academic-research

name	academic-research
description	Academic research methodology pack — systematic literature review, citation integrity, quality evaluation. Activates on: 学术, academic, 论文, paper, 文献, literature, meta-analysis, 元分析, PRISMA, systematic review, 系统性综述, PubMed, 文献综述, 学术研究, 科研
version	0.1.0
type	reference-based
keywords	["学术","academic","论文","paper","文献","literature","meta-analysis","元分析","PRISMA","systematic review","系统性综述","PubMed","文献综述","学术研究","科研"]

Academic Research Capability Pack

Teaches AI agents HOW to do academic research — depth enforcement, citation integrity, quality scoring, and self-evaluation. Derived from ScienceClaw's 629-line SCIENCE.md protocol + ScholarEval rubric + VOYAGER-inspired Reflexion Cycle.

CONSUMES: Research question + optional domain constraints (field, date range, databases). PRODUCES: Evidence-grounded research report + methodology section + citation audit trail + Reflexion Cycle self-evaluation (for non-trivial tasks).

---

Scope Disambiguation

This pack covers academic and scientific research methodology.

This pack — use when:

• User asks about 学术/academic/论文/paper/文献/literature tasks
• Systematic or literature reviews, meta-analyses
• Tasks mentioning PRISMA, PubMed, citation analysis, ScholarEval
• Evaluating research quality or scholarly writing

NOT this pack — defer to research-methodology when:

• Market analysis, technology trend analysis, competitive analysis
• General non-academic "research X" tasks without scientific context
• Business strategy investigation, product analysis

If ambiguous, ask the user: "Is this academic/scientific research or general market/technology research?"

---

Step 1: Detect Research Task Type

Classify the user's request into one of four tiers. Each tier has a mandatory minimum depth derived from ScienceClaw SCIENCE.md lines 111-121.

Tier	Signal Keywords	Min Phases	Min Tool Calls	Session Model
Quick factual	"what is", "define", "quick question", single-fact lookup	1-2	3-5	Single session, no handoff
Literature survey	"review literature", "survey papers", "what does the research say", "文献综述"	1-5	20-40	1-2 sessions with handoff
Comprehensive review	"comprehensive review", "analyze the field", "综合分析", "学术综合分析"	1-6	40-80	Epic: 2-3 phases
Systematic review	"systematic review", "meta-analysis", "PRISMA", "系统性综述", "元分析"	1-6 (iterated)	80+	Epic: 4-6 phases (PRISMA pipeline)
Multimodal research	user uploads image, "pattern analysis", "visual comparison", "artifact image", "图像分析", "纹样"	1-5	20-40	1-2 sessions; load multimodal-research.md + pattern-extraction.md

Example inputs per tier:

Quick factual:

• "What is the current impact factor of Nature Medicine?"
• "Who first described CRISPR-Cas9 gene editing?"
• "What is the sample size formula for a two-arm RCT?"

Literature survey:

• "Survey recent papers on transformer architectures for protein folding"
• "What does the literature say about remote work productivity?"
• "Review papers on CRISPR cancer therapy from 2023-2025"

Comprehensive review:

• "Analyze the field of large language models for drug discovery"
• "Comprehensive review of causal inference methods in economics"
• "Review all approaches to federated learning in healthcare"

Systematic review:

• "Conduct a systematic review of CBT interventions for anxiety"
• "PRISMA-compliant meta-analysis of statin efficacy in primary prevention"
• "Systematic review of AI diagnostic accuracy in radiology"

Multimodal research:

• "Analyze this image of a ceramic bowl — describe the ornamental pattern and classify the motif types"
• "Compare the palmette designs across these three artifacts from different cultures"
• "Extract the visual features from this food plating photograph for sensory evaluation research"

Source: Adapted from SCIENCE.md lines 111-121, adjusted per tad-mapping-blueprint.md Decision 6

---

Step 2: Load References by Task Type

Protocol References (always applicable)

Tier	Protocol References
Quick factual	zero-hallucination.md only
Literature survey	research-protocol.md + zero-hallucination.md + fallback-chains.md
Comprehensive review	ALL protocol references + relevant cluster references
Systematic review	ALL protocol + ALL cluster references

Cluster References (load by research domain)

Load the cluster references that match the research topic. Multiple clusters may apply.

