research-proposal

name	research-proposal
description	Use when the user asks to write or draft a PhD / doctoral research proposal, research plan, 研究计划书, or 开题报告 — a forward-looking plan of background, gap, research questions, methodology, timeline, and significance, in English or Chinese. Triggers: "write a research proposal", "PhD proposal", "doctoral proposal", "研究计划书", "开题报告", "写博士研究计划". Not for backward-looking literature reviews / 综述 / surveys (use medical-imaging-review), nor grant forms bound to a funder's own template (国自然/NSF).
metadata	{"author":"user","version":"2.0.0"}
allowed-tools	["WebSearch","WebFetch","Read","Write","Edit","AskUserQuestion","Glob","Grep","mcp__zotero__zotero_search_items","mcp__zotero__zotero_get_item_metadata","mcp__zotero__zotero_get_item_fulltext","mcp__zotero__zotero_get_annotations","mcp__zotero__zotero_get_notes","mcp__zotero__zotero_search_notes","mcp__zotero__zotero_semantic_search","mcp__zotero__zotero_advanced_search"]

Research Proposal Generator

Generate a forward-looking academic research proposal — a plan for research not yet done — following flagship academic writing conventions, in English or Chinese.

This skill produces the first draft correctly, not a template to be fixed later. Its single most important discipline is citation integrity: a proposal with a fabricated reference is an academic-integrity problem, not a style problem. Read references/CITATION_INTEGRITY.md before Phase 2.

Core Principles

Prose first. Proposals read as flowing, connected paragraphs — not bulleted lists. Reserve lists for a focused set of research questions/objectives (2–4 items) and timeline milestones. Never enumerate contributions, methodology, background, or significance as bullets; narrate them. Full rules and examples: references/WRITING_STYLE_GUIDE.md.

Every citation verified before it is committed. Reference count follows the argument, never a quota — there is no minimum. A PhD proposal typically cites 25–50 sources (humanities often more); a tightly argued 25 beats a padded 45. Every reference must exist (DOI/PMID/arXiv resolves, or Zotero metadata), with author and year matching the source, before it enters the proposal. Unverifiable references are flagged [UNVERIFIED] and disclosed — never fabricated. See references/CITATION_INTEGRITY.md.

Write with verification, not one-shot. Draft section by section; verify each section's citations before moving to the next (Phase 4). Do not generate a full multi-section proposal with dozens of citations in a single pass — that is the structural cause of hallucinated references.

Hedge to the evidence. Use tentative language ("aims to", "may", "is expected to") for proposed work and uncertain claims; state well-established facts plainly. Do not over-claim ("will prove", "revolutionize").

Avoid the LLM tells. These phrases are AI-detector signatures — strip them: "Over the past decade, X has emerged as…", "In recent years,", "It is worth noting that", "plays a crucial/pivotal role", "has garnered significant attention", "delves into", "a testament to". Write specific openings grounded in the actual field instead of generic scene-setting.

Scenario Routing

The default structure below targets PhD/doctoral proposals and academic research plans (Abstract → Introduction → Literature Review → Methodology → Timeline → Significance). Confirm the scenario in Phase 1 and adapt:

Request	Structure
PhD/doctoral proposal, research plan, 研究计划书	Default structure (this skill)
开题报告 (thesis proposal / defense)	Default structure, but weight Literature Review and feasibility/existing-basis more heavily; keep methodology concrete
Humanities dissertation proposal	Default + a Chapter Outline section (see references/DOMAIN_TEMPLATES.md)
基金申请书 / 国自然 / NSF grant	Different structure (立项依据 / 研究内容与目标 / 研究方案与可行性 / 研究基础与工作条件 / 经费预算). Tell the user the default 5-section template is not a grant form; adapt headings to the funder's required template and confirm with the user before writing

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Phase 1: Requirements Gathering

Use AskUserQuestion to collect:

• Research topic / question — core problem to investigate.
• Scenario — PhD proposal / 开题报告 / research plan / grant (routes structure, see above).
• Academic domain — STEM (and whether computational/ML — see references/DOMAIN_TEMPLATES.md), Humanities, or Social Sciences.
• Output language — English or 中文.
• Target word count — default ~3,000 words; range 2,000–4,000 (humanities may extend to ~10,000).
• Optional — target institution/supervisor; existing materials or a Zotero library to draw on.

If the topic is too vague to scope a methodology, ask focused clarifying questions before proceeding.

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Phase 2: Literature Collection (with verification gate)

Read references/LITERATURE_WORKFLOW.md for search strategy and organization.

