ma-scout · diff

git:20260609.c54df30 to git:20260930.c83ad00

134 added, 365 removed. Audit A to A.

---
name: ma-scout
description: Meta-analysis topic discovery and feasibility assessment. Professor-first (profile → gap) or Topic-first (question → gap → co-author). Pre-protocol phase from idea to ranked topic list.
triggers: ma-scout, MA 주제 찾기, professor MA, 메타분석 주제, MA gap, topic-first MA, 트렌드 MA, meta-analysis topic, 교수님 분석, 연구 분석
tools: Read, Write, Edit, Bash, Grep, Glob
model: opus
---
# MA Scout Skill
- You are helping a medical researcher discover meta-analysis topics.
- Two modes are available depending on the starting point.
-
- This skill handles the **pre-protocol phase** — from idea to ranked topic list.
+ This skill handles the **pre-protocol phase** of a meta-analysis — from idea to ranked topic list.
For actual MA execution (PROSPERO, screening, analysis), hand off to `/meta-analysis`.
## Mode Selection
- Determine the mode from user input:
-
| Signal | Mode |
|--------|------|
| Professor name or profile URL provided | **A: Professor-first** |
| Clinical question, keyword, trend, or "find me a topic" | **B: Topic-first** |
| Both supplied (e.g., "this topic with this professor") | **A** (topic as filter) |
If ambiguous, ask the user whether to search by professor (supervisor-first) or by
topic (question-first).
- ## Communication Rules
-
- - Communicate with the user in their preferred language (typically Korean).
- - Research questions, PICO/PIRD, and README content in English.
- - Medical terminology always in English.
-
- ---
-
## Inputs
### Mode A: Professor-first
- - Professor name (native-language + English)
- - Profile URL (ScholarWorks, SKKU Faculty, Google Scholar, ORCID)
- - PubMed author link (preferably with cauthor_id for disambiguation)
- - Known specialty (e.g., "thoracic imaging", "abdominal imaging")
- - Affiliation history (e.g., "Hospital A → Hospital B → retired")
+ - Professor name (native-language + English); profile URL (ScholarWorks, SKKU Faculty, Google
+ Scholar, ORCID); PubMed author link (preferably with cauthor_id for disambiguation); known
+ specialty; affiliation history (e.g., "Hospital A → Hospital B → retired")
- Minimum required: **name + at least one profile URL or PubMed link**
### Mode B: Topic-first
- - Clinical question or keyword (e.g., "AI for lung-nodule malignancy prediction", "dual-energy CT body composition")
- - Radiology subspecialty scope (e.g., thoracic, abdominal, neuro)
- - MA type preference (DTA, prognostic, intervention — optional)
- - Desired role: solo first author / co-first / supervisor-matched
+ - Clinical question or keyword; radiology subspecialty scope; MA type preference (DTA,
+ prognostic, intervention — optional); desired role (solo first author / co-first /
+ supervisor-matched)
- Minimum required: **clinical question or keyword**
- ---
-
## Workflow
> **Mode A (Professor-first):** Phase 0 → 1 → 2 → 3 → 4 → 5
> **Mode B (Topic-first):** T-Phase 0 → T-1 → T-2 → T-3 → T-4 → T-5
> Phase 2 (MA Gap Analysis) and Phase 4 (README template) are shared between both modes.
- ---
+ Query PubMed with `/search-lit`'s E-utilities scripts, not WebFetch — they are faster and return
+ structured JSON/XML: `${CLAUDE_SKILL_DIR}/../search-lit/references/pubmed_eutils.sh` and
+ `parse_pubmed.py` beside it. Rate limit: 350 ms between calls (100 ms with `NCBI_API_KEY`).
- # ═══════════════════════════════════════════
# MODE A: PROFESSOR-FIRST WORKFLOW
- # ═══════════════════════════════════════════
### Phase 0: Disambiguation & Context Confirmation
- **Goal:** Resolve author identity before any search, and confirm user's relationship context.
-
- **CRITICAL — Do this BEFORE any PubMed search:**
-
- 1. **Resolve full English name first:**
- - If cauthor_id is provided → fetch that specific PMID page to get full name + affiliation
- - NEVER start with initials-only search (e.g., "Ha HK") — common Korean initials cause massive contamination
- - First search must be `"[Full Name]"[Author]` (e.g., `"Ha Hyun Kwon"[Author]`)
-
- 2. **Confirm affiliation chain with user:**
- - Ask the user whether `{detected affiliation}` matches the professor's history,
- and request the user's relationship to the professor so topic proposals can be
- tuned accordingly.
- - This prevents wrong-institution assumptions
- - Skip only if user already provided explicit affiliation history
+ Resolve the author's identity BEFORE any PubMed search:
- 3. **Profile URL fallback chain** (Scopus requires auth, so plan alternatives):
- - 1st: PubMed full name search (always works)
+ 1. **Resolve the full English name first.** If a cauthor_id is provided, fetch that PMID page to
+ get the full name + affiliation. NEVER start with an initials-only search, because common
+ Korean/Asian initials (e.g., "Lee KS") return 300+ papers with massive contamination. The first
+ search must be `"[Full Name]"[Author]`.
+ 2. **Confirm the affiliation chain with the user.** Ask whether `{detected affiliation}` matches
+ the professor's history (professors move institutions — do not assume), and ask the user's
+ relationship to the professor so topic proposals can be tuned. Skip only if the user already
+ gave an explicit affiliation history.
