Article
Microbiology
Pajau Vangay, Josephine Burgin, Anjanette Johnston, Kristen L. Beck, Daniel C. Berrios, Kai Blumberg, Shane Canon, Patrick Chain, John-Marc Chandonia, Danielle Christianson, Sylvain V. Costes, Joan Damerow, William D. Duncan, Jose Pablo Dundore-Arias, Kjiersten Fagnan, Jonathan M. Galazka, Sean M. Gibbons, David Hays, Judson Hervey, Bin Hu, Bonnie L. Hurwitz, Pankaj Jaiswal, Marcin P. Joachimiak, Linda Kinkel, Joshua Ladau, Stanton L. Martin, Lee Ann McCue, Kayd Miller, Nigel Mouncey, Chris Mungall, Evangelos Pafilis, T. B. K. Reddy, Lorna Richardson, Simon Roux, Lynn M. Schriml, Justin P. Shaffer, Jagadish Chandrabose Sundaramurthi, Luke R. Thompson, Ruth E. Timme, Jie Zheng, Elisha M. Wood-Charlson, Emiley A. Eloe-Fadrosh
Summary: Microbiome samples are influenced by their environment, highlighting the importance of metadata in interpreting the data. While important contributions have been made in developing community-driven metadata standards, they are not universally embraced. NMDC hosted a workshop to understand the adoption and barriers of these standards.
Article
Biology
David Johnson, Dominique Batista, Keeva Cochrane, Robert P. Davey, Anthony Etuk, Alejandra Gonzalez-Beltran, Kenneth Haug, Massimiliano Izzo, Martin Larralde, Thomas N. Lawson, Alice Minotto, Pablo Moreno, Venkata Chandrasekhar Nainala, Claire O'Donovan, Luca Pireddu, Pierrick Roger, Felix Shaw, Christoph Steinbeck, Ralf J. M. Weber, Susanna-Assunta Sansone, Philippe Rocca-Serra
Summary: The ISA API is a Python library that allows for creation, editing, parsing, and validating of ISA-Tab and ISA-JSON formats using a common data model. It provides rich metadata-handling functionality to support automation and interoperability between different formats.
Review
Biochemistry & Molecular Biology
Marine Djaffardjy, George Marchment, Clemence Sebe, Raphael Blanchet, Khalid Bellajhame, Alban Gaignard, Frederic Lemoine, Sarah Cohen-Boulakia
Summary: Data analysis pipelines are established as an effective means for bioinformatics data analysis and experiments. However, scripting languages are not sufficient for building large-scale pipelines capable of handling big data and running on high performance computing clusters. Scientific workflow systems provide modular, reproducible, and reusable solutions for bioinformatics data analysis pipelines.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Computer Science, Information Systems
Javier Nogueras-Iso, Javier Lacasta, Manuel Antonio Urena-Camara, Francisco Javier Ariza-Lopez
Summary: In recent years, many institutions have launched Open Data initiatives, enabling broader access and utilization of large datasets. While open source platforms have simplified the setup of Open Data portals, few approaches have analyzed how metadata precisely describes related datasets. This research extends a method for checking the quality of geographic metadata to the context of Open Data metadata, aiming to improve metadata quality assessment in the Open Data domain.
Article
Environmental Studies
Doris Pivac, Miodrag Roic, Josip Krizanovic, Rinaldo Paar
Summary: This study examined the availability of cadastral documentation through catalog services and found that the largest percentage of documents is available through the discovery service. However, there was a lack of application of geoinformation metadata standards in these documents.
Article
Biology
Dylan G. E. Gomes, Patrice Pottier, Robert Crystal-Ornelas, Emma J. Hudgins, Vivienne Foroughirad, Luna L. Sanchez-Reyes, Rachel Turba, Paula Andrea Martinez, David Moreau, Michael G. Bertram, Cooper A. Smout, Kaitlyn M. Gaynor
Summary: The biological sciences community recognizes the importance of open, reproducible, and transparent research practices. However, researchers face barriers in sharing their data and code, including knowledge barriers, concerns about reuse, and misaligned career incentives. By identifying and addressing these barriers, we can promote open science goals.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Green & Sustainable Science & Technology
Na Luo, Marco Pritoni, Tianzhen Hong
Summary: Building data is becoming increasingly important for decision makers to improve building performance, but practical analysis and use of the collected data are limited due to various reasons. There is a need for a toolchain to curate and represent building information and performance data in common standardized terminologies and schemas to enable interoperability between tools and applications.
