Research Data Management Practices

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.

The FAIRSCAPE AI-readiness Framework for Biomedical Research

The paper introduces FAIRSCAPE, a framework for packaging biomedical datasets with metadata to enhance AI-readiness, explainability, and FAIR compliance.

Integrated Database of Force-Field Parameters, Experimental Measurements and Molecular Dynamics Simulations

The paper introduces IDA, a database for storing and integrating MD simulation data, force fields, and experimental measurements to enhance data reuse and FAIR compliance.

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.

AI-readiness criteria for biomedical data

The paper defines AI-readiness criteria for biomedical data, encompassing seven dimensions, and evaluates them across flagship datasets to ensure ethical and explainable AI practices.

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.

Data science and its future in large neuroscience collaborations.

The paper surveys data science practices in neuroscience collaborations to identify challenges and propose improvements in data management and training.

FAIR assessment of MINERVA as an opportunity to foster open science and scientific crowdsourcing in systems biomedicine

The paper assesses the FAIRness of the MINERVA platform using the RDA FAIR Data Maturity Model, focusing on the Parkinson's Disease Map and the COVID-19 Disease Map.

traits.build: a data model, workflow and R package for building harmonised ecological trait databases

The paper introduces a data model, workflow, and R package for building harmonised ecological trait databases that adhere to FAIR principles.

From spreadsheet lab data templates to knowledge graphs: A FAIR data journey in the domain of AMR research

This paper describes a journey towards implementing FAIR data practices in antimicrobial resistance research, transitioning from spreadsheet-based data to a knowledge graph framework.

Improving data archiving practices in ancient genomics

This paper evaluates data archiving practices in ancient genomics and identifies gaps, recommending improvements to ensure data reusability and replication.

A platform for lab management, note-keeping and automation

The paper describes a no-code lab management platform using Airtable for integrated sample, procedure, and data management with custom automations.

Accelerating the continuous community sharing of digital neuromorphology data

The paper describes improvements to NeuroMorpho.Org, a digital neuromorphology database, to accelerate data sharing and processing, reducing time from data identification to public release by 63.7%.

Maggot: An ecosystem for sharing metadata within the web of FAIR Data

Maggot is a tool that generates and manages metadata for datasets to support FAIR data sharing and integration within collaborative environments.

Poseidon - A framework for archaeogenetic human genotype data management

Poseidon provides a framework for managing archaeogenetic data to ensure FAIR principles through open, interoperable tools and archives.

FAIR Header Reference genome: A TRUSTworthy standard

The paper introduces FHR, a metadata standard for reference genome data to improve interoperability and data provenance tracking across platforms.

KoNA: Korean Nucleotide Archive as a New Data Repository for Nucleotide Sequence Data

The paper introduces KoNA, a national nucleotide sequence repository in Korea, and describes its infrastructure, data collection, and integration with analysis tools.

From Planning Stage To FAIR Data: A Practical Metadatasheet For Biomedical Scientists

This paper introduces Metadatasheet, a metadata standard designed to improve data management by aligning with the data-lifecycle and enabling structured metadata recording in Microsoft Excel.

PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata

PEPhub is a database and web interface for sharing, editing, and validating biological sample metadata, enabling fast semantic search and interoperability.

OMEinfo: Global Geographic Metadata for -omics Experiments

OMEinfo retrieves and standardizes geographical metadata for -omics experiments, enabling reproducible and consistent analysis of location-based data.

Unrestricted versus Regulated Open Data Governance: A Bibliometric Comparison of SARS-CoV-2 Nucleotide Sequence Databases

This study compares unrestricted and regulated data governance models for SARS-CoV-2 sequence databases using bibliometric analysis to assess their impact on global collaboration and data reuse.

Keys to the cabinet: unlocking biodiversity data in public entomology collections

The paper analyzes digitized Odonata collections to explore geographical distribution and species composition, highlighting the importance of digitization for conservation and climate change research.

A data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence (MISIP)

The paper introduces a data standard (MISIP) to improve reproducibility and reuse of stable isotope probing (SIP) sequencing data by defining essential metadata fields.

Arctos: Community-driven innovations for managing biodiversity and cultural collections

The paper introduces Arctos, a community-driven collection management system for biodiversity and cultural data, emphasizing its role in enabling research, education, and sustainable data governance.

MADAME: a user-friendly bioinformatic tool for data and metadata retrieval in microbiome research

MADAME is a bioinformatic tool that streamlines data and metadata retrieval from public microbiome repositories by allowing users to search by accession codes and generate visual reports.