medorqis 2.1.1__tar.gz

medorqis-2.1.1/LICENSE

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medorqis-2.1.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: medorqis
+Version: 2.1.1
+Summary: MedOrqis — Medical AI Skills Ecosystem: 24 Specialized Clinical AI Skills, Deterministic Safety Guardrails & Zero-Token Calculators.
+Author-email: Tarek Mohamed <seotarek@gmail.com>
+License: Apache-2.0
+Project-URL: Homepage, https://seotarek.github.io/MedOrqis/
+Project-URL: Repository, https://github.com/seotarek/MedOrqis
+Project-URL: Documentation, https://seotarek.github.io/MedOrqis/
+Project-URL: Zenodo_DOI, https://doi.org/10.5281/zenodo.23937802
+Keywords: medical-ai,clinical-decision-support,mcp,claude-skills,gemini-extensions,patient-safety,zero-token
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Healthcare Industry
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: jsonschema>=4.20.0
+Provides-Extra: mcp
+Requires-Dist: mcp>=1.0.0; extra == "mcp"
+Provides-Extra: dev
+Requires-Dist: pytest>=8.0.0; extra == "dev"
+Requires-Dist: pydantic>=2.0.0; extra == "dev"
+Dynamic: license-file
+
+# MedOrqis — Medical AI Skills Ecosystem (v2.1.1)
+
+[![Live Interactive Catalog](https://img.shields.io/badge/Live_Catalog-seotarek.github.io%2FMedOrqis-00e5a3?style=for-the-badge&logo=google-chrome&logoColor=black)](https://seotarek.github.io/MedOrqis/)
+[![DOI](https://img.shields.io/badge/DOI-10.5281%2Fzenodo.23937802-blue.svg?style=for-the-badge&logo=zenodo&logoColor=white)](https://doi.org/10.5281/zenodo.23937802)
+[![Skills CLI](https://img.shields.io/badge/Skills_CLI-npx_skills_add_seotarek%2FMedOrqis-6366f1?style=for-the-badge&logo=vercel)](https://github.com/vercel-labs/skills)
+[![npm version](https://img.shields.io/badge/npm-v2.1.1-cb3837?style=for-the-badge&logo=npm)](https://www.npmjs.com/package/medorqis)
+[![Verification: 36/36 Passed (100%)](https://img.shields.io/badge/Verification-36%2F36%20Passed%20(100%25)-brightgreen.svg?style=for-the-badge)](tests/reports/VERIFICATION_REPORT.md)
+[![GitHub CI](https://img.shields.io/badge/GitHub_CI-passing-success.svg?style=for-the-badge&logo=githubactions&logoColor=white)](https://github.com/seotarek/MedOrqis/actions)
+[![License: Apache-2.0](https://img.shields.io/badge/License-Apache--2.0-blue.svg?style=for-the-badge)](LICENSE)
+
+**MedOrqis** is an open-source, evidence-grounded, cross-platform ecosystem of **24 specialized clinical AI skills**, **12 deterministic zero-token clinical calculators & safety engines**, and multi-platform adapters (Skills CLI, Claude Code, Gemini CLI, Model Context Protocol, and OpenAI).
+
+> [!TIP]
+> 🌐 **Interactive Web Hub & Live Zero-Token Calculators**:  
+> Explore the live searchable 24-skill catalog, test interactive clinical calculators (ESC 2024 CHA₂DS₂-VA, CKD-EPI 2021, Bedside Schwartz, HAS-BLED, NEWS2, DDI Checker), and inspect dialect benchmarks directly in your browser at **[https://seotarek.github.io/MedOrqis/](https://seotarek.github.io/MedOrqis/)**.
+> 
+> ⚡ **Fleet Install in 1-Second (Claude Code, Cursor, Codex, Antigravity, OpenCode)**:  
+> ```bash
+> npx skills add seotarek/MedOrqis
+> ```
+
+Built with an **evidence-first, patient-safety-first architecture**, MedOrqis eliminates medical hallucination risks in high-stakes clinical calculations by executing arithmetic, unit conversions, PHI scrubbing, negation parsing, and drug interaction screenings through a **local, deterministic Python core with zero LLM API token overhead**.
