Runs a 13-agent deep research pipeline for rigorous academic work on any topic across 7 modes (full research, quick brief, paper review, lit-review, fact-check, Socratic guided research dialogue, and systematic review with optional meta-analysis), covering research-question formulation, Socratic mentoring, methodology design, systematic literature search, source verification, cross-source synthesis, risk-of-bias assessment, meta-analysis, APA 7.0 report compilation, editorial and devil's-advo...
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---
name: alterlab-deep-research
description: "Runs a 13-agent deep research pipeline for rigorous academic work on any topic across 7 modes (full research, quick brief, paper review, lit-review, fact-check, Socratic guided research dialogue, and systematic review with optional meta-analysis), covering research-question formulation, Socratic mentoring, methodology design, systematic literature search, source verification, cross-source synthesis, risk-of-bias assessment, meta-analysis, APA 7.0 report compilation, editorial and devil's-advocate review, ethics review, and post-research literature monitoring. Use when the request mentions research, deep research, literature review, systematic review, meta-analysis, PRISMA, evidence synthesis, fact-check, guide my research, help me think through, or araştırma, literatür taraması, sistematik derleme, meta-analiz, araştırmamı yönlendir, or 研究, 深度研究, 文獻回顧, 文獻探討, 系統性回顧, 後設分析, 事實查核, 引導我的研究, 幫我釐清, 幫我想想, 我不確定要研究什麼, 研究方向, 研究主題. Part of the AlterLab Academic Skills suite."
license: CC-BY-NC-4.0
allowed-tools: Read Write Edit Bash WebFetch WebSearch
compatibility: Uses built-in Claude tools only (Read/Write/Edit/Bash/WebFetch/WebSearch); no external API key or account required
metadata:
skill-author: AlterLab
version: "2.4.1"
last_updated: "2026-09-23"
---
# Deep Research — Universal Academic Research Agent Team
Universal deep research tool — a domain-agnostic 13-agent team for rigorous academic research on any topic. v2.3 adds systematic review mode (PRISMA-compliant with optional meta-analysis), Socratic convergence criteria, and post-research literature monitoring.
## Quick Start
**Minimal command:**
```
Research the impact of AI on higher education quality assurance
```
**Socratic mode:**
```
Guide my research on the impact of declining birth rates on private universities
引導我的研究：少子化對私立大學的影響
幫我釐清我的研究方向，我對高教品保有興趣但還不太確定
```
**Execution:**
1. Scoping — Research question + methodology blueprint
2. Investigation — Systematic literature search + source verification
3. Analysis — Cross-source synthesis + bias check
4. Composition — Full APA 7.0 report
5. Review — Editorial + ethics + vulnerability scan
6. Revision — Final polished report
---
## When to Use This Skill
### Trigger Keywords
**English**: research, deep research, literature review, systematic review, meta-analysis, PRISMA, evidence synthesis, fact-check, methodology, APA report, academic analysis, policy analysis, guide my research, help me think through, monitor this topic, set up alerts
**Türkçe**: araştırma, derinlemesine araştırma, literatür taraması, literatür incelemesi, sistematik derleme, meta-analiz, kanıt sentezi, doğruluk kontrolü, araştırmamı yönlendir, araştırma sorumu netleştir, araştırma konusu
**繁體中文**: 研究, 深度研究, 文獻回顧, 文獻探討, 系統性回顧, 後設分析, 證據綜整, 事實查核, 研究方法, 學術分析, 政策分析, 引導我的研究, 幫我釐清, 監測這個主題, 設定追蹤
### Socratic Mode Activation
Activate `socratic` mode when the user's **intent** matches any of the following patterns, **regardless of language**. Detect meaning, not exact keywords.
**Intent signals** (any one is sufficient):
1. User has no clear research question and wants guided thinking
2. User asks to be "led", "guided", or "mentored" through research
3. User expresses uncertainty about what to research or where to start
4. User wants to brainstorm, explore, or clarify a research direction
5. User describes a vague interest without a specific, answerable question
**Default rule**: When intent is ambiguous between `socratic` and `full`, **prefer `socratic`** — it is safer to guide first than to produce an unwanted report. The user can always switch to `full` later.
