radiology-data

name

radiology-data

description

Prepare and audit Data/Code Availability statements, DICOM de-identification plans, repository selection, dataset citations, and FAIR/sharing checks for Radiology (RSNA) and Nature-portfolio imaging+omics submissions. Use when the user needs a data availability statement, must de-identify DICOM imaging, choose a repository (TCIA, Zenodo, GEO, dbGaP, EGA), share code/models, write dataset citations, check FAIR compliance, or needs Extended Data / Supplementary Information / Source Data planning for a Nature-family journal — including controlled-access genomics for radiogenomics. Bilingual-aware (中文作者备注 → submission-ready English). Never overstates availability or invents accessions.

Data & Code Availability + De-identification

Prepare submission-ready Data Availability and Code/Model Availability statements, plan DICOM de-identification, choose repositories, and check FAIR — for imaging and imaging+omics (radiogenomics) studies.

Core stance

• Every result-supporting dataset maps to a concrete access route — public repository + accession, controlled access + steward, or a justified restriction. Avoid bare "available on reasonable request" (editors increasingly reject it; if used, name the controller and conditions). At Nature-portfolio venues this is stated as a condition of publication, not a recommendation — treat it accordingly.
• De-identify before sharing any imaging — DICOM headers and burned-in pixel PHI; defacing for head imaging.
• Cite datasets like literature (DataCite-style: creator, title, repository, year, identifier).
• Share code/models for reproducibility (CLAIM/TRIPOD+AI open-science items).
• Don't overstate or fabricate — no invented accessions; controlled data described honestly with the access process.

When to use

• "Write the Data Availability / Code Availability statement."
• "How do I de-identify these DICOMs for TCIA / a public release?"
• "Which repository for my images / radiomic features / RNA-seq?"
• "Write dataset citations / check FAIR."
• "We have controlled genomics (dbGaP/EGA) — how do I word availability?"
• "What goes in Extended Data vs Supplementary Information vs Source Data?" (Nature-portfolio)

When to open extra files

File	Open when
references/dicom-deidentification.md	De-identifying imaging: DICOM tags, pixel PHI, defacing, standards/tools
references/repositories.md	Choosing a repository for images, features, code/models, and omics (open vs controlled)
references/availability-and-fair.md	Statement templates, dataset citations, FAIR checklist, Chinese-author alignment
references/ai-radiogenomics-public-resources.md	Selecting public datasets for radiology AI/radiogenomics, planning external validation or pretraining, or checking TCIA/GDC/PhysioNet/GEO/dbGaP/EGA-style resource roles

Workflow

1. Inventory result-supporting data: imaging, radiomic feature tables, clinical data, omics (bulk/scRNA/spatial), code, trained models.
2. For public-resource planning, open ai-radiogenomics-public-resources.md and mark each dataset as pretraining, development, internal test, external validation, or citation-only.
3. Classify each as public / depositable / restricted (privacy, consent, DUA, commercial).
4. De-identify imaging (dicom-deidentification.md); confirm no pixel PHI; deface head MRI/CT.
5. Pick repositories (repositories.md): images → TCIA/Zenodo; features/code → Zenodo/ GitHub (+ DOI); expression → GEO; controlled genomics → dbGaP/EGA.
6. Draft statements (availability-and-fair.md) with accessions/placeholders; write dataset citations; run the FAIR check.
7. Flag restrictions honestly: reason, controller, review route, conditions.

Output contract

1. Data inventory — item → sensitivity → access route → repository → accession/placeholder.
2. Data Availability statement and Code/Model Availability statement (submission-ready).
3. Dataset citations (DataCite-style) for any public data used.
4. Public-resource role map — dataset → role (pretraining/development/test/external validation) → overlap/leakage/access risks.
5. De-identification plan (if imaging is shared).
6. FAIR/issues — gaps and fixes; restricted-data wording.
7. Extended Data / Source Data plan (Nature-portfolio only) — which items are main-text, Extended Data, Supplementary Information, and confirmation that Source Data will be exported per figure.
8. 待确认（中文） for Chinese authors — items needing author confirmation.

Handoffs

Reporting-guideline availability items, Reporting Summary → radiology-reporting; dataset discovery → radiology-search; controlled-cohort design → radiology-radiogenomics; figure-level Source Data / Extended Data figure count → radiology-figure/nature-figure-spec.md; display-item plan in the manuscript → radiology-writing. Not legal advice — confirm consent/DUA/IRB terms with your institution.