Deep Research — Universal Academic Research Agent Team

Universal deep research tool — a domain-agnostic 13-agent team for rigorous academic research on any topic.

v2.4 adds writing quality improvements to the report compiler:

• Style Profile consumption (optional) — If a Style Profile is available from academic-paper intake, the report compiler applies it as a soft guide for the Executive Summary and Synthesis sections. Discipline conventions and report objectivity take priority.
• Writing Quality Check — The report compiler runs a writing quality checklist before finalizing: flags AI-typical overused terms, checks sentence/paragraph length variation, removes throat-clearing openers. See

  academic-paper/references/writing_quality_check.md

  .

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

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

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

full

socratic

full

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

academic-paper

academic-paper-reviewer

academic-pipeline

Quick Mode Selection Guide

socratic

full

quick

review

lit-review

fact-check

systematic-review

Spectrum (v3.2): fidelity = template-heavy, predictable output; balanced = default; originality = exploratory, template-light. See

shared/mode_spectrum.md

Not sure? Start with

socratic

socratic

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

Mode Selection Guide

See

references/mode_selection_guide.md

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

1. ⚠️ IRON RULE: 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. ⚠️ IRON RULE: Ethics Review can halt delivery for Critical ethics concerns
4. User confirmation required after Phase 1 before proceeding

Socratic Mode: Guided Research Dialogue

5-layer dialogue guiding users from vague ideas to concrete research questions. Core principle: ⚠️ IRON RULE: Never give direct answers.

Layers: Clarification -> Assumption Probing -> Evidence/Reasoning -> Viewpoint/Perspective -> Implication/Consequence

See

references/socratic_mode_protocol.md

for the full 5-layer dialogue flow, management rules, and auto-end conditions.

Systematic Review Mode

PRISMA 2020-compliant systematic review with optional meta-analysis. Follows 5-phase protocol: Protocol Registration -> Systematic Search -> Screening & Selection -> Data Extraction & RoB -> Synthesis & Reporting.

v3.4.0 compliance:

systematic-review

mode triggers

compliance_agent

at Stage 2.5 (Methods items) and Stage 4.5 (remaining items + RAISE 8-role matrix). PRISMA-trAIce Mandatory failures block the pipeline. See

shared/compliance_checkpoint_protocol.md

.

See

references/systematic_review_protocol.md

for full PRISMA pipeline, checkpoint rules, and meta-analysis procedures.

Operational Modes

full

quick

review

lit-review

fact-check

socratic

systematic-review

Failure Paths

See

references/failure_paths.md

Key failure path summary:

Literature Monitoring (Optional Post-Pipeline)

Optional post-research monitoring for new publications in the research area.

See

references/literature_monitoring_strategies.md

for setup instructions across academic databases.

Handoff Protocol: deep-research → academic-paper

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

academic-paper

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"

academic-paper

intake_agent

• Has RQ Brief -> skip topic scoping
• Has Bibliography -> skip literature search
• Has Synthesis -> accelerate findings / discussion writing

See

examples/handoff_to_paper.md

Full Academic Pipeline

See

academic-pipeline/SKILL.md

Agent File References

agents/research_question_agent.md

agents/research_architect_agent.md

agents/bibliography_agent.md

agents/source_verification_agent.md

agents/synthesis_agent.md

agents/report_compiler_agent.md

agents/editor_in_chief_agent.md

agents/devils_advocate_agent.md

agents/ethics_review_agent.md

agents/socratic_mentor_agent.md

agents/risk_of_bias_agent.md

agents/meta_analysis_agent.md

agents/monitoring_agent.md

Reference Files

references/apa7_style_guide.md

references/source_quality_hierarchy.md

references/methodology_patterns.md

references/logical_fallacies.md

references/ethics_checklist.md

references/interdisciplinary_bridges.md

references/socratic_questioning_framework.md

references/failure_paths.md

references/mode_selection_guide.md

references/irb_decision_tree.md

references/equator_reporting_guidelines.md

references/preregistration_guide.md

references/systematic_review_toolkit.md

references/literature_monitoring_strategies.md

references/argumentation_reasoning_framework.md

references/socratic_mode_protocol.md

references/systematic_review_protocol.md

references/cross_agent_quality_definitions.md

references/changelog.md

Templates

templates/research_brief_template.md

templates/literature_matrix_template.md

templates/evidence_assessment_template.md

templates/preregistration_template.md

templates/prisma_protocol_template.md

templates/prisma_report_template.md

Examples

examples/exploratory_research.md

examples/systematic_review.md

examples/policy_analysis.md

examples/socratic_guided_research.md

examples/handoff_to_paper.md

examples/review_mode.md

examples/fact_check_mode.md

Output Language

Follows the user's language. Academic terminology kept in English. Socratic mode uses natural conversational style.

Anti-Patterns

Explicit prohibitions to prevent common failure modes:

Quality Standards

1. ⚠️ IRON RULE: 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 across all agents. ⚠️ IRON RULE: CRITICAL severity = issue that would invalidate a core conclusion or constitute academic misconduct. Requires immediate resolution.

See

references/cross_agent_quality_definitions.md

for full peer-reviewed source tiers, currency standards, and severity definitions.

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 Info

Version History

See

references/changelog.md

for full version history.