Article

Biodiversity data should be published, cited, and peer reviewed

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Abstract

Concerns over data quality impede the use of public biodiversity databases and subsequent benefits to society. Data publication could follow the well-established publication process: with automated quality checks, peer review, and editorial decisions. This would improve data accuracy, reduce the need for users to 'clean' the data, and might increase data use. Authors and editors would get due credit for a peer-reviewed (data) publication through use and citation metrics. Adopting standards related to data citation, accessibility, metadata, and quality control would facilitate integration of data across data sets. Here, we propose a staged publication process involving editorial and technical quality controls, of which the final (and optional) stage includes peer review, the most meritorious publication standard in science.

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... For all of these reasons, we chose to build the workflow around the third approach, centralized data reformatting where data is curated by a dedicated data aggregator. This approach could interest both parties involved, as the data provider could benefit from the expertise of the data aggregator on data shared, as well as providing advice on metadata information or potential errors (Costello et al., 2013). ...
... However, in contrast to data publication, data sharing, on which the Status of Coral Reefs of the World: 2020 report (Souter et al., 2021) was mainly built, limits the traceability of integrated individual datasets (as they are not associated with a DOI), reducing the reproducibility of the workflow. The trend towards increased data publication should nevertheless help to reduce this problem in the coming years (Costello et al., 2013;Shin et al., 2020). ...
... The need for data integration will likely increase in the coming years (Miller et al., 2019), due to the emergence of new standards on data interoperability (e.g. FAIR data principles, (Wilkinson et al., 2016)) and a trend towards further data sharing (Michener, 2015) or data publication (Costello et al., 2013;Shin et al., 2020), which together sharply increase the volume of accessible data available to the scientific community (Hampton et al., 2013). In this context, the publication of code and workflow are essential to increase the reproducibility of results and to drive ecology towards a more transparent science. ...
Article
Programs and initiatives aiming to protect biodiversity and ecosystems have increased over the last decades in response to their decline. Most of these are based on monitoring data to quantitatively describe trends in biodiversity and ecosystems. The estimation of such trends, at large scales, requires the integration of numerous data from multiple monitoring sites. However, due to the high heterogeneity of data formats and the resulting lack of interoperability, the data integration remains sparsely used and synthetic analyses are often limited to a restricted part of the data available. Here we propose a workflow, comprising four main steps, from data gathering to quality control, to better integrate ecological monitoring data and to create a synthetic dataset that will make it possible to analyse larger sets of monitoring data, including unpublished data. The workflow was designed and applied in the production of the Status of Coral Reefs of the World: 2020 report, where more than two hundred individual datasets were integrated to assess the status and trends of hard coral cover at the global scale. The workflow was applied to two case studies and associated R codes, based on the experience acquired during the production of this report. The proposed workflow allows for the integration of datasets with different levels of taxonomic and spatial precision, with a high degree of reproducibility. It provides a conceptual and technical framework for the integration of ecological monitoring data, allowing for the estimation of temporal trends in biodiversity and ecosystems or to test ecological hypotheses at larger scales.
... However, a single bottom trawl survey (henceforth survey) is typically carried out nationally, regionally or within a delimited management zone (but this is not the case for some of the European surveys). As a result, monitoring protocols differ among surveys, and the data are not always publicly available, while the assessment of species range shifts critically depends on the availability and quality of surveys (Costello et al., 2013;Schindler & Hilborn, 2015). ...
... The network created here greatly improves the visibility of surveys, by presenting their metadata. Further, the availability of data can only be improved by changing the way we share scientific information, for instance by publishing data (Costello et al., 2013) and ensuring quality-controlled use of data. Several bottom trawl surveys are published online, but the most recent years are not always included, or links to access the data are not always maintained, e.g., the Norwegian surveys (Djupevåg, 2018), the southern Gulf of St Lawrence survey (Swain et al., 2016), Mauritania (Kidé et al., 2015), southeast Asian surveys (Garces et al., 2006). ...
... Publishing data, following FAIR principles (Findable, Accessible, Interoperable and Reusable, https://www.go-fair.org/fair-princ iples/) as well as open science principles, could ultimately increase the visibility of surveys but will face the challenge of thoughtfully using the data by prioritizing the need to give credit to the data providers (Costello et al., 2013; Box 1). ...
Article
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Marine biota are redistributing at a rapid pace in response to climate change and shifting seascapes. While changes in fish populations and community structure threaten the sustainability of fisheries, our capacity to adapt by tracking and projecting marine species remains a challenge due to data discontinuities in biological observations, lack of data availability, and mismatch between data and real species distributions. To assess the extent of this challenge, we review the global status and accessibility of ongoing scientific bottom trawl surveys. In total, we gathered metadata for 283,925 samples from 95 surveys conducted regularly from 2001 to 2019. We identified that 59% of the metadata collected are not publicly available, highlighting that the availability of data is the most important challenge to assess species redistributions under global climate change. Given that the primary purpose of surveys is to provide independent data to inform stock assessment of commercially important populations, we further highlight that single surveys do not cover the full range of the main commercial demersal fish species. An average of 18 surveys is needed to cover at least 50% of species ranges, demonstrating the importance of combining multiple surveys to evaluate species range shifts. We assess the potential for combining surveys to track transboundary species redistributions and show that differences in sampling schemes and inconsistency in sampling can be overcome with spatio-temporal modeling to follow species density redistributions. In light of our global assessment, we establish a framework for improving the management and conservation of transboundary and migrating marine demersal species. We provide directions to improve data availability and encourage countries to share survey data, to assess species vulnerabilities, and to support management adaptation in a time of climate-driven ocean changes.
... Moreover, data usage represents a critical potential currency, with higher-quality information being used more frequently. The usage of individual Primary Biodiversity Data can be quantified via linkage with documentation of their use-for example downloading events and, most importantly, publications or reports based on them (Costello et al. 2013). Standardized quantifications of data quality and use should both help justify improvements to data quality and increase incentives for both providers and funding sources to improve data quality. ...
... Increasingly, journals and funding sources require that data used in publications be made openly available (Molloy 2011, Reichmen et al. 2011e.g., Nature Scientific Data, Biodiversity Data Journal). Whereas digital deposition is customary for some kinds of data (e.g., GenBank for gene sequences; DRYAD for more diverse data types; Greenberg et al. 2009), no equivalent expectation or standard mechanism yet exists for Primary Biodiversity Data (Table 1; Chavan and Ingwersen 2009, Costello et al. 2013. Similarly, recent years have seen dramatic increases in online supplemental information and external repositories to document methods and provide code (Campbell et al. 2019). ...
... Furthermore, a broad consensus must be reached regarding mechanism to achieve a standardized identifier system that can be used across aggregators and throughout biodiversity science , Suhrbier et al. 2017, BCN 2018. We advocate for a single registry service to guarantee that a given identifier indeed is universally unique for all biodiversity uses (Costello et al. 2013). ...
... However, a single bottom trawl survey (henceforth survey) is typically carried out nationally, regionally or within a delimited management zone (but this is not the case for some of the European surveys). As a result, monitoring protocols differ among surveys, and the data are not always publicly available, while the assessment of species range shifts critically depends on the availability and quality of surveys (Costello et al., 2013;Schindler & Hilborn, 2015). ...
... The network created here greatly improves the visibility of surveys, by presenting their metadata. Further, the availability of data can only be improved by changing the way we share scientific information, for instance by publishing data (Costello et al., 2013) and ensuring quality-controlled use of data. Several bottom trawl surveys are published online, but the most recent years are not always included, or links to access the data are not always maintained, e.g., the Norwegian surveys (Djupevåg, 2018), the southern Gulf of St Lawrence survey (Swain et al., 2016), Mauritania (Kidé et al., 2015), southeast Asian surveys (Garces et al., 2006). ...
... Publishing data, following FAIR principles (Findable, Accessible, Interoperable and Reusable, https://www.go-fair.org/fair-princ iples/) as well as open science principles, could ultimately increase the visibility of surveys but will face the challenge of thoughtfully using the data by prioritizing the need to give credit to the data providers (Costello et al., 2013; Box 1). ...
Article
Full-text available
Marine biota are redistributing at a rapid pace in response to climate change and shifting seascapes. While changes in fish populations and community structure threaten the sustainability of fisheries, our capacity to adapt by tracking and projecting marine species remains a challenge due to data discontinuities in biological observations, lack of data availability, and mismatch between data and real species distributions. To assess the extent of this challenge, we review the global status and accessibility of ongoing scientific bottom trawl surveys. In total, we gathered metadata for 283,925 samples from 95 surveys conducted regularly from 2001 to 2019. We identified that 59% of the metadata collected are not publicly available, highlighting that the availability of data is the most important challenge to assess species redistributions under global climate change. Given that the primary purpose of surveys is to provide independent data to inform stock assessment of commercially important populations, we further highlight that single surveys do not cover the full range of the main commercial demersal fish species. An average of 18 surveys is needed to cover at least 50% of species ranges, demonstrating the importance of combining multiple surveys to evaluate species range shifts. We assess the potential for combining surveys to track transboundary species redistributions and show that differences in sampling schemes and inconsistency in sampling can be overcome with spatio‐temporal modeling to follow species density redistributions. In light of our global assessment, we establish a framework for improving the management and conservation of transboundary and migrating marine demersal species. We provide directions to improve data availability and encourage countries to share survey data, to assess species vulnerabilities, and to support management adaptation in a time of climate‐driven ocean changes.
... This study investigates why PDA policies that go beyond ''available upon request'' may not be proving effective in realizing the goals of open data efforts. One purported reason for failing to build collections of reusable datasets is that journals lack appropriate enforcement mechanisms and incentive structures to ensure that published datasets are complete and high quality (Costello et al., 2013;Mayernik, 2017). We sought to build on this idea and explain the mechanisms by which journals enforce PDA policies by examining the roles of stakeholders in the PDA process and identifying problematic aspects of the process. ...
... For example, the Global Biodiversity Information Facility houses hundreds of datasets and continues to grow in size and scope. However, as Costello et al. (2013) pointed out, over two-thirds of the datasets have been provided by government organizations rather than from academics. This finding is surprising given that, according to Ware and Mabe (2015) and Costello et al. (2013), academic researchers publish 75% of all scientific papers across scientific disciplines. ...
