Academic Writing SOP — 学术写作标准操作规程

When to Read This Skill

Read this skill when the user asks to:

Draft or edit academic text (papers, reports, theses, proposals)
Format citations or bibliographies
Export/import references (BibTeX, RIS, CSV, JSON, PDF, DOI list)
Write or compile LaTeX documents
Convert markdown to PDF, docx, or other formats
Polish academic language or adjust tone
Prepare a manuscript for submission

FOUR-PHASE ITERATIVE WRITING PROTOCOL

CRITICAL — READ THIS FIRST

You MUST follow this four-phase protocol for ALL writing tasks longer than one paragraph. NEVER produce a complete draft in a single pass and call it done. Each phase has explicit steps. Complete them IN ORDER.

所有超过一段的写作任务必须遵循四阶段迭代流程。不得一次性写完就结束。

Phase 1  材料审查与大纲  Material Review & Outline    ⏸ STOP → wait for user
Phase 2  初稿生成        First Draft Generation       (continuous, mid-draft search if needed)
Phase 3  自检与修订      Self-Review & Revision        ⏸ STOP → present review results
Phase 4  精修与导出      Polish & Export               ⏸ STOP → present final + diff

Version Tagging: Every workspace_save MUST use version tags: {topic}-v1.md, {topic}-v2.md, {topic}-final.md.

Phase 1: 材料审查与大纲 (Material Review & Outline)

Goal: Confirm requirements, audit materials, produce outline with per-section citation needs. Identify gaps BEFORE writing.

Step 1: Gather Requirements

MUST ask (skip items already answered by user):

Target format — journal / conference / thesis / report / proposal?
Venue/style — specific journal, conference, or template?
Citation style — APA 7 / MLA 9 / Chicago / IEEE / other? (Default: APA 7)
Language — English / Chinese / bilingual?
Length target — approximate word/page count?
Existing materials — notes, data, figures, prior drafts in workspace?

Step 2: Audit Available Materials (审查已有材料)

MUST execute:

workspace_list — check outputs/drafts/ and outputs/reports/ for existing work
library_search — search local library for relevant papers
workspace_read — read any existing notes/outlines the user mentions

Step 3: Generate Section Outline (生成大纲)

MUST produce this table for EACH section:

Section	Key Points	Citations Needed	Available	Gap?
Introduction	Research gap, RQ, contributions	5-8	3	YES
Methods	...	...	...	...

Step 4: Material Supplementation Loop (材料补充循环)

IF any section has Gap? = YES:

Tell user: "Sections X, Y need more citations. I will search."
Trigger search-sop — use web_search or academic search tools
Add papers via library_add_paper or library_import_bibtex
Update outline table
REPEAT until gaps filled or search exhausted (document remaining gaps)

NEVER proceed to Phase 2 with known gaps unless user explicitly approves.

⏸ STOP POINT 1 — Present Outline (展示大纲，等待确认)

MUST present: (1) outline table, (2) materials summary, (3) remaining gaps, (4) estimated length.

MUST say: "Please review this outline. Reply with changes, or confirm to proceed."

MUST WAIT. Do NOT proceed to Phase 2 automatically.

Phase 2: 初稿生成 (First Draft Generation)

Goal: Write section by section per outline. Save versioned draft.

Step 1: Write Section by Section (逐节撰写)

For EACH section in order:

Write following outline key points
Embed citations per agreed style (see Appendix A)
Per-section check:
- Every factual claim has citation? If NO → add or flag
- All cited papers verified/in library? If NO → search or flag
- All outline key points covered? If NO → expand
If citation missing mid-section: pause → search (search-sop) → add to library → continue
If section needs a figure: pause → load Plotting SOP → generate figure → workspace_save to outputs/figures/ → embed reference ("See Figure N") → continue

Step 2: Save v1

workspace_save → outputs/drafts/{topic}-v1.md
library_export_bibtex → outputs/exports/bibliography-{topic}.bib   (if BibTeX)

Step 3: Progress Note

Tell user: "First draft (v1) saved. Moving to self-review." List any sections with improvised material.

Do NOT wait for input here. Proceed to Phase 3.

Phase 3: 自检与修订 (Self-Review & Revision)

Goal: Execute mechanical checklist. Fix issues. Save v2. Present results.

Step 1: Self-Check Checklist (自检清单)

MUST check ALL 10 items. Record PASS or FAIL for each.