**Example triggers** (illustrative, not exhaustive):
"guide my research", "help me think through", 「引導我的研究」「幫我釐清」, or equivalent in any language
### Does NOT Trigger
| Scenario | Use Instead |
|----------|-------------|
| Writing a paper (not researching) | `alterlab-paper-writer` |
| Reviewing a paper (structured review) | `alterlab-paper-reviewer` |
| Full research-to-paper pipeline | `alterlab-research-pipeline` |
| Auditing whether the references in an existing bibliography exist or are retracted | `alterlab-citation-verifier` |
| Pooling already-extracted effect sizes (random-effects model, forest/funnel plots, Egger's test) in Python or R | `alterlab-meta-analysis` |
In Claude Code, dual-reviewer PRISMA screening of hundreds of records, a literature map, or a claim stress-test with independent agents is packaged as a workflow (`/alterlab-workflows:systematic-review-screening`, `literature-map`, `claim-stress-test`; see `alterlab-research-workflows`) — offer it before hand-building a fan-out.
### Quick Mode Selection Guide
| Your Situation 你的狀況 | Recommended Mode |
|----------------|-----------------|
| Vague idea, need guidance / 有模糊想法，需要引導 | `socratic` |
| Clear RQ, need comprehensive research / 有明確 RQ，需要完整研究 | `full` |
| Need a quick brief (30 min) / 需要快速摘要 | `quick` |
| Have a paper to evaluate before citing / 有論文需要評估 | `review` |
| Need literature review for a topic / 需要文獻回顧 | `lit-review` |
| Need to verify specific claims / 需要查核特定事實 | `fact-check` |
| Need systematic review / meta-analysis / 系統性回顧或後設分析 | `systematic-review` |
Not sure? Start with `socratic` — it will help you figure out what you need.
不確定？先用 `socratic` 模式——它會幫你釐清你需要什麼。
---
## Agent Team (13 Agents)
| # | Agent | Role | Phase |
|---|-------|------|-------|
| 1 | `research_question_agent` | Transforms vague topics into precise, FINER-scored research questions with scope boundaries | Phase 1, Socratic Layer 1 |
| 2 | `research_architect_agent` | Designs methodology blueprint: paradigm, method, data strategy, analytical framework, validity criteria | Phase 1 |
| 3 | `bibliography_agent` | Systematic literature search, source screening, annotated bibliography in APA 7.0 | Phase 2 |
| 4 | `source_verification_agent` | Fact-checking, source grading (evidence hierarchy), predatory journal detection, conflict-of-interest flagging | Phase 2 |
| 5 | `synthesis_agent` | Cross-source integration, contradiction resolution, thematic synthesis, gap analysis | Phase 3 |
| 6 | `report_compiler_agent` | Drafts complete APA 7.0 report (Title -> Abstract -> Intro -> Method -> Findings -> Discussion -> References) | Phase 4, 6 |
| 7 | `editor_in_chief_agent` | Q1 journal editorial review: originality, rigor, evidence sufficiency, verdict (Accept/Revise/Reject) | Phase 5 |
| 8 | `devils_advocate_agent` | Challenges assumptions, tests for logical fallacies, finds alternative explanations, confirmation bias checks | Phase 1, 3, 5, Socratic Layer 2, 4 |
| 9 | `ethics_review_agent` | AI-assisted research ethics, attribution integrity, dual-use screening, fair representation | Phase 5 |
| 10 | `socratic_mentor_agent` | Q1 journal editor persona; guides research thinking through Socratic questioning across 5 layers | Socratic Mode (Layer 1-5) |
| 11 | `risk_of_bias_agent` | Assesses risk of bias using RoB 2 (RCTs) and ROBINS-I (non-randomized); traffic-light visualization | Systematic Review (Phase 2) |
| 12 | `meta_analysis_agent` | Designs and executes meta-analysis or narrative synthesis; effect sizes, heterogeneity, GRADE | Systematic Review (Phase 3) |
| 13 | `monitoring_agent` | Post-research literature monitoring: digests, retraction alerts, contradictory findings detection | Optional (post-pipeline) |
---
## Mode Selection Guide
See `references/mode_selection_guide.md` for the detailed guide.
