Article
Chemistry, Multidisciplinary
Ingrid Hasenkopf, Robert Mills-Goodlet, Litty Johnson, Ian Rouse, Mark Geppert, Albert Duschl, Dieter Maier, Vladimir Lobaskin, Iseult Lynch, Martin Himly
Summary: Extensive investigation and characterisation of nanoparticle-protein conjugates are important for assessing potential hazards and predicting biological effects. The development of in silico modelling tools can provide alternative approaches and accelerate risk assessment. This study validates emerging in silico protein corona models and provides recommendations for improvement.
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
Cell Biology
Isabel Kemmer, Antje Keppler, Beatriz Serrano-Solano, Arina Rybina, Bugra Oezdemir, Johanna Bischof, Ayoub El Ghadraoui, John E. Eriksson, Aastha Mathur
Summary: Bioimaging is facing challenges in handling, analyzing, and managing the increasingly complex datasets due to the rapid development of microscopy technologies. Efforts and solutions are being developed by the microscopy community to address these challenges, and collaborations within the microscopy ecosystem, as well as research infrastructures like Euro-BioImaging, are shaping the field.
HISTOCHEMISTRY AND CELL BIOLOGY
(2023)
Article
Physics, Multidisciplinary
Thomas E. Exner, Anastasios G. Papadiamantis, Georgia Melagraki, Jaleesia D. Amos, Nathan Bossa, Georgios P. Gakis, Costas A. Charitidis, Geert Cornelis, Anna L. Costa, Philip Doganis, Lucian Farcal, Steffi Friedrichs, Irini Furxhi, Frederick C. Klaessig, Vladimir Lobaskin, Dieter Maier, John Rumble, Haralambos Sarimveis, Blanca Suarez-Merino, Socorro Vazquez, Mark R. Wiesner, Antreas Afantitis, Iseult Lynch
Summary: This article reviews the current state-of-the-art data management solutions in nanosafety research, highlighting the limitations of approaches that are too focused on specific projects or data repositories. The authors propose the development of a functional FAIRification ecosystem that addresses the needs of both data generators and users, by integrating and generalizing unique features from existing tools and approaches.
FRONTIERS IN PHYSICS
(2023)
Article
Biochemical Research Methods
Christian D. D. Powell, Hunter N. B. Moseley
Summary: An updated version of the mwtab Python package for accessing the Metabolomics Workbench data repository was released in 2021. It includes validation facilities to detect and catalog file inconsistencies and errors in publicly available datasets. A website, the MetabolomicsWB File Status, was developed to provide continuous validation and interface for these issues.
BMC BIOINFORMATICS
(2023)
Article
Environmental Sciences
Jennifer M. Bayer, Rebecca A. Scully, Erin K. Dlabola, Jennifer L. Courtwright, Christine L. Hirsch, David Hockman-Wert, Scott W. Miller, Brett B. Roper, W. Carl Saunders, Marcia N. Snyder
Summary: Data resulting from environmental monitoring programs are valuable assets for various users. Sharing well-documented data and metadata allows for research beyond initial program intentions.
ENVIRONMENTAL MONITORING AND ASSESSMENT
(2023)
Article
Computer Science, Information Systems
Lei Zhang, Ke Pang, Jiangtao Xu, Bingxin Niu
Summary: XYJSON is a data interaction transformation model that can handle all data using standard SQL syntax and JSON document data. It solves the problem of increased development workload and difficulty caused by using different control methods for different types of databases under cloud hybrid storage, by establishing a general conversion model between relational and NoSQL data.
JOURNAL OF CLOUD COMPUTING-ADVANCES SYSTEMS AND APPLICATIONS
(2022)
Article
Mathematics
Cristina Georgiana Calancea, Lenuta Alboaie
Summary: Sharing data along the economic supply/demand chain is crucial for improving the performance of a digitized business sector. Designing automatic mechanisms for structured data exchange and implementing FAIR principles are necessary for ensuring the proper development of B2B processes in a regulated environment.
Article
Ecology
Sarah Wiechers, Lara Marie Koesters, Dietmar Quandt, Thomas Borsch, Susann Wicke, Kai Frank Mueller
Summary: DNA barcoding is a useful tool for rapid species identification by comparing DNA sequences to a reference database. BarKeeper is a flexible and open-source tool that supports barcoding projects and phylogenetic studies by managing large datasets of raw sequences and associated metadata. It offers various features for data collection, editing, quality checking, and data analysis, making it a valuable resource for efficient collaborative workflows. Evaluation: 8 out of 10.