#	Check Item	Verify By
1	Structure complete — follows IMRaD or target format?	Compare headings vs outline
2	Every claim cited — no unsupported assertions?	Scan each paragraph
3	Citation format consistent — same style throughout?	Spot-check 5+ citations
4	No fabricated references — all papers real?	`library_search` cross-check
5	Logical flow — transitions between paragraphs?	Read endings→beginnings
6	Academic tone — no casual language?	Scan for colloquialisms
7	Data/figures labeled — numbered, captioned, referenced?	Check each table/figure
8	Abstract ≤250 words (if applicable)?	Word count
9	No orphaned sections — every header has content?	Scan structure
10	Length ±20% of target?	Word count

Step 2: Fix Every FAIL

For EACH failed item:

Describe the problem
Fix it
Re-verify → confirm PASS

If fixing requires new citations → trigger search (same as Phase 1 Step 4).

Step 3: Save v2

workspace_save → outputs/drafts/{topic}-v2.md

⏸ STOP POINT 2 — Present Self-Review (展示自检结果)

MUST present:

Checklist results (10 items, PASS/FAIL)
Change summary (v1 → v2)
Remaining concerns
Ask: "Review {topic}-v2.md. Reply with changes, or confirm for final polish."

MUST WAIT. Do NOT proceed to Phase 4 automatically.

Phase 4: 精修与导出 (Polish & Export)

Goal: Apply feedback, final polish, export, show version diff.

Step 1: Apply User Feedback

For each piece of feedback: locate section → make change → verify consistency. If "no changes" → skip to Step 2.

Step 2: Final Language Polish (最终润色)

MUST apply these 5 passes (details in Appendix F):

Conciseness — cut redundancies
Precision — vague terms → exact values
Flow — smooth transitions, add signposts
Terminology — consistent terms for same concepts
Grammar — agreement, tense, articles

Step 3: Save & Export

workspace_save → outputs/drafts/{topic}-final.md

Export per user request:

Format	Action
docx	`workspace_export({ source: "…-final.md", format: "docx" })`
PDF	`workspace_export(…, format: "pdf")` or md2pdf pipeline (Appendix E)
LaTeX	Save as `.tex` with preamble (Appendix D)
BibTeX	`library_export_bibtex`

If no format specified, ask user.

Step 4: Version Comparison (版本对比)

MUST present diff summary: structural changes, content changes, quality fixes, word counts (v1 / v2 / final).

⏸ STOP POINT 3 — Final Deliverables (展示最终成果)

MUST present: (1) all saved file paths, (2) version diff, (3) all 10 checks PASS, (4) caveats.

Writing task complete.

APPENDICES — Reference Material for the Phases Above

Appendix A: Citation Formatting

Style	In-text	Reference Format
APA 7	(Author, Year)	Author, A. A. (Year). Title. Journal, vol(issue), pp.
MLA 9	(Author page)	Author. "Title." Journal, vol. X, no. Y, Year, pp. Z.
Chicago	Footnote / (Author Year)	Author. Title. Place: Publisher, Year.
IEEE	[1]	[1] A. Author, "Title," Journal, vol. X, no. Y, pp. Z, Year.
Vancouver	(1)	1. Author AA. Title. Journal. Year;Vol(Issue):Pages.
Harvard	(Author Year)	Author, A.A. Year. Title. Journal, Vol(Issue), pp.
Nature	Superscript^1	1. Author, A. A. Title. Journal Vol, Pages (Year).
ACM	[Author Year]	Author. Year. Title. In Proc. Conf., Pages.

Default: APA 7. For CSL/GB/T 7714-2015, read Citation Styles skill.

Appendix B: Citation Integrity Rules

Every cited paper MUST exist in local library or be verifiable via DOI.
Cite primary sources. Secondary only if primary genuinely inaccessible.
Paraphrase → cite. Quote → quotation marks + page numbers.
Cannot verify a paper? Say so. NEVER fabricate references.

Appendix C: Writing Quality Standards

Clarity: Active voice. One idea per sentence. Define acronyms on first use.
Precision: Exact numbers, not "many." Specify units.
Structure: IMRaD unless user specifies otherwise.
Tone: Academic 3rd person default. "We" for multi-author. Adjust per user.
Transitions: Signpost phrases ("However," "In contrast," "Building on this,").