Tool portability. Confirm which tools are available before using tool-specific names. Prefer the user's Zotero library (via the mcp__zotero__* tools) for closed-access papers; use WebSearch for landscape/trends and WebFetch to open DOI / PubMed / arXiv pages and confirm metadata. If a Zotero/arXiv/PubMed MCP is not connected, fall back to WebSearch + WebFetch. Remind the user to add relevant closed-access papers to Zotero.

Sources by role: WebSearch for trends, reviews, and terminology; WebFetch on arXiv / PubMed / publisher pages for open-access primary sources and metadata; Zotero MCP for the user's own library, annotations, and notes. For journal articles the Crossref REST API (WebFetch https://api.crossref.org/works/<DOI>) is the highest-signal existence+metadata check — it returns clean JSON (title / first author / year / venue), more reliable than parsing a publisher HTML page.

Organize candidates by role: background/context, current state-of-the-art, gap-identifying, methodology, and related work.

Verification gate (do not skip)

Before any source is eligible to be cited:

1. Verify each candidate's existence, first author, and year against a first source (DOI/PMID/arXiv page, or Zotero metadata) — Rules 1, 2, 5 of references/CITATION_INTEGRITY.md.
2. Only take specific findings/numbers from sources whose full text or abstract you actually accessed. Do not write internal results for a paper you could not open.
3. Present the verified candidate list (title, author, year, source/DOI) to the user for a quick sanity check before outlining.

Anything that cannot be verified does not enter the reference pool; if the user insists on a half-remembered source, flag it [UNVERIFIED].

Non-interactive / headless runs. If the skill is invoked without an interactive user (a background agent or pipeline), do not deadlock on step 3: record the verified candidate list inline in the deliverable (or a companion citation_verification_log.md) and continue. The recorded list is the audit trail in lieu of a live sanity check.

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Phase 3: Outline Generation

Read references/STRUCTURE_GUIDE.md and references/DOMAIN_TEMPLATES.md for section-by-section and domain guidance.

Standard Outline (default scenario)

# [Research Title]

## Abstract (150-300 words, 5-10%) — background, questions, methodology overview, significance
## 1. Introduction (500-800 words, 15-20%) — background, problem, questions/objectives, scope
## 2. Literature Review (500-1000 words, 20-25%) — framework, current state, gap, positioning
## 3. Methodology (500-800 words, 20-25%) — design, data collection, analysis, validity/limitations
## 4. Timeline (200-300 words, 5-10%) — phases, milestones, optional Gantt
## 5. Significance and Expected Contributions (200-400 words, 10-15%) — theoretical, practical, broader impact
## References — cite what the argument needs (see CITATION_INTEGRITY.md); no minimum, no padding

Add a Chapter Outline section for humanities proposals. Do NOT include appendices — integrate essential content into the body.

Approval gate (RED LINE)

Present the outline and wait for explicit user approval before Phase 4. Do not start writing content on an unapproved outline.

Ask whether the structure, section emphasis, and scope are acceptable, and whether to add/remove/modify sections.

If the user says "you decide" / "你看着办" / defers: state the assumptions you are locking in (scenario, domain, section set, target length, language), present the concrete outline once more as the decision, and proceed only after that — treat silence-plus-deferral as approval of that stated outline, but still surface the assumptions so the user can veto.

If there is no interactive user at all (headless/agent run): record the locked assumptions and the outline inline in the deliverable and treat that recorded outline as approved. This keeps the audit trail without deadlocking on an approval that no one can give.

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Phase 4: Content Writing (write-with-verify)

Load the scaffold as the writing skeleton and fill it section by section:

• English → assets/proposal_scaffold_en.md
• 中文 → assets/proposal_scaffold_zh.md

Read references/WRITING_STYLE_GUIDE.md and apply it. Key hard rules from it: prose over lists; hedge to evidence; PEEL paragraphs (point → evidence+citation → explanation → link); define abbreviations on first use ("coronary CT angiography (CCTA)"); integrate citations into sentences.

Write-with-verify loop — repeat per section:

1. Draft the section as connected prose, placing (Author, Year) citations only from the Phase 2 verified pool.
2. Immediately verify that section's citations: each in-text (Author, Year) has a matching References entry (Rule 3), and every directional/quantitative claim matches its source (Rule 4). See references/CITATION_INTEGRITY.md.
3. Self-check against the LLM tells (Core Principles) and the hallucination red flags in CITATION_INTEGRITY.md.
4. Fix any failure in place before starting the next section. Do not accumulate unverified citations across sections.