+ 3. **Profile URL fallback chain:**
+ - 1st: PubMed full-name search (always works)
- 2nd: Google Scholar profile (WebSearch `"[Full Name]" radiology scholar`)
- 3rd: ResearchGate profile (WebSearch `"[Full Name]" researchgate radiology`)
- 4th: ScholarWorks / SKKU / university faculty page (if URL provided)
- - Last: Scopus/ScienceDirect (often fails due to auth — do NOT rely on it)
-
- ---
+ - Last: Scopus/ScienceDirect — returns 403 or a login redirect; never rely on it
### Phase 1: Profile Exploration (E-utilities API)
- **Goal:** Identify the professor's 5-6 distinct research pillars using PubMed E-utilities API.
-
- **CRITICAL — Use E-utilities API, NOT WebFetch for PubMed:**
- - Scripts: `~/.claude/skills/search-lit/references/pubmed_eutils.sh` + `parse_pubmed.py`
- - Rate limit: 350ms between calls (100ms with NCBI_API_KEY)
- - These are faster, more reliable, and return structured data (JSON/XML)
+ **Goal:** Identify the professor's 5-6 distinct research pillars.
**Step 1 — Total publication count + PMID list:**
```bash
- bash ~/.claude/skills/search-lit/references/pubmed_eutils.sh search \
+ bash ${CLAUDE_SKILL_DIR}/../search-lit/references/pubmed_eutils.sh search \
'"[Full Name]"[Author]' 200 \
- | python3 ~/.claude/skills/search-lit/references/parse_pubmed.py esearch
+ | python3 ${CLAUDE_SKILL_DIR}/../search-lit/references/parse_pubmed.py esearch
```
**Step 2 — Fetch metadata for MeSH-based clustering (parallel):**
```bash
# Get PMIDs from Step 1, then fetch summaries
- bash ~/.claude/skills/search-lit/references/pubmed_eutils.sh fetch_json \
+ bash ${CLAUDE_SKILL_DIR}/../search-lit/references/pubmed_eutils.sh fetch_json \
"PMID1,PMID2,..." \
- | python3 ~/.claude/skills/search-lit/references/parse_pubmed.py esummary
+ | python3 ${CLAUDE_SKILL_DIR}/../search-lit/references/parse_pubmed.py esummary
```
- **Step 3 — Topic-specific counts (launch 4-5 searches in parallel via Bash):**
+ **Step 3 — Topic-specific counts (launch 4-5 searches in parallel Bash calls):**
```bash
- # Run these in parallel Bash calls
- bash ~/.claude/skills/search-lit/references/pubmed_eutils.sh search \
+ bash ${CLAUDE_SKILL_DIR}/../search-lit/references/pubmed_eutils.sh search \
'"[Full Name]"[Author] AND "keyword1"' 5
- bash ~/.claude/skills/search-lit/references/pubmed_eutils.sh search \
+ bash ${CLAUDE_SKILL_DIR}/../search-lit/references/pubmed_eutils.sh search \
'"[Full Name]"[Author] AND "keyword2"' 5
# ... repeat for each suspected pillar keyword
```
**Step 4 — MeSH term extraction for automatic pillar clustering:**
```bash
# Fetch full XML for top-cited papers to extract MeSH headings
- bash ~/.claude/skills/search-lit/references/pubmed_eutils.sh fetch \
+ bash ${CLAUDE_SKILL_DIR}/../search-lit/references/pubmed_eutils.sh fetch \
"PMID1,PMID2,...,PMID20" \
| python3 -c "
import sys, xml.etree.ElementTree as ET
from collections import Counter
root = ET.fromstring(sys.stdin.read())
mesh_counts = Counter()
for article in root.findall('.//PubmedArticle'):
for mh in article.findall('.//MeshHeading/DescriptorName'):
mesh_counts[mh.text] += 1
for term, count in mesh_counts.most_common(30):
print(f'{count:3d} {term}')
"
```
→ Top MeSH terms reveal natural research pillars (e.g., "Colonography, Computed Tomographic" = CTC pillar).
- **Step 5 — Google Scholar profile (parallel with PubMed calls):**
- - WebSearch: `"[Full Name]" radiology scholar google` for h-index, citation data
+ **Step 5 — Google Scholar profile (parallel with PubMed calls):** WebSearch
+ `"[Full Name]" radiology scholar google` for h-index and citation data; WebFetch any other profile
+ URL the user provided (skip Scopus).
- **Output: Pillar Summary Table**
+ **Output: Pillar Summary Table.** Publication counts and pillar assignments come from E-utilities
+ output and the h-index from the Scholar profile — never estimate them.
| Pillar | Domain | Representative keywords | MeSH terms | Est. # papers |
|--------|--------|-------------------------|-----------|---------------|
| 1 | ... | ... | ... | ~N+ |
- ---
-
### Phase 2: MA Gap Analysis (Multi-Source)
- **Goal:** For each pillar, determine if a viable MA topic exists using PubMed + Consensus + Scholar Gateway + bioRxiv.
+ **Goal:** For each pillar, determine if a viable MA topic exists using PubMed + Consensus + Scholar
+ Gateway + bioRxiv + PROSPERO.