Research Domain Signal	Load These Cluster References
Literature search, citation analysis	references/literature-search.md
Academic database queries (general)	references/database-apis-general.md
Life science databases (protein, gene, drug)	references/database-apis-life-sciences.md
Statistical analysis, meta-analysis	references/statistics.md
Paper/grant/report writing	references/writing.md
Figures, plots, charts	references/visualization.md
Biomedical / life science domain	references/domain-biomedical.md
Physical / computational science	references/domain-physical.md
Social science / economics	references/domain-social.md
Experiment design, ethics, reproducibility	references/experiment-design.md
Image analysis, visual evidence, multimodal	references/multimodal-research.md
Ornamental patterns, motifs, cross-cultural visual comparison	references/pattern-extraction.md
Quantitative image measurement, CV tools, similarity scoring, frequency analysis	references/quantitative-analysis.md

Read the loaded reference files and apply their rules during research execution.

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Step 3: Alex/Blake Role Mapping for Research Tasks

Research Activity	Alex (Design)	Blake (Execute)
Research question formulation	Elicits via Socratic Inquiry	—
Search strategy + database selection	Specifies in handoff	—
Search execution	—	Runs curl/API commands
Paper reading + extraction	—	Reads and extracts findings
Quality assessment	Defines criteria in handoff ACs	Applies ScholarEval from scholar-eval.md
Synthesis across sources	—	Synthesizes with citation audit
Report writing	—	Writes report with methodology section
Depth enforcement	Sets minimum tier in handoff	Follows research-protocol.md thresholds
Citation integrity	AC: "every citation traces to tool result"	Self-checks per zero-hallucination.md

Source: tad-mapping-blueprint.md Decision 5

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Step 4: Anti-Premature-Conclusion Checklist

Before concluding ANY research task (except quick factual), apply the 10 Anti-Premature-Conclusion Rules from research-protocol.md and the Completeness Checklist from the same file.

If any item is unchecked, continue working instead of concluding.

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Step 5: TAD Integration

TAD Mechanism	Academic Research Role
Gate 3	Verifies citation integrity (zero-hallucination 4-point check) + ScholarEval score ≥ 0.75 for Accept
Gate 4	Verifies research completeness per tier (did Blake reach the minimum phase and tool-call threshold?)
Knowledge Assessment	Runs after Reflexion Cycle for non-trivial tasks — captures reusable research patterns in project-knowledge
Ralph Loop Layer 1	Checks fallback chain exhaustion (did Blake try alternatives before declaring a source failed?)

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Step 6: Research Memory & Persistence

Research findings persist across sessions via TAD's existing memory stack — no additional infrastructure required.

Memory Need	TAD Solution	How It Works
Cross-session findings	.tad/project-knowledge/*.md	Knowledge Assessment (Gate 3/4) writes reusable discoveries to category files. Blake or Alex reads them on next session via @import in CLAUDE.md.
Semantic recall across sources	NotebookLM via *research-notebook ask	Multi-source notebooks (30-50 sources each) enable cross-source synthesis. Query returns grounded answers with source attribution.
Per-topic evidence archive	.tad/evidence/research/{topic}/	Subdirectories per research topic store raw findings, analysis files, and search logs. Persists across handoffs within an Epic.
Self-evaluation patterns	Completion report Knowledge Assessment	Reflexion Cycle (reflexion-cycle.md) captures what worked and what failed. Written to completion report, promoted to project-knowledge if reusable.
Research notebook portfolio	.tad/research-notebooks/REGISTRY.yaml	Index of all NotebookLM notebooks with topic, source count, and status. Alex creates and curates; Blake queries during implementation.