RENEWABLE & SUSTAINABLE ENERGY REVIEWS
(2021)
Article
Ecology
Ana M. M. Sequeira, Malcolm O'Toole, Theresa R. Keates, Laura H. McDonnell, Camrin D. Braun, Xavier Hoenner, Fabrice R. A. Jaine, Ian D. Jonsen, Peggy Newman, Jonathan Pye, Steven J. Bograd, Graeme C. Hays, Elliott L. Hazen, Melinda Holland, Vardis M. Tsontos, Clint Blight, Francesca Cagnacci, Sarah C. Davidson, Holger Dettki, Carlos M. Duarte, Daniel C. Dunn, Victor M. Eguiluz, Michael Fedak, Adrian C. Gleiss, Neil Hammerschlag, Mark A. Hindell, Kim Holland, Ivica Janekovic, Megan K. McKinzie, Monica M. C. Muelbert, Chari Pattiaratchi, Christian Rutz, David W. Sims, Samantha E. Simmons, Brendal Townsend, Frederick Whoriskey, Bill Woodward, Daniel P. Costa, Michelle R. Heupel, Clive R. McMahon, Rob Harcourt, Michael Weise
Summary: The study emphasizes the importance of a standardization framework to ensure discoverability, interoperability, and effective translation of bio-logging data for addressing global conservation challenges. By using simple templates and automated procedures, data can be transformed into four standardized levels, facilitating data sharing, interoperability, accuracy-of-use, rightful attribution, and data preservation security. Adoption of this framework will support the collection of Essential Ocean Variables and inter-governmental assessments, and establish a starting point for broader efforts in establishing interoperable bio-logging data formats across all fields in animal ecology.
METHODS IN ECOLOGY AND EVOLUTION
(2021)
Article
Computer Science, Information Systems
Paola Ingavelez-Guerra, Vladimir E. Robles-Bykbaev, Angel Perez-Munoz, Jose Hilera-Gonzalez, Salvador Oton-Tortosa
Summary: This article presents a multilevel methodological proposal for the automatic adaptation of open educational resources, aiming to improve accessibility and the correct use of metadata in e-learning environments. The research conducted aims to address the real needs and preferences of students with disabilities and to support the generation and reuse of accessible educational resources.
Article
Psychology
Erin M. Buchanan, Sarah E. Crain, Ari L. Cunningham, Hannah R. Johnson, Hannah Stash, Marietta Papadatou-Pastou, Peder M. Isager, Rickard Carlsson, Balazs Aczel
Summary: As researchers increasingly embrace open and transparent data sharing, providing effective information such as data dictionaries and codebooks is crucial for others to understand data sets. Metadata plays a key role in providing insights and facilitating broader data use, while using freely available web applications can ensure psychology data is findable, accessible, interoperable, and reusable. Proper documentation is essential for making data stored in online repositories like OSF discoverable and readable by a wider audience.
ADVANCES IN METHODS AND PRACTICES IN PSYCHOLOGICAL SCIENCE
(2021)
Article
Biology
Emma J. Griffiths, Ruth E. Timme, Catarina Ines Mendes, Andrew J. Page, Nabil-Fareed Alikhan, Dan Fornika, Finlay Maguire, Josefina Campos, Daniel Park, Idowu B. Olawoye, Paul E. Oluniyi, Dominique Anderson, Alan Christoffels, Anders Goncalves da Silva, Rhiannon Cameron, Damion Dooley, Lee S. Katz, Allison Black, Ilene Karsch-Mizrachi, Tanya Barrett, Anjanette Johnston, Thomas R. Connor, Samuel M. Nicholls, Adam A. Witney, Gregory H. Tyson, Simon H. Tausch, Amogelang R. Raphenya, Brian Alcock, David M. Aanensen, Emma Hodcroft, William W. L. Hsiao, Ana Tereza R. Vasconcelos, Duncan R. MacCannell
Summary: PHA4GE is a global coalition working to improve openness, interoperability, and consistency in public health microbial bioinformatics. They have developed a SARS-CoV-2 contextual data specification package to support data collection and harmonization in public biorepositories.
