Article

An online database and desktop assessment software to simplify systematic reviews in environmental science

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  • Ernst & Young and Ecotec
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Abstract

We describe software to facilitate systematic reviews in environmental science. Eco Evidence allows reviewers to draw strong conclusions from a collection of individually-weak studies. It consists of two components. An online database stores and shares the atomized findings of previously-published research. A desktop analysis tool synthesizes this evidence to test causeeeffect hypotheses. The software produces a standardized report, maximizing transparency and repeatability. We illustrate evidence extraction and synthesis. Environmental research is hampered by the complexity of natural environments, and difficulty with performing experiments in such systems. Under these constraints, systematic syntheses of the rapidly-expanding literature can advance ecological understanding, inform environmental management, and identify knowledge gaps and priorities for future research. Eco Evidence, and in particular its online re-usable bank of evidence, reduces the workload involved in systematic reviews. This is the first systematic review software for environmental science, and opens the way for increased uptake of this powerful approach.

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... Eco Evidence is a freely available framework (Norris et al. 2012), online database of evidence, and supporting software (https://toolkit.ewater.org.au/tools/eco-evidence, accessed 16 February 2018) to facilitate assessment of causal hypotheses in environmental science (Webb et al. 2015b). The history and logic behind the Eco Evidence framework are described in detail elsewhere (Nichols et al. 2011;Norris et al. 2012). ...
... Each study was reviewed for relevant evidence items. Evidence was extracted and was given a weighting based on the study design according to the pre-defined rules in Eco Evidence (Nichols et al. 2011;Norris et al. 2012), and entered into the online Eco Evidence database (Webb et al. 2015b). After extracting evidence items, we assessed the level of support for each cause-effect hypothesis from the conceptual models. ...
... To evaluate support for each hypothesis, we used the Eco Evidence desktop analysis software (Webb et al. 2015b) to sum the individual evidence weights of studies that support the hypothesis, and also sum weights of those that refute it. We used the default threshold of 20 summed points for reaching conclusions. ...
Article
Environmental flows aim to mitigate the impacts of modification of riverine flow regimes by restoring components of the natural flow regime. Explicit evidence-based cause-effect relationships between flow regimes and fish responses are required for defensible flow recommendations. However, flow recommendations are typically based on expert opinion rather than a rigorous test of the available evidence. We used rapid evidence synthesis to systematically review the literature on responses of several native Australian fish to flow-related and other important environmental variables, and tested 13 explicit hypotheses. The hypotheses were related to the condition, reproduction and survival of pygmy perches, carp gudgeons, blackfish and flat-headed gudgeons. The evidence was insufficient to reach strong conclusions for all but three of our hypotheses. Late-spring high flows are associated with increased survival of pygmy perches and carp gudgeons, and exotic fish are associated with decreased survival of these fishes. The evidence that warmer spring water temperatures enhance their reproduction was inconsistent. The dearth of evidence to support or refute most hypotheses points to substantial gaps in our understanding of hydro-ecology of these native Australian fish, highlighting the need for targeted monitoring and research to further understand key flow relationships for these fish species.
... Relevant information from the papers was extracted to a spreadsheet to enable a synthesis of the literature (for convenience it was split into Sheets 2 & 3 in Appendix A). According to the concept, each effect of combined stressors on a response variable (a 'bivariate association' sensu Ziegler et al., 2015) described in a quantitative way forms an 'evidence item' (EI) sensu Webb et al. (2015) that was entered into a separate row of the table. Papers containing more than one EI thus covered several rows of the table. ...
... Here, the knowledge of quantifiable responses to multiple stressors can serve as the basis for risk assessment and appropriate management actions. Decision support systems for causal analysis, such as CADDIS (Norton et al., 2009) and Eco Evidence (Webb et al., 2015 ), use scientific literature to inform evidence-based decision making in environmental management. Both applications rely on literature databases containing information on stressor-response associations reported in the peer-reviewed scientific literature. ...
... 15 alexandra.collins@imperial.ac.uk the accessibility of our research results for environmental management and policy applications. The objective of this initiative is to facilitate inclusion of FWS-published research results in databases that support systematic literature assessments (e.g., Webb et al. 2015, USEPA 2018. Once the research findings are entered into these databases, they can be quickly and repeatedly accessed, increasing the efficiency and timeliness of their application to diverse environmental management questions and tools. ...
