| id | paper_writing_skills_index |
| name | Paper Writing Skills Index |
| description | Routing and workflow skill family for paper-writing tasks. Covers manuscript
drafting, journal and conference papers, grant proposals, lab reports,
group-meeting reports, talks, workshop notes, reviewer rebuttals, academic
HTML/PDF/LaTeX output with editable-block contracts, citation grounding,
evidence checking, and pre-submission quality gates.
|
| tags | ["paper_writing","manuscript","grant","rebuttal","citation","html","latex"] |
Paper Writing Skills
Mode
Two modes control which files and gates are loaded. Set mode in triage.md during Phase 0.
| Mode | Default for | Trigger words (override default) |
|---|
report | all scenarios | (default — no trigger needed) |
submission | journal_article, conference_paper, paper_submission, grant_proposal, revision_response | 投稿、submit、journal、conference、SCI、Nature、Cell、NeurIPS、ICLR、grant、基金、申请书、rebuttal、revision、peer review、深度调研、systematic review、meta-analysis |
If any submission trigger word appears in the user request, set mode: submission regardless of scenario. Otherwise default to report.
Routing + Sequential Pipeline
| Phase | Entry criteria | Actions | Exit criteria |
|---|
| 0. Triage | a user request and any UI scenario labels | Read workflow/SKILL.md ("Triage" section). Choose scenario_id, format_id, theme_id, mode, language, audience, outputs, constraints. | {workdir}/triage.md exists or is updated |
| 1. Materials and evidence | triage is known | Read the chosen scenario file under scenarios/. Inventory materials. submission only: fetch/search papers via paper_fetch.md, build evidence registry (see Evidence Layer below). | {workdir}/materials/inventory.md; submission: also claim_evidence_map.md |
| 2. Outline + claim boundary | materials are known | Read workflow/SKILL.md ("Paper Outline" + "Figure Storyline" sections). submission + novelty claim: also read Knowledge Lineage Audit in scenarios/grant_proposal.md. | outline |
| 3. Section drafting | outline exists | Read writing/SKILL.md. Draft Markdown. | {workdir}/draft/paper.md |
| 4. Quality gates | draft exists | Run gates per mode (see Quality Gates below). | quality reports under {workdir}/quality/ |
| 5. Editable output | draft + quality notes exist | Apply the chosen rendering template + theme per the Editable HTML Contract section below. | {workdir}/report/<slug>_preview.html |
Scenario Routing
| User intent | scenario_id | Required scenario file | Default mode |
|---|
| manuscript, paper submission, write a paper | paper_submission | scenarios/paper_submission.md | submission |
| journal article, SCI, Nature-style paper | journal_article | scenarios/journal_article.md | submission |
| conference paper, workshop paper | conference_paper | scenarios/conference_paper.md | submission |
| grant, proposal, funding application | grant_proposal | scenarios/grant_proposal.md | submission |
| lab report, experiment report | lab_report | scenarios/lab_report.md | report |
| group meeting, weekly report | group_report | scenarios/group_report.md | report |
| conference talk, workshop sharing | conference_talk / workshop_share | scenarios/conference_talk.md / scenarios/workshop_share.md | report |
| reviewer comments, rebuttal, revision response | revision_response | scenarios/revision_response.md | submission |
Family Index
| Layer | File | Contents |
|---|
| Workflow phases | workflow/SKILL.md | 9 phases inlined: triage, material inventory, research question, literature review, paper outline, data analysis summary, figure storyline, reader testing, finalize packet |
| Section writing | writing/SKILL.md | abstract, introduction, method, results, discussion, claim_evidence_check (citation grounding inlined), reviewer_rubric (+ reviewer_rubric_example), response_letter |
| Evidence layer | inlined below | paper_fetch, evidence registry, evidence summary, context-bound answering |
| Quality gates | inlined below | manuscript coverage, format lint, reproducibility; reporting_guideline_check (clinical) at reporting_guideline_check.md |
| Editable HTML contract | inlined below | block shape, attributes, validation pass criteria |
| Themes | themes/kami_academic.md + themes/kami_academic.css | warm parchment academic theme |
Scenario Format Index
HTML output for any format must satisfy the Editable HTML Contract below.