Article
Computer Science, Information Systems
Petar Milic, Natasa Veljkovic, Leonid Stoimenov
Summary: Metadata plays a crucial role in e-government open data platforms, providing a structured environment for data consumption and enabling unique interpretations of data. Research indicates that more attention should be paid to metadata to uncover relationships between datasets.
IEEE TRANSACTIONS ON EMERGING TOPICS IN COMPUTING
(2021)
Article
Biochemical Research Methods
Bryan A. Bartley
Summary: With the increasing automation and data-driven nature of synthetic biology, tools that aid researchers in implementing FAIR data management practices are necessary. Tyto, a lightweight Python tool, addresses the difficulty of adopting standardized annotation practices by providing support for controlled vocabularies in everyday scripting practice.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biology
Bart Nijsse, Peter J. Schaap, Jasper J. Koehorst
Summary: The life sciences are a major source of scientific data. Reusing and connecting these data can lead to new concepts and insights. However, the availability of easy-to-adopt implementations that fulfill the needs of data producers is limited. In response, the FAIR Data Station, a lightweight application written in Java, has been developed to support researchers in managing research metadata according to the FAIR principles. It includes modules for generating metadata templates, validating recorded values, and converting metadata into RDF format.
Review
Electrochemistry
Franco M. Zanotto, Diana Zapata Dominguez, Elixabete Ayerbe, Iker Boyano, Christine Burmeister, Marc Duquesnoy, Marlene Eisentraeger, Jonathan Florez Montano, Alfonso Gallo-Bueno, Lukas Gold, Florian Hall, Nicolaj Kaden, Bernhard Muerkens, Laida Otaegui, Yvan Reynier, Simon Stier, Matthias Thomitzek, Artem Turetskyy, Nicolas Vallin, Jacob Wessel, Xukuan Xu, Jeyhun Abbasov, Alejandro A. Franco
Summary: Using digital twin models in real-time information exchange and parameter correction can optimize the characteristics of the pilot line in lithium-ion battery manufacturing. This article discusses the parameters involved in each step of LIB manufacturing, presents available computational modeling approaches, and explores software implementation details. The importance of these parameters in terms of modeling set-up and validation, measurement accuracy, and rapidity is analyzed. Furthermore, the challenges and opportunities of integrating digital twin pilot lines are presented. The challenges of managing the data produced by these models are also discussed.
BATTERIES & SUPERCAPS
(2022)
Article
Evolutionary Biology
Ambrocio Melvin A. Matias, Iva Popovic, Joshua A. Thia, Ira R. Cooke, Gergely Torda, Vimoksalehi Lukoschek, Line K. Bay, Sun W. Kim, Cynthia Riginos
Summary: Genomic studies have revealed extensive hidden diversity in reef-building corals, which is highly underestimated in terms of evolutionary and ecological relevance. Additionally, symbiotic algae within coral host species can provide adaptive responses to environmental stress and may contribute to coral genetic variation. This study examines the genetic variation of Acropora tenuis coral host and its associated symbiotic algae across the Great Barrier Reef. The results demonstrate three distinct genetic clusters of coral hosts, associated with latitude and inshore-offshore reef position, while symbiotic algae diversity is influenced by reef location relative to shore.
EVOLUTIONARY APPLICATIONS
(2023)
Article
Ecology
Andre Vicente Liz, Dennis Roedder, Duarte Vasconcelos Goncalves, Guillermo Velo-Anton, Pedro Tarroso, Philippe Geniez, Pierre-Andre Crochet, Silvia B. Carvalho, Jose Carlos Brito
Summary: This study reveals a high and widespread diversity of lizards in the arid regions of the Sahara Desert, with their history linked to climate change. Northern Sahara acts as a unique hotspot for diversity, while the southern regions connect wide-ranging lineages from the Red Sea to the Atlantic coast. Terrain and land cover influence genetic diversity and geographic structure.
