orchestrate

Files (7)

• SKILL.md
• data_flow_contract.md · references/
• dialogue_nodes.md · references/
• report_template.md · references/
• report_template_ko.md · references/
• skill.yml
• test_qc_gate_contract.py · tests/

SKILL.md (first lines)

# Orchestrate Skill

Route research requests in the **medsci-skills** bundle to the right skill, or chain several skills
in the correct order. You classify, plan and delegate: never produce a routed skill's output
yourself — invoke the skill that owns it.

---

## Available Skills

| Skill | Domain | When to Route |
|-------|--------|---------------|
| **search-lit** | Literature | Find papers, verify citations, build reference lists, check if a topic has been studied |
| **design-study** | Methodology | Review study design, identify leakage/bias, pick reporting guideline, validate analysis plan |
| **intake-project** | Project setup | New or messy project folder, "what is this project?", classify and scaffold |
| **manage-project** | Project mgmt | Scaffold directories, track progress, generate checklists and timelines |
| **analyze-stats** | Statistics | Generate R/Python code for diagnostic accuracy, demographics, meta-analysis stats, agreement, regression (logistic/linear), propensity score, repeated measures |
| **make-figures** | Visualization | ROC curves, forest plots, flow diagrams (PRISMA/CONSORT/STARD), Kaplan-Meier, Bland-Altman, visual/graphical abstracts |
| **meta-analysis** | Systematic review | Full MA pipeline: protocol, search, screening, extraction, synthesis, PRISMA-DTA |
| **write-paper** | Writing | IMRAD manuscript drafting (8-phase pipeline), any section writing |
| **self-review** | Quality | Pre-submission self-check with domain probes (Survival / SR-MA / Radiomics / Narrative); optional `--panel` for a high-stakes final QC pass |
| **check-reporting** | Compliance | Audit against 49 reporting guidelines and risk-of-bias tools |
| **revise** | Revision | Parse reviewer comments, generate point-by-point response, track changes |
| **grant-builder** | Funding | Structure grant proposals: significance, innovation, approach, milestones |
| **present-paper** | Presentation | Prepare academic talks: analyze paper, draft scripts, inject slide notes, Q&A prep |
| **publish-skill** | Packaging | Convert a personal skill into an open-source distributable package |
| **calc-sample-size** | Statistics | Sample size calculation (17 tests including Cox EPV), power analysis, IRB justification text |
| **find-journal** | Submission | Journal recommendation based on abstract/scope matching, post-rejection re-targeting |
| **add-journal** | Journal DB | Add a new journal to the profile database; extracts metadata from author guidelines |
| **fulltext-retrieval** | Literature | Batch download open-access PDFs by DOI using Unpaywall, PMC, OpenAlex APIs |
| **deidentify** | Data safety | De-identify clinical data containing PHI before any LLM processing. Standalone Python CLI (no LLM). |
| **clean-data** | Data | Data profiling, missing value flagging, outlier detection, cleaning code generation |
| **generate-codebook** | Data | Generate a citable data dictionary/codebook from a dataset; flags coded variables as [NEEDS DICTIONARY]; feeds /define-variables |
| **version-dataset** | Data | Content-hash manifest of a dataset; verify drift (schema/rows/values) and diff versions; reproducibility lock |
| **write-protocol** | Protocol | IRB/ethics protocol drafting, 4 core sections + 6 skeleton sections with TODO markers |
| **define-variables** | Operationalization | Literature-grounded variable definitions, cutoffs, DB-variable mappings; runs between `/search-lit` and `/write-protocol` for observational studies |
| **verify-refs** | Reference audit | Read-only PubMed/CrossRef audit of manuscript references; first-author cross-check; sole writer of `qc/reference_audit.json`. Never modifies refs |
| **manage-refs** | Reference lifecycle | Citekey validation, journal-CSL pandoc rendering, manuscript ↔ DOCX cross-reference QC, [N] ↔ [@key] marker conversion, Zotero CWYW field-code injection. Sole writer of `manuscript_final.docx`, `qc/xref_audit.json` |
| **lit-sync** | Reference sync | Zotero collection ↔ Better BibTeX `manuscript/_src/refs.bib` ↔ Obsidian literature notes. Sole writer of refs.bib (auto-export); upstream of `manage-refs` |
| **obsidian-paper-vault** | Vault build | A folder of PDFs → templated Obsidian literature notes + atomic concept notes synthesized across them. Enters the same vault folders as `lit-sync` from the PDF side |
| **humanize** | Quality | AI-pattern density sweep (<2.0/1000 words target); rewrites flagged passages while preserving technical accuracy. Phase 7.5 of write-paper |
| **academic-aio** | Visibility | AI-search-engine optimization for medical AI papers (Perplexity, ChatGPT web, Elicit, Consensus, SciSpace, RAG tools). Opt-in checklist; never auto-applies edits |