... However, as Costello et al. (2013) pointed out, over two-thirds of the datasets have been provided by government organizations rather than from academics. This finding is surprising given that, according to Ware and Mabe (2015) and Costello et al. (2013), academic researchers publish 75% of all scientific papers across scientific disciplines. Researchers from various subdisciplines have called for increased contributions from the academic community and have offered mechanisms by which the community might review and improve datasets prior to publishing (Chavan and Ingwersen, 2009;Costello, 2009;Costello et al., 2013;Michener, 2015;Piwowar et al., 2007;White et al., 2013). ...
Article
Full-text available
To improve the quality and efficiency of research, groups within the scientific community seek to exploit the value of data sharing. Funders, institutions, and specialist organizations are developing and implementing strategies to encourage or mandate data sharing within and across disciplines, with varying degrees of success. Academic journals in ecology and evolution have adopted several types of public data archiving policies requiring authors to make data underlying scholarly manuscripts freely available. The effort to increase data sharing in the sciences is one part of a broader “data revolution” that has prompted discussion about a paradigm shift in scientific research. Yet anecdotes from the community and studies evaluating data availability suggest that these policies have not obtained the desired effects, both in terms of quantity and quality of available datasets. We conducted a qualitative, interview-based study with journal editorial staff and other stakeholders in the academic publishing process to examine how journals enforce data archiving policies. We specifically sought to establish who editors and other stakeholders perceive as responsible for ensuring data completeness and quality in the peer review process. Our analysis revealed little consensus with regard to how data archiving policies should be enforced and who should hold authors accountable for dataset submissions. Themes in interviewee responses included hopefulness that reviewers would take the initiative to review datasets and trust in authors to ensure the completeness and quality of their datasets. We highlight problematic aspects of these thematic responses and offer potential starting points for improvement of the public data archiving process.
... There is growing recognition that this open sharing of biodiversity data is critical for advancing biodiversity research (Farley et al. 2018). Some of the primary benefits of open biodiversity data include enhanced reproducibility of research (Alston and Rick 2021); making data available for reuse in new research applications (Chawinga and Zinn 2019); enabling researchers to receive credit, in the form of citations, for their efforts producing and sharing data sets (Costello et al. 2013, Brown 2021; and minimizing the duplication of research effort, enabling researchers to prioritize new data collection that fills research gaps (Troudet et al. 2017). As data sharing continues to become normalized, best practices have developed for the sharing of biodiversity data (Kühl et al. 2020). ...
... We recognize many values of small databases, including responsiveness to specific disciplinary requirements (Franz and Sterner 2018) and the cultivation of strong relationships between data curators and communities of data users (Blair et al. 2020, Monfils et al. 2020. However, small open databases may lack the standardization and interoperability that are built into larger data aggregators , they may lack consistent leadership to maintain growing content and keep up with developing best practices (Costello et al. 2013), and they are more likely to become technologically obsolete, rendering the data inaccessible (Vines et al. 2014, Tessarolo et al. 2017, Ball-Damerow et al. 2019, Blair et al. 2020. ...
Article
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Presence-only biodiversity data are increasingly relied on in biodiversity, ecology, and conservation research, driven by growing digital infrastructures that support open data sharing and reuse. Recent reviews of open biodiversity data have clearly documented the value of data sharing, but the extent to which the biodiversity research community has adopted open data practices remains unclear. We address this question by reviewing applications of presence-only primary biodiversity data, drawn from a variety of sources beyond open databases, in the indexed literature. We characterize how frequently researchers access open data relative to data from other sources, how often they share newly generated or collated data, and trends in metadata documentation and data citation. Our results indicate that biodiversity research commonly relies on presence-only data that are not openly available and neglects to make such data available. Improved data sharing and documentation will increase the value, reusability, and reproducibility of biodiversity research.
... although not all published sequences are accompanied by these metadata and there are also some concerns about data quality, e.g. the accuracy of both metadata and annotations (Costello et al., 2013;Culligan et al., 2014). ...
... Publication of data is also often required by funding bodies, probably because making the data available to the whole scientific community makes better use of the resources that they have provided for the research (Pearce and Smith, 2011). Data which has been generated through publicly funded research usually has to be published (Costello et al., 2013). ...
Thesis
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This master thesis explores the perspective of different actors on the issue of digital sequence information on genetic resources (DSI) on the need for benefit-sharing arising from the use of DSI, the form of benefit-sharing and how this could be organized within the Nagoya Protocol‟s framework.
... Citing datasets as professional reward for sharing has been mentioned by researchers in biodiversity and other fields to be a major incentive for making data openly available (Piwowar, 2011;Edmundus et al., 2012;Enke et al., 2012;Kim & Zhang, 2015;Sayogo & Pardo, 2013). The number of publications using GBIF data and citing GBIF has rapidly increased since 2007 (Costello et al., 2013). However, few datasets are cited in a standard format in biodiversity and the citation style is often determined by the editors for their journal (Costello et al., 2013). ...
... The number of publications using GBIF data and citing GBIF has rapidly increased since 2007 (Costello et al., 2013). However, few datasets are cited in a standard format in biodiversity and the citation style is often determined by the editors for their journal (Costello et al., 2013). This is similar to life sciences data in Dryad, where the number of articles citing data in works cited section was only 8% as of 2014 (Mayo, Vision & Hull, 2016). ...
Conference Paper
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Openly available research data promotes reproducibility in science and results in higher citation rates for articles published with data in biological and social sciences. Even though biodiversity is one of the fields where data is frequently reused, information about how data is reused and cited is not often openly accessible from research data repositories. This study explores data citation and reuse practices in biodiversity by using openly available metadata for 43,802 datasets indexed in the Global Biodiversity Information Facility (GBIF). Quantitative analysis of dataset types and citation counts suggests that the number of studies making use of openly available biodiversity data has been increasing in a steady manner. Citation rates vary for different types of datasets based on the quality of data, and similarly to articles, it takes 2-3 years to accrue most citations for datasets. Content analysis of a random sample of unique citing articles (n=101) for 437 cited datasets in a random sample of 1000 datasets suggests that best practice for data citation is yet to be established. 26.7% of articles are mentioned the dataset in references, 12.9% are mentioned in data access statements in addition to the methods section, and only 2% are mentioned in all three sections, which is important for automatic extraction of citation information. Citation practice was inconsistent especially when a large number of subsets (12~50) were used. This calls for adoption of a standard citation model for this field to provide proper attribution when using subsets of data.
... Open methods mean that the details of how the research was conducted are comprehensively and transparently reported, allowing the reader to understand what was done and, in principle, replicate or extend those methods in the future (Munafò et al. 2017). Open data allow readers to verify whether conclusions in the report are backed by the data, support long-term monitoring and comparative studies, and facilitate evidence synthesis (Costello et al. 2013;Costello & Wieczorek 2014;Roche et al. 2014;Haddaway 2015;Culina et al. 2018b). Open data also allow researchers to ask new and different questions, often at a broader scale, to build knowledge and understanding (Tenopir et al. 2011;Poisot et al. 2013) (Appendix S1). ...
... Additionally, open materials can help improve citizen/community science initiatives, which contribute invaluable data to conservation science (e.g., Sullivan et al. 2017;Robinson et al. 2020). Open data also ensure maximum benefits from the costs of data collection (Costello et al. 2013;Hampton et al. 2013;Turner et al. 2015). For example, open data make it easier to find information on a target species or ecosystem (Culina et al. 2018a); they facilitate evidence synthesis (especially meta-analysis), particularly for species that are less-well studied (Culina et al. 2018b); and they allow better-designed and hence more informative studies -for example, by facilitating power analyses to avoid errors of statistical significance and effect sign or magnitude ...
Article
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The knowledge‐action gap in conservation science and practice occurs when research outputs do not result in actions to protect or restore biodiversity. Among the diverse and complex reasons for this gap, three barriers are fundamental: knowledge is often unavailable to practitioners, challenging to interpret, and/or difficult to use. Problems of availability, interpretability, and useability are solvable with open science practices. We consider the benefits and challenges of three open science practices for use by conservation scientists and practitioners. First, open access publishing makes the scientific literature available to all. Second, open materials (methods, data, code, and software) increase the transparency and (re)use potential of research findings. Third, open education resources allow conservation professionals (scientists and practitioners) to acquire the skills needed to make use of research outputs. The long‐term adoption of open science practices would help researchers and practitioners achieve conservation goals more quickly and efficiently, in addition to reducing inequities in information sharing. However, short‐term costs for individual researchers (insufficient institutional incentives to engage in open science and knowledge mobilization) remain a challenge to overcome. Finally, we caution against a passive approach to sharing that simply involves making information available. We advocate for a proactive stance towards transparency, communication, collaboration, and capacity building that involves seeking out and engaging with potential users to maximize the environmental and societal impact of conservation science. This article is protected by copyright. All rights reserved
... Citing datasets as professional reward can be a major incentive for sharing (Piwowar, 2011;Edmundus et al., 2012;Enke et al., 2012;Kim & Zhang, 2015;Sayogo & Pardo, 2013). The number of publications using GBIF data and citing GBIF has rapidly increased since 2007 (Costello et al., 2013). However, few datasets are cited in a standard format in biodiversity and the citation style is often determined by the editors for their journal (Costello et al., 2013). ...
... The number of publications using GBIF data and citing GBIF has rapidly increased since 2007 (Costello et al., 2013). However, few datasets are cited in a standard format in biodiversity and the citation style is often determined by the editors for their journal (Costello et al., 2013). This is similar to life sciences data in Dryad, where the number of articles citing data in works cited section was only 8% as of 2014 (Mayo, Vision, & Hull, 2016). ...