... The Eco Evidence software also provides an online database ( Webb et al. 2015), which stores information about causal relationships extracted from environmental science stud-ies. This information is specifically geared to support cause and effect assessments. ...
Technical Report
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This deliverable gives an overview of the functionality of the Freshwater Information System (FIS) through a number of screenshots and a short explanatory text. FIS is one of the tools that are developed within the MARS project. It is the web-based information system providing access to information and practical tools generated in MARS. FIS contains informative factsheets for DPSIR, stressors, ecosystem services and MARS case studies on the impact of multiple stressors for ecological status as well as a model selection tool for river basin management. The design and functionality has been discussed internally with MARS partners (Deltares, UDE, IGB) and with end-users during workshops in Delft (September 2015) and Den Helder (October 2016). FIS will be integrated in the Freshwater Information Platform, which aims at bringing together the results of many projects dealing with freshwater ecosystems in one a single platform. While the assessment of the ecological status of surface water bodies has become quite straightforward nowadays, almost two decades after the WFD has been launched, the inference of appropriate management options from the assessment is still challenging. More precisely, water body managers face the ecological status assessment of a given water body that usually integrates over several or numerous (multiple) stressors impacting the water body. The challenge is to identify the most-impacting stressor(s) and to distinguish them from the minor ones. Such stressor hierarchies are required to infer the appropriate hierarchy of management options to address the relevant stressors. This report presents tools to assist water body managers in the inference of management options to address the impact of multiple stressors on surface water bodies. The first chapter presents a conceptual model to visualise the published evidence of the impacts of combined stressors (here: nutrient enrichment and fine sediment pollution) on river organisms. The structured evaluation of published evidence can help identify potential interactions of stressors, which then require consideration in water body management. The second chapter presents an approach to diagnose the causes of deterioration of lowland rivers based on the causes' (stressors') effects on selected diagnostic metrics derived from the macrozoobenthos community. The approach uses a Bayesian (Belief) Network (BN) to statistically infer the probabilities of the causes to be causal for the detected effects at the water body. In the third chapter, we present an interactive online tool that builds upon the BN as presented in Chapter 2. The tool provides a graphical interface that allows the user to easily enter evidence (i.e. the states of selected effect variables) to the BN. The results are graphically displayed and accompanied by helpful background information and web links to relevant sources of information.
... One such method is Eco Evidence (Norris et al., 2012;Webb et al., 2015). This approach uses an eight-step method that is consistent with the aims and philosophy of systematic review for hypothesis setting, evidence gathering and synthesis, and reporting on conclusions. ...
Chapter
Failure to address nonflow stressors and flow-mediated connections through catchments is frequently implicated as the cause of disappointing outcomes from experimental environmental water projects. This is a key reason for considering environmental water management as part of an integrated catchment management (ICM) approach, which aligns efforts across government and nongovernment stakeholders to balance protection and use of land, water, and biodiversity. Successful ICM requires an ability to determine the primary stressors affecting environmental function within a catchment. Systematic review of evidence is a practical approach to identification of stressors in river ecosystems and several approaches are available. Implementation of ICM has had mixed results. In Australia, the Victorian catchment management authorities provide a useful case study where environmental water management has been included as part of a broader catchment management program. The Ecosystem Approach provided a set of principles that should be considered in the design of effective ICM in the future.
... Given the proliferation of hydropower dams and other barriers to fish migration in the temperate south, our aim was to assess the evidence for design criteria that would optimise the effectiveness of fishways for non-sport species. We evaluated a total of 19 hypotheses ( Table 1, Table 2) using the Eco Evidence method and software for literature evidence synthesis (Norris et al., 2012;Webb et al., 2015). êTurbine revolution speed éMortality (blade strike) T4 ...