format_id | Scenario file | Required structure | Special constraints |
|---|
journal_article | scenarios/journal_article.md | Title, Abstract, Keywords, Introduction, Results, Discussion, Methods, Data Availability, Code Availability, Acknowledgements, References, SI note | figure/table numbering, data/code statements, guideline checks when applicable |
conference_paper | scenarios/conference_paper.md | Title, Abstract, Introduction, Related Work, Method, Experiments, Results, Discussion, Conclusion, References, Appendix | page limit, baseline and ablation completeness, optional LaTeX |
grant_application | scenarios/grant_proposal.md | title, abstract, background, gap, aims, research content, key scientific questions, technical route, innovation, feasibility, plan, expected outcomes, team, budget, references | form-like blocks, word limits, aim-route consistency |
lab_report | scenarios/lab_report.md | experiment name, date, operator, purpose, materials, steps, raw observations, data processing, results, abnormal events, conclusion, next step | raw observation separated from interpretation |
group_report | scenarios/group_report.md | progress, core question, evidence, current conclusion, blockers, discussion questions, next plan | scan-friendly, short sections |
conference_talk | scenarios/conference_talk.md | opening, audience context, problem, key idea, evidence sequence, takeaway, Q&A, speaker notes | every figure has a spoken takeaway |
workshop_share | scenarios/workshop_share.md | prerequisites, materials, steps, checkpoints, expected outputs, troubleshooting, Q&A | reproducible from a clean environment |
revision_response | scenarios/revision_response.md | Reviewer X Comment Y, Comment, Response, Changes Made, Status | preserve every comment |
Required Outputs
{workdir}/triage.md{workdir}/draft/paper.md (Markdown source of truth){workdir}/report/<slug>_preview.html{workdir}/quality/claim_evidence_report.md{workdir}/quality/reviewer_report.md — submissions, grants, rebuttals, high-risk tasks only
Rendering Templates
Standard rendering flow
- Read report_standard.md for the HTML+CSS template.
- Convert
draft/paper.md to HTML, wrapping major sections per the Editable HTML Contract below.
- Apply the selected theme. Write
{workdir}/report/<slug>_preview.html.
Academic rendering flow (LaTeX → PDF)
- Read the LaTeX template (
latex_cn.md or latex_en.md based on language).
- Convert
draft/paper.md to LaTeX, fill the template, write <slug>.tex.
- Read COMPILE.md — probe available engines before compiling.
- Also produce an HTML preview via report_academic.md.
Evidence Layer
Evidence skills decide where facts come from. Claims may not be invented or
grounded in model memory; they must trace back to a registered piece of evidence.
| Need | Where |
|---|
| Search and fetch open-access papers by DOI / arXiv / PMID | paper_fetch.md |
| Register claims and supporting evidence | Evidence Registry below |
| Ground citations to specific text segments, rerank, attribute sentences | writing/claim_evidence_check.md ("Citation Grounding" section) |
| Write data and code availability statements | scenarios/journal_article.md ("Data and Code Availability" section) |
Default pipeline: paper_fetch → evidence_summary → evidence_registry → draft → citation grounding
Evidence Registry — claim_evidence_map.md
| Claim ID | Claim | Evidence type | Source | Strength | Risk | Action |
|---|
| C1 | … | citation/figure/table/data/user_material/missing | S001 | strong | low | keep |
Evidence types: citation, figure, table, experimental_data, statistical_result, user_material, missing. Claims with missing evidence cannot appear as firm conclusions. If support is partial, narrow the wording.
Evidence Summary — output table
| Evidence ID | Source | Passage/page | Query answered | Summary | Score | Claim IDs |
|---|
Preserve locator detail for later attribution. Separate the source's statement from the agent's interpretation. If evidence does not answer the query, say so; do not force fit.
Context-Bound Answering
Answer only from provided context. Cite context keys, evidence IDs, pages, or material IDs. If context is insufficient, write I cannot answer from the provided context and list what is missing. Do not fall back to model memory.