+
+---
+
+## ⚡ 1-Minute Quick Start & Integration Options
+
+### 🛠️ Option 1: One-Command Fleet Install (Skills CLI)
+Install all 24 skills directly into your active coding agent workspace (Claude Code, Cursor, Antigravity, OpenCode, Codex):
+```bash
+# Install the complete MedOrqis ecosystem (all 24 skills)
+npx skills add seotarek/MedOrqis
+
+# Or install specific clinical skills:
+npx skills add seotarek/MedOrqis --skill emergency-triage-redflags
+npx skills add seotarek/MedOrqis --skill pharmacology-dosing-interactions
+npx skills add seotarek/MedOrqis --skill pediatrics-neonatology
+```
+
+> ⭐ **Support Open-Source Clinical AI**: If MedOrqis helps your workflow or coding agents, please give the repo a **[Star on GitHub](https://github.com/seotarek/MedOrqis)** — it helps the project reach more clinicians and medical AI engineers!
+
+---
+
+### 📦 Option 2: NPX & NPM Interactive Terminal Package (`medorqis`)
+Explore the catalog and copy prompts directly in your terminal:
+```bash
+# Run interactive CLI browser
+npx medorqis
+
+# List all 24 skills grouped by safety tier
+npx medorqis list
+
+# Print copyable Universal AI Prompt for web chat models
+npx medorqis prompt
+
+# Print MCP configuration JSON block
+npx medorqis mcp
+```
+Or install globally or as a project dependency:
+```bash
+npm install -g medorqis
+# or in Node.js apps:
+npm install medorqis
+```
+
+---
+
+### ⚡ Option 3: Universal AI Model Prompting (Zero Install — Any Model)
+You do not need to install anything or run code to use MedOrqis with LLMs! You can send the repository link and prompt directly to **ChatGPT (with web access), Claude 3.5 Sonnet, Google Gemini, Cursor, Grok, or Antigravity**:
+
+> **Copy & Paste into any AI model:**
+> ```text
+> Read the open-source clinical AI skills ecosystem MedOrqis at:
+> https://github.com/seotarek/MedOrqis (Web catalog: https://seotarek.github.io/MedOrqis/)
+> 
+> You are now operating under MedOrqis clinical governance rules (v2.1.1):
+> 1. Enforce zero-hallucination deterministic standards for all medical risk scores and formulas (CHA2DS2-VA ESC 2024, CKD-EPI 2021, Bedside Schwartz, Cockcroft-Gault, Wells DVT/PE, CURB-65, HAS-BLED, NEWS2, Pediatric Dose Capping).
+> 2. Epistemic provenance: Never recommend high-risk interventions based on unconfirmed model hypotheses.
+> 3. Missing Age Gatekeeper: If patient age is unrecorded, do NOT assume a default adult age (30); immediately flag SAFE_ABSTENTION_DATA_DEFICIT.
+> 4. Sentinel Emergency Red Flags: Immediate emergency redirection on acute stroke (FAST), ACS crushing chest pain, anaphylaxis, septic shock, or anticoagulation + active bleeding.
+> 5. Provide evidence-grounded differential diagnosis, drug interaction screening, and red-flag triage across all 24 MedOrqis clinical domains.
+> 
+> Please summarize your activated clinical skills and await clinical input.
+> ```
+
+---
+
+### 🔌 Option 4: Model Context Protocol (MCP Server)
+Run the local MCP stdio server:
+```bash
+python3 mcp_server/medorqis_mcp_server.py
+```
+Add to your Claude Desktop configuration (`claude_desktop_config.json`):
+```json
+{
+  "mcpServers": {
+    "medorqis": {
+      "command": "python3",
+      "args": ["/path/to/MedOrqis/mcp_server/medorqis_mcp_server.py"]
+    }
+  }
+}
+```
+
+---
+
+### 🐍 Option 5: Local Python Developer Setup
+```bash
+git clone https://github.com/seotarek/MedOrqis.git
+cd MedOrqis
+python3 -m pip install -e .
