Research Data Management Practices

A Pilot Evaluation of Open-Weight Large Language Models for Screening RNA-seq Metadata in Public Databases

The paper evaluates open-weight large language models for screening RNA-seq metadata in public databases, finding they significantly improve classification performance over keyword searches.

Non-Invasive Brain Stimulation Data Analysis Structure (NIBS-DAS): A Template for the Layout, Management, and Analysis of NIBS Data

The paper introduces NIBS-DAS, a template for structuring, managing, and analyzing NIBS data to improve data sharing and standardization.

Quantifying data reuse in proteomics using PRIDE downloads statistics and a semi-supervised LLM-based framework

The paper analyzes proteomics dataset reuse using PRIDE download statistics and a semi-supervised LLM-based framework to classify download sources.

The Common Fund Data Ecosystem (CFDE)

The paper describes the Common Fund Data Ecosystem (CFDE), which integrates NIH Common Fund data resources to enable discovery, analysis, and collaboration across heterogeneous datasets.

Introducing the digital PCR data essentials standard to harmonize data structure for clinical and research use

The paper introduces the Digital PCR Data Essentials Standard (DDES) to standardize data structure for dPCR, improving interoperability and reproducibility across platforms and applications.

BiOS: An Open-Source Framework for the Integration of Heterogeneous Biodiversity Data

BiOS integrates heterogeneous biodiversity data through an open-source framework, enhancing interoperability and accessibility for conservation efforts.

Descriptron-GBIF Annotator: A browser-based platform for crowdsourced morphological annotation of biodiversity images to help accelerate morphology based biodiversity data

The paper introduces a browser-based platform for crowdsourced morphological annotation of biodiversity images, enabling scalable data collection and integration with ontologies and standardized formats.

FRED: a universal tool to generate FAIR metadata for omics experiments

FRED generates FAIR-compliant metadata for omics experiments, enabling structured data management and interoperability.

Bioimaging Data Management Workflow for Plasma Medicine

The paper presents a data management workflow for plasma medicine bioimaging to improve reproducibility and data reuse by integrating metadata with imaging data.

ro-crate-rs: Development of a Lightweight RO-Crate Rust Library for Automated Synthetic Biology

This paper introduces ro-crate-rs, a Rust library for creating RO-Crates to manage synthetic biology data, enabling FAIR compliance and reproducibility in automated workflows.

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.

Systematic Survey of Public Datasets for Behavioral Research in Invertebrate Models: Toward FAIR and Standardized Data Sharing

The paper surveys public behavioral datasets for invertebrate models, evaluates their FAIR compliance, and provides guidance for standardized data sharing and AI benchmarking.

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.

μGrowthDB: querying, visualizing, and sharing microbial growth curve data

GrowthDB is a repository for microbial growth curve data that allows querying, visualization, and sharing of growth and metabolite profiles from monocultures and communities.

Sustainability During Instability: Long-Lived Life Science Databases and Science Funding Outlook in the United States

This paper examines the sustainability of long-standing life science databases in the U.S. under changing funding conditions and identifies potential consequences of their closure.

Analyzing the Naming Conventions of Life Science Data Resources to Inform Human and Computational Findability

This study evaluates naming conventions of life science data resources to assess their impact on findability, revealing suboptimal practices and opaqueness in common names.

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.

Advancing FAIR Data Management through AI-Assisted Curation of Morphological Data Matrices

This paper introduces an AI tool for curating morphological data into standardized formats, improving data quality and FAIRness.

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.