---
name: topic-to-manuscript
description: Use when a user needs research topic suggestions ranked by novelty, feasibility, and publishability, then wants one or more selected topics turned into manuscript outlines, evidence maps, or full manuscript packages.
---

# Topic to Manuscript

## Overview

Turn a broad research direction, dataset, disease area, or preliminary result into ranked manuscript-ready topics, then push a chosen topic through evidence scan, outline, package scaffolding, drafting, and self-audit. Use this skill to stop “jump straight to prose” behavior and force a topic-selection stage before manuscript writing.

A manuscript package is not a short memo. Unless the user explicitly asks for a teaser, letter, or ultra-short summary, default to a submission-facing draft that is long enough to feel like a real paper and uses inline citations that are traceable to `references.bib`.

## Core principle

Always work in this order:
1. intake and constraints
2. candidate topic generation
3. evidence scan
4. topic ranking
5. package scaffold
6. outline and figure/table plan
7. manuscript drafting
8. self-audit

If data, methods, or literature support are weak, narrow the claim before writing.

## Required sub-skills

Use these existing skills instead of rebuilding their workflows:
- **REQUIRED:** `research-lookup` for current literature, gap checks, and recent evidence
- **REQUIRED:** `citation-management` for metadata cleanup, DOI/PMID resolution, and `references.bib`
- **REQUIRED:** `scientific-writing` for paragraph-level manuscript drafting
- **USE WHEN NEEDED:** `literature-review` when the topic area is broad, controversial, or under-defined
- **USE WHEN NEEDED:** `research-audit` before calling a manuscript package “ready”

If the topic involves special methods or external validation layers, pull in the relevant domain skill only after the topic is selected.

## Workflow

### 1) Intake

Start from the raw research need, not the user's first phrasing.

Collect or infer:
- disease/domain
- available data assets
- preferred design (cohort, MR, trial emulation, review, etc.)
- primary exposure/outcome pair
- target journal or audience
- need for external validation, sensitivity analysis, or mechanistic add-ons

If the user says “课时选题” but the context is manuscript writing, interpret it as **课题选题 / research topic selection** unless corrected.

If the user has only a broad area but no dataset, no clear study design, and no realistic evidence base yet, stop at a **topic memo + gap list**. Do not pretend a full manuscript is ready to draft.

### 2) Candidate topic generation

When the user has no fixed topic yet, generate 5-8 candidate topics. Each topic should be specific enough to become a paper, not just a broad direction.

For each candidate, include:
- working title
- one-sentence core question
- why it matters now
- minimum required data/methods
- likely study design
- main publication risk

Do **not** write a full manuscript before a topic is chosen.

### 3) Evidence scan and ranking

Before recommending a topic, run a lightweight literature scan with `research-lookup`, then score topics using `references/topic-selection-rubric.md`.

Return a ranked table with these columns:
- rank
- topic
- novelty
- feasibility
- validation potential
- manuscriptability
- total score
- recommendation

Always explain:
- why the top topic is strongest
- why the runner-up is still viable
- why lower-ranked topics should wait, narrow, or merge

### 4) Package scaffold

Once a topic is selected, create a per-topic workspace using `scripts/scaffold_topic_package.py`.

The package must contain:
- `01_topic_brief.md`
- `02_evidence_map.md`
- `03_outline.md`
- `04_manuscript_draft.md`
- `05_revision_notes.md`
- `references.bib`

This prevents mixing ideation, evidence, and prose into one unstable file.

### 5) Outline before prose

Fill the package in this order:
1. topic brief
2. evidence map
3. IMRAD outline
4. figure/table plan
5. manuscript draft
6. revision notes

Use `references/manuscript-workflow.md` for the section order and `references/manuscript-draft-standards.md` for length / inline-citation rules. Use `references/manuscript-package-checklist.md` for the final quality gate.

Before drafting prose, lock three things in `03_outline.md`:
- target manuscript type (default: full original article)
- target word budget by section
- citation plan for introduction, methods, and discussion

### 6) Draft the manuscript

After the outline is stable, switch to `scientific-writing`.

Draft in full paragraphs. Keep claims aligned to available evidence. If the study is observational or incomplete, avoid overstating causality. If key validation layers are optional rather than available, label them as future work or recommended extensions.

**Default draft contract for `04_manuscript_draft.md`:**
- unless the user asked for a short form, write a **full-length original-article draft**, not a 1-2k word memo
- follow the word-budget guidance in `references/manuscript-draft-standards.md`
- use inline citations tied to `references.bib`, preferably Pandoc-style cite syntax such as `[@Chen_2024]` or `[@Chen_2024; @Li_2024]`
- do **not** leave literature-backed paragraphs uncited
- do **not** use naked `(Author et al., 2024)` mentions unless they are paired with the BibTeX key, for example `Chen et al. [@Chen_2024]`
- keep the abstract concise and journal-like; do not let the whole paper become abstract-heavy and body-light

### 7) Self-audit before calling it done

Before handing off a manuscript package, check:
- Is the title tightly aligned with the actual analysis?
- Are novelty claims tied to a real literature gap?
- Are all causal/mechanistic claims supported by the design?
- Is there a realistic journal fit?
- Are missing data or unresolved reviewer risks captured in `05_revision_notes.md`?
- Does the draft length match a real submission-facing manuscript rather than a memo?
- Are inline citations present wherever prior literature is discussed?
- Do cited keys in the draft actually exist in `references.bib`?

If needed, run `research-audit` on the finished package.

## Output contracts

### If the user asks for topic suggestions only

Return:
1. ranked topic table
2. top recommendation with rationale
3. one-line next action for each topic

### If the user asks for a manuscript package

Return:
1. selected topic summary
2. generated package path
3. completed or partially completed core files
4. explicit statement of what is drafted vs still evidence-dependent
5. whether `04_manuscript_draft.md` is a full draft, extended draft, or scoped mini-draft

### If the topic is not yet defensible

Return:
1. a narrowed topic memo
2. the top blockers (data, method, literature, validation)
3. the minimum evidence needed before manuscript drafting starts

### If the user asks for full manuscript writing immediately

Do not skip ranking unless the topic is already clear and defensible. In that case still do a fast evidence scan and state the key risks before drafting. Unless explicitly told otherwise, default to a full-length draft with inline citations rather than a short narrative summary.

## Red flags

Stop and correct course if any of these appear:
- the workflow is hard-coded to one old project or one disease story arc
- placeholder text is being treated as real evidence
- prose starts before evidence mapping
- topic ranking is based on vibe rather than rubric
- causal claims exceed the study design
- extra validation layers are promised without data access
- references are cited without metadata verification
- the full manuscript draft is under ~3000 words even though the user asked for a paper-like deliverable
- paragraphs summarize prior studies but contain no inline citation markers tied to `references.bib`
- `references.bib` is populated, but the draft only says “See references.bib” and does not actually cite those entries inline

## Resources

- Read `references/topic-selection-rubric.md` when scoring candidate topics.
- Read `references/manuscript-workflow.md` when moving from topic choice to outline and prose.
- Read `references/manuscript-draft-standards.md` before drafting or revising `04_manuscript_draft.md`.
- Read `references/manuscript-package-checklist.md` before calling the package complete.
- Run `scripts/scaffold_topic_package.py` to create the per-topic file structure.