+```
+
+---
+
+## 🧮 Pure Deterministic Clinical Calculators (`core/clinical_calculators.py`)
+
+All medical calculations in MedOrqis execute with **zero LLM API token overhead and strict mathematical determinism** via pure Python functions in [`core/clinical_calculators.py`](core/clinical_calculators.py):
+
+| # | Clinical Calculator | Function Name | Clinical Guideline & Standard | Target Population | Safety Gate & Boundary Enforcement |
+|---|---|---|---|---|---|
+| **1** | **CHA₂DS₂-VA** | `calculate_cha2ds2_va_esc2024` | ESC Guidelines 2024 (Sex-Neutral) | Adults ($\ge 18\text{y}$) with AF | Refuses if Age missing (`SAFE_ABSTENTION_DATA_DEFICIT`). Removes 1-point female bias. |
+| **2** | **CHA₂DS₂-VASc** | `calculate_cha2ds2_vasc_aha2023` | ACC/AHA/ACCP/HRS 2023 | Adults ($\ge 18\text{y}$) with AF | Historical comparative baseline for US guidelines ($+1$ for female sex). |
+| **3** | **CKD-EPI 2021** | `calculate_ckd_epi_2021_egfr` | NKF-ASN Task Force / NEJM 2021 | Adults ($\ge 18\text{y}$) | Race-free adult eGFR formula. **Hard Refusal** if Age $< 18$ years (`SAFE_REFUSAL_PEDIATRIC`). |
+| **4** | **Bedside Schwartz** | `calculate_bedside_schwartz_egfr` | Schwartz GJ et al. (JASN 2009) | Pediatrics ($< 18\text{y}$) | Height-based eGFR ($0.413 \times \text{Ht}/\text{SCr}$). **Hard Refusal** if Age $\ge 18$ years (`SAFE_REFUSAL_ADULT`). |
+| **5** | **Cockcroft-Gault** | `calculate_cockcroft_gault_crcl` | FDA Renal Dosing Standards | Adults ($\ge 18\text{y}$) | Automatically calculates IBW and Adjusted Body Weight (AdjBW $0.4$) if BMI $\ge 30$. |
+| **6** | **HAS-BLED** | `calculate_has_bled_score` | Pisters R et al. (Chest 2010) | Adults on Anticoagulation | Flags High Bleeding Risk ($\ge 3$); warns against unmonitored DOAC initiation. |
+| **7** | **CURB-65** | `calculate_curb65_score` | British Thoracic Society (BTS) | Adults with CAP | Stratifies 30-day mortality risk (Outpatient vs Inpatient vs ICU admission). |
+| **8** | **NEWS2** | `calculate_news2_score` | Royal College of Physicians (2017) | Acute Inpatient Care | Physiological aggregate triage across 6 vital signs; automated sepsis escalation. |
+| **9** | **Wells DVT Criteria** | `calculate_wells_dvt_score` | Wells PS et al. (NEJM 2003) | Suspected DVT | Pre-test probability (Unlikely vs Likely); dictates D-dimer vs Compression Ultrasound. |
+| **10** | **Wells PE Criteria** | `calculate_wells_pe_score` | Wells PS et al. (Ann Intern Med 2001) | Suspected PE | Pre-test probability (Unlikely vs Likely); dictates D-dimer vs CT Pulmonary Angiography. |
+
+*(Auxiliary dosing & safety engines: `calculate_pediatric_weight_dose` & `calculate_mosteller_bsa` in `core/clinical_calculators.py`, and Contraindicated DDI Screening in `core/safety_guardrails.py`)*.
+
+---
+
+## 🏥 The 24-Skill Risk-Stratified Taxonomy
+
+### Tier 1: Governance, Research & Operations (Class A)
+- `medorqis-orchestrator`: Context envelope routing and conflict resolution.
+- `ebm-research-biostatistics`: PICO, CASP, RoB-2 appraisal, and GRADE certainty.
+- `medical-documentation-translation`: SOAP, SBAR, and BiDi multilingual medical translation.
+- `healthcare-ops-telemedicine-ehr`: HL7 FHIR mapping and telemedicine intake.
+- `health-cybersecurity-privacy`: PHI scrubbing and prompt injection defense.
+- `public-health-epidemiology`: Screening metrics (sens/spec) and IPC protocols.
+
+### Tier 2: Diagnostic & Chronic Care Support (Class B)
+- `differential-diagnosis-cds`: VINDICATE differential framework.
+- `laboratory-medicine-pathology`: Critical panic values and LOINC mapping.
+- `radiology-medical-imaging`: ACR Appropriateness Criteria and radiation safety.
+- `internal-medicine-chronic`: Multi-morbidity chronic disease care plans.
+- `infectious-diseases-stewardship`: Antimicrobial stewardship and resistance awareness.
+- `nursing-clinical-care`: NEWS2 early warning score and Braden scale.
+- `clinical-nutrition-dietetics`: Caloric requirements and food-drug interactions.
+- `rehabilitation-physical-therapy`: Post-op and stroke rehab protocols.
+
+### Tier 3: High-Risk, Emergency & Vulnerable Populations (Class C)
+- `emergency-triage-redflags`: ABCDE primary survey and emergency redirection.
+- `clinical-safety-auditor`: Pre-output verification and safety gate check.
+- `pharmacology-dosing-interactions`: Renal/hepatic adjustments and DDI checks.