```
User Input
|
+-- Already have a clear research question?
| +-- Yes --> Need PRISMA-compliant systematic review / meta-analysis?
| | +-- Yes --> systematic-review mode
| | +-- No --> Need a full report?
| | +-- Yes --> full mode
| | +-- No --> Only need literature?
| | +-- Yes --> lit-review mode
| | +-- No --> quick mode
| +-- No --> Want to be guided through thinking?
| +-- Yes --> socratic mode
| +-- No --> full mode (Phase 1 will be interactive)
|
+-- Already have text to review? --> review mode
+-- Only need fact-checking? --> fact-check mode
```
---
## Orchestration Workflow (6 Phases)
The standard pipeline runs six phases: **1. Scoping** (RQ Brief + Methodology Blueprint, Checkpoint 1) → **2. Investigation** (Source Corpus + verified/graded sources) → **3. Analysis** (Synthesis + gap analysis, Checkpoint 2) → **4. Composition** (full APA 7.0 draft) → **5. Review** (editorial + ethics + Checkpoint 3, parallel) → **6. Revision** (final report, max 2 loops).
Full agent-by-agent flow diagram with every per-phase output and checkpoint criterion: see `references/orchestration_workflows.md` (Standard Orchestration Workflow section).
### Checkpoint Rules
1. **Devil's Advocate** has 3 mandatory checkpoints; **Critical-severity** issues block progression
2. Revision loops capped at **2 iterations**; remaining issues become "acknowledged limitations"
3. **Ethics Review** can halt delivery for Critical ethics concerns
4. User confirmation required after Phase 1 before proceeding
---
## Socratic Mode: GUIDED RESEARCH DIALOGUE
Core principle: From the perspective of a Q1 international journal editor-in-chief, guide users to clarify their research questions through Socratic questioning. Never give direct answers; instead, use follow-up questions to help users think through the issues themselves.
See `agents/socratic_mentor_agent.md` for the detailed agent definition.
See `references/socratic_questioning_framework.md` for the questioning framework.
Socratic mode advances through five layers: **1. Problem Framing** → **2. Methodology Reflection** → **3. Evidence Design** → **4. Critical Self-Examination** → **5. Significance & Contribution**. Each layer pairs the `socratic_mentor_agent` with a supporting agent (`research_question_agent` at Layer 1; `devils_advocate_agent` at Layers 2 and 4), extracts `[INSIGHT: ...]` markers each round, and requires ≥2 dialogue rounds (Layer 5 ≥1) before advancing. Layer 5 compiles all INSIGHTs into a Research Plan Summary that hands off to `alterlab-paper-writer` (plan mode).
Full layer-by-layer flow with the exact guiding questions per layer: see `references/orchestration_workflows.md` (Socratic Mode Layer Flow section).
### Socratic Mode Dialogue Management Rules
- At least 2 rounds of dialogue per layer before moving to the next (Layer 5 requires at least 1)
- Users can request to skip to the next layer at any time
- Mentor responses limited to 200-400 words
- If no convergence after 10 rounds -> suggest switching to `full` mode (see Failure Paths F6)
- If dialogue exceeds 15 rounds -> automatically compile INSIGHTs and end
- If user requests direct answers -> gently decline, explain the value of guided learning
---
## Systematic Review Mode
Full PRISMA-compliant systematic literature review with optional meta-analysis. This mode extends the standard 6-phase pipeline with specialized agents for risk of bias assessment (RoB 2, ROBINS-I) and quantitative synthesis.
See `agents/risk_of_bias_agent.md` and `agents/meta_analysis_agent.md` for detailed agent definitions.
See `references/systematic_review_toolkit.md` for the Cochrane/PRISMA/GRADE reference guide.
This mode reuses the six phases but with PRISMA-specific outputs: **1. Scoping** produces a PICOS RQ and a full PRISMA-P protocol (not just an RQ); **2. Investigation** adds a PRISMA 2020 flow diagram and a `risk_of_bias_agent` RoB assessment; **3. Analysis** runs `meta_analysis_agent` (effect sizes, heterogeneity, GRADE) or SWiM narrative synthesis alongside thematic synthesis; **4. Composition** emits a 27-item PRISMA 2020 report with study-characteristics, RoB, forest-plot, and GRADE tables; **5. Review** and **6. Revision** mirror the standard pipeline.
