26 papers · ranked by Valyu relevance
Maria Juliana Rodriguez-Cubillos, Tomasz Zieliński, Jason R. Swedlow, T. Ian Simpson + 1 more
Ensuring the availability and accessibility of research data is fundamental to advancing knowledge, as codified in the FAIR principles (Findable, Accessible, Interoperable, and Reusable). Accurate metadata documentation is indispensable for meeting these principles; however, entries in deposition databases often…
Bablu Kumar, Erika Lorusso, Bruno Fosso, Graziano Pesole
Metagenomics, Metabolomics, and Metaproteomics have significantly advanced our knowledge of microbial communities by providing culture-independent insights into their composition and functional potential. However, a critical challenge in this field is the lack of standard and comprehensive metadata associated with raw…
Julien Voisin, Christophe Guyeux, Jacques M. Bahi
—This document summarizes the experience of Julien Voisin during the 2011 edition of the well-known Google Summer of Code. This project is a first step in the domain of metadata anonymization in Free Software. This article is articulated in three parts. First, a state of the art and a categorization of usual metadata…
Fiona Hak, Camille Marchet, Daniel Gautheret, Mélina Gallopin
High-throughput RNA-sequencing has significantly advanced transcriptomic profiling in on-cology. Millions of RNA-seq datasets have accumulated in public databases such as the Sequence Read Archive-SRA. However, fragmented, ambiguous or missing metadata can severely limit accurate cohort selection, introduce bias and…
Anthony Etuk, Felix Shaw, Alejandra Gonzalez-Beltran, David Johnson + 7 more
Scientific innovation is increasingly reliant on data and computational resources. Much of today’s life science research involves generating, processing, and reusing heterogeneous datasets that are growing exponentially in size. Demand for technical experts (data scientists and bioinformaticians) to process these data…
Rita Kukafka, Gunther Eysenbach, Gq Zhang, Xia Jing + 13 more
Background Metadata are created to describe the corresponding data in a detailed and unambiguous way and is used for various applications in different research areas, for example, data identification and classification. However, a clear definition of metadata is crucial for further use. Unfortunately, extensive…
T. J. Khoo, A. Reinsvold Hall, N. Skidmore, S. Alderweireldt + 21 more
'J. K. Anders' 'C. Burr' 'W. Buttinger' 'P. David' 'L. Gouskos' 'L. Gray' 'S. Hageböck' 'A. Krasznahorkay' 'P. Laycock' 'A. Lister' 'З. Маршалл' 'A. B. Meyer' 'T. Novák' 'S. Rappoccio' 'M. Ritter' 'E. Rodrigues' 'J. Rumsevicius' 'L. Sexton-Kennedy' 'Neale R. Smith' 'G. A. Stewart' 'S. Wertz'] In High Energy Physics…
Indresh Singh, Mehmet Kuscuoglu, Derek M. Harkins, Granger Sutton + 2 more
Background The development of high-throughput sequencing and analysis has accelerated multi-omics studies of thousands of microbial species, metagenomes, and infectious disease pathogens. Omics studies are enabling genotype-phenotype association studies which identify genetic determinants of pathogen virulence and drug…
Spyros Blanas, Suren Byna
Advances in technology and computing hardware are enabling scientists from all areas of science to produce massive amounts of data using large-scale simulations or observational facilities. In this era of data deluge, effective coordination between the data production and the analysis phases hinges on the availability…
Christiana McMahon, Spiros Denaxas
Metadata are critical in epidemiological and public health research. However, a lack of biomedical metadata quality frameworks and limited awareness of the implications of poor quality metadata renders data analyses problematic. In this study, we created and evaluated a novel framework to assess metadata quality of…
Mustafa Alshawaqfeh, Salahelden Rababah, Abdullah Hayajneh, Ammar Gharaibeh + 1 more
'Ammar Gharaibeh' 'Erchin Serpedin'] Background Many metagenomic studies have linked the imbalance in microbial abundance profiles to a wide range of diseases. These studies suggest utilizing the microbial abundance profiles as potential markers for metagenomic-associated conditions. Due to the inevitable importance of…
Nathan C. Sheffield, Nathan J. LeRoy, Oleksandr Khoroshevskyi
The genomic data deluge has led to challenges with sharing and integrating genomic data. While substantial effort has been devoted to making genomics data easier to share, one challenge that has received little attention is the related goal of sharing genomic metadata, or attributes of biological samples. Genomic…
Shawn Jones, Valentina Neblitt-Jones, Michele C. Weigle, Martin Klein + 1 more
'Martin Klein' 'Michael L. Nelson'] Abstract—In a perfect world, all articles consistently contain sufficient metadata to describe the resource. We know this is not the reality, so we are motivated to investigate the evolution of the metadata that is present when authors and publishers supply their own. Because…
Ángel Gálvez-Merchán, Kyung Hoi (Joseph) Min, Lior Pachter, A. Sina Booeshaghi
We present a command-line tool, called ffq, for querying metadata from genomic databases.
