042742, R01AR050511, R01AR054966, R01AR063611, R01AR065183]; Foundation for the National Institutes of Health; Dermatology Foundation; National Psoriasis Foundation; Arthritis National Research Foundation; Ann Arbor Veterans Affairs Hospital; Dawn and Dudley Holmes Foundation; Babcock Memorial Trust; Medical Research Council [MR/L011808/1]; German Ministry of Education and Research (BMBF); Doris Duke Foundation [2013106]; National Institute of Health [K08AR060802, R01AR06907]; Taubman Medical Research Institute; Department of Health via the NIHR comprehensive Biomedical Research Center; Kings College London; KCH NHS Foundation Trust; Barbara and Neal Henschel Charitable Foundation; Heinz Nixdorf Foundation; Estonian Ministry of Education and Research [IUT20-46]; Centre of Translational Genomics of University of Tartu (SP1GVARENG); European Regional Development Fund (Centre of Translational Medicine, University of Tartu); German Federal Ministry of Education and Research (BMBF); National Human Genome Research Institute of the National Institutes of Health [R44HG006981]; International Psoriasis Council</p

Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis.

Multiple sclerosis is a common disease of the central nervous system in which the interplay between inflammatory and neurodegenerative processes typically results in intermittent neurological disturbance followed by progressive accumulation of disability. Epidemiological studies have shown that genetic factors are primarily responsible for the substantially increased frequency of the disease seen in the relatives of affected individuals, and systematic attempts to identify linkage in multiplex families have confirmed that variation within the major histocompatibility complex (MHC) exerts the greatest individual effect on risk. Modestly powered genome-wide association studies (GWAS) have enabled more than 20 additional risk loci to be identified and have shown that multiple variants exerting modest individual effects have a key role in disease susceptibility. Most of the genetic architecture underlying susceptibility to the disease remains to be defined and is anticipated to require the analysis of sample sizes that are beyond the numbers currently available to individual research groups. In a collaborative GWAS involving 9,772 cases of European descent collected by 23 research groups working in 15 different countries, we have replicated almost all of the previously suggested associations and identified at least a further 29 novel susceptibility loci. Within the MHC we have refined the identity of the HLA-DRB1 risk alleles and confirmed that variation in the HLA-A gene underlies the independent protective effect attributable to the class I region. Immunologically relevant genes are significantly overrepresented among those mapping close to the identified loci and particularly implicate T-helper-cell differentiation in the pathogenesis of multiple sclerosis

An adaptable integrated modelling platform to support rapidly evolving agricultural and environmental policy

The utility of integrated models for informing policy has been criticised due to limited stakeholder engagement, model opaqueness, inadequate transparency in assumptions, lack of model flexibility and lack of communication of uncertainty that, together, lead to a lack of trust in model outputs. We address these criticisms by presenting the ERAMMP Integrated Modelling Platform (IMP), developed to support the design of new “business-critical” policies focused on agriculture, land-use and natural resource management. We demonstrate how the long-term (>5 years), iterative, two-way and continuously evolving participatory process led to the co-creation of the IMP with government, building trust and understanding in a complex integrated model. This is supported by a customisable modelling framework that is sufficiently flexible to adapt to changing policy needs in near real-time. We discuss how these attributes have facilitated cultural change within the Welsh Government where the IMP is being actively used to explore, test and iterate policy ideas prior to final policy design and implementation