Integration rules:

• Findings that apply beyond a single handoff → write to .tad/project-knowledge/ via Knowledge Assessment
• Findings specific to one research question → keep in .tad/evidence/research/{topic}/
• Findings worth cross-source synthesis → ingest into NotebookLM via *research-notebook ingest
• Do NOT duplicate: choose one persistence path per finding

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Quick Rule Index

Protocol References (Phase 2)

Reference	What It Covers	When to Read
research-protocol.md	6 mandatory phases, depth enforcement, mandatory search protocol	Every non-trivial research task
zero-hallucination.md	Citation integrity, 4-point self-check, empty-result handling	Every task — this is absolute
scholar-eval.md	8-dimension weighted quality rubric (0-1 scale)	When evaluating research quality
reflexion-cycle.md	5-dimension post-task self-evaluation	After completing a research task
fallback-chains.md	Source failure recovery, 3-strike rule, fallback tables	When a search/API fails

Cluster References (Phase 3) — Domain-Specific Judgment Rules

Reference	What It Covers	When to Read
literature-search.md	Multi-database search, PRISMA pipeline, citation networks, bibliography management	Literature reviews, systematic reviews
database-apis-general.md	Semantic Scholar, OpenAlex, PubMed, arXiv, World Bank, CrossRef API templates	Any database query task
database-apis-life-sciences.md	UniProt, ChEMBL, NCBI, PDB, ClinicalTrials, KEGG, STRING API templates	Life science research
statistics.md	Test selection, meta-analysis (DerSimonian-Laird, I²), effect sizes, power analysis, APA reporting	Any quantitative analysis
writing.md	IMRaD structure, grant writing (NIH/NSF), LaTeX, citation styles, journal page limits	Writing research outputs
visualization.md	Publication figures (300+ DPI), journal palettes, chart selection, statistical plots	Creating figures
domain-biomedical.md	Bioinformatics (FDR<0.05), clinical trials, CONSORT, drug discovery, protein analysis	Biomedical research
domain-physical.md	Molecular dynamics, materials screening, signal processing, computational chemistry	Physical/computational science
domain-social.md	Econometrics (DiD, RDD, IV), survey methods, psychometrics, education research	Social science research
experiment-design.md	RCT design, sample size, GRADE, Cochrane RoB, reproducibility, IRB, peer review	Experiment planning
multimodal-research.md	Image analysis protocol, observation-before-interpretation, measurement fallbacks, image citation, cross-image comparison	Image-based research tasks
pattern-extraction.md	Motif identification, line abstraction (3 levels), cross-cultural feature matrix, ornamental vocabulary (guilloche, arabesque, etc.)	Visual pattern / ornament studies
quantitative-analysis.md	image-analysis.py decision matrix, similarity/frequency thresholds, output interpretation, qualitative-quantitative integration	When using CV tools for measurement

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Available Tools

scripts/academic-search.sh — Database Query Helper

Reusable bash script for querying academic databases with rate limiting and structured output.

academic-search.sh <database> "<query>" [--limit N]

Supported databases: semantic-scholar, openalex, pubmed, arxiv, europeana (requires EUROPEANA_API_KEY), usda-food (DEMO_KEY or USDA_API_KEY).

scripts/image-analysis.py — Quantitative Image Analysis

Python toolkit for CV-based image measurement. Requires setup: bash scripts/setup-cv.sh

~/.academic-research-cv-venv/bin/python3 scripts/image-analysis.py edges input.jpg --output edges.svg
~/.academic-research-cv-venv/bin/python3 scripts/image-analysis.py colors input.jpg --output colors.json
~/.academic-research-cv-venv/bin/python3 scripts/image-analysis.py match img1.jpg img2.jpg --output result.json
~/.academic-research-cv-venv/bin/python3 scripts/image-analysis.py frequency input.jpg --output freq.json
~/.academic-research-cv-venv/bin/python3 scripts/image-analysis.py features input.jpg --output features.json

See quantitative-analysis.md for decision matrix and output interpretation.

Use this script during research Phase 1 (Discovery) and Phase 4 (Database Cross-Verification) instead of writing raw curl commands.

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Notes

• Skill evolution: This pack improves via TAD's existing *optimize → proposal → human approval → handoff cycle (not runtime generation). See tad-mapping-blueprint.md Decision 4
• Memory: Uses TAD's file-based project-knowledge + optional NotebookLM notebooks. See Step 6 for the full memory integration mapping
• Source coverage: 86 unique ScienceClaw skills cited across 15 reference files (consolidated from 150 P1+P2 skills)