{
"markdown": "\n\n\n\n**Forensic-grade clinical research engine for Gemini CLI**\n\n[](https://gcli.dev)\n[](https://pubmed.ncbi.nlm.nih.gov)\n[](https://github.com/avivlyweb/pubmed-gemini-extension/releases)\n[](#license)\n\n
\n\n---\n\n# πΈ Nagomi (εγΏ): Calm Clarity in a Crisis of Fraud\n\nNagomi is not just a search tool. It is a **forensic-grade clinical research engine** designed to protect the integrity of medical science. \n\nIn a world where **1 in 500 academic papers are retracted** and AI hallucinations create \"fake evidence\" that looks 100% real, Nagomi acts as your scientific gatekeeper. It uses mathematical logic and deep-database cross-referencing to separate ground-breaking research from AI-generated fabrications.\n\n---\n\n## π¬ See It In Action\n\n\n\n\n\n
\n\n---\n\n## π Why Nagomi? (The Power of Forensic Research)\n\n### β‘ 1 Year of Research in 45 Seconds\n* **The Scenario:** A student spent a full year manually researching diagnostic clusters for shoulder impingement.\n* **The Nagomi Result:** In **45 seconds**, Nagomi performed a PICO-optimized search, audited the methodology of 20+ articles, and generated a more accurate, 2025-aligned clinical algorithm.\n* **Impact:** Massive ROI for clinicians and students who need \"Gold Standard\" answers without the manual labor.\n\n### π΅οΈββοΈ Catching \"Uncatchable\" AI Hallucinations\nNagomi automates scientific logic checks that standard plagiarism tools miss.\n* **The Case:** Detected a **Sequential ID Mismatch** in a student paper.\n* **The Proof:** Proved a cited \"2025 AI Study\" was actually using an ID from a **2020 paper about bladder infections**.\n* **Impact:** Absolute protection for academic integrity and degree quality control.\n\n---\n\n## π οΈ The Clinical Research Suite\n\n| Command | Capability | The Nagomi \"Superpower\" |\n|:--|:--|:--|\n| **`/nagomi:search`** | **PICO-Optimized Search** | Doesn't just find keywords. It extracts **Population, Intervention, Comparison, and Outcome** to find the exact clinical \"DNA\" of your question. |\n| **`/nagomi:synthesis`**| **PhD-Level Collation** | Collates dozens of studies into a weighted **Evidence Compass**. It tells you not just *what* was found, but *how much you should trust it*. |\n| **`/nagomi:verify`** | **Hallucination Hunter** | Scans PDFs/DOIs for **Volume Paradoxes** and **Stolen IDs**. Catch fabrication before it enters your bibliography. |\n| **`/nagomi:analyze`** | **Methodological Audit** | Performs a deep-dive on a single PMID. Grades it **A to D** based on sample size, study design, and risk of bias. |\n| **`/nagomi:export`** | **Seamless Integration** | Instant export to **BibTeX or RIS**. Connects your research directly to Zotero, Mendeley, or LaTeX. |\n\n---\n\n## π§ The ABC-TOM v3.1 Intelligence Layers\n\nNagomi doesn't just \"search\"βit **thinks** like a forensic auditor:\n\n1. **PICO Translation:** Automatically converts casual questions (e.g., \"best gout meds\") into precise clinical search strings.\n2. **Evidence Compass:** A visual weighted verdict that correctly favors Grade A Systematic Reviews over anecdotal Case Reports.\n3. **Volume Paradox Logic:** Identifies \"Frankenstein\" citations where the volume number is mathematically impossible for the cited year.\n4. **Sequential ID Tracking:** Detects when an AI reuses real article IDs from old papers to mask fake new titles.\n5. **Retraction Monitor:** Alerts you if a paper in your list has been officially pulled for fraud since its publication.\n\n---\n\n## Usage Examples\n\n**For Clinicians: Find the \"Best\" Treatment**\n```bash\n/nagomi:search what is the most effective treatment for Achilles tendinopathy\n/nagomi:synthesis yoga vs meditation for neuroplasticity in seniors\n```\n\n**For Professors: Audit Academic Integrity**\n```bash\n/nagomi:verify ~/Downloads/final_submission.pdf\n/nagomi:verify 10.1016/j.mcna.2014.03.005\n```\n\n**For Researchers: Deep-Dive and Export**\n```bash\n/nagomi:analyze 34580864\n/nagomi:export \"chronic heart failure telemonitoring\" format=bibtex\n```\n\n---\n\n## Installation\n\n```bash\ngemini extensions install https://github.com/avivlyweb/pubmed-gemini-extension\n```\n\n**Requirements:** Gemini CLI, Node.js 18+, Python 3.9+\n\n---\n\n## Version History\n\n| Version | Milestone | Features |\n|---------|-----------|----------|\n| **3.1.0** | **The Forensic Update** | Volume Paradox, Sequential IDs, Renamed to Nagomi. |\n| **3.0.0** | **The ABC-TOM Update** | 6-Tier Classification, Grey Literature detection. |\n| **2.5.0** | **The Evidence Update** | Evidence Compass, PICO logic, Weighted Verdicts. |\n\n---\n\n## License\n\nMIT\n\n---\n\n> [!IMPORTANT]\n> Nagomi Clinical Forensic is a research tool for scholarly exploration. It does not constitute medical advice. Clinical decisions should always be mediated by qualified practitioners.\n\n\n\n
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Made with love by Aviv at avivly\n\n