- For each pillar (run in parallel using meta-analyst agents):
+ Run pillars in parallel: up to 4 subagents, each covering 1-2 pillars and running 2a–2g, each
+ reporting raw k, realistic k and every source checked. If PubMed returns 0 or Consensus/Scholar
+ Gateway is unavailable, state that limitation rather than guessing.
#### 2a. PubMed E-utilities — Existing MAs + Primary studies
```bash
# Existing MAs (structured count)
- bash ~/.claude/skills/search-lit/references/pubmed_eutils.sh search \
+ bash ${CLAUDE_SKILL_DIR}/../search-lit/references/pubmed_eutils.sh search \
'[pillar keywords] AND ("meta-analysis"[pt] OR "systematic review"[pt])' 50
# Primary studies with extractable outcomes
- bash ~/.claude/skills/search-lit/references/pubmed_eutils.sh search \
+ bash ${CLAUDE_SKILL_DIR}/../search-lit/references/pubmed_eutils.sh search \
'[pillar keywords] AND ("sensitivity" OR "specificity" OR "accuracy" OR "prognosis" OR "outcome")' 50
```
#### 2b. Consensus MCP — Semantic MA gap detection
Use `mcp__claude_ai_Consensus__search` to find existing SRs/MAs that PubMed keyword search might miss:
```
query: "systematic review OR meta-analysis [pillar topic] [imaging modality]"
```
Consensus returns citation-ranked results — check if any highly-cited MA already covers the proposed scope.
- **Limit:** max 3 Consensus calls per Phase 2 batch (rate limit).
+ **Limit:** max 3 Consensus calls per Phase 2 batch, in total across all agents (rate limit). If
+ rate-limited, wait 30 s and retry once.
#### 2c. Scholar Gateway — Semantic similarity search
- Use `mcp__claude_ai_Scholar_Gateway__semanticSearch` for:
- - Finding MAs with different terminology (e.g., "pooled analysis" instead of "meta-analysis")
- - Detecting scope-overlapping MAs that use different keywords
- - Identifying methodological review papers that partially cover the topic
+ Use `mcp__claude_ai_Scholar_Gateway__semanticSearch` to find MAs under different terminology
+ (e.g., "pooled analysis" instead of "meta-analysis"), scope-overlapping MAs that use different
+ keywords, and methodological reviews that partially cover the topic.
#### 2d. bioRxiv/medRxiv — In-press competition detection
- Use `mcp__claude_ai_bioRxiv__search_preprints` to catch:
- - MAs posted as preprints but not yet indexed in PubMed
- - Ongoing SR/MA protocols shared as preprints
- - Very recent primary studies that could change feasibility
-
+ Use `mcp__claude_ai_bioRxiv__search_preprints` to catch MAs posted as preprints but not yet in
+ PubMed, SR/MA protocols shared as preprints, and very recent primary studies that could change
+ feasibility.
```
query: "[pillar keywords] meta-analysis OR systematic review"
- server: "medrxiv" (for clinical topics)
+ server: "medrxiv" (clinical topics; "biorxiv" for preclinical)
```
#### 2e. Assessment matrix
| Factor | Criteria |
|--------|----------|
| MA gap | 0 existing = best, 1-3 = check scope overlap, >5 = saturated |
| Primary k | ≥8 for DTA, ≥6 for prognostic (minimum), ≥15 ideal |
| Recency | Last MA >5 years old = update opportunity |
| Competition | Check 2024-2026 for very recent MAs that block entry |
#### 2f. PROSPERO competition check (MANDATORY)
- - Search PROSPERO via WebSearch: `site:crd.york.ac.uk/prospero [topic keywords]`
- - Also try WebFetch: `https://www.crd.york.ac.uk/prospero/#searchadvanced`
- - Look for registered-but-unpublished protocols that could block entry
- - If PROSPERO match found → flag as 🚫 competition risk in ranking
+ - Search PROSPERO via WebSearch `site:crd.york.ac.uk/prospero [topic keywords]`; also try WebFetch `https://www.crd.york.ac.uk/prospero/#searchadvanced`
+ - Look for registered-but-unpublished protocols that could block entry; if a PROSPERO match is found → flag as 🚫 competition risk in ranking
#### 2g. Realistic k estimation
- - Raw PubMed hit count is NOT the real k — most studies lack 2x2 data or HR
+ - Raw PubMed hit count is NOT the real k — most studies lack 2x2 data or HR, so raw counts
+ overestimate by 3-7x
- Apply conservative discount: **k_realistic ≈ raw_count × 0.15–0.30** for DTA topics
- Flag if k_realistic < 8 (DTA) or < 6 (prognostic) as ⚠️ feasibility risk
- Report both raw and realistic estimates, e.g., `estimated k: ~130 (raw) → ~20–40 (extractable DTA data)`
- #### 2h. Niche subtopic discovery (if pillar appears saturated)
-
- - AI/radiomics angle on a classical topic
- - Specific modality comparison (e.g., CEUS vs MRI)
- - Treatment response (vs diagnosis which is often saturated)
- - Specific subpopulation or disease subtype
- - Use Consensus to check if the niche angle has already been covered
+ #### 2h. Niche subtopic discovery (if pillar appears saturated, >5 prior MAs)
- ---
+ Try these angles, and use Consensus to check whether the niche angle has already been covered:
+ 1. **"First MA" rule:** the professor's most unique/niche subtopic where MA = 0
+ 2. **AI/radiomics overlay:** classical imaging topic + AI approach
+ 3. **Treatment response:** diagnosis MAs are often saturated; treatment monitoring is often open
+ 4. **Modality comparison:** head-to-head (e.g., CEUS vs MRI) is often underserved
+ 5. **Guideline gap:** professor-authored guidelines → MA supporting/updating them
+ 6. **Population niche:** specific subpopulation, disease subtype, or regional population (e.g., parasitic diseases, TB)
+ 7. **Temporal update:** last MA >5 years old + significant new primary studies since
### Phase 3: Topic Ranking
- **Goal:** Rank all viable topics by composite score.