+- `clinical-toxicology-overdose`: Toxidromes, antidotes, and Poison Control escalation.
+- `pediatrics-neonatology`: Weight-based dose capping and pediatric safety.
+- `obstetrics-gynecology`: Maternal-fetal safety and pre-eclampsia triage.
+- `geriatrics-polypharmacy`: 2023 Beers Criteria and STOPP/START.
+- `mental-health-psychiatry`: Suicide crisis escalation and psychotropic monitoring.
+- `perioperative-surgical-care`: RCRI pre-op risk and anticoagulation bridging.
+- `oncology-palliative-care`: Oncologic emergencies and palliative pain control.
+
+---
+
+## 🌐 Multilingual & Dialect Regression Benchmark
+
+MedOrqis includes a deterministic natural language processing normalizer verified across **126 curated synthetic test fixtures**:
+- **100 Syntactic Negation Sentences**: Handcrafted fixtures verifying regex boundary detection and clause-stop logic across 8 dialects and languages: Modern Standard Arabic (`ar-MSA`), Egyptian (`ar-EG`), Gulf (`ar-GULF`), Levantine (`ar-LEV`), Maghrebi (`ar-MAG`), English (`en-US/GB`), French (`fr-FR`), and Spanish (`es-ES`).
+- **10 BiDi & Unit Token Strings**: Numerical and unit strings verifying bidirectional layout preservation (e.g. Arabic RTL mixing English numbers/units like "500 mg").
+- **16 Trade Brand-to-INN Mappings**: Lookup fixtures mapping regional commercial trade brand names to generic International Nonproprietary Names (e.g. Panadol $\to$ Paracetamol).
+
+> [!CAUTION]
+> **Two-Axis Governance Separation**:
+> - **Automated Syntactic Unit-Test Pass Rate**: **100.0% (126/126 passed)**.
+> - **Bedside Real-World Clinical Validation**: **0.0% (UNVALIDATED IN-VIVO / PENDING CLINICAL TRIALS)**.
+> 
+> See full breakdown and statistical caveats in [LANGUAGE_COVERAGE_MATRIX.md](LANGUAGE_COVERAGE_MATRIX.md).
+
+---
+
+## 🧪 Automated Verification & Provenance
+
+Execute cryptographic file integrity verification and the harmonized clinical test suite (all 36 unit, safety, multilingual, and adapter tests):
+```bash
+# 1. Verify SHA-256 cryptographic fingerprints across all 45 modules
+python3 core/integrity_manifest.py --verify
+
+# 2. Execute the harmonized clinical test suite
+python3 tests/run_all_tests.py
+```
+This automatically verifies:
+1. `tests/unit/test_clinical_calculators.py`: Boundary and formula correctness for all 12 clinical engines.
+2. `tests/safety/test_safety_and_provenance.py`: Epistemic provenance gates, missing age gatekeeper, sentinel emergency red-flags, and contraindicated DDIs.
+3. `tests/multilingual/test_multilingual_benchmark.py`: Negation preservation, BiDi unit fidelity, and brand-to-INN mapping across 126 test cases.
+4. `tests/platform_adapters/test_security_and_adapters.py`: SHA-256 cryptographic file integrity manifest, PHI scrubbing, prompt injection defense, and MCP JSON-RPC protocol.
+
+Artifacts generated:
+- [VERIFICATION_REPORT.md](tests/reports/VERIFICATION_REPORT.md)
+- [LANGUAGE_COVERAGE_MATRIX.md](LANGUAGE_COVERAGE_MATRIX.md)
+- [file_integrity_manifest.json](governance/file_integrity_manifest.json)
+
+---
+
+## ⚖️ Governance & Regulatory Disclaimer
+MedOrqis is an open-source clinical reference architecture and research framework. It is **NOT** a certified Medical Device (SaMD) and does not autonomously diagnose or prescribe. Clinical Decision Support outputs must always be reviewed by a licensed healthcare professional. See [MEDICAL_DISCLAIMER.md](MEDICAL_DISCLAIMER.md) and [SAFETY_AND_GOVERNANCE.md](SAFETY_AND_GOVERNANCE.md).
+
+---
+
+## 📚 Academic Citation & Persistent DOI
+If you use MedOrqis in clinical informatics, medical AI research, or clinical decision support development, please cite our persistent Zenodo repository DOI:
+
+```bibtex
+@software{mohamed_2026_medorqis,
+  author       = {Mohamed, Tarek},
+  title        = {MedOrqis: Medical AI Skills Ecosystem with Deterministic Safety Guardrails & Zero-Token Calculators},
+  month        = nov,
+  year         = 2026,
+  publisher    = {Zenodo},
+  version      = {v2.1.1},
+  doi          = {10.5281/zenodo.23937802},
+  url          = {https://doi.org/10.5281/zenodo.23937802}
+}
+```
+
+---
+
+## 📜 License
+Licensed under the [Apache License, Version 2.0](LICENSE).
