Category Archives: oa.marine

Systematic review of marine environmental DNA metabarcoding studies: toward best practices for data usability and accessibility [PeerJ]

Posted on by
Reply

Abstract:  The emerging field of environmental DNA (eDNA) research lacks universal guidelines for ensuring data produced are FAIR–findable, accessible, interoperable, and reusable–despite growing awareness of the importance of such practices. In order to better understand these data usability challenges, we systematically reviewed 60 peer reviewed articles conducting a specific subset of eDNA research: metabarcoding studies in marine environments. For each article, we characterized approximately 90 features across several categories: general article attributes and topics, methodological choices, types of metadata included, and availability and storage of sequence data. Analyzing these characteristics, we identified several barriers to data accessibility, including a lack of common context and vocabulary across the articles, missing metadata, supplementary information limitations, and a concentration of both sample collection and analysis in the United States. While some of these barriers require significant effort to address, we also found many instances where small choices made by authors and journals could have an outsized influence on the discoverability and reusability of data. Promisingly, articles also showed consistency and creativity in data storage choices as well as a strong trend toward open access publishing. Our analysis underscores the need to think critically about data accessibility and usability as marine eDNA metabarcoding studies, and eDNA projects more broadly, continue to proliferate.

 

Water science must be Open Science | Nature Water

Posted on by
Reply

“Since water is a common good, the outcome of water-related research should be accessible to everyone. Since Open Science is more than just open access research articles, journals must work with the research community to enable fully open and FAIR science…”

Open Science for water research | Luxembourg Institute of Science and Technology

Posted on by
Reply

“For the launch of the new scientific journal Nature Water, researchers Emma and Stan Schymanski contributed an article about the future of water research. This opinion paper focuses on the importance of open science in a field where, due to its global societal relevance, knowledge and research results should be freely accessible by a wide range of stakeholders. The publication also highlights the interdisciplinary expertise brought to Luxembourg by the two FNR ATTRACT fellows on such a topical subject….

Research on water systems can help us face these considerable challenges but needs to consider the global societal relevance of its subject. “Since water is a common good, it should be natural that the outcome of water-related research is accessible to everyone,” explains Dr Stan Schymanski. “It needs to become freely available and re-usable for everybody, without the need for paid licenses to view publications or use data.”

The two researchers insist on the importance of implementing Open Science in its broadest definition. It has to go beyond open access to research articles: it must also include open data and open-source computer code. Additionally, open data should be aligned with the FAIR Principles, which describe how to make data findable, accessible, interoperable and reusable. Open reproducible research can only be achieved through the combination of all these aspects.

Their Nature Water article details how this is vital for the development of Early Warning Systems for floods for example, as reliable forecasting relies heavily on real-time sharing of meteorological data. It is also crucial when studying processes on long time scales such as groundwater recharge, that can take centuries in arid systems. Understanding these natural mechanisms is only possible through free access to long time series of hydrological data across the globe.

After reviewing the tools already available to perform open water research – such as open repositories, templates to facilitate reproducibility assessments, practical guidelines for sharing code and choosing appropriate licenses – the two authors call for substantial additional efforts toward fully open science….”

NETL-Developed Online Database Brings Energy-Related Wastewater Stream Data to Public’s Fingertips | netl.doe.gov

Posted on by
Reply

“Community leaders and water researchers can now access publicly available online datasets curated and processed by NETL to better understand the composition of energy-related wastewater streams. The data will help mitigate environmental risks and identify possible sources of valuable critical minerals (CMs).

The National Energy Water Treatment and Speciation (NEWTS) Database provides information at no cost about the levels of toxins, concentrations of metals and other hazardous materials found in energy-related wastewater streams, which include power plant leachate, acid mine drainage, brackish water and oil and gas produced water. Researchers can input the data into computer software to develop appropriate remediation steps.

The NEWTS team is also developing a database dashboard showing sites across the nation where energy-related wastewater stream samples and composition data have been collected. Using the dashboard, community leaders and the public will be able to quickly obtain data from locations displayed on a map where various government agencies collect and analyze water samples from energy-related wastewater streams….”

New website compiles ocean data from landmark 19th-century scientific voyage | Illinois

Posted on by
Reply

“The HMS Challenger began a four-year voyage 150 years ago to explore the deep sea and the creatures that lived in it. The scientists aboard the ship discovered thousands of new species and recorded massive amounts of data about the oceans. The treasure trove of information they gathered is now available online in the first comprehensive database of the Challenger findings.

A new website devoted to the expedition and the database was launched Dec. 21 – the 150th anniversary of the beginning of the Challenger’s voyage. It is part of the Oceans 1876 project by Gillen D’Arcy Wood, a University of Illinois Urbana-Champaign English professor and a historian of 19th-century environmental history and science. Wood also is the associate director of the Institute for Sustainability, Energy, and the Environment, and the director of its environmental writing program….”