Article
Despite growing evidence of open biodiversity data reuse by scientists, information about how data is reused and cited is rarely openly accessible from research data repositories. This study explores data citation and reuse practices in biodiversity by using openly available metadata for 43,802 datasets indexed in the Global Biodiversity Information Facility (GBIF) and content analyses of articles citing GBIF data. Results from quantitative and content analyses suggest that even though the number of studies making use of openly available biodiversity data has been increasing steadily, best practice for data citation is not yet common. It is encouraging, however, that an increasing number of recent articles (16 out of 23 in 2019) in biodiversity cite datasets in a standard way. A content analysis of a random sample of unique citing articles (n = 100) found various types of background (n = 18) and foreground (n = 81) reuse cases for GBIF data, ranging from combining with other data sources to create species distribution modelling to software testing. This demonstrates some unique research opportunities created by open data. Among the citing articles, 27% mentioned the dataset in references and 13% in data access statements in addition to the methods section. Citation practice was inconsistent especially when a large number of subsets (12 ~ 50) were used. Even though many GBIF dataset records had altmetric scores, most posts only mentioned the articles linked to those datasets. Among the altmetric mentions of datasets, blogs can be the most informative, even though rare, and most tweets and Facebook posts were for promotional purposes.
... Impediments to biodiversity data sharing include lack of professional recognition of scientific data publishing efforts [58], compounded by a lack of infrastructure for easy data sharing [59]. Therefore, it is necessary "to motivate and reward the contribution of data to international integrated databases by bringing such data into the mainstream of respected scientific publication" [60]. This will involve the development of "mechanisms for data citation and indices of data access comparable to those for citation systems in print journals" [61]. ...
... Several other databases, such as the Living Planet Index, also encourage data contributions through their website. Other options include working towards the mainstreaming of data papers by making the publishing of data mandatory in research project proposals and performance assessments [62], and adopting standards related to data citation, accessibility, metadata, and quality control in order to facilitate integration of data across data sets [60,63,64]. ...
Article
Full-text available
Many conservation managers, policy makers, businesses and local communities cannot access the biodiversity data they need for informed decision-making on natural resource management. A handful of databases are used to monitor indicators against global biodiversity goals but there is no openly available consolidated list of global data sets to help managers, especially those in high-biodiversity countries. We therefore conducted an inventory of global databases of potential use in monitoring biodiversity states, pressures and conservation responses at multiple levels. We uncovered 145 global data sources, as well as a selection of global data reports, links to which we will make available on an open-access website. We describe trends in data availability and actions needed to improve data sharing. If the conservation and science community made a greater effort to publicise data sources, and make the data openly and freely available for the people who most need it, we might be able to mainstream biodiversity data into decision-making and help stop biodiversity loss.
... This is in addition to more traditional, but still widely used, expert elicitation and scoring methods, again focused on bio-climatic similarity [47][48][49][50][51]. The increasing availability of species range information via systems such as the global biodiversity information facility (GBIF) [52], as well as climatic correlate data (e.g. via WORLDCLIM [53] and other remote sensing data resources) makes the potential for 'real-time' updating of relative risks by country/region of origin increasingly feasible. As an illustration, Rembold et al. [54] combine climatic information from the European Centre for Medium-Range Weather Forecasts with information of vegetative indices from remote sensing to produce a 'near real time' warning of food security issues and drought in water-limited regions, a principal which could be adapted for IAS surveillance given appropriate datasets. ...
... Lack of agreed standards are a longstanding issue around the comparative analysis in pest management (e.g. [11,25,85]), with multiple calls for how relevant information is stored and made globally accessible [21,52,[86][87][88]. The digital infrastructure around IAS is often extremely complex, with one survey indicating that in the U.S.A. alone, there are over 50 different systems containing data which are known to be relevant to IAS management, prediction or control practice [89]. ...
Article
Invasive alien species (IAS) are one of the most severe threats to biodiversity and are the subject of varying degrees of surveillance activity. Predictive early warning systems (EWS), incorporating automated surveillance of relevant dataflows, warning generation and dissemination to decision makers are a key target for developing effective management around IAS, alongside more conventional early detection and horizon scanning technologies. Sophisticated modelling frameworks including the definition of the ‘risky’ species pool, and pathway analysis at the macro and micro-scale are increasingly available to support decision making and to help prioritise risks from different regions and/or taxa. The main challenges in constructing such frameworks, to be applied to border inspections, are (i) the lack of standardisation and integration of the associated complex digital data environments and (ii) effective integration into the decision making process, ensuring that risk information is disseminated in an actionable way to frontline surveillance staff and other decision makers. To truly achieve early warning in biosecurity requires close collaboration between developers and end-users to ensure that generated warnings are duly considered by decision makers, reflect best practice, scientific understanding and the working environment facing frontline actors. Progress towards this goal will rely on openness and mutual understanding of the role of EWS in IAS risk management, as much as on developments in the underlying technologies for surveillance and modelling procedures.
... Costello and collaborators (2013a) go further and state that datasets should be published in specialized journals or dedicated sections after peer-review under the same standards of a research manuscript. Independent of introducing new metrics or publishing datasets in journals, the push for recognizing data as research production is strong Wolkovich et al., 2012;Costello et al., 2013a;Drew et al., 2013;Piwowar, 2013;Vines et al., 2013). ...
... Both scientific community and individual researchers may be rewarded by the establishment of a data sharing culture in animal behavior sciences. Use of datasets without proper citation would likely be discouraged, researchers would receive recognition for reused products and articles would become more transparent and reproducible (Wolkovich et al., 2012;Costello et al., 2013a;Piwowar, 2013). ...
Preprint
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Published discussions on data stewardship often focus on standardized datasets whose reuse patterns are known. Improvements in stewardship of animal behavior data are virtually absent and lag behind other disciplines such as molecular biology and systematics. In this essay, we discuss best practices of three key aspects related to the collection and archival of behavioral data: data supporting published results; data collected from field observations; and the potential of museum specimens as source of data to animal behavior and ecology. To quantify how much data is shared in publications we reviewed selected journals in animal behavior and behavioral ecology. We found that only an extremely small proportion of the articles published in 2013 made even part of their data available. We discuss about the benefits of making data available, review resources available for data archiving and provide practical guidance for ethologists. We discuss and provide examples of the amount of ethological and ecological data that can be recorded during field observations. To investigate the potential of museum specimens as source of data, we surveyed researchers working in areas related to ecology, animal behavior, and systematics. Both ethologists and systematists agreed that natural history information stored in collections would be a valuable source of data. We make recommendations to enhance data collection and stewardship from the point of view of researchers in animal behavior sciences, considering the special characteristics of the discipline and the type of data that is often produced. We suggest that there is a large amount of crucial data about natural history, ecology and behavior that investigators could glean from collections. Although it is difficult to appreciate the relevance of data for future studies at the time of publication, such data may inspire fruitful opportunities that we cannot afford to lose.
... More researchers and research institutions also need to make their datasets publicly available, ideally including data of published literature, so that other scientists can make use of them to better study the distribution of marine species (e.g. Costello 2009, Costello et al. 2013). More detailed morphological and molecular studies are also likely to reveal a large increase in polychaete diversity not only in poorly-studied areas, but also in well-studied areas. ...
Article
The global biogeography of polychaete worms has never been assessed previously. In the present study, we studied the world distribution patterns of polychaetes based on datasets obtained from the Global Biodiversity Information Facility, the Ocean Biogeographic Information System and our recently published checklist of Indonesian polychaete species. Polychaete biogeographic regions were visualized using ‘Infomap Bioregions’, and the latitudinal species richness gradient of the animals was examined using 3 metrics, i.e. alpha, gamma and estimated species richness (the last metric was adjusted for sampling bias). We identified 11 major polychaete biogeographic regions. The North Atlantic, Australia and Indonesia were the top 3 species-rich biogeographic regions in the world. The total number of polychaete species was higher in the southern hemisphere (~2100 species, 67 families) than in the northern hemisphere (~1800 species, 75 families) despite significantly more data in the latter (>500000 records compared to >26000 records). Contrary to the classical idea of a unimodal distribution pattern, the latitudinal gradient of polychaetes was generally bimodal with a pronounced dip north of the Equator (15°N). We suggest that the slightly higher peak of species richness in the southern (30°S) than in the northern (60°N) hemisphere reflects higher southern endemicities. These patterns are unlikely to be due to sampling bias but rather represent a natural phenomenon, and we found them most significantly correlated with sea temperature.
... Current metadata and provenance have been limited to the modeling of data, which is only one element in a scientific workflow (cf. Costello et al. 2013;Tullis and Kar 2020). To enable full automation and reproducibility, we argue that it is equally, if not more, important to capture runtime information about both the data and the spatial operation, or spatial operation chains, in a complex problem-solving environment. ...
Article
The availability and use of geographic information technologies and data for describing the patterns and processes operating on or near the Earth’s surface have grown substantially during the past fifty years. The number of geographic information systems software packages and algorithms has also grown quickly during this period, fueled by rapid advances in computing and the explosive growth in the availability of digital data describing specific phenomena. Geographic information scientists therefore increasingly find themselves choosing between multiple software suites and algorithms to execute specific analysis, modeling, and visualization tasks in environmental applications today. This is a major challenge because it is often difficult to assess the efficacy of the candidate software platforms and algorithms when used in specific applications and study areas, which often generate different results. The subtleties and issues that characterize the field of geomorphometry are used here to document the need for (1) theoretically based software and algorithms; (2) new methods for the collection of provenance information about the data and code along with application context knowledge; and (3) new protocols for distributing this information and knowledge along with the data and code. This article discusses the progress and enduring challenges connected with these outcomes.
... Hay que resaltar la importancia de contar con registros biológicos publicados y disponibles que contribuyan al conocimiento de la especie y los ecosistemas que habitan, que son vagamente conocidos o poco estudiados, con suficiente esfuerzo de muestreo. Además, la necesidad de esta información, revisada por pares y soportada, asegura la calidad de su uso (Costello et al., 2013). Más aún, los esfuerzos sistemáticos por documentar la distribución de especies son por sí mismos necesarios debido a su impacto en todo tipo de análisis ecológicos (políticas públicas, manejo, valoración de la biodiversidad; Boakes et al., 2010). ...
