Category Archives: oa.ecology

Beyond the Repository – ACM Queue

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“Open source is much more than a repository—it is a rich multilevel ecosystem of human contributors who collaboratively cooperate, in many capacities, to accomplish a shared creative endeavor. Consequently, when studying open source ecosystems, numerous interacting parts must be considered to understand the dynamics of the whole. Research on open source ecosystems is ultimately research about a sociotechnical ecosystem. Researchers should take care to retain the socio- element in research and understand how both their methods and results may impact entire open source ecosystems.

This article describes best practices for open source ecosystems research through multiple overarching best practices. It offers practical guidelines for conducting rigorous, ethical, respectful research that maintains the integrity of the open source ecosystem under consideration….”

Close to open—Factors that hinder and promote open science in ecology research and education | PLOS ONE

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Abstract:  The Open Science (OS) movement is rapidly gaining traction among policy-makers, research funders, scientific journals and individual scientists. Despite these tendencies, the pace of implementing OS throughout the scientific process and across the scientific community remains slow. Thus, a better understanding of the conditions that affect OS engagement, and in particular, of how practitioners learn, use, conduct and share research openly can guide those seeking to implement OS more broadly. We surveyed participants at an OS workshop hosted by the Living Norway Ecological Data Network in 2020 to learn how they perceived OS and its importance in their research, supervision and teaching. Further, we wanted to know what OS practices they had encountered in their education and what they saw as hindering or helping their engagement with OS. The survey contained scaled-response and open-ended questions, allowing for a mixed-methods approach. We obtained survey responses from 60 out of 128 workshop participants (47%). Responses indicated that usage and sharing of open data and code, as well as open access publication, were the most frequent OS practices. Only a minority of respondents reported having encountered OS in their formal education. A majority also viewed OS as less important in their teaching than in their research and supervisory roles. The respondents’ suggestions for what would facilitate greater OS engagement in the future included knowledge, guidelines, and resources, but also social and structural support. These are aspects that could be strengthened by promoting explicit implementation of OS practices in higher education and by nurturing a more inclusive and equitable OS culture. We argue that incorporating OS in teaching and learning of science can yield substantial benefits to the research community, student learning, and ultimately, to the wider societal objectives of science and higher education.

 

“Superior identification index – Quantifying the capability of academic journals to recognize good research

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Abstract:  In this paper we present “superior identification index” (SII), a metric to quantify the capability of academic journals to recognize top papers restricted by specific time window and study field. Intuitively, SII is the percentage of papers from a journal in the top p% papers in the field. SII provides flexible framework to make trade-offs on journal quality and quantity, as p rises it puts more weight on quantity and less weight on quality. Concerns on the p selection are discussed, and extended metrics of SII, including superior identification efficiency (SIE) and paper rank percentile (PRP), were proposed to sketch other dimensions of journal performance. Based on bibliometric data from ecological field, we find that as p increases, the correlation between SIE and JIF first rises then drops, indicating that JIF might most likely reflect “how well a journal identifies the top 26~34% papers in the field”. Hopefully, the new proposed SII metric and its extensions could promote the quality awareness and provide flexible tools for research evaluation.

Slow improvement to the archiving quality of open datasets shared by researchers in ecology and evolution | Proceedings of the Royal Society B: Biological Sciences