Diamond open access – an exciting new era for Aquatic Living Resources with Ifremer and IRD

Posted on by
Reply

“We are pleased to announce a new chapter in our longstanding partnership with Ifremer (French National Research Institute for Ocean Science) and IRD (French National Research Institute for Sustainable Development). These two leading marine science organisations have committed to sponsoring Aquatic Living Resources (ALR) as a diamond open access journal with immediate effect. Diamond open access enables all papers to be freely available without any subscriptions or publication fees for authors thanks to the support of Ifremer and IRD. The ALR archives are also now freely available….”

Open access and the evolving academic publishing landscape of the water sector: Water International: Vol 0, No 0

Posted on by
Reply

“The launch of many new water journals in recent years is a testament to the growth and importance of water research as a problematique, that is, as both a problem in and of itself and as an important correlate of other global challenges. As entire regions start to run dry or suffer repeated flooding due to climate change, it is more important than ever to understand water availability, quality, use and governance. And as the burgeoning industry of ‘nexus’ studies shows, researchers and policy- makers have discovered at, indeed, most elements of society are linked to water. This is a great time to be a water scholar with exciting new opportunities to collaborate with researchers from across the natural and social sciences, engineering. and humanities. Water scholars also have initiated many new journals, book series, etc., that clamour for our insights and academic production. But there are tensions too, linked to the perhaps too-rapid proliferation of journals, their transition to open access (OA) business models, and the unhealthy ways in which these are linked to career prospects for water scholars.”

Sharkipedia: a curated open access database of shark and ray life history traits and abundance time-series | Scientific Data

Posted on by
Reply

Abstract:  A curated database of shark and ray biological data is increasingly necessary both to support fisheries management and conservation efforts, and to test the generality of hypotheses of vertebrate macroecology and macroevolution. Sharks and rays are one of the most charismatic, evolutionary distinct, and threatened lineages of vertebrates, comprising around 1,250 species. To accelerate shark and ray conservation and science, we developed Sharkipedia as a curated open-source database and research initiative to make all published biological traits and population trends accessible to everyone. Sharkipedia hosts information on 58 life history traits from 274 sources, for 170 species, from 39 families, and 12 orders related to length (n?=?9 traits), age (8), growth (12), reproduction (19), demography (5), and allometric relationships (5), as well as 871 population time-series from 202 species. Sharkipedia relies on the backbone taxonomy of the IUCN Red List and the bibliography of Shark-References. Sharkipedia has profound potential to support the rapidly growing data demands of fisheries management, international trade regulation as well as anchoring vertebrate macroecology and macroevolution.

 

Frontiers | Sounding the Call for a Global Library of Underwater Biological Sounds | Ecology and Evolution

Posted on by
Reply

Abstract:  Aquatic environments encompass the world’s most extensive habitats, rich with sounds produced by a diversity of animals. Passive acoustic monitoring (PAM) is an increasingly accessible remote sensing technology that uses hydrophones to listen to the underwater world and represents an unprecedented, non-invasive method to monitor underwater environments. This information can assist in the delineation of biologically important areas via detection of sound-producing species or characterization of ecosystem type and condition, inferred from the acoustic properties of the local soundscape. At a time when worldwide biodiversity is in significant decline and underwater soundscapes are being altered as a result of anthropogenic impacts, there is a need to document, quantify, and understand biotic sound sources–potentially before they disappear. A significant step toward these goals is the development of a web-based, open-access platform that provides: (1) a reference library of known and unknown biological sound sources (by integrating and expanding existing libraries around the world); (2) a data repository portal for annotated and unannotated audio recordings of single sources and of soundscapes; (3) a training platform for artificial intelligence algorithms for signal detection and classification; and (4) a citizen science-based application for public users. Although individually, these resources are often met on regional and taxa-specific scales, many are not sustained and, collectively, an enduring global database with an integrated platform has not been realized. We discuss the benefits such a program can provide, previous calls for global data-sharing and reference libraries, and the challenges that need to be overcome to bring together bio- and ecoacousticians, bioinformaticians, propagation experts, web engineers, and signal processing specialists (e.g., artificial intelligence) with the necessary support and funding to build a sustainable and scalable platform that could address the needs of all contributors and stakeholders into the future.

Help us shape the future of the Blue-Cloud! Please take our short survey

Posted on by
Reply

“The Blue-Cloud project is piloting a web-based Open Science cyberspace to service the needs of marine scientists and researchers in the marine domain. This survey was launched to build a vision for its long-term evolution into 2030, generating value and benefits for a much larger user base and for wider stakeholder communities -including not only scientists & researchers, but also Blue Economy SMEs, maritime industries, policy makers, NGOs and ultimately citizens. Your response to this survey will contribute to shaping strategic policy recommendations towards that end, considering your needs and expectations and aligning with wider developments….”