Quality Gates
Gates produce reports and risk flags — guardrails, not gatekeepers. Flag issues and suggest fixes; do not silently rewrite a draft to hide problems. Aim for ≥80% compliance; prioritize critical issues (missing data, unsupported claims, fabricated citations) over cosmetic formatting.
Run order: manuscript coverage → format lint → reproducibility → claim/evidence → reporting guideline → reviewer simulation → HTML editability → response consistency.
Manuscript Coverage Check
Core sections (required): Title, Abstract, Introduction, Methods, Results, Discussion, References.
Optional (journal-dependent): Keywords, Conclusion, Acknowledgements, Author Contributions, Competing Interests, Data/Code Availability, Supplementary Materials.
| Section | Must contain |
|---|
| Abstract | background → gap → method → results → conclusion |
| Introduction | background → related work → gap → contribution |
| Methods | design, materials, procedure, parameters, analysis |
| Results | main findings, figures, tables, statistics, subsections by question |
| Discussion | interpretation, comparison, limitations, future, take-home |
Output: ## Manuscript Coverage Report with completeness %, present/complete list, missing/incomplete list, recommendation. Gate: ≥90% excellent / 80-89% good / <80% major sections missing.
Format Lint
Check: section structure complete; figure/table numbering sequential with captions; references numbered, no gaps, consistent format; word/page limits met; supplementary files referenced and numbered.
Output: ## Format Lint Report with compliance %, correct categories, issues (severity + location + action), word count vs limit, recommendation.
Common limits (always verify against journal guidelines):
| Journal | Abstract | Main text | Figures | Refs |
|---|
| Nature/Science | 150-200 | 3-4k words | 4-6 | 30-50 |
| Cell | 150 | 5k | 7 | 80 |
| NeurIPS | 250 | 8 pages | — | — |
| PLOS ONE | 300 | none | none | none |
Gate: ≥90% excellent / 80-89% fix flagged / <80% major problems.
Reproducibility Check
Audit categories (each must be present and concrete): software & tools (names, versions, OS, libraries); parameters & settings (hyperparameters, seeds, hardware); data (source, version, splits, availability); code (repo URL, license, dependencies, reproducibility script).
Output: ## Reproducibility Check Report with compliance %, sufficient detail list, missing/vague list (current text + fix), availability statement templates, recommendation. Gate: ≥90% excellent / 80-89% good / 70-79% fair / <70% major revision.
Editable HTML Contract
All HTML outputs must be standalone working files, not app-only previews.
<section class="editable-block" contenteditable="true"
data-block-id="abstract-001" data-section="abstract"
data-source="draft/paper.md" data-format-role="summary">
<h2>Abstract</h2><p>…</p>
</section>
Required: single file with embedded CSS; semantic tags (section, figure, figcaption, table, caption); @page or @media print; no frontend runtime required; no absolute positioning for body layout.
| Attribute | Meaning |
|---|
data-block-id | stable local block identifier |
data-section | manuscript/report section |
data-source | source file, usually draft/paper.md |
data-format-role | summary, claim, evidence, method, response |
Validation (run after every HTML generation): file opens standalone; CSS embedded; main text is semantic HTML not an image; major blocks have contenteditable="true" and all four data-* attributes; print CSS present; figures/tables use semantic tags. If any criterion fails, fix the renderer or source Markdown — do not relax the contract.
Non-Negotiable Rules
- Do not write unsupported claims. Mark missing evidence and downgrade or remove the claim.
- Do not invent citations, DOIs, accession IDs, page numbers, data repositories, reviewer changes, or experimental results.
- Do not let a search result become evidence until it is summarized, attributed, and bound to a specific claim in the Evidence Registry above.
- Do not use Sci-Hub or any access-control bypass. Open PDF fetching may use only legal OA routes in paper_fetch.md.
- Do not output screenshot-like reports. Main text must remain semantic and editable HTML per the Editable HTML Contract above.
- Keep each
SKILL.md below 500 lines.
Sources