| **render-pdf-doc** | Document layout | Non-bibliography academic markdown → PDF (proposal, briefing, anchor doc, IRB cover, reference table), CJK-aware. Boundary opposite of `manage-refs scripts/render_pandoc.sh` |
| **fill-protocol** | Form filling | Institutional Word form filling (.doc/.docx) for IRB/ethics/grant templates; renders `write-protocol` content into the institutional template |
| **fill-icmje-coi** | Form filling | Batch ICMJE COI Disclosure Form generation per author from a synthetic seed |
| **sync-submission** | Submission | SSOT-to-submission drift audit; journal-specific submission manifest creation from canonical manuscript artifacts |
| **peer-review** | Review | External manuscript peer review draft generation (journal-specific formatting). Use ONLY for reviewing other authors' work, never for self-review |
| **review-paper** | Writing | Scaffold/draft a literature review (narrative / scoping PRISMA-ScR / systematic). Distinct from `write-paper` (original research) and `meta-analysis` (pooling) |
| **polish-language** | Quality | Academic-English consistency lint + non-native clarity polish (abbreviations, US/UK spelling, ranges, P/p case, units). Style-only; distinct from `humanize` (AI-tell removal) and `check-reporting` (guideline items) |
| **author-strategy** | Analysis | PubMed author-profile analysis: study-type classification, trajectory-archetype, publication-strategy report from a name |
| **batch-cohort** | Analysis | Generate N analysis scripts from one validated methodology template × many exposure/outcome combinations (same method, swap variables) + summary matrix |
| **replicate-study** | Analysis | Replicate an existing cohort study's methodology on a different database: design extraction, variable-harmonization table, replication-difference report |
| **cross-national** | Analysis | Cross-national comparison study (KNHANES + NHANES + CHNS or parallel surveys): variable harmonization + parallel weighted analysis |
| **ma-scout** | Systematic review | Meta-analysis topic discovery + feasibility (professor-first profile→gap, or topic-first question→gap→co-author) before a protocol exists |
| **find-cohort-gap** | Methodology | Research-gap discovery from a longitudinal cohort DB: profile strengths, match PI expertise, literature-saturation scan, ranked topic proposals |
| **design-ai-benchmarking** | Methodology | Design/validity review for benchmarking AI systems against a human-expert reference panel (rubrics, calibration probes, panel construction, IRR targets) — before data collection |
| **model-selection** | Modeling | Choose the model for an imaging study: a paper-grounded architecture family (task + modality + data scale + imbalance → shortlist), then vet the concrete repo / checkpoint (licence, version pin, weight provenance; flags an evaluation arm on the benchmark the model was developed or tuned on) |
| **imaging-data** | Modeling | Profile an imaging dataset before any modelling decision (spacing/orientation, intensity domain, label integrity, foreground fraction, target volume) and gate it against the plan; then plan/audit DICOM/NIfTI intake, resampling, normalisation and augmentation with a preprocessing manifest + data-stage leakage gate before `model-scaffold` |
| **model-scaffold** | Modeling | Generate a reproducible runnable PyTorch training repo (patient-level seed-locked split, task model, train/eval scripts, repro record) — between choosing an architecture and validating a trained model |
| **radiomics-ml** | Modeling | Produce/audit a radiomics / tabular-ML study (imaging or clinical features → penalised logistic / SVM / RF / gradient-boosting / MLP → outcome) with a nested-CV / feature-stability / calibration / external-validation gate (no GPU) |
| **model-assessment** | Validation | Validate/evaluate a trained imaging model: split-leakage gate + validation design (internal vs external, comparator, sizing); task-correct held-out metrics (Dice + boundary, AUROC + AUPRC with bootstrap CIs, FROC/mAP, calibration, subgroups) → per-case table; uncertainty/OOD/abstention for deployment claims; Grad-CAM/explainability sanity checks + localisation |
| **mllm-eval** | Evaluation | Design/audit an evaluation harness for an LLM/MLLM clinical task (report generation, VQA, extraction/classification): adjudicated reference, clinical-efficacy metrics beyond BLEU/ROUGE, hallucination, contamination, prompt-sensitivity, reader study |
| **model-card** | Documentation | Generate a Model Card + Datasheet + data-quality pass for an engineer-built imaging model from user-supplied facts, with a completeness gate |
| **contribute** | Setup | Offer a local edit (a journal profile, a fix) back as a pull request or issue without typing git; blocks on patient data in the diff and sends nothing until confirmed. Also files a false positive or a failed step |
| **setup-medsci** | Setup | Read-only runtime diagnostic (Python, R, Node, Claude Code, Git, Zotero, MCP servers): pass/fail table with the setup doc for each missing component |

