medsci-skills 4.1.0

package/metadata/skills_catalog.json

@@ -0,0 +1,452 @@
+{
+  "_comment": "AUTO-GENERATED by scripts/gen_skills_catalog_json.py from each skills/<slug>/SKILL.md + skill.yml. Machine-readable skill catalog (single source of truth) consumed by external surfaces such as the aperivue.com storefront to gate skill-list completeness. Do not hand-edit; CI gate: python3 scripts/gen_skills_catalog_json.py --check.",
+  "skill_count": 44,
+  "categories": [
+    {
+      "key": "literature_references",
+      "label": "Literature & References",
+      "slugs": [
+        "fulltext-retrieval",
+        "lit-sync",
+        "manage-refs",
+        "search-lit",
+        "verify-refs"
+      ]
+    },
+    {
+      "key": "data_study_design",
+      "label": "Data & Study Design",
+      "slugs": [
+        "calc-sample-size",
+        "clean-data",
+        "define-variables",
+        "deidentify",
+        "design-ai-benchmarking",
+        "design-study",
+        "generate-codebook",
+        "version-dataset"
+      ]
+    },
+    {
+      "key": "analysis_figures",
+      "label": "Analysis & Figures",
+      "slugs": [
+        "analyze-stats",
+        "batch-cohort",
+        "cross-national",
+        "make-figures",
+        "meta-analysis",
+        "replicate-study"
+      ]
+    },
+    {
+      "key": "writing_manuscript",
+      "label": "Writing & Manuscript",
+      "slugs": [
+        "academic-aio",
+        "humanize",
+        "review-paper",
+        "revise",
+        "write-paper",
+        "write-protocol"
+      ]
+    },
+    {
+      "key": "review_compliance",
+      "label": "Review & Compliance",
+      "slugs": [
+        "check-reporting",
+        "peer-review",
+        "self-review"
+      ]
+    },
+    {
+      "key": "submission_journals",
+      "label": "Submission & Journals",
+      "slugs": [
+        "add-journal",
+        "fill-icmje-coi",
+        "fill-protocol",
+        "find-journal",
+        "grant-builder",
+        "sync-submission"
+      ]
+    },
+    {
+      "key": "project_workflow",
+      "label": "Project & Workflow",
+      "slugs": [
+        "author-strategy",
+        "find-cohort-gap",
+        "intake-project",
+        "ma-scout",
+        "manage-project",
+        "orchestrate"
+      ]
+    },
+    {
+      "key": "presentation_tooling",
+      "label": "Presentation & Tooling",
+      "slugs": [
+        "present-paper",
+        "publish-skill",
+        "render-pdf-doc",
+        "setup-medsci"
+      ]
+    }
+  ],
+  "skills": [
+    {
+      "slug": "academic-aio",
+      "category": "writing_manuscript",
+      "category_label": "Writing & Manuscript",
+      "layer": "C",
+      "owner_domain": "manuscript_optimization",
+      "description": "Medical AI paper optimization for AI search engines (Perplexity, ChatGPT web, Elicit, Consensus, SciSpace) and RAG-based literature tools."
+    },
+    {
+      "slug": "add-journal",
+      "category": "submission_journals",
+      "category_label": "Submission & Journals",
+      "layer": "C",
+      "owner_domain": "journal_profile_authoring",
+      "description": "Add a new journal to the MedSci Skills profile database."
+    },
+    {
+      "slug": "analyze-stats",
+      "category": "analysis_figures",
+      "category_label": "Analysis & Figures",
+      "layer": "B",
+      "owner_domain": "statistical_analysis",
+      "description": "Statistical analysis for medical research papers."
+    },
+    {
+      "slug": "author-strategy",
+      "category": "project_workflow",
+      "category_label": "Project & Workflow",
+      "layer": "D",
+      "owner_domain": "author_profile_analysis",
+      "description": "PubMed author profile analysis."
+    },
+    {
+      "slug": "batch-cohort",
+      "category": "analysis_figures",
+      "category_label": "Analysis & Figures",
+      "layer": "B",
+      "owner_domain": "batch_analysis",
+      "description": "Generate N analysis scripts from a single methodology template × multiple exposure/outcome combinations."