+Medical vocabularies and guidelines are attributed in [DATA_LICENSES_AND_ATTRIBUTIONS.md](DATA_LICENSES_AND_ATTRIBUTIONS.md).

medorqis-2.1.1/README.md

@@ -0,0 +1,235 @@
+# MedOrqis — Medical AI Skills Ecosystem (v2.1.1)
+
+[![Live Interactive Catalog](https://img.shields.io/badge/Live_Catalog-seotarek.github.io%2FMedOrqis-00e5a3?style=for-the-badge&logo=google-chrome&logoColor=black)](https://seotarek.github.io/MedOrqis/)
+[![DOI](https://img.shields.io/badge/DOI-10.5281%2Fzenodo.23937802-blue.svg?style=for-the-badge&logo=zenodo&logoColor=white)](https://doi.org/10.5281/zenodo.23937802)
+[![Skills CLI](https://img.shields.io/badge/Skills_CLI-npx_skills_add_seotarek%2FMedOrqis-6366f1?style=for-the-badge&logo=vercel)](https://github.com/vercel-labs/skills)
+[![npm version](https://img.shields.io/badge/npm-v2.1.1-cb3837?style=for-the-badge&logo=npm)](https://www.npmjs.com/package/medorqis)
+[![Verification: 36/36 Passed (100%)](https://img.shields.io/badge/Verification-36%2F36%20Passed%20(100%25)-brightgreen.svg?style=for-the-badge)](tests/reports/VERIFICATION_REPORT.md)
+[![GitHub CI](https://img.shields.io/badge/GitHub_CI-passing-success.svg?style=for-the-badge&logo=githubactions&logoColor=white)](https://github.com/seotarek/MedOrqis/actions)
+[![License: Apache-2.0](https://img.shields.io/badge/License-Apache--2.0-blue.svg?style=for-the-badge)](LICENSE)
+
+**MedOrqis** is an open-source, evidence-grounded, cross-platform ecosystem of **24 specialized clinical AI skills**, **12 deterministic zero-token clinical calculators & safety engines**, and multi-platform adapters (Skills CLI, Claude Code, Gemini CLI, Model Context Protocol, and OpenAI).
+
+> [!TIP]
+> 🌐 **Interactive Web Hub & Live Zero-Token Calculators**:  
+> Explore the live searchable 24-skill catalog, test interactive clinical calculators (ESC 2024 CHA₂DS₂-VA, CKD-EPI 2021, Bedside Schwartz, HAS-BLED, NEWS2, DDI Checker), and inspect dialect benchmarks directly in your browser at **[https://seotarek.github.io/MedOrqis/](https://seotarek.github.io/MedOrqis/)**.
+> 
+> ⚡ **Fleet Install in 1-Second (Claude Code, Cursor, Codex, Antigravity, OpenCode)**:  
+> ```bash
+> npx skills add seotarek/MedOrqis
+> ```
+
+Built with an **evidence-first, patient-safety-first architecture**, MedOrqis eliminates medical hallucination risks in high-stakes clinical calculations by executing arithmetic, unit conversions, PHI scrubbing, negation parsing, and drug interaction screenings through a **local, deterministic Python core with zero LLM API token overhead**.
+
+---
+
+## ⚡ 1-Minute Quick Start & Integration Options
+
+### 🛠️ Option 1: One-Command Fleet Install (Skills CLI)
+Install all 24 skills directly into your active coding agent workspace (Claude Code, Cursor, Antigravity, OpenCode, Codex):
+```bash
+# Install the complete MedOrqis ecosystem (all 24 skills)
+npx skills add seotarek/MedOrqis
+
+# Or install specific clinical skills:
+npx skills add seotarek/MedOrqis --skill emergency-triage-redflags
+npx skills add seotarek/MedOrqis --skill pharmacology-dosing-interactions
+npx skills add seotarek/MedOrqis --skill pediatrics-neonatology
+```
+
+> ⭐ **Support Open-Source Clinical AI**: If MedOrqis helps your workflow or coding agents, please give the repo a **[Star on GitHub](https://github.com/seotarek/MedOrqis)** — it helps the project reach more clinicians and medical AI engineers!