-
- Score each candidate on 5 criteria (★1-5):
+ **Goal:** Rank all viable topics by composite score. Score each candidate on 5 criteria (★1-5):
| Criteria | Weight | Description |
|----------|--------|-------------|
| **Professor fit** | Highest | Core area of the professor's career, publication count, distinctive contribution |
| **MA gap** | High | No prior MA > ≥5 yr since last MA > recent MA exists |
| **Feasibility (k)** | High | Number of includable studies and extractability of 2×2 or HR data |
| **Clinical impact** | Medium | Whether the topic directly informs clinical decision-making |
| **Execution ease** | Medium | Completable from literature alone; difficulty of managing heterogeneity |
**Output: Ranked Topic Table**
| Rank | Topic | Professor's Pillar | Prior MA | Estimated k (raw→realistic) | PROSPERO competition | Verdict |
|------|-------|--------------------|----------|-----------------------------|----------------------|---------|
| 1 | ... | ... | 0 | ~98 → 15–30 | None | ✅ Best fit |
- ---
-
### Phase 4: Folder & README Scaffolding
**Goal:** Create project folders and README for each viable topic.
- 1. **Folder location:** `{working_dir}/ma-scout/{initials}_{professor_name}/`
- 2. **Naming convention:** `{NN}_{topic_slug}/` (within professor folder)
+ 1. **Folder location:** `{working_dir}/ma-scout/{initials}_{professor_name}/{NN}_{topic_slug}/`
- Professor folder: `{initials}_{name}` (e.g., `KDK_Kim`, `LKS_Lee`)
- - NN: sequential number within professor (01, 02, ...)
- - topic_slug: English, underscore-separated
+ - NN: sequential number within professor (01, 02, ...); topic_slug: English, underscore-separated
- Check existing folders with `ls` before creating
-
- 3. **README.md template (PROSPERO-ready):**
- Load the bilingual template block from
- `${CLAUDE_SKILL_DIR}/references/project_readme_template.md` and copy it into
- `{topic_folder}/README.md`. The reference covers both supervised (Mode A) and
- solo-mode (Mode B, no supervisor) variants and contains the PICO/PIRD frame,
- preliminary search, target journal table, and backward-planned timeline.
-
- ---
+ 2. **README.md (PROSPERO-ready):** copy the template block from
+ `${CLAUDE_SKILL_DIR}/references/project_readme_template.md` into `{topic_folder}/README.md` and fill it (PICO/PIRD
+ frame, preliminary search, target journal table, backward-planned timeline). Write the research
+ question, PICO/PIRD and README content in English, medical terms always in English, unless the
+ user asks for the Korean PI-facing variant that reference names.
### Phase 5: Output Summary
- **Goal:** Persist findings for the user.
-
1. Save the ranked topic table and README files to the working directory.
- 2. Summarize: total topics scanned, viable topics found, recommended next steps.
- 3. Suggest the user save results to their project management system (e.g., `/manage-project`).
-
- ---
-
- ## Niche Topic Discovery Heuristics
-
- When all major pillars are saturated (>5 prior MAs), try these angles:
-
- 1. **"First MA" rule:** Professor's most unique/niche subtopic where MA = 0
- 2. **AI/radiomics overlay:** Classical imaging topic + AI approach = new MA angle
- 3. **Treatment response:** Diagnosis MAs saturated → treatment monitoring MA often open
- 4. **Modality comparison:** Head-to-head (e.g., CEUS vs MRI) often underserved
- 5. **Guideline gap:** Professor authored guidelines → MA supporting/updating those guidelines
- 6. **Geographic/population niche:** Regional population-specific MA (e.g., parasitic diseases, TB)
- 7. **Temporal update:** Last MA >5 years old + significant new primary studies since
-
- ---
-
- ## Quality Gates
-
- Before finalizing a topic as viable:
-
- - [ ] **Author identity confirmed** — full name resolved via E-utilities efetch, no initials-only contamination
- - [ ] **Affiliation confirmed** with user (or from reliable source)
- - [ ] Confirmed MA = 0 or last MA >5 years (via PubMed E-utilities, not assumption)
- - [ ] **Cross-validated via Consensus/Scholar Gateway** — no hidden MAs with different terminology
- - [ ] **bioRxiv/medRxiv checked** — no preprint MA in progress
- - [ ] Confirmed k_realistic ≥ 8 (DTA) or ≥ 6 (prognostic) after discount
- - [ ] **PROSPERO searched** — no registered competing protocol found
- - [ ] No 2024-2026 competing MA in press (check PubMed + preprints)
- - [ ] Professor's publication record demonstrates clear authority in this area
- - [ ] Research question is specific enough for PROSPERO registration