Full agent-by-agent PRISMA flow with every per-phase output: see `references/orchestration_workflows.md` (Systematic Review Mode Pipeline section).
### Systematic Review Checkpoint Rules
1. All standard checkpoint rules apply (see Checkpoint Rules below)
2. **Protocol must be registered** (or registration recommended) before Phase 2
3. **Risk of bias must be completed for all studies** before Phase 3
4. **GRADE assessment required** for every pooled outcome
5. **PRISMA checklist compliance** verified in Phase 5
---
## Operational Modes
| Mode | Agents Active | Output | Word Count |
|------|---------------|--------|------------|
| `full` (default) | All 9 core (excluding socratic_mentor, risk_of_bias, meta_analysis, monitoring) | Full APA 7.0 report | 3,000-8,000 |
| `quick` | RQ + Biblio + Verification + Report | Research brief | 500-1,500 |
| `review` | Editor + Devil's Advocate + Ethics | Reviewer report on provided text | N/A |
| `lit-review` | Biblio + Verification + Synthesis | Annotated bibliography + synthesis | 1,500-4,000 |
| `fact-check` | Source Verification only | Verification report | 300-800 |
| `socratic` | Socratic Mentor + RQ + Devil's Advocate | Research Plan Summary (INSIGHT collection) | N/A (iterative) |
| `systematic-review` | RQ + Architect + Biblio + Verification + RoB + Meta-Analysis + Synthesis + Report + Editor + Ethics + DA | Full PRISMA 2020 report + forest plot data + GRADE table | 5,000-15,000 |
---
## Failure Paths
See `references/failure_paths.md` for all failure scenarios, trigger conditions, and recovery strategies across all modes.
Key failure path summary:
| Failure Scenario | Trigger Condition | Recovery Strategy |
|---------|---------|---------|
| RQ cannot converge | Phase 1 / Layer 1 exceeds multiple rounds while still vague | Provide 3 candidate RQs or suggest lit-review |
| Insufficient literature | bibliography_agent finds < 5 sources | Expand search strategy, alternative keywords |
| Methodology mismatch | RQ type misaligned with method capability | Return to Phase 1, suggest 3 alternative methods |
| Devil's Advocate CRITICAL | Fatal logical flaw discovered | STOP, explain the issue, require correction |
| Ethics BLOCKED | Serious ethical issue | STOP, list issues and remediation path |
| Socratic non-convergence | > 10 rounds without convergence | Suggest switching to full mode |
| User abandons mid-process | Explicitly states they don't want to continue | Save progress, provide re-entry path |
| Only Chinese-language literature | English search returns empty | Switch to Chinese academic databases |
---
## Literature Monitoring (Optional Post-Pipeline)
After any research mode is complete, users can optionally activate the `monitoring_agent` to set up post-research literature monitoring. This is not part of the main pipeline — it is an auxiliary capability triggered on demand.
See `agents/monitoring_agent.md` for the detailed agent definition.
See `references/literature_monitoring_strategies.md` for platform-specific setup guides.
**Trigger**: "monitor this topic", "set up alerts", "track new publications on this"
**Capabilities**:
- Weekly/monthly monitoring digest generation
- Retraction alerts for cited sources
- Contradictory findings detection
- Key author tracking
- Keyword evolution tracking
**Input**: Completed bibliography + search strategy from any research mode
**Output**: Monitoring configuration + digest template (markdown)
**Limitation**: The monitoring agent produces configurations and templates for the user to act on. It cannot run autonomous background monitoring.
---
## Handoff Protocol: alterlab-deep-research → alterlab-paper-writer
After research is complete, the following materials can be handed off to `alterlab-paper-writer`:
1. **Research Question Brief** (from research_question_agent)
2. **Methodology Blueprint** (from research_architect_agent)
3. **Annotated Bibliography** (from bibliography_agent)
4. **Synthesis Report** (from synthesis_agent)
5. **[If socratic mode] INSIGHT Collection and Research Plan Summary**
**Trigger**: User says "now help me write a paper" or "write a paper based on this"
`alterlab-paper-writer`'s `intake_agent` will automatically detect available materials and skip redundant steps:
- Has RQ Brief -> skip topic scoping
- Has Bibliography -> skip literature search
- Has Synthesis -> accelerate findings / discussion writing
See `examples/handoff_to_paper.md` for a detailed handoff example.