+
+---
+
+### 📦 Option 2: NPX & NPM Interactive Terminal Package (`medorqis`)
+Explore the catalog and copy prompts directly in your terminal:
+```bash
+# Run interactive CLI browser
+npx medorqis
+
+# List all 24 skills grouped by safety tier
+npx medorqis list
+
+# Print copyable Universal AI Prompt for web chat models
+npx medorqis prompt
+
+# Print MCP configuration JSON block
+npx medorqis mcp
+```
+Or install globally or as a project dependency:
+```bash
+npm install -g medorqis
+# or in Node.js apps:
+npm install medorqis
+```
+
+---
+
+### ⚡ Option 3: Universal AI Model Prompting (Zero Install — Any Model)
+You do not need to install anything or run code to use MedOrqis with LLMs! You can send the repository link and prompt directly to **ChatGPT (with web access), Claude 3.5 Sonnet, Google Gemini, Cursor, Grok, or Antigravity**:
+
+> **Copy & Paste into any AI model:**
+> ```text
+> Read the open-source clinical AI skills ecosystem MedOrqis at:
+> https://github.com/seotarek/MedOrqis (Web catalog: https://seotarek.github.io/MedOrqis/)
+> 
+> You are now operating under MedOrqis clinical governance rules (v2.1.1):
+> 1. Enforce zero-hallucination deterministic standards for all medical risk scores and formulas (CHA2DS2-VA ESC 2024, CKD-EPI 2021, Bedside Schwartz, Cockcroft-Gault, Wells DVT/PE, CURB-65, HAS-BLED, NEWS2, Pediatric Dose Capping).
+> 2. Epistemic provenance: Never recommend high-risk interventions based on unconfirmed model hypotheses.
+> 3. Missing Age Gatekeeper: If patient age is unrecorded, do NOT assume a default adult age (30); immediately flag SAFE_ABSTENTION_DATA_DEFICIT.
+> 4. Sentinel Emergency Red Flags: Immediate emergency redirection on acute stroke (FAST), ACS crushing chest pain, anaphylaxis, septic shock, or anticoagulation + active bleeding.
+> 5. Provide evidence-grounded differential diagnosis, drug interaction screening, and red-flag triage across all 24 MedOrqis clinical domains.
+> 
+> Please summarize your activated clinical skills and await clinical input.
+> ```
+
+---
+
+### 🔌 Option 4: Model Context Protocol (MCP Server)
+Run the local MCP stdio server:
+```bash
+python3 mcp_server/medorqis_mcp_server.py
+```
+Add to your Claude Desktop configuration (`claude_desktop_config.json`):
+```json
+{
+  "mcpServers": {
+    "medorqis": {
+      "command": "python3",
+      "args": ["/path/to/MedOrqis/mcp_server/medorqis_mcp_server.py"]
+    }
+  }
+}
+```
+
+---
+
+### 🐍 Option 5: Local Python Developer Setup
+```bash
+git clone https://github.com/seotarek/MedOrqis.git
+cd MedOrqis
+python3 -m pip install -e .
+```
+
+---
+
+## 🧮 Pure Deterministic Clinical Calculators (`core/clinical_calculators.py`)
+
+All medical calculations in MedOrqis execute with **zero LLM API token overhead and strict mathematical determinism** via pure Python functions in [`core/clinical_calculators.py`](core/clinical_calculators.py):
+
+| # | Clinical Calculator | Function Name | Clinical Guideline & Standard | Target Population | Safety Gate & Boundary Enforcement |
+|---|---|---|---|---|---|
+| **1** | **CHA₂DS₂-VA** | `calculate_cha2ds2_va_esc2024` | ESC Guidelines 2024 (Sex-Neutral) | Adults ($\ge 18\text{y}$) with AF | Refuses if Age missing (`SAFE_ABSTENTION_DATA_DEFICIT`). Removes 1-point female bias. |
+| **2** | **CHA₂DS₂-VASc** | `calculate_cha2ds2_vasc_aha2023` | ACC/AHA/ACCP/HRS 2023 | Adults ($\ge 18\text{y}$) with AF | Historical comparative baseline for US guidelines ($+1$ for female sex). |
+| **3** | **CKD-EPI 2021** | `calculate_ckd_epi_2021_egfr` | NKF-ASN Task Force / NEJM 2021 | Adults ($\ge 18\text{y}$) | Race-free adult eGFR formula. **Hard Refusal** if Age $< 18$ years (`SAFE_REFUSAL_PEDIATRIC`). |
