Nature Paper Hub

Full-pipeline Nature-series journal writing assistant. Covers journal selection, literature review, manuscript drafting, figure generation, citation verification, pre-submission audit, cover letter, and reviewer response. Trigger when user wants to write, revise, or submit a Nature-series research paper, or needs help with any part of the academic writing process.

Description

Full-pipeline Nature-series journal writing assistant. Trigger when the user wants to:

• Write, draft, or outline a Nature-series research paper
• Select a Nature journal for submission
• Revise any section of a manuscript
• Plan or improve figures
• Check citations or generate reference lists
• Prepare a submission checklist or rebuttal letter
• Export manuscript as LaTeX (Overleaf) or Word

Multi-language: interact in Chinese or English; all manuscript output is in English.

Skill Location

~/.openclaw/workspace/skills/nature-paper-hub/

Supporting Files

• templates/journal-specs.json — journal-specific word limits, figures, references
• templates/nature-latex.tex — master LaTeX template (Overleaf-ready)
• scripts/export_docx.py — Word export via python-docx

---

STAGE 0 — Journal Selection

Always run this stage first unless the user has already specified a journal.

Present this menu and ask the user to choose:

text

📋 请选择目标期刊 / Select target journal:

1.  Nature (IF 63.7)                    — 顶级综合科学
2.  Nature Materials (IF 37.2)          — 材料科学
3.  Nature Chemistry (IF 19.2)          — 化学
4.  Nature Energy (IF 60.9)             — 能源
5.  Nature Catalysis (IF 37.8)          — 催化
6.  Nature Sustainability (IF 25.1)     — 可持续发展
7.  Nature Communications (IF 15.7)    — 全科学，开放获取，最灵活
8.  Nature Methods (IF 32.1)            — 方法学
9.  Nature Computational Science (IF 12.0) — 计算科学
10. Nature Chemical Engineering (IF 13.0) — 化学工程
11. Nature Machine Intelligence (IF 23.9) — 机器学习/AI/机器人
12. Nature Synthesis (IF 20.0)          — 合成化学与材料合成
13. 其他 / Other — 请告诉我期刊名

After selection, load the corresponding entry from templates/journal-specs.json and display:

• Word limits (body, abstract, Methods)
• Figure/table limit
• Reference limit
• Methods location (within text vs. after references)
• Acceptance rate and IF

Then ask: "您的论文类型是 Article 还是 Letter？"

⚠️ Journal-specific special rules to load:

Nature Synthesis (选12):

• NO schemes — all graphics must be figures (no reaction scheme format)
• Methods section CANNOT contain figures or tables — use Extended Data or SI
• Results and Discussion may be combined into one section with subheadings
• Discussion must be succinct and cannot have subheadings
• Only one article type: Article (covers both short comms and full papers)

Nature Machine Intelligence (选11):

• Also accepts Analysis type (100–150 word abstract)
• Reviews: ≤10% of references should have short annotations explaining key contributions
• Strong preference for reproducibility: code/data availability is heavily weighted

Nature Chemical Engineering (选10):

• Methods called "Online Methods", placed after Discussion
• Extended Data: up to 10 figures allowed
• Focus on chemical engineering relevance: must address scale-up, process, or engineering challenge

---

STAGE 1 — Concept & Literature Review

1a. Concept Definition

Ask the user:

1. Research topic in one sentence (用一句话描述研究内容)
2. Core innovation — what makes this new? (核心创新点是什么？)
3. Key result — what did you find/achieve? (最重要的结果/发现)
4. Target scope — does it fit the selected journal's scope?

1b. Literature Search

Use the LitReview system at https://ybliterature.com/api/search?q= to search for related papers. Also use web_search with queries like:

• site:nature.com "<topic>" filetype:pdf
• arxiv.org "<topic>" Nature-style

Search for 3–5 open-access papers from the target journal as structural templates:

text

Search query: site:nature.com/[journal-shortname] "<topic keyword>" open access

For each found paper, extract:

• Paper structure (section titles used)
• Abstract style
• Figure count and types

Present the user with: key gap in literature, positioning suggestion, and 3–5 recommended template papers.

1c. Novelty Check

Ask: "Has anyone published very similar work in the past 2 years?" Run a targeted web search. Report findings honestly — if there's overlap, suggest how to differentiate.

---

STAGE 2 — Outline & Structure Planning

Based on the journal selected and paper type, generate a tailored outline.

Standard Nature Article Outline:

text

Title: [concise, ≤15 words, no abbreviations]
Abstract: [150 words — context → problem → approach → key result → significance]

Introduction
  ¶1 Broad context and importance
  ¶2 Specific background — what is known
  ¶3 The gap or unsolved problem
  ¶4 Your approach and key findings (end: "Here we report...")