---

## Classification Logic

Classify each request into one of these intents.

### Single-skill requests (route directly)

Route to the skill whose Available Skills row matches: name it with a one-line reason, then invoke
it. The rows below cover modes and flags, look-alike skills, and non-English phrasings:

| User says something like... | Route to |
|-----------------------------|----------|
| "I have a messy folder, help me organize" | `/intake-project` |
| "Set up a new project" / "Create project scaffold" | `/manage-project init` |
| "Review my manuscript before submission" | `/self-review` |
| "Brutally / harshly check before submission" / "top-tier journal final check" / "multi-reviewer / panel review" / "review it from stats, clinical, and imaging angles" / "혹독하게 제출 전 점검" | `/self-review --panel --json` |
| "Review someone else's manuscript" / "Journal club critique draft" / "외부 논문 리뷰 답변" | `/peer-review` |
| "Which journal should I submit to?" / "Find a journal" / "I was rejected, where else?" | `/find-journal` |
| "Sync submission" / "Retarget journal" / "Check SSOT drift" | `/sync-submission` |
| "Add a journal profile" / "저널 프로필 추가" | `/add-journal` |
| "Download PDFs" / "Get full texts" / "PDF 다운로드" | `/fulltext-retrieval` |
| "Visual abstract 만들어줘" / "Graphical abstract" / "GA 생성" | `/make-figures` |
| "De-identify my data" / "Remove PHI" / "비식별화" / "익명화" / "Anonymize patient data" | `/deidentify` |
| "Write an IRB protocol" / "Draft ethics submission" / "Research protocol" | `/write-protocol` |
| "Fill IRB protocol form" / "기관 양식 채워줘" / "심사면제 요청서 채움" / "동의면제 양식" | `/fill-protocol` |
| "Define my variables" / "Justify cutoff" / "Phenotype definition" / "변수 정의 근거" / "ad-hoc 정의 피하기" | `/define-variables` |
| "Write a case report" / "I have an interesting case" | `/write-paper` (case-report mode) |
| "Generate a cover letter" / "Write cover letter for submission" | `/write-paper` (Phase 8+, requires completed manuscript) |
| "Render manuscript to DOCX" / "Build final .docx" / "Cascade reformat references" / "Apply journal CSL" / "Re-render with Vancouver" / "회람용 docx" / "Zotero CWYW injection" | `/manage-refs` |
| "Render proposal to PDF" / "Anchor doc PDF" / "한글 학술 PDF" / "Briefing handout PDF" / "IRB cover PDF" / "non-bib markdown → PDF" | `/render-pdf-doc` |
| "Sync Zotero" / "Refresh refs.bib" / "Better BibTeX export" / "Zotero ↔ Obsidian 동기화" / "literature note 만들어줘" | `/lit-sync` |
| "PDF를 Obsidian 노트로" / "논문 요약 노트 만들어줘" / "이 폴더의 PDF 정리해줘" / "build a paper vault" / "second brain" / "extract concepts from papers" | `/obsidian-paper-vault` |
| "ICMJE COI 양식 일괄 생성" / "공저자 COI 폼 만들기" / "Disclosure form batch" | `/fill-icmje-coi` |
| "AI search optimization" / "Perplexity-friendly abstract" / "RAG visibility" / "GEO checklist" / "Elicit/Consensus 노출" | `/academic-aio` |
| "Remove AI patterns" / "AI 티 제거" / "humanize this section" / "GPT 흔적 지워줘" | `/humanize` |

### Multi-skill workflows (plan then execute sequentially)

The **Nodes** column lists the decision forks to render in interactive mode (Dialogue Protocol
below); N1–N11 are defined in `${CLAUDE_SKILL_DIR}/references/dialogue_nodes.md`.

| Scenario | Skill chain | Nodes |
|----------|-------------|-------|
| **New project, no prior work** | `intake-project` -> `search-lit` -> `design-study` -> `manage-project init` | N1, N2 (if user wants manuscript output), N3 |
| **Data ready, need a paper** | `manage-project init` -> `analyze-stats` -> `make-figures` -> `write-paper` | N6 (PHI gate), N3, N4 (journal timing), N2 |
| **Draft exists, prepare for submission** | `self-review` -> `check-reporting` -> `verify-refs` -> `humanize` -> `academic-aio` (opt-in `--aio`) -> `manage-refs` (DOCX build + xref QC `--strict`) -> `manage-project checklist` | N4 (if not yet locked), N8 (only if self-review returns fatal) |
| **Submission rendering & cascade reformat** | `manage-refs` (Workflow A pandoc citeproc, or B Zotero CWYW) -> `manage-refs scripts/check_xref.py --strict` -> `verify-refs` -> `sync-submission build` | N10 (Workflow A vs B selection — see manage-refs SKILL.md decision tree) |
| **Cascade rejection re-target** | `find-journal` (exclude rejected) -> `manage-refs` (re-render with new CSL) -> `write-paper` Phase 8+ (new cover letter) -> `sync-submission build --journal {new}` | N4 |
| **Non-bibliography academic deliverable (proposal/briefing/anchor doc)** | `write-protocol` -> `fill-protocol` (institutional form available) ⫶ `render-pdf-doc` (markdown-only, no form) | N11 (form available vs not) |
| **Reference housekeeping cycle** | `lit-sync` (Zotero ↔ refs.bib auto-export) -> `manage-refs scripts/check_citation_keys.py` -> `verify-refs --strict` (first-author cross-check) | — |
| **ICMJE COI batch (multi-author submission)** | `fill-icmje-coi` (per-author docx generation from synthetic seed) -> manual circulation | — |
| **Medical-AI paper, AI-search visibility pass** | `self-review` -> `humanize` -> `academic-aio` (title, abstract, summary box, README / CITATION.cff / HF card) | N4, N9 (section entry for re-edit scope) |

From Aperivue/medsci-skills, MIT.

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