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README.md
README.md
 
 
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Clinical Database

车同轨，书同文，行同伦。

This repository is the public method repository for the clinical database standardization project.

It provides:

  • directory contracts
  • policy-registry contracts
  • database-specific critical semantics contracts
  • Layer 3 retained-output layout governance
  • database lineage and version tracking
  • onboarding playbooks
  • public workflow entrypoints
  • release governance and release-note surfaces
  • generated public exports and coverage summaries
  • GitHub-safe public variable-card contracts
  • early standard-system MVP draft specs
  • public database scaffolding entrypoints
  • reusable scripts
  • Layer 1 database skeletons
  • public tutorials
  • detailed public review checklists

It does not provide:

  • raw database files
  • local parquet copies
  • patient-level Layer 2 to Layer 5 outputs

Start Here

  1. Read docs/GETTING_STARTED.md.
  2. Check docs/DATABASE_LINEAGE_AND_VERSION_MATRIX.md.
  3. Read docs/STANDARD_SYSTEM_MATURITY_ROADMAP.md to understand how the current repository baseline grows into a stricter standard system.
  4. Read docs/standard_system_mvp/VARIABLE_CLASS_LANDSCAPE_AND_ROLLOUT.md for the current variable-class map and rollout order.
  5. Read docs/standard_system_mvp/README.md for the current governed MVP batch and runtime-evidence surface.
  6. Read the class-2 bundle under docs/standard_system_mvp, including the class definition, current closure, total closure review, MIMIC expansion decision, duration-summary approvals, Amsterdam next ICU and ICU/MCU admission approvals, baseline-snapshot approvals, grouped/proxy split approval, first window-summary approval, Amsterdam first-day urine-output candidate/formal review, Amsterdam hospital-LOS candidate boundary review, and BMI derived-baseline candidate/formal reviews.
  7. Read the class-3 and opening class-5 bundle under docs/standard_system_mvp, including the first binary-state approval, Amsterdam same-name candidate/formal review for invasive mechanical ventilation active, the MIMIC respiratory-support single-status expansions through NIV, HFNC, supplemental oxygen, and tracheostomy, the Amsterdam respiratory-support third-layer audit, the cross-database vasopressor-support and RRT active approvals, and the MIMIC plus Amsterdam RRT child split into CRRT-family, non-CRRT, and exact modality episode layers.
  8. Read docs/standard_system_mvp/CLASS1_FIRST_BATCH_APPROVAL_SUMMARY.md for the first formal content-approval closure of the reviewed MIMIC-IV-3.1 class-1 batch.
  9. Read docs/standard_system_mvp/STD_HEART_RATE_FORMAL_APPROVAL_REVIEW.md for the current formal approval review of std_heart_rate.
  10. Read docs/standard_system_mvp/CLASS1_CURRENT_APPROVAL_CLOSURE.md for the current broader 11-variable class-1 closure state.
  11. Install dependencies with pip install -r requirements.txt.
  12. Place your officially obtained source data into the expected sibling local-work path Methods/Clinical_Database/local_work/Layer 1/<database>/... outside this public repository.
  13. Read Framework_Guideline/Layer3_Directory_Contract.md before creating retained Layer 3 outputs.
  14. Run the public workflow entrypoints in scripts/public_workflow.py.
  15. Use prepare-release, validate-layer3-layout, and check-public-repository to keep the public release surface coherent.

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