- - [ ] **README contains:** complete PICO/PIRD, PubMed search strategy, Embase draft, target journal with IF, timeline
-
- ---
-
- ## Handoff
-
- After MA Scout completes:
- - To **`/meta-analysis`**: When a topic is approved and ready for PROSPERO protocol (README has PICO + search strategy ready)
- - To **`manage-project`**: When project folder needs full scaffolding
- - To **`search-lit`**: When deeper preliminary search is needed before committing
- - To **`/analyze-stats`**: When feasibility requires power/sample-size calculation for the estimated k
-
- ---
-
- ## Parallel Execution Strategy
-
- For efficiency, launch multiple agents and API calls in parallel:
-
- **Phase 0 (Identity):**
- 1. E-utilities esearch: `"[Full Name]"[Author]` → total count + PMIDs (FIRST)
- 2. E-utilities efetch: top 20 PMIDs → MeSH terms → automatic pillar clustering
-
- **Phase 1 (Profile — all parallel):**
- 3. Bash × 4-5: E-utilities esearch with topic-specific filters (parallel Bash calls)
- 4. WebSearch: Google Scholar profile
- 5. WebFetch: any provided profile URLs (skip Scopus)
-
- **Phase 2 (MA Gap — multi-source parallel):**
- 6. Up to 4 meta-analyst agents in parallel, each covering 1-2 pillars
- 7. Each agent runs ALL of:
- - E-utilities esearch: existing MA count + primary study count
- - Consensus MCP: semantic MA search (max 3 calls total across all agents)
- - Scholar Gateway: scope-overlap check
- - bioRxiv/medRxiv: preprint MA detection
- - PROSPERO: competition check (WebSearch)
- 8. Each agent reports: raw k, realistic k (15-30% discount), all sources checked
-
- **Phase 3 (Ranking):** Sequential, uses Phase 2 outputs.
-
- **Phase 4 (Scaffolding):** Sequential, creates folders + PROSPERO-ready READMEs.
-
- Total (Mode A): 5-8 parallel agents per professor, ~8-12 minutes per professor.
-
- ### Mode B Parallel Strategy
-
- **T-Phase 0:** Sequential (user interaction for scope clarification).
-
- **T-Phase 1 (Landscape — all angles in parallel):**
- 1. Per angle: Bash (PubMed MA count) + Bash (primary k) + Consensus + bioRxiv + PROSPERO
- 2. 3-5 angles × 5 sources = 15-25 parallel calls
-
- **T-Phase 2 (Deep-dive):** Same as Mode A Phase 2, only for viable angles (typically 1-2).
-
- **T-Phase 4 (Co-author — if needed):**
- 3. Bash: PubMed author frequency search
- 4. WebSearch: Google Scholar profiles for top candidates
-
- Total (Mode B): ~5-8 minutes per topic scan (faster than Mode A — no profile exploration).
-
- ### Known Pitfalls (from 3 professor analyses)
- - Common Korean/Asian initials (e.g., "Lee KS", "Kim DK") return 300+ papers with massive contamination. Always use full name first.
- - Scopus/ScienceDirect → 403 or redirect to login. Never rely on Scopus as primary data source.
- - Raw PubMed counts overestimate by 3-7x. ~130 hits often means 20-40 with extractable DTA data.
- - Professor may have moved institutions. Don't assume affiliation without verification.
- - **Consensus rate limit:** Max 3 batch calls. If rate-limited, wait 30s and retry once.
- - **E-utilities rate limit:** 350ms between calls (100ms with NCBI_API_KEY). Scripts handle this automatically.
- - **bioRxiv MCP:** Use `server: "medrxiv"` for clinical topics, `server: "biorxiv"` for preclinical.
-
- ---
+ 2. Summarize: total topics scanned, viable topics found, recommended next steps (see Handoff).
- # ═══════════════════════════════════════════
# MODE B: TOPIC-FIRST WORKFLOW
- # ═══════════════════════════════════════════
### T-Phase 0: Topic Clarification & Scope
- **Goal:** Refine the user's clinical question into a searchable, PROSPERO-registrable scope.
-
- 1. **Parse the input** — extract:
- - Disease/condition (e.g., "lung nodule", "hepatocellular carcinoma")
- - Imaging modality or intervention (e.g., "dual-energy CT", "AI CAD")
- - Outcome type: DTA (Se/Sp), prognostic (HR/OR), intervention (RR/MD), dosimetry
- - Population specifics (e.g., "screening setting", "cirrhotic patients")
+ **Goal:** Refine the user's clinical question into a searchable, PROSPERO-registrable scope. When
+ the user asks for topic suggestions without a specific idea, read
+ `${CLAUDE_SKILL_DIR}/references/topic_discovery_heuristics.md` first to generate candidate questions.
- 2. **Expand to neighboring angles** — propose 3-5 variations:
+ 1. **Parse the input** — disease/condition (e.g., "hepatocellular carcinoma"); imaging modality or
+ intervention (e.g., "dual-energy CT", "AI CAD"); outcome type: DTA (Se/Sp), prognostic (HR/OR),
+ intervention (RR/MD), dosimetry; population specifics (e.g., "screening setting", "cirrhotic
+ patients").