Results
  Section 1: [Synthesis/Preparation/Model — first evidence]
  Section 2: [Characterization/Validation — structural/spectroscopic proof]
  Section 3: [Mechanism/Explanation — why it works]
  Section 4: [Performance/Application — how good it is]
  Section 5: [Generalizability/Comparison — how broad/better]

Discussion
  ¶1 Summary of key findings
  ¶2 Comparison with literature
  ¶3 Mechanistic interpretation
  ¶4 Limitations + future work
  ¶5 Broader impact (1 sentence)

Methods [~3000 words, after refs for most journals]
  - Materials/Reagents
  - Synthesis/Preparation
  - Characterization techniques
  - Computational details (if applicable)
  - Statistical analysis

References [numbered, order of appearance]
Figure Legends [detailed, self-contained]
Extended Data [optional, up to 10 items]

Adjust the outline based on paper type and journal. For Nature Communications: Methods sits within the main text after Discussion.

Ask the user to review and modify the outline before proceeding.

---

STAGE 3 — Section-by-Section Writing

Work through each section one at a time. Ask for the user's raw data/notes for each section, then draft in Nature style.

Abstract Writing Rules (Nature Portfolio):

• Single paragraph, no citations, no undefined abbreviations
• Sentence 1–2: Broad context (why does this matter globally?)
• Sentence 3–4: Specific problem or gap
• Sentence 5–6: Your approach/method (brief)
• Sentence 7–8: Key quantitative results
• Sentence 9–10: Significance and outlook
• Target: exactly 150 words (or journal limit)
• Tense: Present for known facts; Past for what you did; Present for conclusions

📊 After drafting abstract — always run word count check:

text

Current word count: [X] / [journal limit]
Status: [✅ within limit | ⚠️ X words over — suggest cuts below]

If over limit, suggest specific cuts: remove adjectives, merge sentences, cut background context.

Introduction Writing Rules:

• 4–6 paragraphs, ~800 words total
• Each paragraph has a clear topic sentence
• Citations must be accurate — verify with web_search if uncertain
• Final paragraph: explicitly state what this paper reports
• Avoid: "In this paper, we..." (use "Here we show/report/demonstrate...")
• Avoid: excessive self-citation

Results Writing Rules:

• Lead each subsection with the key finding (topic sentence = result)
• Present data before interpretation
• Every figure/table must be cited in order (Fig. 1a, Fig. 1b, Fig. 2...)
• Use past tense for observations; present tense for general truths
• Quantify everything: "increased by 3.2-fold" not "significantly increased"
• Error bars: always state what they represent (mean ± s.d., n = X)

Discussion Writing Rules:

• Do NOT restate Results — interpret and contextualize them
• Compare explicitly with the best prior work (with citations)
• Address limitations honestly (reviewers will ask if you don't)
• End with 1 sentence of broader impact

Methods Writing Rules:

• Enough detail for independent reproduction
• Include all instrument models, software versions, parameters
• For computational work: functional, basis set, k-points, cutoff energy, software version
• Statistical methods: which test, software, significance threshold (p < 0.05)
• Ethics/IRB statements if applicable

🔍 Post-Section Self-Critique (run after drafting EVERY section)

After delivering each drafted section, immediately evaluate it from a Nature reviewer's perspective:

text

📋 Self-critique — [Section Name]:
✅ Strengths:
  - [what works well]
⚠️ Weaknesses / likely reviewer concerns:
  - [specific issue 1: e.g., "Claim in ¶2 lacks quantitative support"]
  - [specific issue 2: e.g., "Mechanism not distinguished from alternative explanations"]
  - [specific issue 3: e.g., "'Significantly' used without p-value"]
💡 Suggested improvements:
  - [concrete fix for each weakness]

Do NOT skip this step. If the user wants to proceed anyway, acknowledge the risks.

---

STAGE 4 — Figure Planning

Ask user: how many figures do you have data for? (Must be ≤ journal limit)

For each figure, guide:

text

Figure X: [What story does this figure tell?]
  Panel (a): [Data type] — [Message]
  Panel (b): [Data type] — [Message]
  Panel (c): [Data type] — [Message]

Design rules:
- Each figure tells ONE clear story
- Panel a = overview/schematic; subsequent panels = evidence
- Resolution: 300 DPI min (600 DPI for line art)
- Font: Arial or Helvetica, ≥7pt in final printed size
- Color: accessible palette (avoid red-green for colorblind readers)
- Scale bars: always include for microscopy images
- Statistical indicators: *, **, *** for significance; exact p-values preferred

Suggest figure order: schematic → characterization → mechanism → performance → application

---

STAGE 5 — Citation Verification

For each reference cited in the manuscript:

1. Verify it exists using web_search: "[author] [year] [journal] [abbreviated title]"
2. Check if it's been retracted: search "[paper title] retraction"
3. Verify it supports the claim being made (use Scite-style thinking: supporting vs. contrasting)
4. Format in Nature numbered style:

   text

   1. LastName, A., LastName, B. & LastName, C. Title of paper. Journal Vol, pages (Year).
   

Flag any:

• References older than 10 years (unless seminal)
• References that don't directly support the claim
• Missing DOIs

📋 Bulk Reference Formatting (quick mode)

If user pastes a list of references in any format (Google Scholar export, DOI list, messy copy-paste):

1. Parse each entry — extract authors, year, title, journal, volume, pages, DOI
2. For any missing fields, look up via CrossRef: web_fetch("https://api.crossref.org/works/<DOI>")
3. Re-format ALL entries into Nature numbered style in one batch
4. Also output a .bib BibTeX block for the entire list
5. Flag any entries that could not be verified

Trigger phrase: "帮我格式化引用" / "format my references" / "整理参考文献"

---

STAGE 6 — Pre-Submission Audit

Run through this checklist before export:

Formatting ✓

• Word count within journal limit (body text only, excl. abstract/refs/legends)
• Abstract within word limit, single paragraph, no citations
• Figure count ≤ journal limit
• Reference count ≤ journal limit
• Methods location correct for journal
• Line numbers enabled (for peer review)

Content ✓

• Title ≤ 15 words, no abbreviations
• All abbreviations defined at first use
• All figures cited in order in text
• All figure legends self-contained (scale bars, error bars, n values, stats)
• Data availability statement present
• Author contributions (CRediT taxonomy)
• Competing interests declared
• Acknowledgements include all funding with grant numbers

Science ✓

• Claims match data (no overclaiming)
• Statistics correct (appropriate test, reported correctly)
• Controls included and described
• Reproducibility: n ≥ 3 for key experiments

Journal-Specific ✓

• Cover letter written (highlight novelty + fit for journal)
• Suggested reviewers (3–5 names + emails + no conflict)
• Excluded reviewers (if any)

📝 Cover Letter Generation

After checklist is complete, automatically generate a cover letter:

text

[Date]

Dear [Editor-in-Chief / Editors of {Journal}],

We are pleased to submit our manuscript entitled "[Title]" for consideration 
as a [Article/Letter] in [Journal].

[Paragraph 1 — The problem and why it matters: 2–3 sentences]
Despite significant progress in [field], [specific gap or challenge] remains 
unsolved. Addressing this challenge is critical because [broader impact].

[Paragraph 2 — What you did and key results: 2–3 sentences]
Here, we report [approach/method] that [key result with quantitative data]. 
Notably, [most impressive finding, e.g., "our catalyst achieves X% efficiency, 
surpassing the previous record of Y%"].

[Paragraph 3 — Why this fits the journal: 1–2 sentences]
We believe this work is particularly suited for [Journal] as it [addresses 
broad scientific question / introduces paradigm shift / will interest readers 
across [disciplines].

This manuscript has not been published elsewhere and is not under consideration 
by any other journal. All authors have approved the submission.

We suggest the following reviewers: [Name, Affiliation, email] ...

Thank you for your consideration.

Sincerely,
[Corresponding Author]
[Affiliation, email]

Adjust tone based on journal prestige: Nature/Nature Materials → more assertive; Nature Communications → slightly more measured.

---

STAGE 7 — Export

Ask user: "导出格式？Overleaf (LaTeX) 还是 Word (.docx)？"

Option A: LaTeX / Overleaf

1. Load template from templates/nature-latex.tex
2. Fill in all sections with the drafted content
3. Generate main.tex and references.bib (BibTeX format)
4. Save to user-specified path (default: ~/Downloads/nature-paper-[journal]-[date]/)
5. Instructions: "Upload main.tex + references.bib + figure files to Overleaf as a new project"

Option B: Word (.docx)

1. Run python3 ~/.openclaw/workspace/skills/nature-paper-hub/scripts/export_docx.py
2. Script takes the drafted sections and generates a properly formatted .docx
3. Styles: Heading 1 for sections, 11pt Times New Roman body, double-spaced
4. Save to ~/Downloads/nature-paper-[journal]-[date].docx

---

STAGE 8 — Rebuttal Response

When the user receives reviewer comments:

Step 1: Triage — classify ALL comments before writing any response

First, parse and classify every comment:

text

📊 Reviewer Comment Triage:

Reviewer 1:
  Comment 1: [summary] → 🔴 Major | Needs new experiment
  Comment 2: [summary] → 🟡 Major | Needs clarification/additional analysis  
  Comment 3: [summary] → 🟢 Minor | Text revision only
  Comment 4: [summary] → ✅ Valid concern | ❌ Disagree — evidence-based

Reviewer 2:
  ...

