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:

Scoping — Research question + methodology blueprint
Investigation — Systematic literature search + source verification
Analysis — Cross-source synthesis + bias check
Composition — Full APA 7.0 report
Review — Editorial + ethics + vulnerability scan
Revision — Final polished report

Trigger Conditions

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

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):

User has no clear research question and wants guided thinking
User asks to be "led", "guided", or "mentored" through research
User expresses uncertainty about what to research or where to start
User wants to brainstorm, explore, or clarify a research direction
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)	`academic-paper`
Reviewing a paper (structured review)	`academic-paper-reviewer`
Full research-to-paper pipeline	`academic-pipeline`

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)


research_question_agent
research_architect_agent
bibliography_agent
source_verification_agent
synthesis_agent
report_compiler_agent
editor_in_chief_agent
devils_advocate_agent
ethics_review_agent
socratic_mentor_agent
risk_of_bias_agent
meta_analysis_agent
monitoring_agent

#	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)

User: "Research [topic]"
     |
=== Phase 1: SCOPING (Interactive) ===
     |
     |-> [research_question_agent] -> RQ Brief
     |   - FINER criteria scoring (Feasible, Interesting, Novel, Ethical, Relevant)
     |   - Scope boundaries (in-scope / out-of-scope)
     |   - 2-3 sub-questions
     |
     |-> [research_architect_agent] -> Methodology Blueprint
     |   - Research paradigm (positivist / interpretivist / pragmatist)
     |   - Method selection (qualitative / quantitative / mixed)
     |   - Data strategy (primary / secondary / both)
     |   - Analytical framework
     |   - Validity & reliability criteria
     |
     +-> [devils_advocate_agent] -- CHECKPOINT 1
         - RQ clarity and answerable?
         - Method appropriate for question?
         - Scope too broad or too narrow?
         - Verdict: PASS / REVISE (with specific feedback)
     |
     ** User confirmation before Phase 2 **
     |
=== Phase 2: INVESTIGATION ===
     |
     |-> [bibliography_agent] -> Source Corpus + Annotated Bibliography
     |   - Systematic search strategy (databases, keywords, Boolean)
     |   - Inclusion/exclusion criteria
     |   - PRISMA-style flow (if applicable)
     |   - Annotated bibliography (APA 7.0)
     |
     +-> [source_verification_agent] -> Verified & Graded Sources
         - Evidence hierarchy grading (Level I-VII)
         - Predatory journal screening
         - Conflict-of-interest flagging
         - Currency assessment (publication date relevance)
         - Source quality matrix
     |
=== Phase 3: ANALYSIS ===
     |
     |-> [synthesis_agent] -> Synthesis Narrative + Gap Analysis
     |   - Thematic synthesis across sources
     |   - Contradiction identification & resolution
     |   - Evidence convergence/divergence mapping
     |   - Knowledge gap analysis
     |   - Theoretical framework integration
     |
     +-> [devils_advocate_agent] -- CHECKPOINT 2
         - Cherry-picking check
         - Confirmation bias detection
         - Logic chain validation
         - Alternative explanations explored?
         - Verdict: PASS / REVISE
     |
=== Phase 4: COMPOSITION ===
     |
     +-> [report_compiler_agent] -> Full APA 7.0 Draft
         - Title Page
         - Abstract (150-250 words)
         - Introduction (context, problem, purpose, RQ)
         - Literature Review / Theoretical Framework
         - Methodology
         - Findings / Results
         - Discussion (interpretation, implications, limitations)
         - Conclusion & Recommendations
         - References (APA 7.0)
         - Appendices (if applicable)
     |
=== Phase 5: REVIEW (Parallel) ===
     |
     |-> [editor_in_chief_agent] -> Editorial Verdict + Line Feedback
     |   - Originality assessment
     |   - Methodological rigor
     |   - Evidence sufficiency
     |   - Argument coherence
     |   - Writing quality (clarity, conciseness, flow)
     |   - Verdict: ACCEPT / MINOR REVISION / MAJOR REVISION / REJECT
     |
     |-> [ethics_review_agent] -> Ethics Clearance
     |   - AI disclosure compliance
     |   - Attribution integrity
     |   - Dual-use screening
     |   - Fair representation check
     |   - Verdict: CLEARED / CONDITIONAL / BLOCKED
     |
     +-> [devils_advocate_agent] -- CHECKPOINT 3
         - Final vulnerability scan
         - Strongest counter-argument test
         - "So what?" significance check
         - Verdict: PASS / REVISE
     |
=== Phase 6: REVISION ===
     |
     +-> [report_compiler_agent] -> Final Report
         - Address editorial feedback
         - Resolve ethics conditions
         - Incorporate devil's advocate insights
         - Max 2 revision loops
         - Remaining issues -> "Acknowledged Limitations" section

Checkpoint Rules

Devil's Advocate has 3 mandatory checkpoints; Critical-severity issues block progression
Revision loops capped at 2 iterations; remaining issues become "acknowledged limitations"
Ethics Review can halt delivery for Critical ethics concerns
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.