JOURNAL OF BIOGEOGRAPHY
(2023)
Review
Ecology
Erica S. Nielsen, Jeffrey O. Hanson, Silvia B. Carvalho, Maria Beger, Romina Henriques, Francine Kershaw, Sophie von der Heyden
Summary: Integrative and proactive conservation approaches are essential for the long-term survival of biodiversity. Molecular data, although rarely used, can provide valuable insights for conserving biodiversity at different levels. This article bridges the gap between molecular ecology and systematic conservation planning, providing a practical guide for incorporating molecular data into spatial conservation planning tools. The proposed framework enhances interdisciplinary collaboration, which is key to achieving ambitious global conservation goals in the coming decade.
TRENDS IN ECOLOGY & EVOLUTION
(2023)
Article
Biodiversity Conservation
Eric D. Crandall, Rachel H. Toczydlowski, Libby Liggins, Ann E. Holmes, Maryam Ghoojaei, Michelle R. Gaither, Briana E. Wham, Andrea L. Pritt, Cory Noble, Tanner J. Anderson, Randi L. Barton, Justin T. Berg, Sofia G. Beskid, Alonso Delgado, Emily Farrell, Nan Himmelsbach, Samantha R. Queeno, Thienthanh Trinh, Courtney Weyand, Andrew Bentley, John Deck, Cynthia Riginos, Gideon S. Bradburd, Robert J. Toonen
Summary: Genetic diversity within species is important for species resilience and conservation policies, but most studies lack the necessary spatial and temporal metadata for reusability and acknowledging sovereignty. We conducted a datathon and found that metadata decayed over time, with successful restoration through papers and online repositories being more effective than contacting authors directly. The rapid decay of metadata availability should prompt updates to data-sharing policies and researcher practices.
CONSERVATION BIOLOGY
(2023)
Article
Ecology
Maria Joao Paul, Dan Rosauer, Pedro Tarroso, Guillermo Velo-Anton, Silvia B. Carvalho
Summary: Understanding the drivers of biodiversity patterns is crucial, and this study aims to identify if global-scale drivers of phylogenetic diversity and endemism are also predictive at regional scales using Iberian amphibians as a case study. The results show that water-energy availability and historical climate instability are important drivers of amphibian diversity in Iberia, but the strength of these predictors is weaker at the regional scale compared to the global scale.
ECOLOGY AND EVOLUTION
(2023)
Article
Cell Biology
Gal Chaim Nuta, Yuval Gilad, Nadav Goldberg, Sara Meril, Marcela Bahlsen, Silvia Carvalho, Noga Kozer, Haim Barr, Yael Fridmann Sirkis, Kamil Hercik, Petra Brehova, Radim Nencka, Shani Bialik, Miriam Eisenstein, Adi Kimchi
Summary: Autophagy is a process of cellular content degradation and recycling, which has been found to play a crucial role in advanced stages of cancer by maintaining tumor cell homeostasis and promoting continuous growth under hypoxic or nutrient-starved conditions. Autophagy also supports alternative cellular trafficking pathways and provides a mechanism for the non-canonical secretion of inflammatory cytokines. This opens up potential therapeutic opportunities for using autophagy inhibitors in cancer treatment and acute inflammatory responses.
Article
Biodiversity Conservation
Thomas J. Richards, Katrina McGuigan, J. David Aguirre, Adriana Humanes, Yves-Marie Bozec, Peter J. Mumby, Cynthia Riginos
Summary: Global environmental change is happening rapidly, with coral reefs being one of the most threatened ecosystems. To ensure the survival of wild populations, adaptation is necessary. However, our understanding of the complex ecological and evolutionary dynamics of corals is limited, hindering predictions about their ability to adapt to future conditions.
GLOBAL CHANGE BIOLOGY
(2023)
Article
Ecology
Andre P. Samayoa, J. David Aguirre, Erwan Delrieu-Trottin, Libby Liggins
Summary: This study examined the historical biogeography of endemic marine fishes in subtropical islands of the Southwest Pacific. The results showed that most species originated in mainland Australia and that both geographical proximity and climatic differences played a significant role in determining colonization and speciation.
