Research Data Management Practices

'PhyTaxR', a set of phytoplankton taxonomic curation tools in R

PhyTaxR provides an R package for harmonizing phytoplankton taxonomic records by resolving inconsistencies and retaining uncertainty through automated and semi-automated workflows.

Community needs for FAIR pathogen data: a cross-sectional survey of infectious-disease researchers and educators

This paper surveys infectious-disease stakeholders to identify barriers to FAIR pathogen data and prioritize training and infrastructure needs.

A data model for longitudinal multi-modal biomedical cohorts

The paper introduces a data model for longitudinal multimodal biomedical cohorts, demonstrating its ability to manage heterogeneous data across multiple modalities and study visits.

A semi-automated tool for improving Assessments and Lab Tests data annotation in ImmPort

The paper introduces a semi-automated tool to improve data annotation in ImmPort by streamlining template population and ensuring formatting consistency.

From Public Archive to Reusable Resource: Characterizing Gut Microbiome Metadata in the NCBI SRA

The paper analyzes gut microbiome metadata from the NCBI SRA to assess its structure, completeness, and reusability for large-scale studies and AI model development.

A Standardized Methodology for FAIRness Assessment and Multi-Dimensional Scoring in Agrosystem Research Data Infrastructures

This paper introduces a standardized framework for assessing FAIRness in agrosystem research data infrastructures using a multi-dimensional scoring system.

The second life of collection - how the scientific value of natural history holdings can be deliberately increased

The paper proposes a framework to increase the scientific value of natural history collections through curated actions and a dynamic analysis of their multidimensional value.

The Shape of Biological Metadata: Measuring Repository Richness with Entity-Based NLP Metrics

The paper quantifies metadata richness in three biological repositories using NLP metrics, finding differences in word count, information density, and entity consistency across repositories.

The StrainDiscoveryDatabase: an open framework for standardized microbial strain data

The paper introduces the StrainDiscoveryDatabase (SDD), a unified microbial strain dataset that resolves data fragmentation and synonymy to support AI-driven bioindustrial applications.

Making Accelerating Medicines Partnership Data Findable and Interoperable through a Common Data Model: Extending OMOP for Multi-Source Multimodal Data

The paper extends the OMOP Common Data Model to support multimodal data integration across AMP projects by adding extension tables and a CDE Registry.

SeqDesk: a sequencing-facility management system for standards-compliant and FAIR (meta)data submission

SeqDesk is a sequencing-facility management system that ensures FAIR-compliant metadata submission by integrating standards-compliant metadata capture into routine operations.

A collaborative submission model for building high-quality data resources at scale through partnership: lessons from single-cell genomics

The paper describes a collaborative submission model for building high-quality single-cell genomics data resources, emphasizing partnership between contributors and curators to improve metadata quality and resource scalability.

Nipoppy: A framework for standardizing neuroimaging studies to facilitate international derived-data sharing

Nipoppy standardizes neuroimaging data workflows to enable reproducible and comparable multi-center data sharing.

A Modular, AI-assisted Digitization Toolkit for Resource-Constrained Herbaria: A Case Study from Zimbabwe

This paper presents an AI-assisted toolkit for digitizing herbarium collections in resource-constrained settings, showing it reduces time and cost compared to manual methods.

COSMOS: A FAIR-aligned infrastructure for clinical trial data validation, warehousing, and interactive discovery

COSMOS provides an open-source infrastructure for validating, storing, and querying clinical trial data in Secure Data Environments.

Who Funds Open Data Sharing? Analysis of data availability statements in biomedical publications

The paper analyzes data availability statements in biomedical publications to assess open data sharing rates across funders, journals, and institutions.

The Portable Microhaplotype Object and Tools

The paper introduces a standardized format for storing phased targeted sequencing data and provides tools to create and manipulate this format.

Metadata Collector: An Open-Source Platform for Standardized Metadata Management in Multi Centre Sequencing Projects

Metadata Collector is an open-source platform designed to standardize metadata management in multi-centre sequencing projects, ensuring FAIR-aligned and reproducible metadata across distributed research groups.

The HuBMAP Framework for Advancing Data FAIRness

The paper describes the HuBMAP framework for creating FAIR data through standardized metadata reporting across diverse assays and institutions.

TaxonMatch: taxonomic integration and tree construction from heterogeneous biological databases

TaxonMatch integrates taxonomic data from heterogeneous databases by reconciling synonyms and resolving inconsistencies to create unified taxonomic structures.

Elab2ARC: A Browser-Based Workspace for Converting Free-Text Protocols into rich FAIR digital objects

elab2ARC converts ELN records into FAIR-compliant research objects, automating metadata extraction and structured data organization.

First Survey of Publicly Available Metagenomic Sequencing Data Across 24 Middle Eastern and North African Countries: The MENA Microbiome Database

The paper compiles and harmonizes metagenomic data from 24 MENA countries, revealing geographic sampling biases and country-level ecological patterns in microbiomes.

Revealing the Hidden Landscape of Public Metabolomics Data Reuse in MetaboLights

This study characterizes the reuse of MetaboLights metabolomics datasets in the literature, finding most reuse is for method development and highlighting issues with inconsistent citation.

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.