Research Data Management Practices

Building an open infrastructure for molecular neuroimaging: standards and tools from the OpenNeuroPET initiative

The paper describes the OpenNeuroPET initiative, which develops standards and open-source tools to standardize and share PET neuroimaging data, enhancing reproducibility and collaboration.

10 recommendations for strengthening citizen science for improved societal and ecological outcomes: A co-produced analysis of challenges and opportunities in the 21st century

Co-produced analysis of 46 survey responses and nine STARDIT case studies identifies eleven core challenges in citizen science and formulates 10 recommendations for infrastructure, FAIR data, and contributor support.

IDR searcher: a search engine solution for public image resource

The paper introduces IDR searcher, an open-source search engine for public bioimaging resources, aiming to improve dataset discovery and address disparities in accessing quality datasets.

bMINTY: Enabling Reproducible Management of High-Throughput Sequencing Analysis Results and their Metadata

bMINTY provides a structured, portable framework for managing post-alignment sequencing data and metadata to enhance reproducibility and reuse of scientific findings.

Persistent hindrances to data re-use in single-cell genomics

The paper assesses challenges in reusing scRNA-seq data from GEO, finding that only ~40% provide usable processed data and <10% include cell-type annotations.

EcoKMER: One-stop shop for spatio-temporal metagenomic exploration using DataFed

An R-Shiny app built on DataFed lets researchers filter metagenomic sample metadata by location, date and environmental variables, then download only matching sequence files via Globus.

Funders' expectations for open science in cardiovascular research: A Scoping review of the largest cardiovascular research funders

This study reviews open science expectations of cardiovascular research funders, finding common mandates for data sharing and open access but inconsistent monitoring and support.

Major Update and Improved Validation Functionality in the mwtab Python Library and the Metabolomics Workbench File Status Website

The paper updates the mwtab Python library and mwFileStatusWebsite to improve validation and support growing metabolomics datasets in the Metabolomics Workbench.

The CFDE Workbench: Integrating Metadata and Processed Data from Common Fund Programs

The CFDE Workbench integrates metadata and processed data from Common Fund programs to enable FAIR and AI-ready cross-program knowledge discovery.

Large-scale Manual Curation and Harmonization of Metadata from Metagenomic and Cancer Genomic Repositories: Challenges and Solutions

The paper curates and harmonizes metadata from metagenomic and cancer genomic repositories to improve data reusability and cross-study integration.

Enhanced semantic classification of microbiome sample origins using Large Language Models (LLMs)

This paper uses large language models to automate the annotation of microbiome sequencing records, achieving better performance than a keyword-based approach.

Facilitating analysis of open neurophysiology data on the DANDI Archive using large language model tools

This paper introduces an AI-powered chat assistant and notebook generator to facilitate reuse of open neurophysiology data from the DANDI Archive.

DeltaBreed: A BrAPI-centric breeding data information system

DeltaBreed is a breeding data management system that integrates with BrAPI-compliant applications and provides interoperability test cases and future development plans.

A roadmap for fair reuse of public microbiome data

The paper proposes a roadmap for fair reuse of public microbiome data by introducing a Data Reuse Information tag (DRI) to facilitate communication between data creators and consumers.

The GSA Family in 2025: A Broadened Sharing Platform for Multi-Omics and Multimodal Data

The paper introduces the GSA Family, a platform for sharing multi-omics and multimodal data, with expanded databases and improved features.

Tier-based standards for FAIR sequence data and metadata sharing in microbiome research

This paper proposes tiered badges and an evaluation tool to assess data sharing compliance in microbiome research and finds that nearly half of publications fail to meet minimum sequence data availability standards.

The Rise of Open Data Practices Among Bioscientists at the University of Edinburgh

This study tracks the increase in open data practices in biosciences at the University of Edinburgh from 2014 to 2023, showing a rise in data-sharing completeness and FAIRness.

Eye-Tracking-BIDS: the Brain Imaging Data Structure extended to gaze position and pupil data

This paper extends the BIDS standard to include eye-tracking data and metadata, improving organization and transparency for gaze position and pupil recordings.

From Ice Cores to Dinosaurs: Physical Collections Managers' Research Data Curation Perceptions and Behaviors

This study examines how physical collection managers perceive and manage data curation across disciplines to improve reusability and discoverability of physical collections.

The FAIR Data Point Populator: collaborative FAIRification and population of FAIR Data Points

The paper introduces a tool for FAIR metadata creation that improves collaboration, schema adherence, and scalability compared to existing tools.

Capacity building needed to reap the benefits of access to biodiversity collections

This study analyzes biodiversity specimen data from the Caribbean to show that digitization benefits mainly the Global North, highlighting the need for capacity building in the Global South.

Ozboneviz: An Australian Precedent in FAIR 3D Imagery and Extended Biodiversity Collections

Ozboneviz provides FAIR 3D imagery of Australasian vertebrate skeletons to enhance research and public engagement with biodiversity collections.

Sharing Data from the Human Tumor Atlas Network through Standards, Infrastructure, and Community Engagement

The paper describes how the Human Tumor Atlas Network shares data through standards, infrastructure, and community engagement, making datasets accessible via multiple platforms.

mvh: an R tool to assemble and organize virtual herbaria from openly available specimen images

The paper introduces an R package called mvh for assembling and organizing virtual herbaria from openly available specimen images, achieving a 99% success rate in downloading images.

Application of a new data management system to the study ofthe gut microbiome of children who are small for theirgestational age

The paper introduces a data management system for gut microbiome studies in children small for gestational age, enhancing quality control and data sharing through a web interface.

COVID-19-related research data availability and quality according to the FAIR principles: A meta-research study

This study evaluates FAIRness of COVID-19 research data by analyzing 5,700 open-access articles and their repositories, finding significant variation in compliance with FAIR principles.

Identifying genomic data use with the Data Citation Explorer

The paper introduces the Data Citation Explorer, an automated tool that identifies genomic data use in publications, improving metadata quality and data sharing.

Ensemble automated approaches for producing high quality herbarium digital records

The paper develops an ensemble method combining rule-based and large language model approaches to improve the accuracy of converting OCR text from herbarium labels into standardized digital data records.

Contextualising samples: Supporting reference genomes of European biodiversity through sample and associated metadata collection

The paper describes the ERGA Pilot project's efforts to establish standards for sample collection and metadata gathering to support reference genome generation for European biodiversity.

Setting up an institutional OMERO environment for bioimage data: perspectives from both facility staff and users

The paper describes the implementation of OMERO for bioimage data management at a research facility, highlighting challenges and strategies for compliance with FAIR principles.