Article
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Vivint als Andes: registres notables de la distribució altitudinal de l’os andí Tremarctos ornatus (Ursidae) a Boyacá, Colòmbia Malgrat la importància d’aquesta espècie, l’os andí encara presenta importants buits d’informació pel que fa a distribució. És endèmic als Andes i ocupa el gradient d’elevació complet, tot i que els registres que ho constaten són escassos. Presentem evidència recent de la seva presència en àrees periglacials (> 4.000 m) i boscos tropicals (< 1.000 m) als Andes Orientals de Colòmbia. Aportem 23 registres nous en elevacions marginals, incloent-hi els primers publicats referents al departament de Boyacá, basats en registres existents i en el nostre treball de camp. Aquesta informació és important per augmentar el coneixement sobre ús d’hàbitat i distribució de l’os andí, la qual cosa permetrà millorar la presa de decisions per a la gestió de l’espècie i dels ecosistemes associats. Dades publicades a GBIF (Doi: 10.15470/32uicm)
... Such reporting would not only require the disclosure of the keywords and the databases but also of the exact search strings and the chosen filters available at the individual databases. Such details require space, which has long been considered scarce in peerreviewed journals but is now less of an issue thanks to online appendices, which are offered by an increasing number of journals (Aguinis et al., 2018;Costello et al., 2013;Mallett et al., 2012). Accordingly, more recent entries among the 133 database-driven reviews (e.g., Stumbitz et al., 2018;Theurer et al., 2018) made use of online supplements offering more detailed information on the database search process. ...
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Systematic review techniques are about to become the “new normal” in reviews of management research. However, we do not yet have much advice on how to organize the sample selection process as part of such reviews. This paper addresses this void and analyzes this vital part of systematic reviews in more detail. In particular, it offers a critical review of systematic literature reviews published in the Academy of Management Annals and the International Journal of Management Reviews between 2004 and 2018. Based on this methodological literature review, the paper presents issues to consider in the most critical choices during the sample selection process. Further, this review identifies several descriptive features such as the mean number of research items included in systematic reviews, the mean number of databases used, and the mean coverage period of such reviews. These numbers may be used as benchmark figures in future reviews.
... Accurate distribution modelling warrants the inclusion of non-climatic environmental variables, such as species dispersal ability and distance constrained variables (e.g., distance to built-up environments and farmlands, proximity to water sources), which can alter the distribution of bats [118][119][120]. Covering multiple threats, especially anthropogenic disturbances and fine-scale land-use modifications will help harness the maximum predictive power from ENMs since species responses to changing environments can either emerge from or become modified by interactions between threats [121,122]. ...
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Bats perform critical ecosystem functions, including the pollination, seed dispersal, and regulation of invertebrate populations. Yet, bat populations are declining worldwide primarily due to habitat loss and other anthropogenic stressors. Thus, studies on bat ecology, particularly on environmental determinants of bat occupancy, are paramount to their conservation. High mobility, nocturnal behavior, and roosting site selection of bats make conventional surveys challenging. Moreover, little is known about geographic distribution, habitat suitability, and responses to climate change among tropical bat species. To bridge these research gaps, we applied ecological niche modeling to two Ceylonese bat species, Kerivoula malpasi and Kerivoula picta, to map their geographic distribution. Seasonal variations in temperature and precipitation were critical environmental predictors of bat distribution in general. Southwestern lowland forests contained the most optimal habitats for the relatively wide-ranging Kerivoula picta, while the central highlands provided the most suitable habitats for the narrow-ranging Kerivoula malpasi. No tangible changes in the highly suitable habitats were evident in response to projected climate change for either species. Yet, the optimal ranges of K. malpasi can become fragmented in the future, whereas the most optimal habitats for K. picta are likely to become spatially contiguous in the future. Habitat availability or fundamental niche alone is insufficient to reliably forecast species persistence, thus we caution against considering these two bat species as resilient to climate change. Our findings will enable the conservation authorities to initiate preemptive conservation strategies, such as the establishment of landscape-scale habitat connectivity and management of buffer zones around conservation lands. We also encourage conservation authorities to employ ecological niche models to map potential species distributions and to forecast range shifts due to climate change.
... Scientific reach might also be extended into other 65 than the original research areas [Chao, 2011], and researchers' reputations could improve by 66 good sharing practices, possibly initiating new collaborations. Moreover, there is a 67 movement towards regarding datasets as full-fledged research output that can be cited in 68 itself [Costello et al., 2013;Neumann and Brase, 2014]. This would mean that sharing data in 69 the near future will have a direct positive influence on a researchers' scientific impact. ...
Preprint
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While reusing research data has evident benefits for the scientific community as a whole, decisions to archive and share these data are primarily made by individual researchers. For individuals, it is less obvious that the benefits of sharing data outweigh the associated costs, for example time and money. In this sense the problem of data sharing resembles a typical game in interactive decision theory, more commonly known as game theory. Within this framework we analyse how measures to promote sharing and reuse of research data affect individuals who do and do not share data. We find that the scientific community can benefit from top-down policies to enhance sharing data even when the act of sharing itself implies a cost. Namely, if (almost) everyone shares, many individuals receive benefits, as datasets in our model can be reused to achieve a higher efficiency (i.e. more publications, higher quality papers). Surprisingly, as sharing implies a cost, even sharing individuals themselves, in a community in which sharing is common, can gain a higher efficiency than individuals who do not share, in a community in which sharing is not common. In addition to these findings, we find that measures to ensure better data retrieval and quality can compensate for sharing costs by further enabling reuse. Nevertheless, an individual researcher who decides not to share omits the costs of sharing. Assuming that the natural tendency will be to use a strategy that will lead to maximisation of individual efficiency, we see the average scientific community efficiency in our model steadily drop as more individuals decide not to share. With this in mind, we conclude that the key to motivate the researcher to share data lies in reducing the costs associated with sharing, or even better, turning it into a benefit.
... Scientific reach might also be extended into other 63 than the original research areas [Chao, 2011], and researchers' reputations could improve by 64 good sharing practices, possibly initiating new collaborations. Moreover, there is a 65 movement towards regarding datasets as full-fledged research output that can be cited in 66 itself [Costello et al., 2013;Neumann and Brase, 2014]. This would mean that sharing data in 67 the near future will have a direct positive influence on a researchers' scientific impact. ...
Preprint
Full-text available
While reusing research data has evident benefits for the scientific community as a whole, decisions to archive and share these data are primarily made by individual researchers. For individuals, it is less obvious that the benefits of sharing data outweigh the associated costs, i.e. time and money. In this sense the problem of data sharing resembles a typical game in interactive decision theory, more commonly known as game theory. Within this framework we analyse in this paper how different measures to promote sharing and reuse of research data affect sharing and not sharing individuals. We find that the scientific community can benefit from top-down policies to enhance sharing data even when the act of sharing itself implies a cost. Namely, if (almost) everyone shares, many individuals can gain a higher efficiency as datasets can be reused. Additionally, measures to ensure better data retrieval and quality can compensate for sharing costs by enabling reuse. Nevertheless, an individual researcher who decides not to share omits the costs of sharing. Assuming that the natural tendency will be to use a strategy that will lead to maximisation of individual efficiency it is seen that, as more individuals decide not to share, there is a point at which average efficiency for both sharing and non-sharing researchers becomes lower than was originally the case and scientific community efficiency steadily drops. With this in mind, we conclude that the key to motivate the researcher to share data lies in reducing the costs associated with sharing, or even better, turning it into a benefit.
... DMPs can be encouraged by rewarding adherence through additional funding, and by having archived data, code, protocols, and software contribute to promotion and tenure packages. Increasing the number and status of journals dedicated to publishing datasets would encourage conservation scientists (e.g., ECR) to publish valuable data and increase the potential for data reuse efforts (Costello, Michener, Gahegan, Zhang, & Bourne, 2013;Geldmann et al., 2020). Moreover, increasing the potential to publish context-specific studies would provide an important venue for local research (e.g., Ecological Evidence and Solutions; Konno et al., 2020). ...
Article
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Scientific evidence is fundamental for guiding effective conservation action to curb biodiversity loss. Yet, research resources in conservation are often wasted due to biased allocation of research effort, irrelevant or low‐priority questions, flawed studies, inaccessible research outputs, and biased or poor‐quality reporting. We outline a striking example of wasted research resources, highlight a powerful case of data rescue/reuse, and discuss an exemplary model of evidence‐informed conservation. We suggest that funding agencies, research institutions, NGOs, publishers, and researchers are part of the problem and solutions, and outline recommendations to curb the waste of research resources, including knowledge co‐creation and open science practices.
... Many of these strategies, however, face major challenges in terms of data acquisition, analysis and implementation 14 . In addition, the reluctance to share data among scientists 15 may often frustrate progress in reef science, management and conservation 16 . Clearly this increasing demand of scientific outputs needs to be pursued collectively as a top priority 16 in order to take up the challenges of managing Anthropocene reefs effectively in a rapidly changing world [4][5][6]17 . ...
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Addressing the global decline of coral reefs requires effective actions from managers, policymakers and society as a whole. Coral reef scientists are therefore challenged with the task of providing prompt and relevant inputs for science-based decision-making. Here, we provide a baseline dataset, covering 1300 km of tropical coral reef habitats globally, and comprised of over one million geo-referenced, high-resolution photo-quadrats analysed using artificial intelligence to automatically estimate the proportional cover of benthic components. The dataset contains information on five major reef regions, and spans 2012–2018, including surveys before and after the 2016 global bleaching event. The taxonomic resolution attained by image analysis, as well as the spatially explicit nature of the images, allow for multi-scale spatial analyses, temporal assessments (decline and recovery), and serve for supporting image recognition developments. This standardised dataset across broad geographies offers a significant contribution towards a sound baseline for advancing our understanding of coral reef ecology and thereby taking collective and informed actions to mitigate catastrophic losses in coral reefs worldwide.
... However, a data paper should include all the available data, rather than just those described in the original article (Osawa, 2017). This simultaneous release of data can promote an author's reputation, employment opportunities, standing at work and ability to secure funding (Costello, 2009;Costello, Michener, Gahegan, Zhang, & Bourne, 2013). Thus, making data broadly available could provide several benefits to researchers-both data providers and users. ...