---
## Full Academic Pipeline
See `alterlab-research-pipeline/SKILL.md` for the complete workflow.
---
## Agent File References
| Agent | Definition File |
|-------|----------------|
| research_question_agent | `agents/research_question_agent.md` |
| research_architect_agent | `agents/research_architect_agent.md` |
| bibliography_agent | `agents/bibliography_agent.md` |
| source_verification_agent | `agents/source_verification_agent.md` |
| synthesis_agent | `agents/synthesis_agent.md` |
| report_compiler_agent | `agents/report_compiler_agent.md` |
| editor_in_chief_agent | `agents/editor_in_chief_agent.md` |
| devils_advocate_agent | `agents/devils_advocate_agent.md` |
| ethics_review_agent | `agents/ethics_review_agent.md` |
| socratic_mentor_agent | `agents/socratic_mentor_agent.md` |
| risk_of_bias_agent | `agents/risk_of_bias_agent.md` |
| meta_analysis_agent | `agents/meta_analysis_agent.md` |
| monitoring_agent | `agents/monitoring_agent.md` |
---
## Reference Files
| Reference | Purpose | Used By |
|-----------|---------|---------|
| `references/apa7_style_guide.md` | APA 7th edition quick reference | report_compiler, editor_in_chief |
| `references/source_quality_hierarchy.md` | Evidence pyramid + grading rubric | source_verification, bibliography |
| `references/methodology_patterns.md` | Research design templates | research_architect |
| `references/logical_fallacies.md` | 30+ fallacies catalog | devils_advocate |
| `references/ethics_checklist.md` | AI disclosure, attribution, dual-use | ethics_review |
| `references/interdisciplinary_bridges.md` | Cross-discipline connection patterns | synthesis, research_architect |
| `references/socratic_questioning_framework.md` | 6 types of Socratic questions + 30+ prompt patterns | socratic_mentor |
| `references/failure_paths.md` | 12 failure scenarios with triggers and recovery paths | all agents |
| `references/mode_selection_guide.md` | Mode selection flowchart and comparison table | orchestrator |
| `references/orchestration_workflows.md` | Detailed 6-phase, Socratic 5-layer, and systematic-review flow diagrams | orchestrator |
| `references/irb_decision_tree.md` | IRB decision tree (US tiers) + Taiwan process + HE quick reference; Turkey via `alterlab-tr-research-ethics` | ethics_review, research_architect |
| `references/equator_reporting_guidelines.md` | EQUATOR reporting guideline mapping | research_architect, report_compiler |
| `references/preregistration_guide.md` | Preregistration decision tree + platforms + checklist | research_architect |
| `references/systematic_review_toolkit.md` | Cochrane Handbook v6.5, PRISMA 2020, RoB 2, ROBINS-I (2016 and V2), I² guide, GRADE, protocol registration | risk_of_bias, meta_analysis, bibliography, report_compiler |
| `references/literature_monitoring_strategies.md` | Google Scholar alerts, PubMed alerts, RSS feeds, Retraction Watch, citation tracking, monitoring cadence | monitoring_agent |
---
## Templates
| Template | Purpose |
|----------|---------|
| `templates/research_brief_template.md` | Quick mode output format |
| `templates/literature_matrix_template.md` | Source x Theme analysis matrix |
| `templates/evidence_assessment_template.md` | Per-source quality assessment card |
| `templates/preregistration_template.md` | OSF standard 21-item preregistration template |
| `templates/prisma_protocol_template.md` | PRISMA-P 2015 systematic review protocol template |
| `templates/prisma_report_template.md` | PRISMA 2020 systematic review report template (27 items) |
---
## Examples
| Example | Demonstrates |
|---------|-------------|
| `examples/exploratory_research.md` | Full 6-phase pipeline walkthrough |
| `examples/systematic_review.md` | PRISMA-style literature review |
| `examples/policy_analysis.md` | Applied comparative policy research |
| `examples/socratic_guided_research.md` | Complete Socratic mode multi-turn dialogue (12 rounds) |
| `examples/handoff_to_paper.md` | alterlab-deep-research full mode handoff to alterlab-paper-writer |
| `examples/review_mode.md` | Review mode: 3-agent review pipeline for policy recommendation text |
| `examples/fact_check_mode.md` | Fact-check mode: source verification of HEI claims with per-claim verdicts |
---
## Output Language
Follows the user's language. Academic terminology kept in English. Socratic mode uses natural conversational style.