+    },
+    {
+      "slug": "calc-sample-size",
+      "category": "data_study_design",
+      "category_label": "Data & Study Design",
+      "layer": "A",
+      "owner_domain": "study_design",
+      "description": "Interactive sample size calculator for medical research."
+    },
+    {
+      "slug": "check-reporting",
+      "category": "review_compliance",
+      "category_label": "Review & Compliance",
+      "layer": "A",
+      "owner_domain": "reporting_compliance",
+      "description": "Check manuscript compliance with medical research reporting guidelines."
+    },
+    {
+      "slug": "clean-data",
+      "category": "data_study_design",
+      "category_label": "Data & Study Design",
+      "layer": "B",
+      "owner_domain": "data_preparation",
+      "description": "Interactive data profiling and cleaning assistant for medical research."
+    },
+    {
+      "slug": "cross-national",
+      "category": "analysis_figures",
+      "category_label": "Analysis & Figures",
+      "layer": "B",
+      "owner_domain": "cross_national_comparison",
+      "description": "End-to-end cross-national comparison study using KNHANES + NHANES + CHNS (or other parallel surveys)."
+    },
+    {
+      "slug": "define-variables",
+      "category": "data_study_design",
+      "category_label": "Data & Study Design",
+      "layer": "C",
+      "owner_domain": "variable_operationalization",
+      "description": "Literature-grounded variable operationalization for observational research."
+    },
+    {
+      "slug": "deidentify",
+      "category": "data_study_design",
+      "category_label": "Data & Study Design",
+      "layer": "A",
+      "owner_domain": "data_preparation",
+      "description": "De-identify clinical research data before LLM-assisted analysis."
+    },
+    {
+      "slug": "design-ai-benchmarking",
+      "category": "data_study_design",
+      "category_label": "Data & Study Design",
+      "layer": "D",
+      "owner_domain": "study_design",
+      "description": "Design and validity review for studies that benchmark one or more AI systems against a human-expert panel as the reference."
+    },
+    {
+      "slug": "design-study",
+      "category": "data_study_design",
+      "category_label": "Data & Study Design",
+      "layer": "D",
+      "owner_domain": "study_design",
+      "description": "Study design and validity review for radiology and medical AI research."
+    },
+    {
+      "slug": "fill-icmje-coi",
+      "category": "submission_journals",
+      "category_label": "Submission & Journals",
+      "layer": "A",
+      "owner_domain": "form_filling",
+      "description": "Batch-generate per-author ICMJE Conflict of Interest Disclosure Forms (`coi_disclosure.docx`) for manuscript submission."
+    },
+    {
+      "slug": "fill-protocol",
+      "category": "submission_journals",
+      "category_label": "Submission & Journals",
+      "layer": "A",
+      "owner_domain": "form_filling",
+      "description": "Fill institutional Word form templates (.doc/.docx) for IRB protocols, ethics applications, grant proposals, and other structured research documents while preserving the original styles, table layouts…"
+    },
+    {
+      "slug": "find-cohort-gap",
+      "category": "project_workflow",
+      "category_label": "Project & Workflow",
+      "layer": "D",
+      "owner_domain": "research_gap_analysis",
+      "description": "Research gap finder for longitudinal cohort databases."
+    },
+    {
+      "slug": "find-journal",
+      "category": "submission_journals",
+      "category_label": "Submission & Journals",
+      "layer": "D",
+      "owner_domain": "journal_recommendation",
+      "description": "Journal recommendation engine for medical manuscripts."
+    },
+    {
+      "slug": "fulltext-retrieval",
+      "category": "literature_references",
+      "category_label": "Literature & References",
+      "layer": "A",
+      "owner_domain": "literature_discovery",
+      "description": "Batch download open-access PDFs by DOI using legitimate OA APIs (Unpaywall, PMC, OpenAlex, Crossref)."
+    },
+    {
+      "slug": "generate-codebook",
+      "category": "data_study_design",
+      "category_label": "Data & Study Design",
+      "layer": "A",
+      "owner_domain": "data_documentation",
+      "description": "Generate a citable data dictionary / codebook from a tabular dataset (CSV/TSV/Excel/Parquet/Stata/SAS)."
+    },
+    {
+      "slug": "grant-builder",
+      "category": "submission_journals",
+      "category_label": "Submission & Journals",
+      "layer": "C",
+      "owner_domain": "grant_proposal",
+      "description": "Grant and challenge proposal support for radiology and medical AI projects."