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Data papers, such as those published by Ecological Research, encourage the retrieval and archiving of valuable unpublished, undigitized ecological observational data. However, scientists remain hesitant to submit their data to such forums. In this perspective paper, we describe lessons learned from the Long‐Term Ecological Research, the Global Biodiversity Information Facility and marine biological databases and discuss how data sharing and publication are both powerful and important for ecological research. Our aim is to encourage readers to submit their unpublished, undigitized ecological observational data then the data may be archived, published and used by other researchers to advance knowledge in the field of ecology. Coupling data sharing and syntheses with the development of innovative informatics would allow ecology to enter the realm of big science and provide seeds for a new and robust agenda of future ecological studies. We promote the continuous retrieval, archiving and publication of ecological observational data and advance their analysis and evaluation through the utilization of published open data. The following figure shows the numbers of published data papers of Ecological Research and Ecology.
... Producing available data takes time because it depends on each national jurisdiction and the need to acknowledge the work and expertise of the data collectors and owners. Publishing the data could ultimately increase the visibility and give credit to the data providers (Costello et al., 2013b) and should follow FAIR principles (Findable, Accessible, Interoperable and Reusable, https://www.go-fair.org/fair-principles/). In ecology, the Global Biodiversity Information Facility (GBIF) is a successful example of "an international network and research infrastructure funded by the world's governments and aimed at providing anyone, anywhere, open access to data about all types of life on Earth" and led to many scientific outocomes that would be impossible otherwise, with clear economic and societal benefits. ...
Thesis
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Ecosystems worldwide are subject to an unprecedented loss of biodiversity, largely resulting from a range of human impacts such as over-exploitation, habitat loss and climate change. To understand the consequences of this biodiversity crisis on both land and oceans, scientists tried quantifying the relationship between biodiversity and ecosystem functioning (ability of an ecosystem to perform and maintain a suite of key properties such as biomass and flux of energy), ultimately trying to answer: what is the importance of biodiversity for ecosystems? A positive influence of biodiversity on ecosystem functioning has been shown in many experimental studies, demonstrating enhanced biomass production under higher number of species. However, the extent to which such findings hold in natural systems is unknown, especially in large and complex marine ecosystems. To address this knowledge gap, we use high-resolution monitoring data on fish community composition and abundance in continental shelf seas across the North Atlantic and statistical modeling to test the existence of links between biodiversity and ecosystem functions at both regional and continental scales. This empirical approach is complemented with a mathematical food web model to establish theoretical hypotheses about the contribution of biodiversity and food web structure on several ecosystem functions. We demonstrate that while a positive relationship between the number of species and several ecosystem functions is expected in theory, that link is not necessarily emergent from observations of real fish communities. We highlight that the metric of biodiversity and ecosystem function evaluated matters to determine the overall ecosystem performance. This thesis is an attempt to understand the role of fish biodiversity for marine ecosystem functioning across several ecosystems and to develop hypotheses on the role of biodiversity in complex food webs. Quantifying the importance of biodiversity for ecosystem functioning is necessary for our understanding of ecosystem complexity in ecology, enhance biodiversity and ecosystem conservation and has the potential to trigger policy towards conservation of ecosystems.
... Herbarium collections and the data they hold are valuable, not only for the traditional studies of taxonomy and systematics, but also for ecology, bioengineering, conservation, food security and the human social and cultural elements of scientific collection (Baird 2010, James et al. 2018). The value and universality of herbarium specimens are recognised in most countries, where national and large regional herbaria are actively developing and improving (Costello et al. 2013, Cranston et al. 2014, Kovtonyuk 2017, Pearse et al. 2017. The digitisation and open access to the collections have become a common trend in biodiversity collections management, the latest stage in improving the inventory and modernisation of herbarium collections of the leading botanical institutions in the world (Heberling et al. 2019, Le Bras et al. 2017, Seregin 2020, Kovtonyuk et al. 2019a. ...
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The Central Siberian Botanical Garden of the Siberian Branch of the Russian Academy of Sciences (CSBG SB RAS) is the largest botanical institution in the Asian part of Russia. Founded in 1946, CSBG SB RAS is historically a consortium of two herbarium collections with their own acronyms (NS and NSK) and registration in the Index Herbariorum (Thiers 2020). At present the NS+NSK collections contain about 800,000 herbarium specimens comprising vascular plants (680,000), mosses (25,000), lichens (80,000) and fungi (15,000) gathered, not only in Siberia, but also in the European part of Russia and other parts of the Eurasian and American continents. CSBG SB RAS has the third largest collection in Russia after the Komarov Botanical Institute of RAS (LE) and Moscow State University (MW) collections. The dataset consists of 5,384 records of digitised herbarium specimens of vascular plants belonging to 111 families, collected since the 19th century in 54 administrative regions from the European part of Russia and kept in NS+NSK collections. Herbarium specimens were digitised using two special scanners, both ObjectScan 1600, according to international standards, at 600 dpi, with a barcode, 24-colour scale and spatial scale bar and placed into the CSBG SB RAS Digital Herbarium. For each specimen, the species name, locality, collection date, collector, ecology and revision label are recorded. More than 94% of the records have coordinates that fall within the area of European Russia, west of the Ural Mountains.
... Hay que resaltar la importancia de contar con registros biológicos publicados y disponibles que contribuyan al conocimiento de la especie y los ecosistemas que habitan, que son vagamente conocidos o poco estudiados, con suficiente esfuerzo de muestreo. Además, la necesidad de esta información, revisada por pares y soportada, asegura la calidad de su uso (Costello et al., 2013). Más aún, los esfuerzos sistemáticos por documentar la distribución de especies son por sí mismos necesarios debido a su impacto en todo tipo de análisis ecológicos (políticas públicas, manejo, valoración de la biodiversidad; Boakes et al., 2010). ...
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Living in the Andes: noteworthy records on the altitudinal distribution of the Andean bear Tremarctos ornatus (Ursidae) in Boyacá, Colombia. Despite the importance of Andean bears, much relevant information regarding their distribution is lacking. Endemic to the Andes, the species is known to occupy the entire elevation gradient, but records to support this assumption are scarce. Here we present recent evidence of their presence in peri–glacial (> 4,000 m) and tropical forests (< 1.000 m) areas in the Eastern Andes of Colombia. Based on existing records and our own field work, we report 23 new records for marginal elevations, including the first records to be published for the Boyacá department. This information is valuable in order to increase our knowledge of Andean bear habitat use and distribution and thereby improve decision–making for the management of the species and its associated ecosystems.
... Una característica fundamental de este tipo de contribución es que los datos que describen han de estar disponibles de forma pública en algún repositorio estable y en línea. Aunque los artículos de datos van un paso más allá del depósito de los datos junto con sus metadatos en un repositorio, ya que representan una garantía de accesibilidad y calidad debido a que requieren, además, una revisión por pares (Costello et al. 2013). En dicha revisión, además de evaluarse la calidad del artículo, se revisan los pasos seguidos para la publicación y puesta a punto de los datos que se presentan. ...
... The mobilization of long-tail datasets should therefore have high priority before data collectors retire or die which inevitably will lead to the ultimate loss of raw data and metadata (Michener et al., 1997). This requires sociological change such as incentives and reducing barriers to data sharing through citation and use metrics (Costello et al., 2013) and through supporting education and establishing community standards (Kattge et al., 2020;Michener, 2015). Ultimately, this would reduce research costs, improve collaborative efforts and increase research opportunities (Uhlir and Schröder, 2007). ...
Article
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Trait data represent the basis for ecological and evolutionary research and have relevance for biodiversity conservation, ecosystem management and earth system modelling. The collection and mobilization of trait data has strongly increased over the last decade, but many trait databases still provide only species-level, aggregated trait values (e.g. ranges, means) and lack the direct observations on which those data are based. Thus, the vast majority of trait data measured directly from individuals remains hidden and highly heterogeneous, impeding their discoverability, semantic interoperability, digital accessibility and (re-)use. Here, we integrate quantitative measurements of verbatim trait information from plant individuals (e.g. lengths, widths, counts and angles of stems, leaves, fruits and inflorescence parts) from multiple sources such as field observations and herbarium collections. We develop a workflow to harmonize heterogeneous trait measurements (e.g. trait names and their values and units) as well as additional information related to taxonomy, measurement or fact and occurrence. This data integration and harmonization builds on vocabularies and terminology from existing metadata standards and ontologies such as the Ecological Trait-data Standard (ETS), the Darwin Core (DwC), the Thesaurus Of Plant characteristics (TOP) and the Plant Trait Ontology (TO). A metadata form filled out by data providers enables the automated integration of trait information from heterogeneous datasets. We illustrate our tools with data from palms (family Arecaceae), a globally distributed (pantropical), diverse plant family that is considered a good model system for understanding the ecology and evolution of tropical rainforests. We mobilize nearly 140,000 individual palm trait measurements in an interoperable format, identify semantic gaps in existing plant trait terminology and provide suggestions for the future development of a thesaurus of plant characteristics. Our work thereby promotes the semantic integration of plant trait data in a machine-readable way and shows how large amounts of small trait data sets and their metadata can be integrated into standardized data products.
... Como cualquier otro artículo científico, es una publicación que da visibilidad al contenido y reconocimiento académico a sus autores (Chavan y Penev, 2011). Al ser sometidos a revisión por pares, igual que cualquier otro artículo de investigación actúa como una garantía de accesibilidad y calidad de los datos y metadatos (Costello et al., 2013). En los últimos años, ha aumentado el número de revistas que incluyen esta modalidad de publicación o que se dedican exclusivamente a ellos (data journals) como la revista Biodiversity data Journal. ...