+| **4** | **Bedside Schwartz** | `calculate_bedside_schwartz_egfr` | Schwartz GJ et al. (JASN 2009) | Pediatrics ($< 18\text{y}$) | Height-based eGFR ($0.413 \times \text{Ht}/\text{SCr}$). **Hard Refusal** if Age $\ge 18$ years (`SAFE_REFUSAL_ADULT`). |
+| **5** | **Cockcroft-Gault** | `calculate_cockcroft_gault_crcl` | FDA Renal Dosing Standards | Adults ($\ge 18\text{y}$) | Automatically calculates IBW and Adjusted Body Weight (AdjBW $0.4$) if BMI $\ge 30$. |
+| **6** | **HAS-BLED** | `calculate_has_bled_score` | Pisters R et al. (Chest 2010) | Adults on Anticoagulation | Flags High Bleeding Risk ($\ge 3$); warns against unmonitored DOAC initiation. |
+| **7** | **CURB-65** | `calculate_curb65_score` | British Thoracic Society (BTS) | Adults with CAP | Stratifies 30-day mortality risk (Outpatient vs Inpatient vs ICU admission). |
+| **8** | **NEWS2** | `calculate_news2_score` | Royal College of Physicians (2017) | Acute Inpatient Care | Physiological aggregate triage across 6 vital signs; automated sepsis escalation. |
+| **9** | **Wells DVT Criteria** | `calculate_wells_dvt_score` | Wells PS et al. (NEJM 2003) | Suspected DVT | Pre-test probability (Unlikely vs Likely); dictates D-dimer vs Compression Ultrasound. |
+| **10** | **Wells PE Criteria** | `calculate_wells_pe_score` | Wells PS et al. (Ann Intern Med 2001) | Suspected PE | Pre-test probability (Unlikely vs Likely); dictates D-dimer vs CT Pulmonary Angiography. |
+
+*(Auxiliary dosing & safety engines: `calculate_pediatric_weight_dose` & `calculate_mosteller_bsa` in `core/clinical_calculators.py`, and Contraindicated DDI Screening in `core/safety_guardrails.py`)*.
+
+---
+
+## 🏥 The 24-Skill Risk-Stratified Taxonomy
+
+### Tier 1: Governance, Research & Operations (Class A)
+- `medorqis-orchestrator`: Context envelope routing and conflict resolution.
+- `ebm-research-biostatistics`: PICO, CASP, RoB-2 appraisal, and GRADE certainty.
+- `medical-documentation-translation`: SOAP, SBAR, and BiDi multilingual medical translation.
+- `healthcare-ops-telemedicine-ehr`: HL7 FHIR mapping and telemedicine intake.
+- `health-cybersecurity-privacy`: PHI scrubbing and prompt injection defense.
+- `public-health-epidemiology`: Screening metrics (sens/spec) and IPC protocols.
+
+### Tier 2: Diagnostic & Chronic Care Support (Class B)
+- `differential-diagnosis-cds`: VINDICATE differential framework.
+- `laboratory-medicine-pathology`: Critical panic values and LOINC mapping.
+- `radiology-medical-imaging`: ACR Appropriateness Criteria and radiation safety.
+- `internal-medicine-chronic`: Multi-morbidity chronic disease care plans.
+- `infectious-diseases-stewardship`: Antimicrobial stewardship and resistance awareness.
+- `nursing-clinical-care`: NEWS2 early warning score and Braden scale.
+- `clinical-nutrition-dietetics`: Caloric requirements and food-drug interactions.
+- `rehabilitation-physical-therapy`: Post-op and stroke rehab protocols.
+
+### Tier 3: High-Risk, Emergency & Vulnerable Populations (Class C)
+- `emergency-triage-redflags`: ABCDE primary survey and emergency redirection.
+- `clinical-safety-auditor`: Pre-output verification and safety gate check.
+- `pharmacology-dosing-interactions`: Renal/hepatic adjustments and DDI checks.
+- `clinical-toxicology-overdose`: Toxidromes, antidotes, and Poison Control escalation.
+- `pediatrics-neonatology`: Weight-based dose capping and pediatric safety.
+- `obstetrics-gynecology`: Maternal-fetal safety and pre-eclampsia triage.
+- `geriatrics-polypharmacy`: 2023 Beers Criteria and STOPP/START.
+- `mental-health-psychiatry`: Suicide crisis escalation and psychotropic monitoring.
+- `perioperative-surgical-care`: RCRI pre-op risk and anticoagulation bridging.
+- `oncology-palliative-care`: Oncologic emergencies and palliative pain control.