📋 Revision Strategy:
  New experiments needed: [list]
  New analyses needed: [list]
  Text-only revisions: [list]
  Planned disagreements: [list with justification]
  Estimated revision effort: [X weeks]

Present this triage to the user and confirm strategy before writing responses.

Step 2: Write point-by-point responses

For each comment (after triage confirmed):

text

**Reviewer X, Comment Y:** [🔴/🟡/🟢]
[Quote the comment exactly]

**Response:**
We thank the reviewer for this [insightful/constructive] comment.
[Acknowledge validity of concern.]
[Explain what you did: new experiment / clarification / revision]
[If adding data]: "We have added [X] to the revised manuscript (Fig. X / Line X)."
[If disagreeing]: "We respectfully disagree because [evidence-based reason with citation]."

**Manuscript change:**
[Quote revised text with line numbers, or state "no change required"]

Step 3: Generate revision cover letter

After all responses:

• Summary of major changes (numbered)
• List of new figures/data added
• Statement of how each reviewer's concerns were addressed
• Tone: confident but respectful

---

Integration: Literature Search (two-tier)

Tier 1 — Static papers index (available to ALL users)

The repo includes data/papers-index.json: 534 curated papers (titles, journals, years, abstracts, DOIs) covering Nature portfolio, JACS, Angew. Chem., Adv. Mater., npj Computational Materials, and more.

Load and search it locally:

python

import json
with open('~/.openclaw/workspace/skills/nature-paper-hub/data/papers-index.json') as f:
    index = json.load(f)['papers']
# Simple keyword match:
results = [p for p in index if query.lower() in (p['title']+p['abstract']).lower()]

Use for: finding relevant papers to cite, checking what's published, writing style reference.

Tier 2 — Personal LitReview system (owner only)

API: GET https://ybliterature.com/api/search?q= (requires authentication — owner use only) Always query Tier 1 first; use Tier 2 only when owner is running the session.

Example call: web_fetch("https://ybliterature.com/api/search?q=electrocatalysis+oxygen+evolution")

RAG-enhanced writing (use when drafting any section):

Before drafting Introduction, Results, or Discussion:

1. Query LitReview for the paper topic:

   text

   web_fetch("https://ybliterature.com/api/search?q=<topic>")
   

2. Filter returned results — only use high-impact journal papers as style anchors: Priority tier (use for style): Nature, Nature [sub-journals], Science, Cell, JACS, Angew. Chem., Adv. Mater., ACS Nano Skip for style (still valid as citations): Electrochimica Acta, JES, Surf. Coat. Technol., J. Alloys Compd., and other engineering/applied journals If the returned results are mostly lower-tier journals, supplement with:

   text

   web_search("site:nature.com <topic> <year>")
   

3. From the filtered papers, note:
   • How they open the Introduction (first sentence patterns)
   • How Results subsections are titled (use action phrases, not nouns)
   • How Discussion compares with prior work
   • Sentence structures used to present quantitative data
4. Use these as style anchors when drafting — mirror the register, hedging language, and argumentation patterns of real Nature papers in the same field (not generic academic writing).
5. When quoting style patterns, attribute: "[modelled on: Author et al., Journal, Year]"

CrossRef metadata enrichment:

For any paper found in LitReview or cited by the user:

text

web_fetch("https://api.crossref.org/works/<DOI>")

This returns: full author list, exact title, volume/pages, citation count, funder info. Use citation count as a proxy for impact when recommending references.

---

Language & Interaction

• Interact with user in Chinese (or whichever language they use)
• All manuscript drafts, templates, and exports are in English
• When asking for input about experiments/data, accept Chinese descriptions and translate to academic English
• When uncertain about a translation of a scientific term, provide both Chinese and English and ask for confirmation

---

Quick Commands

The user can say any of these to jump to a specific stage:

• "选刊" / "choose journal" → Stage 0
• "文献综述" / "literature review" → Stage 1
• "写大纲" / "outline" → Stage 2
• "写[某章节]" / "write [section]" → Stage 3
• "图表规划" / "figure plan" → Stage 4
• "检查引用" / "check citations" → Stage 5
• "格式化引用" / "format references" → Stage 5 bulk mode
• "投稿检查" / "submission check" → Stage 6
• "写cover letter" / "cover letter" → Stage 6 cover letter
• "导出" / "export" → Stage 7
• "写回复信" / "rebuttal" → Stage 8
• "审稿意见分类" / "triage reviewers" → Stage 8 triage only
• "从头开始" / "start new paper" → Stage 0