Article
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Los datos en una investigación son considerados como las materias primas para la extracción de información o conocimiento científico que sustenta las publicaciones y la toma de medidas. Existe la creencia de que cuando la investigación termina y se publica, los datos utilizados pierden su valor y tienden a desecharse o almacenarse, invisibles e inaccesibles para otros investigadores. Esta es una visión superficial que esconde la realidad de que los datos son uno de los productos primarios más valiosos de la ciencia, con múltiples valores adicionales que permiten afirmar que pueden llegar a ser más importantes incluso que las propias publicaciones. Pero para que se pueda expresar este valor, debe seguirse una serie de aspectos metodológicos que incluyen desde la estructuración apropiada de las matrices o ficheros, su documentación a través de metadatos, la selección y asignación de las licencias, el identificador digital o su publicación como Artículo de datos. En la presente revisión se discuten algunas de estas prácticas para revalorizar los datos de las investigaciones ecológicas y poder explotarlos en toda su extensión, dado el desconocimiento generalizado de la infraestructura existente y los métodos para hacerlos disponibles, recuperables y utilizables por tiempo indefinido. Para ello se responden las preguntas básicas: ¿por qué y para qué? ¿cómo? ¿dónde? y ¿cuándo? Se termina haciendo un llamado al cam bio desde la visión tradicional que se enfoca solo en el análisis de los datos. Se requiere una nueva visión que ponga más énfasis en la organización de los datos y su documentación para hacerlos públicos, conjuntamente con los artículos. ABSTRACT Research data are considered the raw material for acquiring scientific knowledge for articles and decision-making process. There is a believe that once research finished and papers are published, data loss value and can be disposal or keep in forgotten corners, invisibles and inaccessible for any other scientist. This is a shallow view that ignores the reality that data is one of the most valuable results in science, with additional values that raise them to even more important place than papers. But for getting this value a series of steps and procedures should be followed from matrix structure or file ordering, documentation with proper metadata, selection and assignment of licenses and digital identification or their publication as data papers. In current review, some of these practices are discussed to reinforce ecological research data values, due to the generalized ignorance on current available infrastructure and method to secure their available, retrieval, and use for all time. To do that, I answer the basic questions of why? why for? how? where? and when? I ended by making a call for a vision change from current focus on data. A new emerging vision includes more efforts directed to Data organization and documentation for data sharing, along with the papers.
... The exchange of relevant information and data from the field observations is needed to develop effective conservation prioritization. This is also to bolster biodiversity protection and to minimize the negative impacts of the rapidly changing human environment on ecosystem service provisions and sustainability [1]. The rate of imperilment has been higher than the previously projected extinction risks and many species have poor ability to recover quickly from these losses [2]. ...
Article
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The Philippines is among the most threatened biodiversity hotspots. Developing effective conservation requires science-based evidence from field data and observations. Yet, many important biodiversity information remain unpublished, particularly from academic institutions and NGOs. Here, we synthesized 34-year data from biodiversity studies from Bicol University in Luzon Island, Philippines. We found a large number of studies that increased in the post-2000 period with the majority of the studies focused on community surveys and animal and wildlife studies. While there is a massive number of studies, we found clear disproportionate distribution in terms of geographic and thematic areas. Our results may be based on a regional level, but if taken carefully, it has important implications and applications to other higher education institutions in the Philippines in promoting biodiversity studies and conservation in the country.
... However, this type of scientific research is far from being easily carried out, as many may think when they disown and/or relegate to the background the importance and the scientific nature of this type of contribution (Cotterill & Foissner 2010). This becomes explicit when we look at the publication metrics of inventories in journals that publish such articles compared to others that do not (Costello et al. 2013). Carrying out structured species inventories requires well-grounded knowledge of the biology of the target group (data that are mainly obtained in natural history studies) and appropriate collecting techniques, in addition to the taxonomic knowledge of the group, what implies consulting experts and/or having access to proper identification keys (Silveira et al. 2010). ...
Article
Katydids were surveyed in the Iguaçu National Park (ParNa Iguaçu), the largest preserve of the Interior Atlantic Forest in Brazil. Sampling was carried out in three different areas of the ParNa Iguaçu, including its two predominant phytophysiognomies (Seasonal Semidecidual Forest and Mixed Ombrophilous Forest), and consisted of diurnal and nocturnal active searching for katydids and also using light traps. After collected, specimens were reared until adulthood in order to record their calling songs. Almost a thousand katydids were collected, belonging to 89 species and five subfamilies. Phaneropterinae appeared as the most speciose subfamily (57 species), followed by Conocephalinae (22), Meconematinae and Pseudophyllinae, each one with four species, and Pterochrozinae (two species). Several species were recorded for the first time for the Paraná State, for the South Region of Brazil, and also for the country. Calling songs of 34 species were recorded, 29 of them unknown to science. The description of the sound produced by species of some supraspecific taxa (e.g., Aniarae, Cosmophylla and Scaphurae) is here presented for the first time. Data reinforce the relevance of ParNa Iguaçu for the maintenance of thousands of species from different taxonomic groups and also highlight the catastrophic effects that continuous pressures and threats on the preserve, despite the successive attempts to downgrade this conservation unit, may have on the outstanding biodiversity that is harboured by ParNa Iguaçu.
... Additionally, of the papers that examined species traits, only 31% of those reported the traits of those species. Despite broad calls for data sharing across scientific communities (Costello et al. 2013;Reichman et al. 2011;Trisos et al. 2021), very few scientists share trait data, even for common, broadly distributed species. While some of these trait data are published in online repositories (e.g., PanTHERIA, Jones et al. 2009;TRY, Kattge et al. 2011), many taxa are not represented, and existing databases are not complete. ...
Article
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Since the 1990s, recognition of urban biodiversity research has increased steadily. Knowledge of how ecological communities respond to urban pressures can assist in addressing global questions related to biodiversity. To assess the state of this research field in meeting this aim, we conducted a systematic review of the urban biodiversity literature published since 1990. We obtained data from 1209 studies that sampled ecological communities representing 12 taxonomic groups. While advances have been made in the field over the last 30 years, we found that urban biodiversity research has primarily been conducted in single cities within the Palearctic and Nearctic realms, within forest remnants and residential locations, and predominantly surveys plants and birds, with significant gaps in research within the Global South and little integration of multi-species and multi-trophic interactions. Sample sizes remain limited in spatial and temporal scope, but citizen science and remote sensing resources have broadened these efforts. Analytical approaches still rely on taxonomic diversity to describe urban plant and animal communities, with increasing numbers of integrated phylogenetic and trait-based analyses. Despite the implementation of nature-based solutions across the world’s cities, only 5% of studies link biodiversity to ecosystem function and services, pointing to substantial gaps in our understanding of such solutions. We advocate for future research that encompasses a greater diversity of taxonomic groups and urban systems, focusing on biodiversity hotspots. Implementing such research would enable researchers to move forward in an equitable and multidisciplinary way to tackle the complex issues facing global urban biodiversity. Graphical abstract Word cloud from titles of 1209 publications on urban biodiversity from 1990–2018.
... This was done for specific collections (see Saint-Hilaire herbarium, Pignal et al. 2013), libraries (i.e., Biodiversity Heritage Library) and animal and plant collections. Expectations then turned out to be true: new species were discovered, and novel research was being performed based on the examination of such digitized specimens, despite the discussion of the issue of quality (Smith et al. 2011;Costello et al. 2013;Soltis 2017). These new data demanded new technologies, such as specific software to aid species image analysis (i.e., RECOLNAT 2020) and morphological research (Borges et al. 2020), and even machine learning has been employed (Pryer et al. 2020). ...
Article
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The digital era provides new opportunities for taxonomists, as well as for everyone that studies biodiversity. Many herbaria have been able to digitize their collections, a process that started with the typing of label data, moving more recently towards the digitization of each sample with the simultaneous acquisition of high-resolution images. Here we discuss some of the challenges we faced in digitizing samples and provide a series of suggestions to avoid common mistakes for herbaria that have yet to start the process. We used a professional camera, database management software, and a barcode scanner to digitize the collections of herbaria CRI, ECT, FURB, LUSC, and UFRN. Pre-revision of samples with prior restoration when needed, barcode fixation, and a good database allowed faster digitization of samples. Good database software and the formation of a network among small herbaria accelerated digitization and increased the number of images available of Brazilian biodiversity. Thus far, our joint efforts made 118,000 specimen images available online with the purpose of accelerating botanical research.
... Los ecosistemas marino-costeros y su biodiversidad están experimentando una presión cada vez mayor en todo el mundo debido a la contaminación, a la mala planificación de infraestructura, a la sobrepesca y al cambio climático (He & Silliman, 2019). Conocer la biodiversidad marina es esencial para evaluar el estado, los cambios y el alcance de la pérdida en estos ecosistemas (Costello, Michener, Gahegan, Zhang, & Bourne, 2013;Worm et al., 2006). Los hábitats marino-costeros tropicales, como los arrecifes de coral, los manglares, zonas intermareales y los lechos de pastos marinos, han sido el foco de investigación en las últimas décadas. ...
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Introducción: Los hábitats costeros de todo el mundo están experimentando una presión cada vez mayor debido a la contaminación, el desarrollo costero, la pesca y el cambio climático. Identificar y registrar la biodiversidad costera es esencial para evaluar la salud, los cambios y el alcance de la pérdida de biodiversidad de los ecosistemas. Los hábitats costeros tropicales como los arrecifes de coral y los lechos de pastos marinos han sido el foco de investigación de los científicos durante las últimas décadas; sin embargo, se han descuidado otros ecosistemas, como los bosques de macroalgas, los fondos de sedimentos submareales (20-30 m de profundidad) y los arrecifes rocosos. Objetivo: Este trabajo reporta la biodiversidad marina asociada con arrecifes rocosos, arrecifes de coral, bosques de Sargazo y fondos submareales sedimentarios (20-30 m de profundidad), en un área tropical de afloramiento estacional (Península de Santa Elena, Bahía de Santa Elena e Islas Murciélago, Costa Rica). Métodos: Durante la Expedición Santa Elena (21 de abril-2 de mayo de 2018), se visitaron un total de 28 sitios para registrar la biodiversidad en cuatro hábitats diferentes (arrecifes rocosos y de coral, bosques de sargazo y fondos de sedimentos submareales), utilizando SCUBA, en muestreos sistemáticos, evaluaciones visuales y en algunos fondos de sedimentos se utilizó una draga de arrastre por 20 minutos. Resultados: Se identificaron un total de 254 taxones, siendo los peces óseos el grupo más diverso con 91 especies, seguido de los gasterópodos (25 spp.), las algas rojas (21 spp.) y los antozoos (19 spp.). Se reportan cuatro nuevos registros para el Pacífico continental de Costa Rica, incluida la subclase de una anémona tubícola (Ceriantharia). Conclusiones: Los resultados muestran que la península de Santa Elena, la bahía de Santa Elena y las islas Murciélago albergan hábitats poco comunes y no estudiados, como bosques del alga parda Sargassum, fondos de sedimentos, arrecifes construidos por el coral masivo Pavona gigantea, que es muy inusual, y comunidades de arrecifes rocosos dominadas por colonias calcáreas de poliquetos (Salmacina tribranchiata).