OceanDocs Home

Posted on by

“OceanDocs is supported by the Intergovernmental Oceanographic Commission (IOC) to collect, preserve and facilitate discovery and access to all research output from members of the ocean research and observation community and specifically their Ocean Data and Information Networks (ODINS). It is one of a number of complementary thematic digital marine and aquatic repositories including the Aquatic Commons, which is supported by the International Association of Aquatic and Marine Science Libraries and Information Centers (IAMSLIC).”

Welcome to Aquatic Commons – Aquatic Commons

Posted on by

“The Aquatic Commons is a thematic digital repository covering the natural marine, estuarine /brackish and fresh water environments . It includes all aspects of the science, technology, management and conservation of these environments, their organisms and resources, and the economic, sociological and legal aspects. It is complementary to OceanDocs, which is supported by the Intergovernmental Oceanographic Commission (IOC)/ International Oceanographic Data and Information Exchange (IODE) specifically to collect, preserve and facilitate access to all research output from members of their Ocean Data and Information Networks (ODINS). Click to read more information about this repository….”

A database of zooplankton biomass in Australian marine waters – PubMed

Posted on by

Abstract:  Zooplankton biomass data have been collected in Australian waters since the 1930s, yet most datasets have been unavailable to the research community. We have searched archives, scanned the primary and grey literature, and contacted researchers, to collate 49187 records of marine zooplankton biomass from waters around Australia (0-60°S, 110-160°E). Many of these datasets are relatively small, but when combined, they provide >85 years of zooplankton biomass data for Australian waters from 1932 to the present. Data have been standardised and all available metadata included. We have lodged this dataset with the Australian Ocean Data Network, allowing full public access. The Australian Zooplankton Biomass Database will be valuable for global change studies, research assessing trophic linkages, and for initialising and assessing biogeochemical and ecosystem models of lower trophic levels.

 

Popular preprint servers face closure because of money troubles

Posted on by

“The rise of preprint repositories has helped scientists worldwide to share results and get feedback quickly. But several platforms that serve researchers in emerging economies are struggling to raise money to stay afloat. One, which hosts research from Indonesia, has decided to close because of this funding shortfall.

INA-Rxiv, which was set up in 2017, was one of the first repositories to host studies from a particular region. Previous platforms served specific disciplines: for example, arXiv, the original preprint repository, hosts physical-sciences research, and bioRxiv is a popular repository for biology studies. Other region or language-specific repositories followed, including ArabiXiv, which hosts Arabic-language research; AfricArxiv and IndiaRxiv. Managers of these repositories say they increase exposure for research from the regions, and facilitate collaborations.

INA-Rxiv, ArabiXiv, AfricArxiv and IndiaRxiv are run by volunteers around the world, but the servers are hosted online by the non-profit Center for Open Science (COS), based in Charlottesville, Virginia. The centre’s platform hosts 26 repositories, including more than a dozen that are discipline-specific.

In December 2018, the COS informed repository managers that from 2020, it would be introducing fees, charged to repository managers, to cover maintenance costs. The charges, which were finalized last December, start at about US$1,000 a year, and increase as repositories’ annual submissions grow….”

OCLE: A European open access database on climate change effects on littoral and oceanic ecosystems – ScienceDirect

Posted on by

“Studies on historical and future distribution of marine species are frequently limited by the lack of relevant data on abiotic components (IPCC, 2014), especially when working over large areas (Robinson et al., 2017). Important advances have been achieved in the last years regarding availability of global information on physical and chemical driven forces affecting species distributions. WorldClim (Hijmans et al., 2005) marked a milestone in terrestrial species distribution studies, as it opened the opportunity to address global research studies with high resolution. Other databases including historical and projected variables in the terrestrial environment, mainly temperature and precipitation, such as Climond (Kriticos et al., 2012), Climate wizard (Girvetz et al., 2009) or Chelsea (Karger et al., 2016) have emerged recently. However, in the marine environment the number of global databases is limited. Bio-Oracle is the most valuable reference because it provides surface and benthic layers for water temperature, salinity, nutrients, chlorophyll, sea ice, current velocity, phytoplankton, primary productivity, iron and light at high resolution and global coverage (Assis et al., 2017; Tyberghein et al., 2012). Other remarkable databases are MARSPEC (Sbrocco and Barber, 2013), offering variables derived from bathymetry, slope, salinity and sea surface temperature, Aquamaps (Ready et al., 2010), focused on marine animals, or Hexacoral (Fautin and Buddemeier, 2002), with the aim to understand spatial and temporal patterns in biogeochemistry and biogeography. Some databases cover both land and sea areas, such as the MERRAclim (Vega et al., 2017), which offers decadal data of 19 derived variables of air temperature and humidity atmospheric water vapour….

Trying to comply with these requirements and using the best data available, to our best knowledge, this study presents the open access database on climate change effects on littoral and oceanic ecosystems (OCLE), an ecological-driven database of present and future hazards for marine life in Europe….”