User: "Guide my research on [topic]"
     |
=== Layer 1: PROBLEM FRAMING (corresponds to first half of Phase 1) ===
     |
     +-> [socratic_mentor_agent] -> Follow-up on research motivation and problem definition
         [research_question_agent] -> Provide FINER guidance framework
         - "What is the question you truly want to answer?"
         - "Why does this question matter? To whom?"
         - "If your research succeeds, how would the world be different?"
         Extract [INSIGHT: ...] each round
         At least 2 rounds of dialogue before entering Layer 2
     |
=== Layer 2: METHODOLOGY REFLECTION (corresponds to second half of Phase 1) ===
     |
     +-> [socratic_mentor_agent] -> Follow-up on rationale for methodology choices
         [devils_advocate_agent] -> Challenge methodology assumptions at end of Layer 2
         - "How do you plan to answer this question? Why this approach?"
         - "Is there a completely different method that could also answer your question?"
         - "What is the biggest weakness of your method?"
         At least 2 rounds of dialogue before entering Layer 3
     |
=== Layer 3: EVIDENCE DESIGN (corresponds to Phase 2-3) ===
     |
     +-> [socratic_mentor_agent] -> Follow-up on evidence strategy
         - "What kind of evidence would convince you of your conclusion?"
         - "What evidence would make you change your conclusion?"
         - "What are you most worried about not finding?"
         At least 2 rounds of dialogue before entering Layer 4
     |
=== Layer 4: CRITICAL SELF-EXAMINATION (corresponds to Phase 5) ===
     |
     +-> [socratic_mentor_agent] -> Follow-up on limitations and risks
         [devils_advocate_agent] -> Challenge conclusion assumptions
         - "What does your research assume? What if those assumptions don't hold?"
         - "How would someone with the opposite view refute you?"
         - "What negative impact could your research have?"
         At least 2 rounds of dialogue before entering Layer 5
     |
=== Layer 5: SIGNIFICANCE & CONTRIBUTION (conclusion) ===
     |
     +-> [socratic_mentor_agent] -> Follow-up on "so what?"
         - "Why should readers care about your findings?"
         - "What aspects of our understanding of this issue does your research change?"
         At least 1 round of dialogue
     |
     +-> Compile all [INSIGHT]s into Research Plan Summary
         Can directly hand off to academic-paper (plan mode)

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.

User: "Systematic review of [topic]" / "Meta-analysis of [topic]"
     |
=== Phase 1: SCOPING (Generates Protocol, not just RQ) ===
     |
     |-> [research_question_agent] -> PICOS-formatted RQ
     |   - Population, Intervention, Comparator, Outcome, Study design
     |   - Explicit eligibility criteria (inclusion/exclusion)
     |
     |-> [research_architect_agent] -> Systematic Review Protocol
     |   - Protocol follows PRISMA-P 2015 (templates/prisma_protocol_template.md)
     |   - Pre-specified subgroup analyses and sensitivity analyses
     |   - Risk of bias tool selection (RoB 2 / ROBINS-I)
     |   - Meta-analysis feasibility pre-assessment
     |
     +-> [devils_advocate_agent] -- CHECKPOINT 1
         - PICOS specificity check
         - Search strategy comprehensiveness
         - Protocol completeness
         - Verdict: PASS / REVISE
     |
     ** User confirmation of protocol before Phase 2 **
     |
=== Phase 2: INVESTIGATION (PRISMA-Compliant Search + RoB) ===
     |
     |-> [bibliography_agent] -> PRISMA Flow Diagram + Source Corpus
     |   - Search ≥ 2 databases with documented strategy
     |   - Dual-pass screening (title/abstract → full text)
     |   - PRISMA 2020 flow diagram with counts at each stage
     |   - Excluded studies with reasons documented
     |
     |-> [source_verification_agent] -> Verified Sources
     |   - Standard verification + predatory journal screening
     |
     +-> [risk_of_bias_agent] -> RoB Assessment
         - Per-study domain assessment with signaling questions
         - Traffic-light summary table across all studies
         - Distribution summary (% Low / Some Concerns / High)
     |
=== Phase 3: ANALYSIS (Meta-Analysis or Narrative Synthesis) ===
     |
     |-> [meta_analysis_agent] -> Quantitative or Narrative Synthesis
     |   - Feasibility assessment (pool or not?)
     |   - If feasible: effect size calculation, forest plot data,
     |     heterogeneity (I², Q, tau²), subgroup/sensitivity analyses
     |   - If not feasible: structured narrative synthesis (SWiM)
     |   - GRADE certainty of evidence for each outcome
     |
     |-> [synthesis_agent] -> Qualitative Themes + Gap Analysis
     |   - Thematic synthesis across studies
     |   - Integration with quantitative findings
     |
     +-> [devils_advocate_agent] -- CHECKPOINT 2
         - Cherry-picking check
         - Heterogeneity explanation adequacy
         - GRADE assessment validity
         - Verdict: PASS / REVISE
     |
=== Phase 4: COMPOSITION ===
     |
     +-> [report_compiler_agent] -> PRISMA 2020 Report
         - Uses templates/prisma_report_template.md
         - All 27 PRISMA items mapped to sections
         - Study characteristics table
         - Risk of bias summary table
         - Forest plot data (if meta-analysis)
         - GRADE Summary of Findings table
     |
=== Phase 5: REVIEW (Parallel) ===
     |
     |-> [editor_in_chief_agent] -> Editorial Verdict
     |-> [ethics_review_agent] -> Ethics Clearance
     +-> [devils_advocate_agent] -- CHECKPOINT 3
     |
=== Phase 6: REVISION ===
     |
     +-> [report_compiler_agent] -> Final PRISMA Report