JOURNAL OF BIOGEOGRAPHY
(2023)
Article
Environmental Sciences
Graeme S. Cumming, Maja Adamska, Michele L. Barnes, Jon Barnett, David R. Bellwood, Joshua E. Cinner, Philippa J. Cohen, Jennifer M. Donelson, Katharina Fabricius, R. Quentin Grafton, Alana Grech, Georgina G. Gurney, Ove Hoegh-Guldberg, Andrew S. Hoey, Mia O. Hoogenboom, Jacqueline Lau, Catherine E. Lovelock, Ryan Lowe, David J. Miller, Tiffany H. Morrison, Peter J. Mumby, Martin Nakata, John M. Pandolfi, Garry D. Peterson, Morgan S. Pratchett, Timothy Ravasi, Cynthia Riginos, Jodie L. Rummer, Britta Schaffelke, Thomas Wernberg, Shaun K. Wilson
Summary: SDG 14 aims to secure marine sustainability by 2030, and understanding the changing seascape, global actions, and the collaboration between science and society are vital for achieving this goal in the Asia-Pacific region. Through a horizon scan, researchers identified nine emerging research priorities that can contribute to marine sustainability, including understanding seascape evolution, drivers of change, and the costs and benefits to people. Researchers can contribute by developing interdisciplinary understandings, emphasizing equity and justice, and improving knowledge of cross-scale processes.
REGIONAL ENVIRONMENTAL CHANGE
(2023)
Editorial Material
Ecology
Gareth B. Jenkins, Andrew P. Beckerman, Celine Bellard, Ana Benitez-Lopez, Aaron M. Ellison, Christopher G. Foote, Andrew L. Hufton, Marcus A. Lashley, Christopher J. Lortie, Zhaoxue Ma, Allen J. Moore, Shawn R. Narum, Johan Nilsson, Bridget O'Boyle, Diogo B. Provete, Orly Razgour, Loren Rieseberg, Cynthia Riginos, Luca Santini, Benjamin Sibbett, Pedro R. Peres-Neto
Summary: We urge journals to mandate archiving open data in a user-friendly format for readers. Consistent implementation will allow contributors to receive recognition through open data citation and promote scientific advancements.
ECOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Natalie J. Forsdick, Jana Wold, Anton Angelo, Francois Bissey, Jamie Hart, Mitchell Head, Libby Liggins, Dinindu Senanayake, Tammy E. Steeves
Summary: This article emphasizes the importance of careful and considered data management in the context of increasing accessibility to large-scale biodiversity genomic datasets. It recognizes the challenges associated with managing such datasets and provides guidance and resources for biodiversity genomics researchers.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Biochemistry & Molecular Biology
Ben Te Aika, Libby Liggins, Claire Rye, E. Owen Perkins, Jun Huh, Rudiger Brauning, Tracey Godfery, Michael A. Black
Summary: The Aotearoa Genomic Data Repository (AGDR) is an initiative that aims to securely store and share non-human genomic data from Aotearoa New Zealand, following the principles of Maori Data Sovereignty. The repository allows access to data only to those who hold guardianship rights and have been approved to access the data. This article describes the development of AGDR from both cultural and technical perspectives and outlines its operational processes.
MOLECULAR ECOLOGY RESOURCES
(2023)
Review
Plant Sciences
Christopher E. Cornwall, Wendy A. Nelson, J. David Aguirre, Caitlin O. Blain, Lucy Coyle, Roberta D'Archino, Matthew J. Desmond, Christopher D. Hepburn, Libby Liggins, Nick T. Shears, Mads S. Thomsen
Summary: The impacts of global climate change on New Zealand's seaweed ecosystems, including increasing marine heatwaves, coastal darkening, and ocean acidification, have been observed. These impacts have already led to negative effects on canopy forming brown algae and are predicted to cause poleward range shifts and reduced growth rates of seaweed species. The interaction between global climate change and local stressors, such as overfishing, will determine the future of New Zealand's seaweed ecosystems.
NEW ZEALAND JOURNAL OF BOTANY
(2023)
Article
Biochemistry & Molecular Biology
Cynthia Riginos, Marlene Jahnke
Summary: Comparative methods are crucial for understanding biodiversity distribution, yet current research primarily focuses on single species. In this study, Zbinden et al. utilized landscape genetics to investigate the landscape genomics of 31 fish species in the White River Basin, revealing the significant impact of stream hierarchy on fish population structure. These findings provide empirical evidence for conservation and fisheries management.