radiology-data

Imaging Data Lifecycle, Availability & De-identification

Build or audit a living data-lifecycle/DMP record, prepare submission-ready Data Availability and Code/Model Availability statements, plan DICOM de-identification, choose repositories, and check FAIR — for imaging and imaging+omics 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.
• A DMP is a living operational artifact. Freeze a funder/institution policy passport, then version data objects, controls, sharing, preservation, retention/destruction, costs, owners and amendments. A publication availability paragraph is not a lifecycle plan.
• FAIR is not automatically public. Protected imaging/genomic data can use a controlled access route; privacy, consent, DUA and community/institutional governance remain binding.

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)
• "Write/update the funder DMP/DMS plan, retention schedule or data-access workflow."
• "A collaborator requested post-publication images/data — what evidence and approval are needed?"

When to open extra files

File	Open when
references/cohort-assembly-and-id-reconciliation.md	Local imaging/clinical/annotation tables do not line up by patient ID; protocol-heterogeneity screening and inclusion/exclusion counts for the cohort flow
references/data-dictionary-spec.md	Building or auditing the field-level data dictionary (variables, coding, missing codes, provenance)
references/chinese-clinical-text-abstraction.md	Extracting variables from Chinese discharge summaries / pathology / radiology reports (manual abstraction, regex, LLM-assisted prefill)
references/outcome-and-followup-data.md	Defining event/censor/time-origin fields, follow-up acquisition and completeness, too-short follow-up, missing-data strategy
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/data-lifecycle-management-plan.md	Building or updating a funder/institution policy passport, living DMP/DMS plan, preservation/retention/destruction schedule or post-publication access-request route
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
templates/data-lifecycle-plan.md	A durable object/lifecycle inventory, imaging release gate and amendment log is requested

Workflow

1. Freeze the applicable policy passport when a DMP/DMS, retention or access decision is in scope. Use VERIFIED_CURRENT / VERIFY_FROM_CURRENT_POLICY / NOT_APPLICABLE / STOP_POLICY_UNRESOLVED; never copy one funder's current format into another regime.
2. Inventory result-supporting data: imaging, radiomic feature tables, clinical data, omics (bulk/scRNA/spatial), code, trained models.
3. For lifecycle planning, open data-lifecycle-management-plan.md; bind raw and derived imaging/clinical/omics/code/model objects to storage, access, metadata/QC, sharing, preservation, retention/destruction, cost, owner and amendment controls.
4. For public-resource planning, open ai-radiogenomics-public-resources.md and mark each dataset as pretraining, development, internal test, external validation, or citation-only.
5. Classify each as public / depositable / restricted (privacy, consent, DUA, commercial).
6. De-identify imaging (dicom-deidentification.md); freeze a closed object/payload/package manifest and apply profile-appropriate checks to attributes, descriptors, structured content, graphics, pixels/faces, encapsulated documents, video/waveform/private payloads and package artifacts. Unknown or unsupported payloads fail closed. Reconcile the released archive to the manifest, resolve every flag and record coverage/exclusions/residual risk. Do not claim absolute absence of PHI from a partial or unaudited check.
7. Pick repositories (repositories.md): images → TCIA/Zenodo; features/code → Zenodo/ GitHub (+ DOI); expression → GEO; controlled genomics → dbGaP/EGA.
8. Draft statements (availability-and-fair.md) with accessions/placeholders; write dataset citations; run the FAIR check.
9. Flag restrictions honestly: reason, controller, review route, conditions. For retention, destruction or post-publication requests, require the authorized steward and a versioned receipt.

Output contract

1. Policy passport and lifecycle state — when applicable: exact authority/source/date, object inventory, controls, preservation/retention/destruction, costs, owner and amendment log.
2. Data inventory — item → sensitivity → access route → repository → accession/placeholder.
3. Data Availability statement and Code/Model Availability statement (submission-ready).
4. Dataset citations (DataCite-style) for any public data used.
5. Public-resource role map — dataset → role (pretraining/development/test/external validation) → overlap/leakage/access risks.
6. De-identification plan and closed release-surface manifest (if imaging is shared) — every object/payload/package artifact, SOP Class or media type, disposition, hash, QA coverage, exception and residual-risk state.
7. FAIR/issues — gaps and fixes; restricted-data wording.
8. 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.
9. Access-request/closeout state — when applicable: request authority, release manifest, retention/destruction hold and unresolved steward action.
10. 待确认（中文） for Chinese authors — items needing author confirmation.

Handoffs

Series/phase/sequence acceptance, acquisition/reconstruction, quantitative transforms, artifacts, dose, phantom/test-retest and protocol drift → radiology-acquisition-qc; this skill retains inventory, provenance, de-identification, access and sharing ownership. 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 and table-level source-data crosswalk → radiology-table; display-item plan in the manuscript → radiology-writing; package manifest → radiology-submission; project provenance → radiology-pipeline; replay level and executable reproduction package → radiology-reproducibility; delivery owners/cadence → radiology-research-ops. Not legal advice — confirm consent/DUA/IRB terms with your institution.