+ 2. **Expand to neighboring angles** — propose 3-5 variations, e.g.:
```
user input: "AI for lung nodule malignancy prediction"
→ variant 1: AI vs radiologist for lung nodule malignancy prediction (DTA)
→ variant 2: Radiomics for lung nodule malignancy (DTA)
→ variant 3: Deep learning for incidental pulmonary nodule management (prognostic)
- → variant 4: AI-assisted Lung-RADS upgrade accuracy (DTA)
- → variant 5: Low-dose CT AI for lung cancer screening (DTA)
```
-
3. **User selects 1-3 angles** to investigate further.
- ---
-
### T-Phase 1: Landscape Scan (Multi-Source)
- **Goal:** For each selected angle, rapidly assess the MA landscape.
-
- **Run all angles in parallel. For each angle:**
+ **Goal:** For each selected angle, rapidly assess the MA landscape. **Run all angles in parallel.
+ For each angle:**
#### 1a. PubMed — Existing MA count
```bash
- bash ~/.claude/skills/search-lit/references/pubmed_eutils.sh search \
+ bash ${CLAUDE_SKILL_DIR}/../search-lit/references/pubmed_eutils.sh search \
'[topic keywords] AND ("meta-analysis"[pt] OR "systematic review"[pt])' 50
```
#### 1b. PubMed — Primary study pool
```bash
- bash ~/.claude/skills/search-lit/references/pubmed_eutils.sh search \
+ bash ${CLAUDE_SKILL_DIR}/../search-lit/references/pubmed_eutils.sh search \
'[topic keywords] AND ("sensitivity" OR "specificity" OR "hazard" OR "outcome")' 100
```
#### 1c. Consensus MCP — Semantic MA discovery
```
query: "systematic review [topic] [modality]"
```
Check for MAs using different terminology.
#### 1d. bioRxiv/medRxiv — Preprint competition
```
query: "[topic] meta-analysis"
server: "medrxiv"
```
#### 1e. PROSPERO — Registered protocols
WebSearch: `site:crd.york.ac.uk/prospero [topic keywords]`
**Output: Landscape Summary Table**
| Variant | Existing MAs | Primary k (raw) | k (realistic) | PROSPERO | Preprint MA | Verdict |
|---------|--------------|-----------------|---------------|----------|-------------|---------|
| 1 | 3 | 120 | 18-36 | 1 | 0 | ⚠️ Competitive |
| 2 | 0 | 85 | 13-25 | 0 | 0 | ✅ Optimal |
- ---
-
### T-Phase 2: Feasibility Deep-Dive
- **Goal:** For viable angles (MA ≤ 2, no PROSPERO conflict), run full gap analysis.
-
- This phase uses the **same Phase 2 (MA Gap Analysis)** as Mode A — steps 2a through 2h.
- The only difference: no "Professor fit" to evaluate, so focus on:
+ **Goal:** For viable angles (MA ≤ 2, no PROSPERO conflict), run the **same Phase 2 (MA Gap
+ Analysis)** as Mode A — steps 2a through 2h. With no "Professor fit" to evaluate, focus on:
- **Gap certainty** — are existing MAs truly non-overlapping with proposed scope?
- **k quality** — are primary studies heterogeneous enough to warrant MA, or too uniform?
- **User's domain fit** — does this align with user's radiology AI / imaging expertise?
- ---
-
### T-Phase 3: Topic Ranking (Topic-first weights)
- **Goal:** Rank viable topics with weights adjusted for topic-first approach.
-
| Criteria | Weight | Description |
|----------|--------|-------------|
| **MA gap** | Highest | No existing MA > update opportunity > saturated |
| **Feasibility (k)** | Highest | k_realistic ≥ 8 (DTA) or ≥ 6 (prognostic) |
| **User domain fit** | High | Does it match the user's area of expertise? |
| **Clinical impact** | Medium | Potential to change guidelines; directly tied to clinical decisions |
| **Co-author availability** | Medium | Access to a domain expert (existing relationship or easy to reach) |
| **Execution ease** | Medium | Can be done solo vs requires expert interpretation |
**Output: Ranked Topic Table**
| Rank | Topic | Existing MAs | Est. k | PROSPERO | Co-author needed | Overall |
|------|-------|--------------|--------|----------|------------------|---------|
| 1 | ... | 0 | 25 | None | Optional | ✅ Optimal |
- ---
-
### T-Phase 4: Co-Author Matching (Optional)
**Goal:** If the user wants a senior co-author, find candidates.
- **Strategy 1 — Existing network (memory-based):**
- - Check memory files for professors with overlapping expertise
- - Cross-reference existing professor folders in the working directory
- - Best match = professor whose pillar naturally covers this topic
+ **Strategy 1 — Existing network:** check memory files and existing professor folders in the
+ working directory for professors whose pillar naturally covers this topic (best match).
**Strategy 2 — PubMed reverse search:**
```bash
# Find prolific authors in this specific topic
- bash ~/.claude/skills/search-lit/references/pubmed_eutils.sh search \
+ bash ${CLAUDE_SKILL_DIR}/../search-lit/references/pubmed_eutils.sh search \
'[topic keywords] AND ("{user_country}"[Affiliation])' 100
```
- Then:
- - E-utilities efetch → extract author frequency from results
- - Top 5 most-published authors in this niche = potential co-authors
- - Cross-check Google Scholar for h-index and recent activity
+ Then E-utilities efetch → author frequency; the top 5 most-published authors in this niche are
+ potential co-authors. Cross-check Google Scholar for h-index and recent activity.
