Research Data Management Practices

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.

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

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

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 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.

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

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.

The paper describes the development of a metadata federation system for NIH Common Fund data to improve discoverability without data movement.

NDI provides a platform-independent data interface and database to standardize and share neuroscience data across labs and analyses.

The paper curates a collection of skin microbiome datasets with enriched metadata and provides a framework for data retrieval and analysis.

plantR provides an R package and workflow to manage and standardize species records from biological collections, improving data quality and usability across taxonomy and ecology.

The paper introduces PEP, a metadata standard for biological projects, to improve data portability and tool compatibility across bioinformatics workflows.

The paper links nucleotide sequence data from the European Nucleotide Archive to scientific publications, enabling analysis of global scientific knowledge trends and data provenance.

This paper proposes tiered metadata specifications for light microscopy to improve data quality, reproducibility, and interoperability, inspired by genomic standards like Encode.

The paper introduces HED for event annotation in neuroimaging data, demonstrating its application to a BIDS dataset and providing best practices for event design and annotation.

The paper introduces an R Shiny application for analyzing circadian behavior sequence data from mice, producing behavior variables and promoting FAIR data practices.

KnowMore automates knowledge discovery across FAIR SPARC datasets by integrating data science methods and machine learning to generate visualizations for comparative analysis.

OpenNeuro is an open archive for sharing brain imaging data following FAIR principles, hosting over 600 datasets from 20,000 participants across species and modalities, with over 150 publications citing its data.

The paper introduces a cloud-based platform called ORCESTRA for reproducible processing and sharing of multimodal biomedical data in a FAIR manner.

The paper describes a FAIR-compliant file format for neuroanatomical structure modeling and its updates to support data reuse and interoperability.

The paper introduces the ISA API, a Python library for handling ISA-Tab and ISA-JSON metadata formats, enabling programmatic manipulation and interoperability in life science experiments.

The paper introduces InsectBrainDatabase (IBdb), a platform for managing and sharing insect neuroanatomical and functional data, enabling cross-species comparisons and data reuse.

MICHA is a pipeline that FAIRifies chemosensitivity assays by automatically annotating compounds, samples, reagents, and data processing methods, enabling interoperable and reusable drug screening data.

The paper introduces the GSA family of repositories to manage explosive growth and diverse data types in genomic data archiving.

The paper examines gene name errors in supplementary files and finds they persist despite prior warnings, with new software identifying higher error rates.

FlywheelTools provides software for reproducible data curation and manipulation on the Flywheel platform, addressing challenges in converting neuroimaging data to BIDS format.

The paper introduces a decoupled, modular curation architecture for data platforms, enabling flexible and scriptable workflows without modifying existing infrastructure.

ICSCB provides a standardized portal to search over 16,000 stem cell lines from global resources, enabling disease-specific cell line collection.

The paper curates and standardizes metadata for ancient metagenomic samples to improve data retrieval and interoperability.

The paper presents a computational workflow to assess FAIRness of datasets in life sciences using two real use cases and proposes a FAIR balloon plot for visualization.