... Los ecosistemas marino-costeros y su biodiversidad están experimentando una presión cada vez mayor en todo el mundo debido a la contaminación, a la mala planificación de infraestructura, a la sobrepesca y al cambio climático (He & Silliman, 2019). Conocer la biodiversidad marina es esencial para evaluar el estado, los cambios y el alcance de la pérdida en estos ecosistemas (Costello, Michener, Gahegan, Zhang, & Bourne, 2013;Worm et al., 2006). Los hábitats marino-costeros tropicales, como los arrecifes de coral, los manglares, zonas intermareales y los lechos de pastos marinos, han sido el foco de investigación en las últimas décadas. ...
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The North Pacific and the South Pacific of Nicaragua is a region of great biological, geological, economic and social wealth. There the dry forest mixes with the rain forest, the sea with the islands and nature with the people. It is a region influenced by the Papagayo upwelling, the emergence of cold marine waters during the dry season, which generates an abundance of life in the sea. As a sample of this marine wealth, in this Special Issue, more than half of the contributions are dedicated to advances in the knowledge of the marine biodiversity of the region. Contributions from the social sciences, geology and physics of the region are also included. Within these areas, the publications provide information on maritime border management, archaeology and sustainable tourism, coastal geology, projected climate changes, as well as various oceanographic aspects of the area. We hope that this Special Issue on the North Pacific of Costa Rica and the South Pacific of Nicaragua will promote more research in the region and help inform decision-making processes and educational activities. We thank the authors for their manuscripts, as well as the more than sixty reviewers who with their comments and suggestions helped to improve the quality of the manuscripts.
... Los ecosistemas marino-costeros y su biodiversidad están experimentando una presión cada vez mayor en todo el mundo debido a la contaminación, a la mala planificación de infraestructura, a la sobrepesca y al cambio climático (He & Silliman, 2019). Conocer la biodiversidad marina es esencial para evaluar el estado, los cambios y el alcance de la pérdida en estos ecosistemas (Costello, Michener, Gahegan, Zhang, & Bourne, 2013;Worm et al., 2006). Los hábitats marino-costeros tropicales, como los arrecifes de coral, los manglares, zonas intermareales y los lechos de pastos marinos, han sido el foco de investigación en las últimas décadas. ...
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Subtidal habitats diversity of Santa Elena Peninsula and Murciélago Islands, North Pacific, Costa Rica Introduction: Worldwide, coastal habitats are experiencing increasing pressure from pollution, coastal development , fisheries, and climate change. Identifying and recording coastal biodiversity is essential to assess ecosystem health, changes and the extent of biodiversity loss. Coastal tropical habitats such as coral reefs and seagrass beds have been the research focus for scientists during the last decades; however, other ecosystems have been neglected, such as macroalgae forests, subtidal (20-30 m deep) sedimentary bottoms, and rocky reefs. Objective: Our study reports the marine biodiversity associated with rocky reefs, coral reefs, Sargassum forests and sedimentary subtidal bottoms (20-30 m deep), in a tropical seasonal upwelling area (Santa Elena Peninsula, Santa Elena Bay, and Murciélago Islands, Costa Rica). Methods: During the 'Santa Elena Expedition' (April 21-May 2 2018), a total of 28 sites were visited in order to record the biodiversity across four different habitats (rocky and coral reefs, Sargassum forests, subtidal sedimentary bottoms), using SCUBA and both systematic surveys and visual assessments; in some sedimentary bottoms a 20-minute dredge tows were done. Results: A total of 254 taxa were identified, being bony fishes the most diverse group (91 species), followed by gastropods (25 spp.), red algae (21 spp.) and anthozoans (19 spp.). We report four new records for the Pacific mainland of Costa Rica, including the subclass of tube-dwelling sea anemone (Ceriantharia). Conclusions: Our results show that Santa Elena Peninsula, Santa Elena Bay, and Murciélago Islands harbor uncommon and unstudied habitats, such as Sargassum forests, sedimentary bottoms, reefs constructed by the stony coral Pavona gigantea-which is very unusual-and rocky reef communities dominated by calcareous colonies of polychaetes (Salmacina tribranchiata).
... Sharing data, expertise, knowledge, and information is key to creating change for developing-world scientists (Gaikwad & Chavan, 2006). Recent initiatives offer opportunities to make biodiversity information (and biological collections) accessible to everyone globally (Costello, Michener, Gahegan, Zhang, & Bourne, 2013). Data sharing not only broadcasts the data that one has to the world but also brings the world's data together for use by oneself, and this two-way information flow benefits scientists in both the developed and developing worlds (Sousa-Baena, Garcia, & Peterson, 2013). ...
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Biodiversity remains relatively unknown and understudied in many parts of the developing world with significant information gaps, in stark contrast to many areas in the developed world, where knowledge about biodiversity can approach encyclopedic. Access to resources, such as funding, data, information, expertise, and biological collections (often collected by colonial‐era scientists from across the developing world), is often quite limited for developing‐world scientists. The life of a biodiversity scientist in the developing world is therefore one of manifold dilemmas and challenges, as well as numerous opportunities. Although collaborations exist between developing‐world scientists and developed‐world scientists, too many of those collaborations are not deep or permanent, and developing‐world scientists are too often relegated to a subordinate role. The focus in this contribution is on providing suggestions for how to open and build access to resources for developing‐world scientists. Everyone benefits if developing‐world and developed‐world scientists work together collaboratively to pose interesting and novel questions, generate new data, update existing data, carry out analyses, and arrive at interesting insights and interpretations. In this way, the biodiversity science community can replace “parachute” science with “global science.”
... Finally, increased funding, institutional and data sharing requirements within grants, and career recognition of data generation could all greatly enhance data availability for other taxa from more-diverse and less-accessible areas and facilitate the sharing of the data needed to understand global biodiversity patterns (Costello et al. 2013b, 2015b, La Sorte and Somveille 2019. Though more difficult than making BAD arguments and simply using what data are available, these steps will be necessary for scientists to realistically predict and prevent biodiversity loss. ...
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Spatial patterns of biodiversity are inextricably linked to their collection methods, yet no synthesis of bias patterns or their consequences exists. As such, views of organismal distribution and the ecosystems they make up may be incorrect, undermining countless ecological and evolutionary studies. Using 742 million records of 374 900 species, we explore the global patterns and impacts of biases related to taxonomy, accessibility, ecotype and data type across terrestrial and marine systems. Pervasive sampling and observation biases exist across animals, with only 6.74% of the globe sampled, and disproportionately poor tropical sampling. High elevations and deep seas are particularly unknown. Over 50% of records in most groups account for under 2% of species and citizen-science only exacerbates biases. Additional data will be needed to overcome many of these biases, but we must increasingly value data publication to bridge this gap and better represent species' distributions from more distant and inaccessible areas, and provide the necessary basis for conservation and management.
... Where possible, maps should be made "open" that is, they should be available to anyone with the possibility of redistribution in any form with minimal copyright or licensing restrictions. A lack of a data publishing culture, especially in the marine biodiversity sciences, is often regarded as the largest hindrance to effective data sharing (Costello et al. 2013). Providing incentives for open and FAIR data, including appropriate acknowledgement and tracking of provenanceor the original sources of the datais therefore crucial to facilitate contributions to the evidence base necessary for progressing toward SDG 14 and related targets. ...
... Recording and publishing marine biodiversity of echinoderms with precise taxonomic identifications is necessary to improve research and management efforts in this Marine Protected Area, and to properly evaluate the natural response of anthropogenic impacts on these ecosystems (Worm et al., 2006;Costello, Michener, Gahegan, Zhang & Bourne, 2013). An update of the research and study of echinoderms is presented under the BioMar-ACG Project, to complement the ACG marine biodiversity baseline compilation (Cortés, 2017). ...
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Introducción: El estudio de la diversidad marina del Pacífico Norte de Costa Rica inició con expediciones extranjeras aisladas en la década de 1930, y fue desarrollado sistemáticamente a mediados de la década de 1990 por el Centro de Investigaciones en Ciencias del Mar y Limnología de la Universidad de Costa Rica, como consecuencia ahora se reporta un total de 1 479 especies en esta región. Objetivo: Presentar una actualización de la riqueza de equinodermos del Área de Conservación Guanacaste. Métodos: Realizamos muestreos exhaustivos en 25 localidades y estimamos la similitud entre sitios con base en la riqueaza de familias y la heterogeneidad ambiental. Resultados: Encontramos 61 taxa, que representan el 26% de las especies reportadas para la costa pacífica del país. De estas, 43 especies son nuevos registros para el Área de Conservación Guanacaste y siete para las costas de Costa Rica y el Pacífico centroamericano. Tres morfoespecies no coinciden con las descripciones disponibles para las especies del Pacífico Tropical Oriental. Por último, hallamos un ejemplar del holoturoideo Epitomapta tabogae y otro del ofiuroideo Ophioplocus hancocki, considerados endémicos para Panamá y las Islas Galápagos respectivamente. La proximidad entre los sitios muestreados y la redundancia de ciertas familias pueden explicar por qué no se encontraron diferencias entre las localidades. Conclusiones: La riqueza de equinodermos de esta área de conservación es al menos 20% mayor que la reportada anteriormente, alcanzando niveles similares a los de otros sitios de alta diversidad del Pacífico Tropical Oriental.
... Recording and publishing marine biodiversity of echinoderms with precise taxonomic identifications is necessary to improve research and management efforts in this Marine Protected Area, and to properly evaluate the natural response of anthropogenic impacts on these ecosystems (Worm et al., 2006;Costello, Michener, Gahegan, Zhang & Bourne, 2013). An update of the research and study of echinoderms is presented under the BioMar-ACG Project, to complement the ACG marine biodiversity baseline compilation (Cortés, 2017). ...
