Nature Writing

---
name: nature-writing
description: >-
  Write or complete scientific manuscript sections from attached drafts, papers,
  notes, or project files; infer the target journal and retrieve available evidence
  to produce readable prose with verification markers for unresolved claims.
  Use for 完成写作、根据这个文件写、根据项目内容写论文、补全引言、填补占位符,
  manuscript drafting, restructuring, outlines, Results evidence allocation,
  and initial-submission materials. Requests to explain or review a file alone
  do not authorize rewriting it. Supports Nature and configured journal routes.
---

# Nature-Style Scientific Writing — Router

This skill is split into two layers:

- A **static layer** under `static/` that holds versioned, reusable content fragments (core stance + workflow, paper-type playbooks, per-section drafting guidance, initial-submission guidance, language-specific rules, per-journal style).
- A **dynamic layer** (this file plus `manifest.yaml`) that detects the request's axes and loads only the fragments needed for the current job.

Do not try to apply the drafting logic from memory or from this router. Always load fragments from disk as described below.

## Completion intent and scope

A manuscript file plus “完成写作 / 帮我写完 / 根据这个文件写”, a project
plus “根据项目内容写作”, or a request to fill manuscript placeholders invokes
**complete-draft behavior** without a special command. Infer scope from the
request, active conversation and document headings; a named section stays that
section. A multi-section draft may be completed within its existing scope; a
project-only request for a paper supports a full manuscript where evidence permits.
Do not infer permission to rewrite from a file attachment alone or a question
about its contents. Explicit outline-only, routing-test, review-only, translation,
language, and staged-approval requests keep their narrower scope.

Read `static/core/evidence-completion.md` through `always_load`. It defines
project discovery, evidence retrieval and first-pass completion for all journals.
For manuscript work it governs missing-input handling and whether clarification
is needed when older section examples say “ask”, “confirm”, or “fill [X]”. Those
examples are planning aids, not author fill-in forms. Preserve scientific evidence
constraints; a marker never makes an invented fact acceptable.

## Routing protocol

Follow these five steps every time the skill is invoked.

### 1. Load the manifest and the core layer

Read [manifest.yaml](manifest.yaml). It declares the axes (`task`, `paper_type`, `section`, `language`, `journal`), the allowed values, and the file paths each value maps to.

Also read every file listed under `always_load`. These hold the default stance, writing workflow, and output format that apply to every drafting job.

### 2. Detect the axis values for this request

For each axis in the manifest, decide the value using the manifest's `detect:` hint and the user's input:

- `task` — manuscript / submission-package. Use `submission-package` for first-submission materials, never for revision correspondence.
- `paper_type` — research / methods / hypothesis / algorithmic / review. Default: research.
- `section` — abstract / intro / related-work / method / experiments / discussion / conclusion / title. May be multiple. Infer from the supplied material first; use the completion workflow for unresolved scope.
- `language` — en or zh-to-en. Detect from the user's notes themselves.
- `journal` — asc / eaai / isa / kbs / neurocomputing / measurement / ieee-trel / eswa / nature / nature-family / nat-comms / nat-mach-intell / generic.
  Use the manifest’s aliases and applicability rules; default to `generic`.
  Match named journal targets rather than general topic words. Nature means
  the flagship journal; use each configured subjournal’s own key.

State the detected axis values in one short line to the user before drafting, so they can correct you cheaply.

For Expert Systems with Applications (`ESWA`, `Expert Syst. Appl.`), use
`journal=eswa` and read `static/fragments/journal/eswa.md`. Its shared
ESWA contract overrides incompatible Nature-specific journal defaults;
retain the normal scientific workflow and evidence safeguards. For layout
jobs that skip prose axes, read `../nature-shared/journal-formats/eswa.md` directly
when ESWA submission requirements affect the layout.

### 3. Load the matching fragments

For every axis except `section`, read the file mapped in the manifest.
Skip section routing for `task=submission-package` or free-floating prose without a section context.

Resolve each requested section before loading its guidance:

1. Look up `journal_sections[journal]` in the manifest. If present, read its
   `profile` and check the stated manuscript/domain applicability. Do not assume
   a journal match alone makes a narrow corpus applicable.
2. If applicable and the section has a mapping, read that mapped file **instead
   of** the default `axes.section.values` fragment and its generic deep section
   reference (for example `references/introduction.md`). The mapped file contains
   both the section plan and detailed journal-specific writing/revision logic.
3. If absent or inapplicable, use the original section fragment and on-demand
   references. Keep the recognized journal and its submission requirements;
   do not substitute another journal's profile.
4. For multiple sections, resolve each separately. For a full manuscript, first
   identify the actual sections/functions, then read the relevant mapped guides.
   Do not require separate Related Work or Discussion headings to use their logic.

Paths in the manifest are relative to this skill directory; links inside a
reference are relative to that reference. Journal adaptations live beside their
original counterparts with a `-<journal>.md` suffix and a matching
`-<journal>-zh.md` Chinese version. Writing owns the shared chapter
content; polishing points to those exact files instead of maintaining a second
copy. When a mapped guide requests a finer template, follow its matching journal-specific links. English is the default reference
language; do not load both languages unless comparison is requested. No files are discovered merely by
being placed in a folder. Apply this resolved section choice to later instructions
in core workflows, task fragments, or reference tables as well. With an active
override, do not additionally load the default deep section guide or Nature-only
corpus/style examples; load general examples only when requested or needed and
compatible with the selected guide. Preserve shared evidence/ethics constraints,
terminology, paper-type guidance, language rules, and the original output format.
The selected guide controls section organization where defaults differ; the
current journal contract controls official requirements, never the corpus.