Conference Paper
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The development of hydropower and other infrastructure that disrupts river connectivity poses a serious threat to highly endemic and genetically distinct freshwater fish species in temperate parts of the Southern Hemisphere. Such locations have been neglected in previous reviews on fish passage. Fishways have long been constructed to mitigate the impacts of riverine barriers on fish, yet they have failed for all but the largest, strongest swimming taxa. This is a particular problem in the temperate south, where the majority of species are small-bodied with low swimming performance. Using the Eco Evidence method for rapid evidence synthesis, we undertook an assessment of evidence for effective fishway design focusing on species representative of the temperate south. Systematic literature searches resulted in 630 publications. Through a rigorous screening process these were reduced to 46 publications containing 76 evidence items across 19 hypotheses relating to design criteria for upstream and downstream passage. Each evidence item was weighted according to the robustness of its study design. These weightings contributed towards the support or rejection of each hypothesis using well-established thresholds. We found an overwhelming lack of evidence for effective fishway design in the temperate south. Particular deficiencies were found with regard to the design of effective facilities for downstream passage. The attraction and entrance of upstream migrating fish into fishways is also relatively under-researched. Given the urgent need for effective fishways in the temperate south, these results justify an approach to fishway design based on a combination of empirical data and expert knowledge. In the meantime, significant resources should be assigned to improve the evidence base through high quality research. The particular deficiencies identified here could guide that research agenda.
... In these cases, the narrow scope restricts the size of the evidence-base, reducing the work involved in all steps of the synthesis process, but can introduce bias. Some rapid review approaches, such as Eco Evidence, have documented methods, use systematic searches, have clear inclusion criteria and weight relevant studies by quality, which provides a robust, yet rapid review of the evidence for causal associations (Norris et al., 2012;Webb et al., 2015b). ...
... Eco Evidence is a synthesis method with an online database and analysis software for use in environmental causal assessments (available from www.toolkit.net.au/tools/eco-evidence). It provides a robust method for synthesis of research findings available in the literature to assess cause-effect hypotheses regarding the effects of human activities or environmental rehabilitation ( Nichols et al. 2011;Norris et al. 2012;Webb et al. 2015b). The method was also designed to help improve the accessibility of primary research to policy-makers and managers. ...
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Implementing policies to return water to the environment is challenging. We developed an approach to integrate ecological responses with river management models to provide a link between flow and ecology. This paper aims to summarize the findings of a multifaceted project bringing together multiple lines of evidence to achieve a proof-of-concept approach for optimizing water use to support water policy and management decisions. We developed an eco-hydrology model that represents rivers, water storages, operational constraints, flow management, an ecological response and consumptive irrigation demands, which is linked to climate. To demonstrate the proof of concept, we describe a case study where modelling optimization seeks solutions to minimize terrestrial vegetation encroachment (an ecological response) and maximize irrigation net value through flow management. The solutions provide a range of alternative ‘optimal’ management options to consider. Ultimately, hydrological modelling that integrates both consumptive use and ecological response simultaneously is important to enhance stakeholder understanding of the complexities and trade-offs involved in implementing different decisions. Although proof of concept at this stage, the approaches offer potential for integration of river management models and quantitative ecological response models (derived by considering available evidence from many sources) to support water policy and management decisions.
... The need for tools and a standardized approach to environmental causal assessments were the primary motivations for developing Eco Evidence (www.toolkit.net.au/tools/eco -evidence), which comprises an evidence synthesis method (Nichols et al. 2011, an online database, and analysis software (Webb et al. 2015). The goal was to provide a robust and streamlined method and associated tools for systematic literature review to assess cause-effect hypotheses regarding the effects of human activities and rehabilitation on the environment , Nichols et al. 2011. ...
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... location, study design, level of replication, effect size, quality and strength of the dependence) further aid in interpreting and weighting individual associations in the context of new hypotheses and analyses. The extraction of such information from Mims and Olden (2012) is detailed in Webb et al. (2015). We are developing an open-access, online and machinereadable repository of associations, external, but complementary, to the traditional written manuscript and scientific publication paradigm. ...
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Responsible care and management of Earth’s resources requires scientific support, but the pool of underused research is growing rapidly. Environmental science research studies describe associations between variables (e.g. statistical relationships between stressors and responses). We propose open-access and online sharing of such associations. This concept differs from various efforts around the world to promote sharing of primary research data, but holds similar goals of improved use of existing knowledge. The initiative is made possible by recent developments in information technology and evolving online culture (e.g. crowdsourcing and citizen science). We have begun to connect existing projects that catalog and store associations, thereby moving toward a single virtual repository. Researchers and decision makers may share and re-use associations for myriad purposes, including: increasing efficiency and timeliness of systematic reviews, environmental assessments and meta-analyses, identifying knowledge gaps and research opportunities, providing evolved metrics of research impact, and demonstrating connections between research and environmental improvement.