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Abstract:  Many leading journals in ecology and evolution now mandate open data upon publication. Yet, there is very little oversight to ensure the completeness and reusability of archived datasets, and we currently have a poor understanding of the factors associated with high-quality data sharing. We assessed 362 open datasets linked to first- or senior-authored papers published by 100 principal investigators (PIs) in the fields of ecology and evolution over a period of 7 years to identify predictors of data completeness and reusability (data archiving quality). Datasets scored low on these metrics: 56.4% were complete and 45.9% were reusable. Data reusability, but not completeness, was slightly higher for more recently archived datasets and PIs with less seniority. Journal open data policy, PI gender and PI corresponding author status were unrelated to data archiving quality. However, PI identity explained a large proportion of the variance in data completeness (27.8%) and reusability (22.0%), indicating consistent inter-individual differences in data sharing practices by PIs across time and contexts. Several PIs consistently shared data of either high or low archiving quality, but most PIs were inconsistent in how well they shared. One explanation for the high intra-individual variation we observed is that PIs often conduct research through students and postdoctoral researchers, who may be responsible for the data collection, curation and archiving. Levels of data literacy vary among trainees and PIs may not regularly perform quality control over archived files. Our findings suggest that research data management training and culture within a PI’s group are likely to be more important determinants of data archiving quality than other factors such as a journal’s open data policy. Greater incentives and training for individual researchers at all career stages could improve data sharing practices and enhance data transparency and reusability.

 

Past and future uses of text mining in ecology and evolution | Proceedings of the Royal Society B: Biological Sciences

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Abstract:  Ecology and evolutionary biology, like other scientific fields, are experiencing an exponential growth of academic manuscripts. As domain knowledge accumulates, scientists will need new computational approaches for identifying relevant literature to read and include in formal literature reviews and meta-analyses. Importantly, these approaches can also facilitate automated, large-scale data synthesis tasks and build structured databases from the information in the texts of primary journal articles, books, grey literature, and websites. The increasing availability of digital text, computational resources, and machine-learning based language models have led to a revolution in text analysis and natural language processing (NLP) in recent years. NLP has been widely adopted across the biomedical sciences but is rarely used in ecology and evolutionary biology. Applying computational tools from text mining and NLP will increase the efficiency of data synthesis, improve the reproducibility of literature reviews, formalize analyses of research biases and knowledge gaps, and promote data-driven discovery of patterns across ecology and evolutionary biology. Here we present recent use cases from ecology and evolution, and discuss future applications, limitations and ethical issues.

 

LAUNCH: Laudato Si’ Integral Ecology Collection | laudato-si

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“In Laudato Si’, Pope Francis emphasised the importance of a united, global response to the current ecological crisis. Dialogue and learning on integral ecology, however, is often hindered by limited access to the academic publications on the subject, which are not affordable for many individuals and institutions in lower-income countries.

 

The Laudato Si’ Integral Ecology Collection was developed to address this problem by making open access a selection of key texts on integral ecology. The collection will provide a valuable resource for lay readers, students, and those undertaking more advanced academic study. Publications in the collection could also be read as part of a reading group or an online course.

At the launch, we will hear from academics and practitioners in the Global South on their current access to academic material on integral ecology and how this collection will support their work. We will also hear about the origins of collection and plans for its future development. There will be an opportunity for Q&A with panellists.”

Knowledge Unlatched and Laudato Si’ Research Institute Make a Collection of at least 11 Books on Integral Ecology Open Access – Knowledge Unlatched

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“Knowledge Unlatched (KU) and the Laudato Si’ Research Institute at Campion Hall, Oxford (LSRI) have joined forces to make 11 titles from the field of Integral Ecology Open Access (OA). This collection of e-books, the Laudato Si’ Integral Ecology Collection, is made possible thanks to the “KU Reverse” model from Knowledge Unlatched and to the generous co-funding from the University of Notre Dame, Georgetown University (Environmental Justice Program), with support from the Yale Forum on Religion and Ecology.

In his encyclical Laudato Si’, Pope Francis emphasized the importance of a united, global response to the current ecological crisis. Dialogue and learning on integral ecology, however, is often hindered by limited access to the academic publications on the subject, which are not affordable for many individuals and institutions in lower-income countries. The Laudato Si’ Integral Ecology Collection was developed to address this problem by making OA a selection of key texts on integral ecology. The collection will provide a valuable resource for lay readers, students, and those undertaking more advanced academic study. Publications in the collection could also be read as part of a reading group or an online course.

The titles will be made available OA to users all over the world after the official launch of the Collection on March 3, 2022 and hosted in a special module on the Open Research Library….”

