Research Data Management Practices

Factors influencing taxonomic unevenness in scientific research: A mixed-methods case study of non-human primate genomic sequence data generation

This study identifies factors contributing to uneven genomic data generation among non-human primates using quantitative analysis and qualitative interviews with researchers.

COPO: a metadata platform for brokering FAIR data in the life sciences

COPO provides a metadata platform to enable FAIR data sharing in life sciences by standardizing metadata description and repository integration.

Community Standards for Open Cell Migration Data

This paper presents standardization efforts for cell migration data to improve data sharing and analysis.

The Dementias Platform UK (DPUK) Data Portal

The DPUK Data Portal provides secure access to cohort data for dementia research, supporting multi-modal analyses and collaborations across multiple institutions.

SpiderSeqR: an R package for crawling the web of high-throughput multi-omic data repositories for data-sets and annotation

SpiderSeqR streamlines access to multi-omic data repositories by integrating GEO and SRA, enabling unified search, annotation conversion, and query management.

Automated Gene Data Integration with Databio

Databio provides fast and accurate gene data annotation with identifier conversion for downstream analysis.

An Automated Open-Source Workflow for Standards-Compliant Integration of Small Animal Magnetic Resonance Imaging Data

The paper presents an open-source workflow to convert small animal MRI data from ParaVision to BIDS format, improving data standardization and compatibility.

Discovering Data Access and Use Requirements Using the Data Tags Suite (DATS) Model

The paper introduces metadata elements in the DATS schema to describe data access, use conditions, and consent for biomedical data reuse.

The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences

The paper assesses the value and sustainability of ELIXIR Core Data Resources, showing their critical role in preserving biological data and highlighting funding challenges.

CNSA: a data repository for archiving omics data

CNSA provides a data repository for archiving omics data, including raw and analytical data, with a focus on data management and standardization.

Efficient data management infrastructure for the integration of imaging and omics data in life science research

The paper proposes a FAIR-compliant data management system integrating imaging and omics data using Service Oriented Architecture principles, demonstrating its use in plant biology and hepatocellular carcinoma studies.

An evaluation of Nephrology Literature for Transparency and Reproducibility Indicators: Cross-sectional Review

This study evaluates reproducibility in nephrology literature, finding low rates of data availability, analysis scripts, and pre-registration.

FAIRshake: toolkit to evaluate the findability, accessibility, interoperability, and reusability of research digital resources

FAIRshake evaluates the FAIRness of research digital resources through community-driven metrics, automated assessments, and visualization tools, revealing opportunities for improvement.

Evaluating FAIR Maturity Through a Scalable, Automated, Community-Governed Framework

The paper introduces a framework to evaluate FAIRness of digital resources through automated, community-governed maturity indicators and compliance tests.

opentsv prevents the corruption of scientific data byExcel

Opentsv prevents Excel from corrupting scientific data by allowing safe opening of delimited data files without name conversions.

NWB:N 2.0: An Accessible Data Standard for Neurophysiology

Version 2.0 of the Neurodata Without Borders neurophysiology format centres on the schema, with an accompanying software stack and community aimed at making recordings easier to reuse.

The COMPARE Data Hubs

The paper describes an informatics platform for structured data storage and pre-publication sharing of pathogen sequencing data with stakeholders.

Geocoding genomic databases using GBIF

The paper discusses methods to geocode genomic sequence records using GBIF to add spatial information when it is missing.

baRcodeR with PyTrackDat: Open-source labelling and tracking of biological samples for repeatable science

The paper introduces baRcodeR and PyTrackDat to improve reproducibility in biological sample labeling, tracking, and data curation.

Extracting human data from published figures: implications for data science and bioethics

This paper demonstrates that data from old human patient studies can be extracted from publication figures and reanalyzed, raising ethical concerns about data sharing.

Liberating links between datasets using lightweight data publishing: an example using plant names and the taxonomic literature

The paper demonstrates using datasette to publish lightweight links between plant taxonomic names and their associated literature.

Data management and sharing in neuroimaging: Practices and perceptions of MRI researchers

The paper surveys MRI researchers on their data management practices and perceptions, finding variability in practices and limited adoption of emerging standards like open access publishing.

Assessment of the impact of shared data on the scientific literature

The paper assesses the impact of shared data on scientific literature using a brain imaging case study, showing increased publication rates and broader scientific collaboration.

MEG-BIDS: an extension to the Brain Imaging Data Structure for magnetoencephalography

MEG-BIDS extends the BIDS standard to organize MEG data, enabling efficient storage, sharing, and integration with MRI data.

25 Years of Molecular Biology Databases: A Study of Proliferation, Impact, and Maintenance

The paper analyzes 3055 database articles from Nucleic Acids Research to study the proliferation, impact, and maintenance of molecular biology databases over 25 years.

Uniform Resolution of Compact Identifiers for Biomedical Data

The paper describes the harmonization of identifier resolution services to enable persistent, machine-resolvable citations for biomedical data.

Experimental Directory Structure (Exdir): An alternative to HDF5 without introducing a new file format

The paper introduces Exdir, an open standard for organizing data storage in experimental pipelines as an alternative to HDF5, improving data sharing and reproducibility.

Standardized Informatics Computing Platform for Advancing Biomedical Discovery Through Data Sharing

The paper introduces BRICS, a standardized informatics computing platform for managing biomedical research data, enabling data sharing and analysis across multiple domains.

GEOMetaCuration: A web-based application for accurate manual curation of Gene Expression Omnibus metadata

GEOMetaCuration is a web-based tool for curating Gene Expression Omnibus metadata, streamlining the process and enabling collaborative curation efforts.

Parallel sequencing lives, or what makes large sequencing projects successful

The paper compares two Hi-C samples, showing how adherence to FAIR principles leads to successful sequencing projects.