+    },
+    {
+      "slug": "humanize",
+      "category": "writing_manuscript",
+      "category_label": "Writing & Manuscript",
+      "layer": "C",
+      "owner_domain": "ai_pattern_removal",
+      "description": "Detect and remove AI writing patterns from academic manuscripts and response-to-reviewers letters."
+    },
+    {
+      "slug": "intake-project",
+      "category": "project_workflow",
+      "category_label": "Project & Workflow",
+      "layer": "D",
+      "owner_domain": "project_intake",
+      "description": "Intake and normalize a new radiology research project."
+    },
+    {
+      "slug": "lit-sync",
+      "category": "literature_references",
+      "category_label": "Literature & References",
+      "layer": "A",
+      "owner_domain": "zotero_sync",
+      "description": "Sync research references from .bib files to Zotero library + Obsidian literature notes."
+    },
+    {
+      "slug": "ma-scout",
+      "category": "project_workflow",
+      "category_label": "Project & Workflow",
+      "layer": "D",
+      "owner_domain": "ma_topic_discovery",
+      "description": "Meta-analysis topic discovery and feasibility assessment."
+    },
+    {
+      "slug": "make-figures",
+      "category": "analysis_figures",
+      "category_label": "Analysis & Figures",
+      "layer": "B",
+      "owner_domain": "figure_generation",
+      "description": "Generate publication-ready figures and visual abstracts for medical research papers."
+    },
+    {
+      "slug": "manage-project",
+      "category": "project_workflow",
+      "category_label": "Project & Workflow",
+      "layer": "D",
+      "owner_domain": "project_management",
+      "description": "Research project management for medical manuscripts."
+    },
+    {
+      "slug": "manage-refs",
+      "category": "literature_references",
+      "category_label": "Literature & References",
+      "layer": "A",
+      "owner_domain": "manuscript_lifecycle",
+      "description": "Cross-cutting reference manager for medical manuscripts."
+    },
+    {
+      "slug": "meta-analysis",
+      "category": "analysis_figures",
+      "category_label": "Analysis & Figures",
+      "layer": "B",
+      "owner_domain": "meta_analysis_integrity",
+      "description": "Systematic review and meta-analysis pipeline for medical research."
+    },
+    {
+      "slug": "orchestrate",
+      "category": "project_workflow",
+      "category_label": "Project & Workflow",
+      "layer": "D",
+      "owner_domain": "orchestration",
+      "description": "General-purpose research orchestrator."
+    },
+    {
+      "slug": "peer-review",
+      "category": "review_compliance",
+      "category_label": "Review & Compliance",
+      "layer": "C",
+      "owner_domain": "external_peer_review",
+      "description": "Peer review assistant for medical journals."
+    },
+    {
+      "slug": "present-paper",
+      "category": "presentation_tooling",
+      "category_label": "Presentation & Tooling",
+      "layer": "C",
+      "owner_domain": "presentation",
+      "description": "Academic presentation preparation — paper-driven (journal club, grand rounds, seminar) and lecture/teaching decks (course material, workshop slides, conference talks)."
+    },
+    {
+      "slug": "publish-skill",
+      "category": "presentation_tooling",
+      "category_label": "Presentation & Tooling",
+      "layer": "B",
+      "owner_domain": "skill_publishing",
+      "description": "Convert a personal agent skill into a distributable, open-source-ready skill."
+    },
+    {
+      "slug": "render-pdf-doc",
+      "category": "presentation_tooling",
+      "category_label": "Presentation & Tooling",
+      "layer": "A",
+      "owner_domain": "document_layout",
+      "description": "Render academic Markdown documents (English or Korean) to publication-quality PDF via pandoc + xelatex."
+    },
+    {
+      "slug": "replicate-study",
+      "category": "analysis_figures",
+      "category_label": "Analysis & Figures",
+      "layer": "B",
+      "owner_domain": "study_replication",
+      "description": "Replicate an existing cohort study's methodology on a different database."
+    },
+    {
+      "slug": "review-paper",
+      "category": "writing_manuscript",
+      "category_label": "Writing & Manuscript",
+      "layer": "C",
+      "owner_domain": "manuscript_authoring",
+      "description": "Scaffold and draft medical/AI literature reviews (narrative, scoping PRISMA-ScR, or systematic)."