Chapter
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1. Whilst it is widely recognised that a natural flow regime is important for sustaining riverine ecosystems, the relative importance of the various components of flow regime for riparian vegetation dynamics is poorly understood. We sought to determine the current extent of knowledge on the importance of seasonal flow timing for riparian plants by conducting a systematic review of the literature using causal criteria analysis. 2. Using a definition of ‘riparian’ that included riverine, wetland and floodplain systems, we found sufficient evidence to provide strong support for the existence of causal relations between seasonal flow timing and a number of riparian plant processes, namely rates of waterborne dispersal (hydrochory), germination and growth, as well as riparian community composition. There was insufficient evidence to infer a causal relationship between flow timing and the reproduction or survival of riparian plants. 3. Thus, we argue that seasonal flow timing is important for many of the processes that generate and sustain riparian vegetation communities. River regulation, and/or flow management aimed at restoring ecological values, should consider flow timing and its implication for riparian flora. Because of regulation, many of the rivers of south-eastern Australia have inverted seasonal flow patterns. Whilst direct evidence of the effects of this inversion on the flora of these rivers is lacking, the results of our causal analysis allow us to predict how these plant communities may have been affected. 4. However, these predictions must be treated with caution because of the reliance of some of the causal analyses on wetland studies. For riverine flora, further research is particularly needed on the effects of seasonal flow timing on hydrochory, survival and reproduction. 5. Causal criteria analysis provides a defensible and efficient means for assessing the extent of evidence for or against ecological hypotheses of this kind. In this case, systematic review of the literature provided strong evidence to support a number of causal links between seasonal flow timing and riparian vegetation dynamics, whilst also efficiently identifying knowledge gaps.
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The environmental movement of the 20(th) century has evolved into a large, diverse and well-financed global community that is increasingly required to prove its worth. Though the environmental sector collects and uses data to determine the status of ecological and social systems, the effectiveness of the programs and policies it uses to affect this status remains largely untested. As governments and donor institutions insist on greater transparency, accountability and evidence of what works and what does not, much is being learned from other fields (e.g. health services, education, international development) and increasingly sophisticated approaches are emerging to manage effectiveness. For example, program evaluation, adaptive management, and systematic review provide frameworks and methods to collect and use information to measure and improve performance. However, the critical data and collaborations necessary for an effectiveness revolution are marginalized by technical, cultural and political obstacles. Learning from other fields, the environmental sector must exploit key leverage points, such as flows of information and self-organization, to overcome impediments and create incentives to initiate and realize an era of effectiveness in environmental management.
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Computerized clinical decision support (CDS) aims to aid decision making of health care providers and the public by providing easily accessible health-related information at the point and time it is needed. natural language processing (NLP) is instrumental in using free-text information to drive CDS, representing clinical knowledge and CDS interventions in standardized formats, and leveraging clinical narrative. The early innovative NLP research of clinical narrative was followed by a period of stable research conducted at the major clinical centers and a shift of mainstream interest to biomedical NLP. This review primarily focuses on the recently renewed interest in development of fundamental NLP methods and advances in the NLP systems for CDS. The current solutions to challenges posed by distinct sublanguages, intended user groups, and support goals are discussed.
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Ecology is inherently cross-disciplinary, drawing together many types of information to address questions about the natural world. Finding and integrating relevant data to assist in these analyses is crucial, but is difficult owing to ambiguous terminology and the lack of sufficient information about datasets. Ontologies provide a formal mechanism for defining terms and their relationships, and can improve the location, interpretation and integration of data based on its inherent meaning. Ontologies have assisted other disciplines (e.g. molecular biology) in unifying and enriching descriptions of data, and ecology can benefit from similar approaches. We review ontology efforts in ecology, and describe how these can benefit research by enhancing the location and interpretation of relevant data for confronting crucial ecological questions.
Advancing ecological research with ontologies What constitutes a good literature review and why does its quality matter? Environ. Model. Softw. 43 Environmental flows can reduce the encroachment of terrestrial vegetation into river channels: a systematic literature review
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