Christian Lovis, Dennis Kadioglu, Holger Storf, Amanda Blatch-Jones + 5 more
Background In the field of medicine and medical informatics, the importance of comprehensive metadata has long been recognized, and the composition of metadata has become its own field of profession and research. To ensure sustainable and meaningful metadata are maintained, standards and guidelines such as the FAIR…
Pietro Franceschi, Roman Mylonas, Nir Shahaf, Matthias Scholz + 7 more
'Panagiotis Arapitsas' 'Domenico Masuero' 'Georg Weingart' 'Silvia Carlin' 'Urska Vrhovsek' 'Fulvio Mattivi' 'Ron Wehrens'] Due to their sensitivity and speed, mass-spectrometry based analytical technologies are widely used to in metabolomics to characterize biological phenomena. To address issues like metadata…
Amir Tosson, Mohammad Reza, Christian Gutt
A Case Study of X-Ray Photon Correlation Spectroscopy Authors: ['Amir Tosson' 'Mohammad Reza' 'Christian Gutt'] Abstract—Metadata is one of the most important aspects for advancing data management practices within all research communities. Definitions and schemes of metadata are inter alia of particular significance in…
Renato Liguori, Michael Huttner, Fulvia Ferrazzi
Next-generation sequencing (NGS) projects generate increasingly complex metadata that are critical for reproducibility, interoperability, and compliance with FAIR principles. Nevertheless, metadata curation in multi-institutional settings often still relies on spreadsheets, manual data entry and curation, as well as…
Fabien Campagne, William ER Digan, Manuele Simi
Data analysis tools have become essential to the study of biology. Tools available today were constructed with layers of technology developed over decades. Here, we explain how some of the principles used to develop this technology are sub-optimal for the construction of data analysis tools for biologists. In contrast…
Gorm E. Shackelford, Philip A. Martin, Amelia S. C. Hood, Alec P. Christie + 2 more
Meta-analysis is often used to make generalizations across all available evidence at the global scale. But how can these global generalizations be used for evidence-based decision making at the local scale, if only the local evidence is perceived to be relevant to a local decision? We show how an interactive method of…
Eftychia Eva Kontou, Axel Walter, Oliver Alka, Julianus Pfeuffer + 5 more
Metabolomics experiments generate highly complex datasets, which are time and work-intensive, sometimes even error-prone if inspected manually. Therefore, new methods for automated, fast, reproducible, and accurate data processing and dereplication are required. Here, we present UmetaFlow, a computational workflow for…
Authors not listed
In drug discovery, metabolite identification data is used to identify metabolic soft spots in research molecules to facilitate reduced metabolism in subsequently designed compounds. In addition, knowledge about exact metabolite structures enables the assessment of risks associated with active, reactive, or toxic…
Authors not listed
Untargeted metabolomics is a powerful approach for exploring the chemical diversity and dynamics of biological systems. However, the types of questions that can be addressed depend not only on experimental design but also on the data processing and analysis workflows employed, many of which require advanced…
Mahnoor Zulfiqar, Michael R. Crusoe, Birgitta König-Ries, Christoph Steinbeck + 2 more
Scientific workflows facilitate the automation of data analysis tasks by integrating various software and tools executed in a particular order. To enable transparency and reusability in workflows, it is essential to implement the FAIR principles. Here, we describe our experiences implementing the FAIR principles for…
Authors not listed
Metabolomics studies require complex data processing pipelines to ensure data quality and extract meaningful biological insights. GetFeatistics is an R-package developed to streamline the elaboration and statistical analysis of metabolomics data. For targeted analyses, the package enables calibration curve-based…
Matthew Lewis, Elena Chekmeneva, Stephane Camuzeaux, Caroline Sands + 11 more
Metabolomics utilising liquid chromatography mass spectrometry (LC-MS) offers biomedical researchers a powerful means of assessing and comparing human phenotypes via measurement of the metabolome in biological samples. Platforms for LC-MS-based global profiling quantify hundreds or thousands of small molecule…