Modeling Eastern Russian High Arctic Geese (Anser fabalis, A. albifrons) during moult and brood rearing in the ‘New Digital Arctic’ | Scientific Reports

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Abstract:  Many polar species and habitats are now affected by man-made global climate change and underlying infrastructure. These anthropogenic forces have resulted in clear implications and many significant changes in the arctic, leading to the emergence of new climate, habitats and other issues including digital online infrastructure representing a ‘New Artic’. Arctic grazers, like Eastern Russian migratory populations of Tundra Bean Goose Anser fabalis and Greater White-fronted Goose A. albifrons, are representative examples and they are affected along the entire flyway in East Asia, namely China, Japan and Korea. Here we present the best publicly-available long-term (24 years) digitized geographic information system (GIS) data for the breeding study area (East Yakutia and Chukotka) and its habitats with ISO-compliant metadata. Further, we used seven publicly available compiled Open Access GIS predictor layers to predict the distribution for these two species within the tundra habitats. Using BIG DATA we are able to improve on the ecological niche prediction inference for both species by focusing for the first time specifically on biological relevant population cohorts: post-breeding moulting non-breeders, as well as post-breeding parent birds with broods. To assure inference with certainty, we assessed it with 4 lines of evidence including alternative best-available open access field data from GBIF.org as well as occurrence data compiled from the literature. Despite incomplete data, we found a good model accuracy in support of our evidence for a robust inference of the species distributions. Our predictions indicate a strong publicly best-available relative index of occurrence (RIO). These results are based on the quantified ecological niche showing more realistic gradual occurrence patterns but which are not fully in agreement with the current strictly applied parsimonious flyway and species delineations. While our predictions are to be improved further, e.g. when synergetic data are made freely available, here we offer within data caveats the first open access model platform for fine-tuning and future predictions for this otherwise poorly represented region in times of a rapid changing industrialized ‘New Arctic’ with global repercussions.

 

 

Preprinting is positively associated with early career researcher status in ecology and evolution – Wolf – 2021 – Ecology and Evolution – Wiley Online Library

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Abstract:  The usage of preprint servers in ecology and evolution is increasing, allowing research to be rapidly disseminated and available through open access at no cost. Early Career Researchers (ECRs) often have limited experience with the peer review process, which can be challenging when trying to build publication records and demonstrate research ability for funding opportunities, scholarships, grants, or faculty positions. ECRs face different challenges relative to researchers with permanent positions and established research programs. These challenges might also vary according to institution size and country, which are factors associated with the availability of funding for open access journals. We predicted that the career stage and institution size impact the relative usage of preprint servers among researchers in ecology and evolution. Using data collected from 500 articles (100 from each of two open access journals, two closed access journals, and a preprint server), we showed that ECRs generated more preprints relative to non-ECRs, for both first and last authors. We speculate that this pattern is reflective of the advantages of quick and open access research that is disproportionately beneficial to ECRs. There is also a marginal association between first author, institution size, and preprint usage, whereby the number of preprints tends to increase with institution size for ECRs. The United States and United Kingdom contributed the greatest number of preprints by ECRs, whereas non-Western countries contributed relatively fewer preprints. This empirical evidence that preprint usage varies with the career stage, institution size, and country helps to identify barriers surrounding large-scale adoption of preprinting in ecology and evolution.