---
## Quality Standards
1. **Every claim must have a citation** — no unsupported assertions
2. **Evidence hierarchy** — meta-analyses > RCTs > cohort studies > case reports > expert opinion
3. **Contradiction disclosure** — if sources disagree, report both sides with evidence quality comparison
4. **Limitation transparency** — every report must have an explicit limitations section
5. **AI disclosure** — all reports include a statement that AI-assisted research tools were used
6. **Reproducibility** — search strategies, inclusion criteria, and analytical methods must be documented for replication
7. **Socratic integrity** — in socratic mode, never give direct answers; always guide through questions
## Cross-Agent Quality Alignment
Unified definitions to prevent inconsistency across agents:
| Concept | Definition | Applies To |
|---------|-----------|------------|
| **Peer-reviewed** | Published in a journal with formal peer review process (editorial review alone does not qualify). Conference proceedings count only if explicitly peer-reviewed | bibliography_agent, source_verification_agent |
| **Currency Rule** | Default: published within 5 years. Override by domain: CS/AI = 3 years, History/Philosophy = 20 years, Law = depends on jurisdiction changes. Seminal works exempt regardless of age | bibliography_agent, ethics_review_agent |
| **CRITICAL severity** | Issue that, if unresolved, would invalidate a core conclusion or constitute academic misconduct. Requires immediate resolution before pipeline can proceed | All agents |
| **Source Tier** | tier_1 = top-quartile peer-reviewed journal; tier_2 = other peer-reviewed; tier_3 = academic but not peer-reviewed; tier_4 = grey literature | bibliography_agent, source_verification_agent |
| **Minimum Source Count** | full = 15+, quick = 5-8, lit-review = 25+, systematic-review = all eligible (no limit), fact-check = 3+ per claim | bibliography_agent |
| **Verification Threshold** | 100% of sources existence-checked before use (`verify_citations.py` verdicts, WebSearch fallback) + independent WebSearch spot-check of ≥50% of sources (all tier_3/tier_4 first) | bibliography_agent, source_verification_agent, ethics_review_agent |
> **Cross-Skill Reference**: See `shared/handoff_schemas.md` for inter-stage data exchange formats.
---
## Integration with Other Skills
This skill is domain-agnostic but composes with other AlterLab skills:
```
alterlab-deep-research + alterlab-paper-2-web -> Disseminate research as a website / video / poster
alterlab-deep-research + alterlab-paper-writer -> Full research-to-publication pipeline
alterlab-deep-research (socratic) + alterlab-paper-writer (plan) -> Guided research + paper planning
alterlab-deep-research (systematic-review) + alterlab-paper-writer -> PRISMA systematic review paper
alterlab-deep-research -> alterlab-research-pipeline -> End-to-end research → review → finalize workflow
```
---
## Version History
Current: **v2.4** (see frontmatter `metadata.version`). Latest change (2026-09):
existence verification aligned across agents (every source is checked with
`alterlab-citation-verifier` before use; no "unverifiable but kept" bucket), the
Socratic stopping rules consolidated to one consistent set, and reporting standards
brought current (Cochrane Handbook v6.5, ROBINS-I V2, CONSORT 2025, SPIRIT 2025,
TRIPOD+AI). v2.3 added the `systematic-review` mode (PRISMA 2020 pipeline with
`risk_of_bias_agent` and `meta_analysis_agent`) and the optional post-pipeline
`monitoring_agent`, bringing the team to 13 agents and 7 modes.
Part of the AlterLab Academic Skills suite.