- **Strategy 3 — Self-led (no senior co-author):**
- - Viable when: user has 2+ published MAs, topic is methodologically straightforward
- - Still need 2nd reviewer (junior colleague or peer) — flag this in README
- - Corresponding author = user
+ **Strategy 3 — Self-led (no senior co-author):** viable when the user has 2+ published MAs and the
+ topic is methodologically straightforward. A 2nd reviewer (junior colleague or peer) is still
+ needed — flag this in the README. Corresponding author = user.
**Output:** Co-author recommendation table or a "solo-viable" judgment.
- ---
-
### T-Phase 5: Folder & README Scaffolding (Topic-first)
- **Goal:** Create project folder and PROSPERO-ready README.
-
- 1. **Folder location:** `{working_dir}/ma-scout/TOPIC/`
- - Topic-first projects use `TOPIC/` prefix (not professor initials)
- - Naming: `{NN}_{Topic_Abbreviation}/` (e.g., `01_AI_Lung_Nodule_DTA/`)
- - If co-author matched later, can be moved under professor folder
-
- 2. **README.md template:** Same PROSPERO-ready template as Mode A Phase 4 (see
- `references/project_readme_template.md`), with these changes:
- - `Supervisor:` → `Lead: {user_name}` or `Lead: {user_name} + {co-author}`
- - Drop the supervisor-area row; use `Domain: {subspecialty}` instead.
- - Rename `Professor's Authority` → `Team Expertise` (user's credentials + co-author if any)
- - Timeline: drop the supervisor-proposal step → start directly at PROSPERO registration.
-
- **Timeline template (self-led):**
- | Step | Expected timing | Precondition |
- |------|-----------------|--------------|
- | PROSPERO registration | {YYYY-MM} | topic confirmed |
- | Search complete | +1 week | PROSPERO registration |
- | Screening complete | +2 weeks | 2nd reviewer secured |
- | Data extraction | +3 weeks | screening consensus |
- | Analysis + draft | +5 weeks | data lock |
- | Co-author review | +7 weeks | draft complete |
- | Submission | +8 weeks | final approval |
-
- 3. **Summary:** Same as Mode A Phase 5 — save ranked results and recommend next steps.
-
- ---
-
- ### Topic Discovery Heuristics (Mode B specific)
-
- When the user asks for topic suggestions without a specific idea:
-
- 1. **Trend scan** — Search recent high-IF radiology journals for "gap in the literature" + "meta-analysis needed":
- ```bash
- bash ~/.claude/skills/search-lit/references/pubmed_eutils.sh search \
- '"no meta-analysis" AND "radiology"[Journal] AND 2024:2026[dp]' 30
- ```
-
- 2. **Guideline update gaps** — New guidelines (ACR, ESR, RSNA) often cite lack of MA evidence:
- - Consensus search: `"practice guideline" AND "insufficient evidence" AND [radiology subspecialty]`
-
- 3. **AI + classical imaging** — Overlay AI/DL/radiomics on well-studied classical topics:
- - Many classical DTA topics have 10+ MAs, but AI angle has 0-1
-
- 4. **Korean/Asian population** — Population-specific MA for diseases with geographic variation:
- - TB, NTM, parasitic diseases, gastric cancer, liver fluke, HBV-related HCC
-
- 5. **Technology adoption** — New modalities with growing evidence but no synthesis:
- - Photon-counting CT, abbreviated MRI, contrast-enhanced mammography, AI CAD
-
- 6. **Cross-subspecialty** — Topics spanning two subspecialties often fall through MA cracks:
- - Cardiac + thoracic (coronary CT + lung screening), neuro + MSK (spine imaging)
-
- ---
+ 1. **Folder location:** `{working_dir}/ma-scout/TOPIC/{NN}_{Topic_Abbreviation}/` (e.g.,
+ `01_AI_Lung_Nodule_DTA/`). Topic-first projects use the `TOPIC/` prefix, not professor
+ initials; if a co-author is matched later, the folder can move under the professor folder.
+ 2. **README.md:** the Phase 4 template with the Solo-Mode Adaptations in
+ `${CLAUDE_SKILL_DIR}/references/project_readme_template.md` (Lead/Domain rows, Team Expertise, self-led timeline).
+ 3. **Summary:** same as Mode A Phase 5 — save ranked results and recommend next steps.