 

Four key challenges in the open?data revolution – Salguero?Gómez – 2021 – Journal of Animal Ecology – Wiley Online Library

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Abstract:  In Focus: Culina, A., Adriaensen, F., Bailey, L. D., et al. (2021) Connecting the data landscape of long-term ecological studies: The SPI-Birds data hub. Journal of Animal Ecology, https://doi.org/10.1111/1365-2656.13388. Long-term, individual-based datasets have been at the core of many key discoveries in ecology, and calls for the collection, curation and release of these kinds of ecological data are contributing to a flourishing open-data revolution in ecology. Birds, in particular, have been the focus of international research for decades, resulting in a number of uniquely long-term studies, but accessing these datasets has been historically challenging. Culina et al. (2021) introduce an online repository of individual-level, long-term bird records with ancillary data (e.g. genetics), which will enable key ecological questions to be answered on a global scale. As well as these opportunities, however, we argue that the ongoing open-data revolution comes with four key challenges relating to the (1) harmonisation of, (2) biases in, (3) expertise in and (4) communication of, open ecological data. Here, we discuss these challenges and how key efforts such as those by Culina et al. are using FAIR (Findable, Accessible, Interoperable and Reproducible) principles to overcome them. The open-data revolution will undoubtedly reshape our understanding of ecology, but with it the ecological community has a responsibility to ensure this revolution is ethical and effective.

 

 

 

SORTEE (SOCIETY FOR OPEN, RELIABLE, AND TRANSPARENT ECOLOGY AND EVOLUTIONARY BIOLOGY)

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“SORTEE is a service organization which brings together researchers working to improve reliability and transparency through cultural and institutional changes in ecology, evolutionary biology, and related fields broadly defined. Anyone interested in improving research in these disciplines is welcome to join, regardless of experience. The society is international in scope, membership, and objectives.is a service organization which brings together researchers working to improve reliability and transparency through cultural and institutional changes in ecology, evolutionary biology, and related fields broadly defined. Anyone interested in improving research in these disciplines is welcome to join, regardless of experience. The society is international in scope, membership, and objectives….”

 

ESA Data Policy – Ensuring an Openness to Science – Ecotone | News and Views on Ecological Science

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“ESA has adopted a society-wide open research policy for its publications to further support scientific exploration and preservation, allow a full assessment of published research, and streamline policies across our family of journals. An open research policy provides full transparency for scientific data and code, facilitates replication and synthesis, and aligns ESA journals with current standards. As of Feb. 1, 2021, all new manuscript submissions to ESA journals must abide by the following policy: 

As a condition for publication in ESA journals, all underlying data and statistical code pertinent to the results presented in the publication must be made available in a permanent, publicly accessible data archive or repository, with rare exceptions (see “Details” for more information). Archived data and statistical code should be sufficiently complete to allow replication of tables, graphs, and statistical analyses reported in the original publication, and perform new or meta-analyses. As such, the desire of authors to control additional research with these data and/or code shall not be grounds for withholding material. …”

Help me redesign the scientific paper | Dynamic Ecology

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“If scientists spend taxpayer money to generate irreproducible results, the public’s logical response should be to either withhold funds or demand a new process that emphasizes reproducibility….

Collaborative Independent Review is one way that funders, journals and scientists could implement a more reproducible paper….

Diversity and Distributions – Wiley Online Library

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“We are pleased to announce that Diversity and Distributions will join the Wiley Open Access portfolio as of 1st January 2019, when all articles (including the entire back catalogue) will become free to read, download and share for all. This exciting development will place the journal at the forefront of open science in the community. 

To cover the cost of publishing, all submissions received after 8th October 2018 will be subject to an Article Publication Charge (APC). Ability to pay the APC should not be a barrier to the publication of important science. Authors without funding for publication charges will be provided with a waiver of the APC. Automatic APC waivers and discounts will be given to authors from countries on the Waivers and Discounts List.

 A 20% discount on the APC is available to members of the International Biogeography Society. …”

Majority of journal’s editorial board resigns after publisher’s handling of letter about move to open access – Retraction Watch

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“A leading journal in ecology and evolution is going through an evolution of its own, following the resignation of its editor in chief and more than half of its editorial board.

The mass exodus at Diversity & Distributionscame after Wiley, which publishes the journal, allegedly blocked it from running a letter protesting the company’s decision to make D & D open access (the company disputes the claim, as we’ll detail in a bit). A letter about the issue, signed by scores of researchers worldwide, decried Wiley’s move….”