Data Archiving & Permissions

Policies, best practices, and resources for responsibly sharing cancer genomics and biomarker data with the Journal of Cancer Genetics and Biomarkers (JCGB).

• Transparency: Readers must be able to trace results back to raw or processed data and analytical code.
• Reusability: Data should be deposited with clear licenses, metadata, and formats that enable integration and re-analysis.
• Respect: Sensitive datasets require governance aligned with participant consent, community expectations, and legal frameworks.
• Longevity: Use stable repositories that offer persistent identifiers (DOIs, accession numbers) and long-term preservation guarantees.

Choose repositories according to data type, access requirements, and compliance mandates.

• Study overview (objectives, design, cohort characteristics)
• Data dictionary describing variables, units, and codes
• File structure map indicating directories, naming conventions, and dependencies
• Detailed methods or laboratory protocols (include reagents, instruments, software)
• Quality control procedures and filtering rules
• Version history documenting updates or corrections

• Use community schemas (MIAME for microarrays, MINSEQE for RNA-seq, HUPO-PSI for proteomics).
• Include controlled vocabulary terms (MeSH, HPO, ICD-10) for disease classification.
• Provide sample-level metadata (age, sex, ethnicity, tumour type, staging) with anonymisation.
• Document data processing pipelines, software versions, and parameter settings.

JCGB encourages open licenses while recognising the need for controlled access in sensitive contexts.

• Controlled Access: Deposit in repositories offering access committees (EGA, dbGaP, controlled Synapse projects). Provide Data Use Agreements (DUAs).
• De-identification: Remove direct identifiers, convert dates to offsets relative to diagnosis, and aggregate geolocation data.
• Genomic Sovereignty: For indigenous or marginalised communities, align with community-specific governance, benefit-sharing agreements, and indigenous data frameworks (CARE principles).
• Third-Party Data: Obtain permissions from original custodians; document agreement terms in the manuscript.

Include a dedicated section in the manuscript after acknowledgments. Examples:

• “Whole-genome sequencing data are available in the European Genome-phenome Archive (EGA) under accession EGAS00001008721. Access requests can be submitted through the EGA Data Access Committee.”
• “Metabolomic peak tables associated with this study are deposited in Metabolomics Workbench (ST002345) under CC BY 4.0 license.”
• “Due to participant confidentiality agreements, de-identified clinical data are available upon request to the corresponding author and subject to institutional review.”

• Host code in public repositories with version control.
• Tag releases corresponding to the manuscript and archive them via Zenodo for DOI generation.
• Provide README files with setup instructions, dependencies, and example data.
• Use containerisation (Docker, Singularity) or workflow description languages (CWL, Nextflow, WDL) for complex pipelines.
• Indicate licensing (MIT, Apache 2.0, GPL) to clarify reuse rights.

• Compress large datasets (tar.gz) and split into manageable segments (≤5 GB) where repository limits apply.
• Provide checksum files (MD5, SHA256) to verify integrity.
• For extremely large data (petabyte-scale imaging), coordinate with JCGB to arrange cloud-based sharing or institutional hosting.

• JCGB permits repository embargoes aligned with journal publication. Specify embargo end date in the metadata.
• If presenting at conferences, ensure repository links honour embargo deadlines and note them in the cover letter.
• JCGB supports preprints (bioRxiv, medRxiv). Link datasets upon preprint release for transparency.

• During peer review, JCGB may request reviewer access to datasets or code. Provide temporary credentials where necessary.
• Post-acceptance, JCGB verifies repository accessibility, metadata completeness, and licensing.
• Failure to provide verifiable data may delay publication or result in rejection.

• Use repository versioning to issue updates or corrections.
• Notify JCGB of significant changes so errata or addenda can be published.
• Document version history in README files and repository metadata.

Complete this checklist before final submission to ensure your archiving plan meets JCGB’s standards and legal obligations:

• Consent Alignment: Confirm that participant information sheets and consent forms explicitly cover the level of data sharing you intend (open, controlled, summary-only). Document any deviations and secure re-consent or waivers when necessary.
• Institutional Approvals: Obtain a letter or email confirmation from your institutional data governance office or privacy board approving the external release of data. Store the approval in project records and reference it in the manuscript if required.
• Data Transfer Agreements: Execute DTAs among collaborating institutions, specifying permitted uses, security obligations, breach response procedures, and data retention timelines.
• Security Architecture: Encrypt datasets prior to upload, enforce multi-factor authentication, and maintain access logs for controlled repositories. For cloud-hosted data, comply with ISO 27001 or equivalent standards.
• Retention & Destruction Policy: Define how long raw and processed data will be retained post-publication and outline procedures for secure destruction when retention periods end.
• Community Engagement: For indigenous or community-led research, document engagement sessions, co-authorship agreements, and benefit-sharing commitments in alignment with the CARE principles.
• Machine-Readable Metadata: Validate JSON, XML, or CSV metadata files against repository schemas. Ensure ontology tags, units, and identifiers are accurate and consistent across files.
• Emergency Contacts: Provide repositories with a generic institutional email (e.g., [email protected]) to ensure continuity if personnel change.

Last updated: September 2025. JCGB reviews data policies annually to align with evolving legal, ethical, and technological standards.