Systematic Review Checkpoint Rules

All standard checkpoint rules apply (see Checkpoint Rules below)
Protocol must be registered (or registration recommended) before Phase 2
Risk of bias must be completed for all studies before Phase 3
GRADE assessment required for every pooled outcome
PRISMA checklist compliance verified in Phase 5

Operational Modes

Mode	Agents Active	Output	Word Count
`full` (default)	All 9 core (excluding socratic_mentor, RoB, meta-analysis)	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: deep-research → academic-paper

After research is complete, the following materials can be handed off to

academic-paper

Research Question Brief (from research_question_agent)
Methodology Blueprint (from research_architect_agent)
Annotated Bibliography (from bibliography_agent)
Synthesis Report (from synthesis_agent)
[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"

academic-paper

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

academic-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/irb_decision_tree.md`	IRB decision tree + Taiwan process + HE quick reference	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 v6.4, PRISMA 2020, RoB 2, ROBINS-I, 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`	deep-research full mode handoff to academic-paper
`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

Every claim must have a citation — no unsupported assertions
Evidence hierarchy — meta-analyses > RCTs > cohort studies > case reports > expert opinion
Contradiction disclosure — if sources disagree, report both sides with evidence quality comparison
Limitation transparency — every report must have an explicit limitations section
AI disclosure — all reports include a statement that AI-assisted research tools were used
Reproducibility — search strategies, inclusion criteria, and analytical methods must be documented for replication
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% DOI check + 50% WebSearch spot-check	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 can be combined with domain-specific skills:

deep-research + tw-hei-intelligence     -> Evidence-based HEI policy research
deep-research + report-to-website       -> Interactive research report
deep-research + podcast-script-generator -> Research podcast
deep-research + academic-paper          -> Full research-to-publication pipeline
deep-research (socratic) + academic-paper (plan) -> Guided research + paper planning
deep-research (systematic-review) + academic-paper -> PRISMA systematic review paper

Version History

Version	Date	Changes
2.3	2026-03-08	Added systematic-review mode (7th mode): PRISMA 2020 compliant pipeline with risk_of_bias_agent (RoB 2 + ROBINS-I), meta_analysis_agent (effect sizes, heterogeneity, GRADE, narrative synthesis), 2 new templates (PRISMA protocol + report), systematic_review_toolkit reference. Added monitoring_agent (post-pipeline literature monitoring with digests, retraction alerts, author tracking) + literature_monitoring_strategies reference. Enhanced socratic_mentor_agent with 4 convergence signals, 4-type question taxonomy, and auto-end triggers. Added Quick Mode Selection Guide to SKILL.md
2.2	2025-03-05	Added synthesis anti-patterns, Socratic quantified thresholds & auto-end conditions, reference existence verification (DOI + WebSearch), enhanced ethics reference integrity check (50% + Retraction Watch), mode transition matrix, cross-agent quality alignment definitions
2.1	2026-03	Added IRB decision tree, EQUATOR reporting guidelines, preregistration guide + template; enhanced ethics_review_agent with human subjects dimension; enhanced research_architect_agent with ethics/EQUATOR/preregistration integration; enhanced methodology_patterns with EQUATOR cross-references
2.0	2026-02	Added socratic mode (10th agent), failure paths, mode selection guide, handoff protocol, 2 new examples, 3 new references
1.0	2026-02	Initial release: 9 agents, 5 modes, 6-phase pipeline

deep-research

NPX Install

Tags

SKILL.md Content