Do **not** read every fragment in `static/`. Load only what step 2 selected.

### 4. Draft using the loaded material

Apply the loaded fragments in this priority order:

1. Core stance + evidence completion (`static/core/stance.md`, `static/core/evidence-completion.md`) — retrieve claim, evidence and boundary from the supplied materials before drafting.
2. Paper-type playbook — argument chain, drafting order.
3. Resolved section-specific drafting rules and structure from step 3.
4. Task-specific submission rules when `task=submission-package`.
5. Journal-specific framing and constraints.
6. Language-specific sentence and paragraph rules (apply last).

For `task=manuscript`, run `static/core/workflow.md` end-to-end. Plan internally and deliver prose in the same task; do not turn ordinary completion requests into outline-approval rounds.

When drafting or restructuring Results, or compressing a full manuscript's main
text, also load `../nature-shared/core/main-text-discipline.md` before building
the paragraph map. Classify every result by function, allocate it across main
text, captions, Methods/source data, and SI, then draft the shortest sufficient
evidence chain. Do not equate a complete analysis record with a complete main
text.

When the target is flagship Nature, Nature Communications, Nature Machine
Intelligence, or another Nature Portfolio title, load the matching shared
Nature-style corpus guidance for the section being drafted:

- Results or Discussion →
  `../nature-shared/core/nature-results-discussion.md`
- Introduction or whole-manuscript narrative →
  `../nature-shared/core/nature-introduction.md`
- Abstract → `../nature-shared/core/nature-abstract.md`

Use these files for claim escalation, question-chain alignment,
discovery-centred compression, and synthesis. They were initially distilled
from published NMI papers and generalized as Nature-style defaults; do not
present them as official policy, and let the target journal's current rules
override them.

For any Discussion drafting, restructuring, or section audit, also load
`../nature-shared/core/discussion-argument-language.md`. Use it to select the
opening anchor, control the reverse-funnel expansion, distinguish literature
positioning from citation decoration, calibrate modal strength to evidence,
and turn limitations and future work into claim-specific reasoning. This is
general writing guidance rather than an official journal rule.

For `task=submission-package`, follow `static/fragments/task/submission-package.md` and `references/submission-package.md` instead. Build the deliverable matrix and readiness audit; do not force manuscript paragraph architecture onto administrative submission materials.

For missing manuscript evidence, follow `static/core/evidence-completion.md`: retrieve, narrow or omit unsupported claims, and return prose with verification notes rather than fill-in blanks. Administrative submission fields retain the submission-package workflow.

### 5. Reach for references only when needed

The files under `references/` are deep references and the example library, not defaults. Open them on demand per the `references.on_demand` table in the manifest. Typical triggers:

- The user asks for a concrete example or template → `references/examples/index.md`.
- A section's draft has structural problems that the section fragment alone does not explain → the matching `references/<section>.md`.
- The user needs a broad-audience `Nature` abstract opening or asks about a `summary paragraph` → `references/nature-summary-paragraph.md`.
- The user asks "does this paragraph flow?" → `references/paragraph-flow.md`.
- The user asks for a self-review or rejection-risk audit → `references/paper-review.md`.
- The user asks what belongs in the main text, captions, or SI; wants a shorter
  Results section; or is adding reviewer-driven explanation →
  `../nature-shared/core/main-text-discipline.md`.
- The user requests a complete first-submission package, templates, or a submission-readiness audit → `references/submission-package.md`.
- The target is the flagship journal Nature and exact submission or formatting
  requirements matter → `../nature-shared/journal-formats/nature.md`.
- The target is Nature Machine Intelligence and exact content-type, submission,
  data/code or production requirements matter →
  `../nature-shared/journal-formats/nature-machine-intelligence.md`.
- Any Nature / Nature Portfolio target needs Results claim progression,
  evidence-bound interpretation, robustness placement, or Discussion synthesis
  → `../nature-shared/core/nature-results-discussion.md`.
- Any target needs a Discussion function chain, evidence-calibrated modal
  language, claim-specific limitations, non-redundant literature positioning,
  or uncertainty-driven future work →
  `../nature-shared/core/discussion-argument-language.md`.
- Any Nature / Nature Portfolio target needs an Introduction funnel, exact gap,
  literature logic, question-first novelty, study roadmap, or alignment with
  Results → `../nature-shared/core/nature-introduction.md`.
- Any Nature / Nature Portfolio target needs abstract evidence-chain,
  main/supporting-claim, numeric-result, or final-payoff decisions →
  `../nature-shared/core/nature-abstract.md`.
- The work involves regulated or specialist research compliance →
  `../nature-shared/core/research-compliance.md`.

## Submission boundary

- `nature-writing` owns **initial submission** materials prepared before peer review.
- `nature-response` owns revision cover letters, rebuttals, point-by-point responses, marked manuscripts, appeals, and other post-decision correspondence.
- Route graphical abstracts and TOC graphics to `nature-figure`; route simulated pre-submission peer review to `nature-reviewer`.

## Why this split

- The static layer is versioned and reviewable. Register journal aliases and the journal fragment in the manifest. For journal-specific chapter logic, additionally register a profile and section paths under `journal_sections`; no further router change is needed for the next journal.
- The dynamic layer keeps each invocation cheap: only the fragments relevant to this draft enter context, instead of the full multi-thousand-line reference set.
- The router itself is short on purpose. Update fragments, not this file, when adding scope.
- This structure mirrors `nature-polishing` so shared content can later be lifted into a `nature-shared/` layer used by both skills.