Citation style by domain: STEM/Social Sciences → APA (Author, Year); Humanities → MLA or Chicago; 中文 → GB/T 7714. Keep one style consistent throughout.

Figures: suggest 3–5 figures at appropriate locations (not in the Abstract), each with a title, content description, and style note. Format and placement guidance is in references/WRITING_STYLE_GUIDE.md.

中文 output: 规范学术语体；hedging（"本研究旨在探讨…" 而非 "本研究将证明…"）；参考文献遵循 GB/T 7714。

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Phase 5: Output and Review

Save as proposal_{topic_slug}_{YYYY-MM-DD}.md in the user's working directory.

Verify against references/QUALITY_CHECKLIST.md. Before delivering, the citation gate must pass:

• grep -nE "xxx|XXXX|\[TBD\]|\[UNVERIFIED\]|10\.xxxx|\[.*占位.*\]" returns 0 hits — or every remaining [UNVERIFIED] has been explicitly disclosed to the user and never presented as confirmed.
• Every in-text (Author, Year) reconciles with the References list (no orphans either direction).
• At least 20% of references, and every quantitative/directional claim, spot-checked against sources.
• No placeholder [brackets] or "TBD" left in the body — except applicant-specific scaffold fields the user must personalize ([University/Institution Name], [Your Field], [Month Year]) and [Figure N Suggestion] labels, which are intentional and may remain.

Offer format conversion:

pandoc proposal.md -o proposal.docx        # Word
pandoc proposal.md -o proposal.pdf         # PDF (needs LaTeX)

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Reference Files

File	Read when
references/CITATION_INTEGRITY.md	Before Phase 2 and throughout Phase 4/5 — the 5 citation rules; non-negotiable
references/STRUCTURE_GUIDE.md	Phase 3 — section-by-section writing guide
references/DOMAIN_TEMPLATES.md	Phase 1/3 — STEM (incl. computational/ML), humanities, social sciences differences
references/WRITING_STYLE_GUIDE.md	Phase 4 — academic writing style, hedging, transitions, figures
references/QUALITY_CHECKLIST.md	Phase 5 — final verification before delivery
references/LITERATURE_WORKFLOW.md	Phase 2 — literature collection workflow
assets/proposal_scaffold_en.md	Phase 4 — English writing skeleton
assets/proposal_scaffold_zh.md	Phase 4 — Chinese writing skeleton

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Workflow Summary

Phase 1 Requirements (interactive) → Phase 2 Literature + verification gate → Phase 3 Outline + approval red line → Phase 4 Content, section-by-section write-with-verify → Phase 5 Output + citation gate + checklist.

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Error Handling

• No Zotero results / MCP unavailable — inform the user, fall back to WebSearch + WebFetch on open-access sources, suggest adding papers to Zotero and retrying.
• A reference cannot be verified / looks fabricated — do not write it into the References list. Flag [UNVERIFIED] inline and tell the user; never invent a DOI or author list to complete it.
• Topic too vague — ask clarifying questions; narrow scope; offer well-formed research-question examples.
• Over the word limit — prioritize Introduction and Methodology; condense the literature review to the load-bearing citations; offer an expanded version as a separate file.

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Version Notes

v2.0.0 was rewritten after diagnosis found the v1.0.0 skill generated many references with zero authenticity guardrails, a one-shot generation step, a hard "minimum 40 references" gate that incentivized padding, and internally contradictory numbers.

Earlier failure (v1.0.0)	Current fix (v2.0.0)
No citation verification anywhere	Added CITATION_INTEGRITY.md with 5 rules; gates in Phase 2/4/5
Hard "minimum 40 references"	Removed; "cite what the argument needs; typically 25–50; never pad"
Phase 4 = one-shot generation	Replaced with section-by-section write-with-verify
No literature-verification gate before writing	Phase 2 verify-before-cite + user sanity check
Contradictory numbers (40/30-50 refs, 60%/80% recency)	Unified: no minimum; ~60% recent where the field moves fast
Scaffolds never loaded by the workflow	Phase 4 explicitly loads assets/proposal_scaffold_{en,zh}.md
AI-tell sentence templates provided as models	Removed; added "avoid the LLM tells" guidance
Outline approval implicit	Made a red line, with "你看着办" handling
Task tool declared but unused; WebFetch missing	Removed Task; added WebFetch
Coronary-imaging examples throughout	Diluted with cross-domain examples; added computational/ML sub-template
Bulleted contributions in scaffolds vs prose-first rule	Scaffolds now demonstrate prose contributions/implications