METHODS IN ECOLOGY AND EVOLUTION
(2023)
Article
Genetics & Heredity
Peter W. Harrison, Alexey Sokolov, Akshatha Nayak, Jun Fan, Daniel Zerbino, Guy Cochrane, Paul Flicek
Summary: The FAANG project aims to create high-quality functional annotation of animal genomes globally, supporting research and enhancing understanding of functional elements. It provides resources to improve farmed animal production, disease resistance, and genetic diversity in both terrestrial and aquatic animal agriculture communities.
FRONTIERS IN GENETICS
(2021)
Article
Computer Science, Information Systems
Francisco Delgado, Jose R. Hilera, Raul Ruggia, Salvador Oton, Hector R. Amado-Salvatierra
Summary: This article presents a new metadata specification for international social security exchanges called Exchange Social Security Information Metadata (ESSIM), based on Dublin Core elements. The proposal aims to ensure interoperability between social security institutions from different countries, strengthening the protection of social security rights for mobile workers and improving cross-border communication between social security institutions. The goal is to include this specification in ICT Guidelines developed by the International Social Security Association to facilitate future adoption as an international standard.
JOURNAL OF INFORMATION SCIENCE
(2021)
Article
Public, Environmental & Occupational Health
Yin Jin, Wang Junren, Jiang Jingwen, Sun Yajing, Chen Xi, Qin Ke
Summary: This paper conducts an in-depth research on the construction method and application of breast cancer-specific database system based on full data lifecycle, aiming to support the application of data in clinical practices, scientific research, and teaching, and fully tap the value of medical big data.
FRONTIERS IN PUBLIC HEALTH
(2021)
Proceedings Paper
Energy & Fuels
Arafath Nihar, Alan J. Curran, Ahmad M. Karimi, Jennifer L. Braid, Laura S. Bruckman, Mehmet Koyuturk, Yinghui Wu, Roger H. French
Summary: The study applies FAIR principles to photovoltaic time series data to increase their reusability in the research community. Key requirements for a FAIRified dataset include a defined data format and accessible metadata. A data model separating photovoltaic data and metadata, using JSON-LD for registration, along with secure APIs for data access, ensures long-term scalability and maintainability.
2021 IEEE 48TH PHOTOVOLTAIC SPECIALISTS CONFERENCE (PVSC)
(2021)
Article
Computer Science, Information Systems
Luiz Olavo Bonino da Silva Santos, Kees Burger, Rajaram Kaliyaperumal, Mark D. D. Wilkinson
Summary: This paper presents and discusses the FAIR Data Point (FDP), a software architecture that aims to define a common approach to publishing semantically-rich and machine-actionable metadata according to the FAIR principles. The FDP includes core components and features, an approach to metadata provision, criteria for evaluating adherence to FDP specifications, and a service for registering, indexing, and searching for metadata content of available FDPs.
Article
Biochemistry & Molecular Biology
Molly A. Bogue, Robyn L. Ball, Vivek M. Philip, David O. Walton, Matthew H. Dunn, Georgi Kolishovski, Anna Lamoureux, Matthew Gerring, Hongping Liang, Jake Emerson, Tim Stearns, Hao He, Gaurab Mukherjee, John Bluis, Sejal Desai, Beth Sundberg, Beena Kadakkuzha, Govindarajan Kunde-Ramamoorthy, Elissa J. Chesler
Summary: The Mouse Phenome Database (MPD) is a biomedical data repository supported by the US National Institutes of Health, which collects and manages phenotype and genotype data from mouse experiments worldwide. With rich metadata and a suite of analysis tools, MPD enables users to analyze and visualize these data within and across studies and populations.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Noe Sturm, Andreas Mayr, Thanh Le Van, Vladimir Chupakhin, Hugo Ceulemans, Joerg Wegner, Jose-Felipe Golib-Dzib, Nina Jeliazkova, Yves Vandriessche, Stanislav Bohm, Vojtech Cima, Jan Martinovic, Nigel Greene, Tom Vander Aa, Thomas J. Ashby, Sepp Hochreiter, Ola Engkvist, Guenter Klambauer, Hongming Chen
JOURNAL OF CHEMINFORMATICS
(2020)
Editorial Material
Chemistry, Multidisciplinary
Rajarshi Guha, Egon Willighagen, Barbara Zdrazil, Nina Jeliazkova
JOURNAL OF CHEMINFORMATICS
(2021)
Article
Chemistry, Medicinal
Nikolay Kochev, Nina Jeliazkova, Gergana Tancheva
Summary: SLN is a comprehensive linear notation for representing chemical objects and can support challenging tasks in cheminformatics research. Ambit-SLN is an open-source software library developed for processing chemical objects using SLN, including functionalities for substructure matching and conversion to other chemical formats. This tool can also be used for generating combinatorial structure sets.