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Introduction: The study of the marine diversity of the North Pacific of Costa Rica began with isolated foreign expeditions in the 1930s and was systematically developed in the mid-1990s by the Center for Research in Marine Sciences and Limnology, Universidad de Costa Rica, as consequence there are now a total of 1 479 reported species in this region. Objective: Present an update to the echinoderm richness of the Guanacaste Conservation Area. Methods: We sampled 25 localities exhaustively and estimated similarity between sites based on the family richness and environmental heterogeneity. Results: We found 61 taxa, which represent 26 % of the echinoderm reported species for the country's Pacific coast. Of these, 43 species are new records for the Guanacaste Conservation Area, and seven for Costa Rica and Central American Pacific coasts. We found three morpho-species that do not match to available descriptions of the Eastern Tropical Pacific echinoderm species. We also found the holothuroid Epitomapta tabogae, and the ophiuroid Ophioplocus hancocki, previously thought endemic to Panama and the Galapagos Islands, respectively. The proximity of the sampled sites and the redundancy of certain families may explain why we did not find important differences among localities. Conclusions: The echinoderm richness of this conservation area is at least 20 % higher than previously reported, reaching similar levels to those in other high diversity sites of the Eastern Tropical Pacific.
... La gestión de los Datos Abiertos requiere tener en cuenta aspectos técnicos como la instalación de repositorios comunes y la estandarización de datos y metadatos, estrategias de financiación sostenibles para el mantenimiento perdurable en el tiempo de estos repositorios, y una definición clara de derechos de propiedad y comportamiento exigido a los usuarios (Bendix et al., 2012). Esta gestión representa un reto importante y debe superar numerosas dificultades habitualmente relacionadas con la falta de concienciación y reticencias de los autores de los datos para compartirlos (Costello, 2013). Los retos técnicos para diseñar sistemas de gestión de datos fiables, eficientes y estandarizados que aseguren su interoperabilidad y una financiación reducida y poco fiable asignada a la gestión de datos, hacen que la perdurabilidad de estos datos en el tiempo esté en cuestión (Bendix et al., 2012). ...
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En los últimos años el ecosistema Open en el que se inscriben movimientos como el Open Source Software, el Open Access y más recientemente el Open Data, está generando profundos cambios en las estrategias de investigadores y centros de investigación, empresas y administraciones. En este artículo se hace una revisión de estos conceptos, de las iniciativas Open más relevantes para las áreas de trabajo de AZTI en investigación marina, y de iniciativas internas de AZTI que se acercan a estos movimientos. Finalmente, se presentan una serie de consideraciones y reflexiones acerca de los cambios que el ecosistema Open y las iniciativas relacionadas con el mismo, están suponiendo en las estrategias de los diferentes agentes, así como sobre las oportunidades y sinergias que se pueden generar y la necesidad de adaptar los sistemas de gestión y los procesos organizativos
... In contrast to groups of organisms from other ecosystems (e.g., aboveground terrestrial 31 ) for which the Global Biodiversity Information Facility (GBIF) constitutes already the main global data hub 32,33 , soil organisms are poorly represented. In fact, distribution data on soil taxa are spread across the literature, museum archives, and a number of non-interoperable platforms (e.g., EDAPHOBASE (https://portal.edaphobase.org/), ...
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Soils harbor a substantial fraction of the world’s biodiversity, contributing to many crucial ecosystem functions. It is thus essential to identify general macroecological patterns related to the distribution and functioning of soil organisms to support their conservation and consideration by governance. These macroecological analyses need to represent the diversity of environmental conditions that can be found worldwide. Here we identify and characterize existing environmental gaps in soil taxa and ecosystem functioning data across soil macroecological studies and 17,186 sampling sites across the globe. These data gaps include important spatial, environmental, taxonomic, and functional gaps, and an almost complete absence of temporally explicit data. We also identify the limitations of soil macroecological studies to explore general patterns in soil biodiversity-ecosystem functioning relationships, with only 0.3% of all sampling sites having both information about biodiversity and function, although with different taxonomic groups and functions at each site. Based on this information, we provide clear priorities to support and expand soil macroecological research. Soil organism biodiversity contributes to ecosystem function, but biodiversity and function have not been equivalently studied across the globe. Here the authors identify locations, environment types, and taxonomic groups for which there is currently a lack of biodiversity and ecosystem function data in the existing literature.
Chapter
This chapter describes the current state-of-the-art and some of the drivers for the rapid development of digital terrain analysis and modeling over the past five decades. The chapter starts with brief descriptions of the role of digital elevation models (DEMs), scale, and terrain analysis software. The attention then shifts to the major accomplishments of the past 20 years and current state-of-the-art. This part describes the typical digital terrain analysis workflow, focusing on innovations and the methods used today for the construction of DEMs, the calculation of land-surface parameters, the delineation of landforms and land-surface objects, and the measurement of error and uncertainty. The next part focuses on future issues, needs and opportunities. There is a need to find ways to: (1) clarify and strengthen the role of theory; (2) rediscover and use existing knowledge; (3) develop new digital terrain analysis methods; (4) use provenance, credibility, and digital terrain application-context knowledge; (5) develop high-fidelity, multi-resolution DEMs; (6) develop and embrace new visualization opportunities; and (7) adopt and use new information technologies and workflows. The chapter concludes with some final comments and a call for action that uses two examples to show how geomorphometry can be adapted and used to help solve some of the problems that threaten the environment and human wellbeing.
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Recent emphasis and requirements for open data publication have led to significant increases in data availability in the Earth sciences, which is critical to long-tail data integration. Currently, data are often published in a repository with an identifier and citation, similar to those for papers. Subsequent publications that use the data are expected to provide a citation in the reference section of the paper. However, the format of the data citation is still evolving, particularly with regards to citing dynamic data, subsets, and collections of data. Considering the motivations of both data producers and consumers, the most pressing need is to create user-friendly solutions that provide credit for data producers and enable accurate citation of data, particularly integrated data. Providing easy-to-use data citations is a critical foundation that is required to address the socio-technical challenges around data integration. Studies that integrate data from dozens or hundreds of datasets must often include data citations in supplementary material due to page limits. However, citations in the supplementary material are not indexed, making it difficult to track citations and thus giving credit to the data producer. In this paper, we discuss our experiences and the challenges we have encountered with current citation guidance. We also review the relative merits of the currently available mechanisms designed to enable compact citation of collections of data, such as data collections, data papers, and dynamic data citations. We consider these options for three data producer scenarios: a domain-specific data collection, a data repository, and a large-scale, multidisciplinary project. We posit that a new mechanism is also needed to enable citation of multiple datasets and credit to data producers.
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The scientific monitoring of the Southern Ocean French fishing industry is based on the use the Pecheker database. Pecheker is dedicated to the digital curation of the data collected on field by scientific observers and which analysis allows the scientists of the Muséum national d’Histoire naturelle institution to provide guidelines and advice for the regulation of the fishing activity, the protection of the fish stocks and the protection of the marine ecosystems. The template of Pecheker has been developed to make the database adapted to the ecosystem-based management concept. Considering the global context of biodiversity erosion, this modern approach of management aims to take account of the environmental background of the fisheries to ensure their sustainable development. Completeness and high quality of the raw data is a key element for an ecosystem-based management database such as Pecheker. Here, we present the development of this database as a case study of fisheries data curation to be shared with the readers. Full code to deploy a database based on the Pecheker template is provided in supplementary materials. Considering the success factors we could identify, we propose a discussion about how the community could build a global fisheries information system based on a network of small databases including interoperability standards.
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Citizen science has become increasingly popular to collect data on biodiversity as it can cover a large area and is cost-effective. However, gaps in biodiversity data are common especially related to data of herpetofauna, which is not received much attention. Project Amfibi Reptil Kita (ARK) is one of the programs created to collect data on the distribution of the herpetofauna in Indonesia. This research aims to analyse the contribution of citizen science through project ARK in increasing data of herpetofauna in Indonesia for the last four years. Most of the data in ARK (56.3%) were obtained during herpblitz, however, the percentage (43.86%) tend to increase in 2020. In total 433 species were reported consisting of 152 species of amphibian and 281 reptiles. Most of the data (70%) reported were from Java region. The lowest recorded data come from Papua and Maluku region. The most frequently reported amphibian species was Duttaphrynus melanostictus and the reptile species was Bronchocela jubata. A total of 416 member-contributed data in ARK project. The result of ARK has been used to describe new species and model spatial distribution. It shows, ARK has been important in documenting the diversity of herpetofauna in Indonesia.
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Crustaceans are an important component of deep-sea biodiversity. A brief review of the history of expeditions and studies related to deep-sea crustaceans in Costa Rica is presented. We briefly discuss studies on crustaceans from the Costa Rican deep-sea environments, and we provided an updated list of species recorded for the Pacific and the Caribbean. A total of 147 species has been reported from Costa Rican deep sea; 8 species have been reported from the Caribbean, 138 from the Pacific, and 1 from both basins. Decapoda was the most diverse group with 87 species, followed by Copepoda (23 spp.) and Peracarida (19 spp.). The first deep-sea exploration in Costa Rica began with foreign efforts, with national projects and participation increasing in recent years. Most research dealing with crustaceans has been focused on reproductive biology, in collaboration with the deepwater shrimp fisheries. Future efforts to study the Costa Rican deep-sea will incorporate collaboration with foreign expeditions and private companies since the country does not have enough funding invested in its deep sea. Finally, we discuss the current threats to deep-sea crustaceans, as well as future perspectives for the study of this fascinating group in Costa Rica.
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Natural history collections play a vital role in biodiversity research and conservation by providing a window to the past. The usefulness of the vast amount of historical data depends on their quality, with correct taxonomic identifications being the most critical. The identification of many of the objects of natural history collections, however, is wanting, doubtful or outdated. Providing correct identifications is difficult given the sheer number of objects and the scarcity of expertise. Here we outline the construction of an ecosystem for the collaborative development and exchange of image recognition algorithms designed to support the identification of objects. Such an ecosystem will facilitate sharing taxonomic expertise among institutions by offering image datasets that are correctly identified by their in-house taxonomic experts. Together with openly accessible machine learning algorithms and easy to use workbenches, this will allow other institutes to train image recognition algorithms and thereby compensate for the lacking expertise.