+    },
+    {
+      "slug": "revise",
+      "category": "writing_manuscript",
+      "category_label": "Writing & Manuscript",
+      "layer": "B",
+      "owner_domain": "reviewer_response",
+      "description": "Parse peer reviewer comments and generate a structured Response to Reviewers document with tracked manuscript changes."
+    },
+    {
+      "slug": "search-lit",
+      "category": "literature_references",
+      "category_label": "Literature & References",
+      "layer": "A",
+      "owner_domain": "literature_discovery",
+      "description": "Literature search and citation management for medical research."
+    },
+    {
+      "slug": "self-review",
+      "category": "review_compliance",
+      "category_label": "Review & Compliance",
+      "layer": "D",
+      "owner_domain": "own_manuscript_critique",
+      "description": "Pre-submission self-review for the user's own manuscripts, applying a reviewer perspective."
+    },
+    {
+      "slug": "setup-medsci",
+      "category": "presentation_tooling",
+      "category_label": "Presentation & Tooling",
+      "layer": "A",
+      "owner_domain": "environment_setup",
+      "description": "Diagnostic checklist for the MedSci Skills runtime."
+    },
+    {
+      "slug": "sync-submission",
+      "category": "submission_journals",
+      "category_label": "Submission & Journals",
+      "layer": "A",
+      "owner_domain": "submission_packaging",
+      "description": "Audit SSOT-to-submission drift and create journal submission manifests from canonical manuscript artifacts."
+    },
+    {
+      "slug": "verify-refs",
+      "category": "literature_references",
+      "category_label": "Literature & References",
+      "layer": "A",
+      "owner_domain": "reference_integrity",
+      "description": "Audit-only verification of manuscript references against PubMed and CrossRef."
+    },
+    {
+      "slug": "version-dataset",
+      "category": "data_study_design",
+      "category_label": "Data & Study Design",
+      "layer": "A",
+      "owner_domain": "dataset_versioning",
+      "description": "Dataset version control for research reproducibility."
+    },
+    {
+      "slug": "write-paper",
+      "category": "writing_manuscript",
+      "category_label": "Writing & Manuscript",
+      "layer": "C",
+      "owner_domain": "manuscript_drafting",
+      "description": "Full-pipeline medical/scientific paper writing."
+    },
+    {
+      "slug": "write-protocol",
+      "category": "writing_manuscript",
+      "category_label": "Writing & Manuscript",
+      "layer": "C",
+      "owner_domain": "protocol_drafting",
+      "description": "IRB/ethics committee research protocol generator."
+    }
+  ]
+}

package/package.json

@@ -0,0 +1,48 @@
+{
+  "name": "medsci-skills",
+  "version": "4.1.0",
+  "description": "MedSci Skills — a medical/scientific research skill suite for AI coding agents (Claude Code, Codex, Cursor, Copilot). The npm package is a terminal-friendly installer shortcut; the canonical distribution remains the GitHub repository and the Claude Code plugin marketplace.",
+  "license": "SEE LICENSE IN LICENSE",
+  "homepage": "https://github.com/Aperivue/medsci-skills#readme",
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/Aperivue/medsci-skills.git"
+  },
+  "bugs": {
+    "url": "https://github.com/Aperivue/medsci-skills/issues"
+  },
+  "bin": {
+    "medsci-skills": "bin/medsci-skills.js"
+  },
+  "files": [
+    "skills/",
+    "installers/install.py",
+    "installers/install-macos.command",
+    "installers/install-windows.cmd",
+    "installers/install-windows.ps1",
+    "metadata/skills_catalog.json",
+    "bin/medsci-skills.js",
+    "README.md",
+    "README_FIRST.md",
+    "LICENSE"
+  ],
+  "engines": {
+    "node": ">=18"
+  },
+  "keywords": [
+    "medical-research",
+    "radiology",
+    "meta-analysis",
+    "systematic-review",
+    "reporting-guidelines",
+    "biostatistics",
+    "peer-review",
+    "claude-code",
+    "agent-skills",
+    "research-pipeline"
+  ],
+  "scripts": {
+    "prepack": "find skills installers -name __pycache__ -type d -prune -exec rm -rf {} + 2>/dev/null; true",
+    "test": "bash tests/test_npm_package.sh"
+  }
+}