MOLECULAR INFORMATICS
(2021)
Article
Nanoscience & Nanotechnology
Nina Jeliazkova, Margarita D. Apostolova, Cristina Andreoli, Flavia Barone, Andrew Barrick, Chiara Battistelli, Cecilia Bossa, Alina Botea-Petcu, Amelie Chatel, Isabella De Angelis, Maria Dusinska, Naouale El Yamani, Daniela Gheorghe, Anna Giusti, Paloma Gomez-Fernandez, Roland Grafstrom, Maciej Gromelski, Nicklas Raun Jacobsen, Vedrin Jeliazkov, Keld Alstrup Jensen, Nikolay Kochev, Pekka Kohonen, Nicolas Manier, Espen Mariussen, Agnieszka Mech, Jose Maria Navas, Vesselina Paskaleva, Aurica Precupas, Tomasz Puzyn, Kirsten Rasmussen, Peter Ritchie, Isabel Rodriguez Llopis, Elise Runden-Pran, Romica Sandu, Neeraj Shandilya, Speranta Tanasescu, Andrea Haase, Penny Nymark
Summary: The proposal of a FAIR-aligned Nanosafety Data Interface aims to improve findability, accessibility, and interoperability of nanosafety data, providing a path towards standardized and optimized use of existing data to promote safe and sustainable nanotechnology.
NATURE NANOTECHNOLOGY
(2021)
Letter
Chemistry, Multidisciplinary
Rajarshi Guha, Nina Jeliazkova, Egon Willighagen, Barbara Zdrazil
JOURNAL OF CHEMINFORMATICS
(2021)
Editorial Material
Nanoscience & Nanotechnology
Roland Grafstrom, Andrea Haase, Pekka Kohonen, Nina Jeliazkova, Penny Nymark
NATURE NANOTECHNOLOGY
(2022)
Review
Nanoscience & Nanotechnology
Ewelina Wyrzykowska, Alicja Mikolajczyk, Iseult Lynch, Nina Jeliazkova, Nikolay Kochev, Haralambos Sarimveis, Philip Doganis, Pantelis Karatzas, Antreas Afantitis, Georgia Melagraki, Angela Serra, Dario Greco, Julia Subbotina, Vladimir Lobaskin, Miguel A. Banares, Eugenia Valsami-Jones, Karolina Jagiello, Tomasz Puzyn
Summary: This Review discusses the importance of a comprehensive system for defining nanomaterial descriptors in enabling a safe-and-sustainable-by-design concept for engineered nanomaterials. The unique nanoscale properties of engineered nanomaterials can pose risks to human health and the environment, making it crucial to design new nanomaterials with safety and sustainability in mind. Physicochemical characteristics, such as chemical composition and size, play a key role in the biological activity of nanomaterials, and nanodescriptors can be used to optimize their functionality and minimize health and environmental hazards. The successful integration of experimental data and computational models is essential for the safe adoption of nanomaterials on a large scale.
NATURE NANOTECHNOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Jeaphianne van Rijn, Antreas Afantitis, Mustafa Culha, Maria Dusinska, Thomas E. Exner, Nina Jeliazkova, Eleonora Marta Longhin, Iseult Lynch, Georgia Melagraki, Penny Nymark, Anastasios G. Papadiamantis, David A. Winkler, Hulya Yilmaz, Egon Willighagen
Summary: Management of nanomaterials and nanosafety data requires a unique identifier for each nanomaterial, which is provided by the European Registry of Materials Identifier. This identifier ensures the linking of internal project documentation with publicly released data and knowledge for specific nanomaterials, and has been applied in H2020-funded nanosafety projects.
JOURNAL OF CHEMINFORMATICS
(2022)
Article
Computer Science, Information Systems
Atanas Terziyski, Stoyan Tenev, Vedrin Jeliazkov, Nina Jeliazkova, Nikolay Kochev