IMRaD Section Guidelines

Introduction — literature gap, research question, contribution summary
Methods — materials, procedures, statistical tests, sample size justification
Results — data first, figures/tables referenced, no interpretation
Discussion — compare prior work, limitations, implications, future work
Abstract — standalone summary (background, methods, results, conclusion; ≤250 words)

Other sections: Literature Review (humanities), Theory/Model (econ/physics), Related Work (CS), Case Study (law/business).

Appendix D: LaTeX Writing SOP

Compilation: xelatex → biber/bibtex → xelatex ×2 → output.pdf Use exec: cd <dir> && xelatex -interaction=nonstopmode main.tex

Template	Use Case	Package
article/revtex	Journal	`revtex4-2`, `elsarticle`
beamer	Presentations	`beamer`
thesis	Graduation	`THUThesis`, `SJTUThesis`, `ustcthesis`
IEEE conf	CS/EE	`IEEEtran`
ACM	CS	`acmart`

Formulas: Inline $...$ , display \[...\] or equation, align align/aligned. Numbering: equation auto, equation* suppresses. Cross-ref: \label{eq:x} + \eqref{eq:x}.

Overleaf: Use \input{} to split; switch to xelatex for CJK.

Appendix E: Export & Conversion

Export

Format	Tool	Use Case
BibTeX `.bib`	`library_export_bibtex`	LaTeX, Overleaf, JabRef
RIS `.ris`	`library_export_bibtex(format:'ris')`	EndNote, Mendeley, Zotero
CSV/JSON/MD	`workspace_save`	Spreadsheet, API, docs

Import

Format	Tool
BibTeX	`library_import_bibtex`
RIS	`library_import_ris`
PDF	`library_add_paper` (extract DOI)
DOI list	`library_batch_add`
CSV	Parse + `library_batch_add`

Pandoc

pandoc input.md -o output.docx --reference-doc=template.docx          # md→docx
pandoc input.md -o output.pdf --pdf-engine=xelatex -V CJKmainfont="Noto Serif CJK SC"  # md→pdf
pandoc input.docx -o output.md --extract-media=./media                 # docx→md
pandoc input.md -o output.pdf --citeproc --bibliography=refs.bib --csl=apa.csl  # +bib

For CJK: always specify CJK fonts. Use --reference-doc for consistent docx styling.

md2pdf

Use md2pdf-export skill's Puppeteer pipeline. Setup: bash skills/md2pdf-export/scripts/setup-env.sh. Convert: node skills/md2pdf-export/scripts/md2pdf.js input.md [--format A4 --toc --theme github]

Appendix F: Language Polishing Guidelines

Preserve meaning — NEVER alter scientific content or conclusions
Grammar — agreement, tense consistency, articles, parallel structure
Conciseness — "in order to" → "to", "it is important to note that" → "notably"
Hedging — "may suggest," "appears to indicate" (avoid over-hedging)
Terminology — same term for same concept throughout
CJK → English — restructure topic-comment → subject-verb-object

Present changes as tracked edits (original vs. revised).

Appendix G: RC Local Tools Reference

Task	Tool	Pattern
Save draft	`workspace_save`	`outputs/drafts/{topic}-v1.md`
Save revision	`workspace_save`	`outputs/drafts/{topic}-v2.md`
Save final	`workspace_save`	`outputs/drafts/{topic}-final.md`
Review draft	`workspace_read`	`outputs/drafts/{file}`
List workspace	`workspace_list`	Check existing materials
Export Word	`workspace_export`	`{ source: "…", format: "docx" }`
Export PDF	`workspace_export`	`{ source: "…", format: "pdf" }`
Export bib	`library_export_bibtex`	`.bib` subset
Search library	`library_search`	Check available citations
Add paper	`library_add_paper`	Add found paper
Link to task	`task_link_file`	Link file to task
Compile LaTeX	`exec`	`cd {dir} && xelatex -interaction=nonstopmode main.tex`
Pandoc	`exec`	`pandoc {in} -o {out} [opts]`

Appendix H: Related Research-Plugins Skills

writing/composition/ — academic structure, ML paper writing, abstract crafting
writing/citation/ — Zotero, BibTeX management, APA/MLA/Chicago
writing/latex/ — LaTeX syntax, Overleaf, formula rendering
writing/templates/ — thesis templates (THUThesis, SJTUThesis), conference
writing/polish/ — language polishing, tone, grammar tools
tools/document/ — PDF parsing (GROBID), format conversion, large docs

Writing SOP