+
+---
+
+## 🌐 Multilingual & Dialect Regression Benchmark
+
+MedOrqis includes a deterministic natural language processing normalizer verified across **126 curated synthetic test fixtures**:
+- **100 Syntactic Negation Sentences**: Handcrafted fixtures verifying regex boundary detection and clause-stop logic across 8 dialects and languages: Modern Standard Arabic (`ar-MSA`), Egyptian (`ar-EG`), Gulf (`ar-GULF`), Levantine (`ar-LEV`), Maghrebi (`ar-MAG`), English (`en-US/GB`), French (`fr-FR`), and Spanish (`es-ES`).
+- **10 BiDi & Unit Token Strings**: Numerical and unit strings verifying bidirectional layout preservation (e.g. Arabic RTL mixing English numbers/units like "500 mg").
+- **16 Trade Brand-to-INN Mappings**: Lookup fixtures mapping regional commercial trade brand names to generic International Nonproprietary Names (e.g. Panadol $\to$ Paracetamol).
+
+> [!CAUTION]
+> **Two-Axis Governance Separation**:
+> - **Automated Syntactic Unit-Test Pass Rate**: **100.0% (126/126 passed)**.
+> - **Bedside Real-World Clinical Validation**: **0.0% (UNVALIDATED IN-VIVO / PENDING CLINICAL TRIALS)**.
+> 
+> See full breakdown and statistical caveats in [LANGUAGE_COVERAGE_MATRIX.md](LANGUAGE_COVERAGE_MATRIX.md).
+
+---
+
+## 🧪 Automated Verification & Provenance
+
+Execute cryptographic file integrity verification and the harmonized clinical test suite (all 36 unit, safety, multilingual, and adapter tests):
+```bash
+# 1. Verify SHA-256 cryptographic fingerprints across all 45 modules
+python3 core/integrity_manifest.py --verify
+
+# 2. Execute the harmonized clinical test suite
+python3 tests/run_all_tests.py
+```
+This automatically verifies:
+1. `tests/unit/test_clinical_calculators.py`: Boundary and formula correctness for all 12 clinical engines.
+2. `tests/safety/test_safety_and_provenance.py`: Epistemic provenance gates, missing age gatekeeper, sentinel emergency red-flags, and contraindicated DDIs.
+3. `tests/multilingual/test_multilingual_benchmark.py`: Negation preservation, BiDi unit fidelity, and brand-to-INN mapping across 126 test cases.
+4. `tests/platform_adapters/test_security_and_adapters.py`: SHA-256 cryptographic file integrity manifest, PHI scrubbing, prompt injection defense, and MCP JSON-RPC protocol.
+
+Artifacts generated:
+- [VERIFICATION_REPORT.md](tests/reports/VERIFICATION_REPORT.md)
+- [LANGUAGE_COVERAGE_MATRIX.md](LANGUAGE_COVERAGE_MATRIX.md)
+- [file_integrity_manifest.json](governance/file_integrity_manifest.json)
+
+---
+
+## ⚖️ Governance & Regulatory Disclaimer
+MedOrqis is an open-source clinical reference architecture and research framework. It is **NOT** a certified Medical Device (SaMD) and does not autonomously diagnose or prescribe. Clinical Decision Support outputs must always be reviewed by a licensed healthcare professional. See [MEDICAL_DISCLAIMER.md](MEDICAL_DISCLAIMER.md) and [SAFETY_AND_GOVERNANCE.md](SAFETY_AND_GOVERNANCE.md).
+
+---
+
+## 📚 Academic Citation & Persistent DOI
+If you use MedOrqis in clinical informatics, medical AI research, or clinical decision support development, please cite our persistent Zenodo repository DOI:
+
+```bibtex
+@software{mohamed_2026_medorqis,
+  author       = {Mohamed, Tarek},
+  title        = {MedOrqis: Medical AI Skills Ecosystem with Deterministic Safety Guardrails & Zero-Token Calculators},
+  month        = nov,
+  year         = 2026,
+  publisher    = {Zenodo},
+  version      = {v2.1.1},
+  doi          = {10.5281/zenodo.23937802},
+  url          = {https://doi.org/10.5281/zenodo.23937802}
+}
+```
+
+---
+
+## 📜 License
+Licensed under the [Apache License, Version 2.0](LICENSE).
+Medical vocabularies and guidelines are attributed in [DATA_LICENSES_AND_ATTRIBUTIONS.md](DATA_LICENSES_AND_ATTRIBUTIONS.md).