Research Data Management Practices

SODA: Software to Support the Curation and Sharing of FAIR Autonomic Nervous System Data

SODA is an open-source software that guides researchers in curating and sharing FAIR autonomic nervous system data according to SPARC guidelines.

OBIA: An Open Biomedical Imaging Archive

OBIA is a biomedical imaging archive that stores and provides access to imaging and clinical data from 937 individuals across multiple modalities and anatomical sites.

MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations

The paper indexes and analyzes 250,000 molecular dynamics simulation files to create a search engine prototype for MD data.

The Metabolomics Workbench File Status Website: A Metadata Repository Promoting FAIR Principles of Metabolomics Data

The paper describes a website that validates metabolomics data files in the Metabolomics Workbench and provides a tool for format validation and error detection.

A Template for Translational Bioinformatics: Facilitating Multimodal Data Analyses in Preclinical Models of Neurological Injury

The paper introduces a data framework for managing multimodal preclinical data in neurological injury research, enabling integration and analysis of diverse data types.

MESSES: Software for Transforming Messy Research Datasets into Clean Submissions to Metabolomics Workbench for Public Sharing

MESSES transforms messy research datasets into clean submissions for the Metabolomics Workbench, improving metadata capture and ease of deposition.

Enhancing Collaborative Neuroimaging Research: Introducing COINSTAC Vaults for Federated Analysis and Reproducibility

This paper introduces COINSTAC Vaults to enhance collaborative neuroimaging research through federated analysis and reproducibility by hosting standardized datasets.

Experimental Data Connector (XDC): Integrating the Capture of Experimental Data and Metadata Using Standard Formats and Digital Repositories

The paper introduces XDC, a tool that connects digital repositories for experimental data and metadata using standard formats, enabling reproducible and exchangeable datasets.

Towards Self-Describing and FAIR Bulk Formats for Biomedical Data

The paper introduces a self-describing format for bulk biomedical data called PFB, showing performance improvements over JSON and SQL for data import/export.

Data architecture for a large-scale neuroscience collaboration

The paper describes a modular data architecture for a neuroscience collaboration, enabling data contribution, access, and analysis across multiple labs.

Developing a standardized but extendable framework to increase the findability of infectious disease datasets

The paper develops a metadata schema based on Schema.org to improve the findability of infectious disease datasets and computational tools across repositories.

LISTER: Semi-automatic metadata extraction from annotated experiment documentation in eLabFTW

LISTER automates metadata extraction from eLabFTW experiment documentation to enhance data findability and reusability.

FAIR Data Station for Lightweight Metadata Management & Validation of Omics Studies

The paper introduces FAIR Data Station, a tool for managing and validating metadata in omics studies to support FAIR principles through standardized workflows and metadata export.

SODAR: managing multi-omics study data and metadata

SODAR is a software package that manages multi-omics study data and metadata using a web interface and APIs, supporting the ISA-Tab format and iRODS storage.

CureSCi Metadata Catalog - Making sickle cell studies findable

The paper introduces a metadata catalog to enhance findability of sickle cell disease studies using FAIR principles through curated metadata and search tools.

TemplateFlow: FAIR-sharing of multi-scale, multi-species brain models

TemplateFlow provides a FAIR framework for sharing and managing multi-scale, multi-species brain models to improve reproducibility in neuroimaging.

pISA-tree - a data management framework for life science research projects using a standardised directory tree

pISA-tree organizes life science research data using a standardized directory structure based on the ISA model, enabling metadata generation and integration with bioinformatics pipelines and repositories.

A review of the International Seabed Authority database DeepData: challenges and opportunities in the UN Ocean Decade

The paper reviews the International Seabed Authority's DeepData database, identifying challenges in data quality and FAIRness, and recommends improvements for better integration with global systems.

EGIDExpress: An Interactive Shiny Web App to Visualize and Share Large Biological Datasets

EGIDExpress is a web app that visualizes and shares large EGID datasets, enabling data exploration and hypothesis generation for researchers.

Sharing GWAS summary statistics results in more citations: evidence from the GWAS catalog

This study finds that sharing GWAS summary statistics leads to about 75% more citations, regardless of journal impact factor, encouraging authors to share data in repositories like the GWAS catalog.

Metadata preservation and stewardship for genomic data is possible, but must happen now

The paper quantifies the loss of spatiotemporal metadata in genomic datasets over time and advocates for improved metadata preservation practices.

Curation of BIDS (CuBIDS): a workflow and software package for streamlining reproducible curation of large BIDS datasets

CuBIDS streamlines reproducible curation of large BIDS datasets by validating metadata, managing variability, and preparing data for preprocessing pipelines.

A community driven GWAS summary statistics standard

The paper defines a standard format for GWAS summary statistics to improve data sharing and analysis.

The Neurodata Without Borders ecosystem for neurophysiological data science

The paper describes the Neurodata Without Borders (NWB) ecosystem, which enables FAIR neurophysiological data management and analysis across species and modalities.

Taxonbridge: an R package to create custom taxonomies based on the NCBI and GBIF taxonomies

Taxonbridge merges GBIF and NCBI taxonomies to create consistent, deduplicated custom taxonomies for extant and extinct species.

Overcoming the Reproducibility Crisis - Results of the first Community Survey of the German National Research Data Infrastructure for Neuroscience.

A survey of the German neuroscience community identifies key barriers to reproducible research and outlines strategies for improving research data management.

Open Data Commons for Preclinical Traumatic Brain Injury Research: Empowering Data Sharing and Big Data Analytics

The paper introduces ODC-TBI, a platform for sharing preclinical TBI data, enabling big data analytics and machine learning to address heterogeneity in TBI research.

The LOTUS Initiative for Open Natural Products Research: Knowledge Management through Wikidata

The paper introduces the LOTUS initiative, which curates and shares 750,000+ structure-organism pairs via Wikidata to improve data interoperability and knowledge management in natural products research.

PET-BIDS, an extension to the brain imaging data structure for positron emission tomography

The paper introduces PET-BIDS, an extension of the BIDS standard for PET data, and provides curated datasets and tools for its use.

SPARClink: an interactive tool to visualize the impact of the SPARC program

SPARClink visualizes the impact of SPARC program datasets and publications by tracking their usage in external resources and creating a knowledge graph to demonstrate FAIR data practices' influence.