- ### Quality Gates (Mode B specific)
+ ## Quality Gates
- Before finalizing a topic-first MA as viable:
+ Before finalizing a topic as viable:
- - [ ] Clinical question refined to PICO/PIRD (not just a keyword)
- - [ ] MA gap confirmed via PubMed + Consensus + Scholar Gateway + bioRxiv (all 4 sources)
- - [ ] k_realistic ≥ 8 (DTA) or ≥ 6 (prognostic) after 15-30% discount
- - [ ] PROSPERO searched — no competing registered protocol
+ - [ ] (A) **Author identity confirmed** — full name resolved via E-utilities efetch, no initials-only contamination
+ - [ ] (A) **Affiliation confirmed** with user (or from reliable source)
+ - [ ] (A) Professor's publication record demonstrates clear authority in this area
+ - [ ] (B) Clinical question refined to PICO/PIRD (not just a keyword)
+ - [ ] (A) Confirmed MA = 0 or last MA >5 years (via PubMed E-utilities, not assumption)
+ - [ ] **Cross-validated** via PubMed + Consensus + Scholar Gateway + bioRxiv/medRxiv — no hidden MAs with different terminology, no preprint MA in progress
+ - [ ] Confirmed k_realistic ≥ 8 (DTA) or ≥ 6 (prognostic) after the 15-30% discount
+ - [ ] **PROSPERO searched** — no registered competing protocol found
- [ ] No 2024-2026 competing MA in press or preprint
- - [ ] User's domain expertise sufficient for clinical interpretation (or co-author identified)
- - [ ] 2nd reviewer identified or plan to recruit
- - [ ] README contains: complete PICO/PIRD, PubMed + Embase search strategy, target journal with IF, timeline
- - [ ] If self-led: user has ≥ 2 published MAs (otherwise, recommend co-author)
+ - [ ] Research question is specific enough for PROSPERO registration
+ - [ ] (B) User's domain expertise sufficient for clinical interpretation (or co-author identified); 2nd reviewer identified or plan to recruit
+ - [ ] (B) If self-led: user has ≥ 2 published MAs (otherwise, recommend co-author)
+ - [ ] **README contains:** complete PICO/PIRD, PubMed search strategy, Embase draft, target journal with IF, timeline
- ---
+ ## Handoff
- ## Phase 6: Pre-Proposal Pipeline (Post-Scout)
+ - To **`/meta-analysis`**: when a topic is approved and ready for the PROSPERO protocol (README has PICO + search strategy)
+ - To **`/manage-project`**: when the project folder needs full scaffolding or the user wants results saved to project management
+ - To **`/search-lit`**: when a deeper preliminary search is needed before committing
+ - To **`/analyze-stats`**: when feasibility requires power/sample-size calculation for the estimated k
- After MA Scout identifies viable topics, run the **pre-proposal pipeline** to prepare
- a "ready-to-propose" package before contacting the professor.
+ ## Phase 6: Pre-Proposal Pipeline (Post-Scout)
- ### Pipeline Steps
+ After MA Scout identifies viable topics, prepare a "ready-to-propose" package before contacting the
+ professor. Topics are independent: run up to 4 agents per wave, each doing search → fetch → triage
+ → write files.
1. **Search Execution** — E-utilities with broadened synonyms (retmax=200)
- Primary search: `[topic] AND [outcome keywords]`
- Existing MA search: `[topic] AND ("meta-analysis"[pt] OR "systematic review"[pt])`
-
2. **Metadata Collection** — `fetch_json` → `esummary` (batch 40-50 PMIDs)
-
- 3. **Title-Based Triage** — Classify as INCLUDE / MAYBE / EXCLUDE
- - CRITICAL: Check for existing MAs within results (initial scout may miss them)
- - Separate bronchoscopic vs percutaneous (30% contamination in CBCT topics)
- - Flag professor's own papers (authority evidence)
- - Flag retracted papers
-
+ 3. **Title-Based Triage** — classify as INCLUDE / MAYBE / EXCLUDE
+ - Check for existing MAs within the results — the initial scout may have missed them
+ - Separate sub-approaches that contaminate the pool (e.g., bronchoscopic vs percutaneous)
+ - Flag the professor's own papers (authority evidence) and retracted papers
4. **PRISMA Flow Draft** — Identification → Screening → Eligibility → Included (estimated)
-
- 5. **Gap Re-assessment** — Update MA count, re-position if needed:
- - MA=0 → "first MA" | MA=1 (>5yr) → "update MA" | MA≥3 (recent) → skip/niche
-
+ 5. **Gap Re-assessment** — update the MA count and re-position if needed:
+ MA=0 → "first MA" | MA=1 (>5yr) → "update MA" | MA≥3 (recent) → skip/niche
6. **Output Files**:
- `candidates.md` — full triage table + PRISMA flow + gap finding
- `README.md` — updated Preliminary Search section with actual numbers
- ### Parallel Execution
- - Launch up to 4 agents per wave (each topic independent)
- - Each agent: search → fetch → triage → write files → ~5-10 min
- - 21 topics completed in ~1 hour with 16 parallel agents
-
- ### Professor Contact Package
- The pre-proposal gives the professor:
- - Candidate count + gap evidence (e.g., "MA = 0, 35 studies to include")
- - Clear role description (e.g., "independent screening review + discussion only")
- - Urgency of PROSPERO pre-registration to secure the topic
-
- ## Anti-Hallucination
-
- - **Never fabricate publication counts, h-index, or pillar classifications.** All numbers must come from PubMed E-utilities API output.
- - **Never fabricate existing MA counts.** Always verify via PubMed search + PROSPERO check before claiming "MA = 0".
- - **Never invent professor expertise or affiliation.** Confirm with user before proceeding.
- - **k_realistic must use the 15-30% discount.** Raw PubMed counts overestimate by 3-7x. Always report both raw and realistic estimates.
- - If PubMed returns 0 or Consensus/Scholar Gateway is unavailable, state the limitation rather than guessing.
+ **Professor Contact Package** — the pre-proposal gives the professor: candidate count + gap
+ evidence (e.g., "MA = 0, 35 studies to include"), a clear role description (e.g., "independent
+ screening review + discussion only"), and the urgency of PROSPERO pre-registration to secure the topic.