Agent skill

manuscript-ingest

Ingest a submitted manuscript into plain text (`output/PAPER.md`) so downstream review skills can extract claims with source pointers. **Trigger**: ingest paper, manuscript text, provide paper, paper.md, 输入论文, 导入稿件, 审稿输入. **Use when**: You are running the `peer-review` pipeline and need `output/PAPER.md` before `claims-extractor`. **Skip if**: `output/PAPER.md` already exists and looks like the full manuscript text. **Network**: none. **Guardrail**: Do not summarize or rewrite the paper; store the raw text (or a faithful extraction) so claims stay traceable.

View SKILL.md on GitHub Repository
Stars 377
Forks 25

Install this agent skill to your Project

npx add-skill https://github.com/WILLOSCAR/research-units-pipeline-skills/tree/main/.codex/skills/manuscript-ingest

SKILL.md

Manuscript Ingest (paper -> text)

Goal: create output/PAPER.md as the single source of truth for the submitted manuscript text.

Downstream skills (e.g., claims-extractor) rely on this file to produce traceable claims (section/page/quote pointers).

Inputs

One of the following (choose the simplest):

  • The user pastes the manuscript text in chat (recommended).
  • A local PDF provided by the user (extract to text, then paste into output/PAPER.md).

Optional context:

  • GOAL.md (review focus / constraints)

Outputs

  • output/PAPER.md

Procedure

  1. Decide the input route
  • If GOAL.md exists, treat it as the review focus/constraints (but do not rewrite the paper to fit it).
  • If the user can paste text: use that.
  • If only PDF is available: extract text (any faithful extraction is OK; do not paraphrase).
  1. Write output/PAPER.md
  • Include the full text in order.
  • Preserve section headings if possible.
  • If page numbers are available, keep simple markers like \n\n[page 7]\n\n (helps traceability).
  1. Quick sanity check
  • Confirm output/PAPER.md contains the paper body (not just title/abstract).
  • Confirm key sections exist (Intro/Method/Experiments/Conclusion), if the paper has them.

Acceptance

  • output/PAPER.md exists.
  • The file contains the full manuscript text (or a faithful extraction), sufficient to quote with pointers.

Troubleshooting

I only have a PDF and the extracted text is messy

Fix:

  • Keep the messy text anyway, but preserve:
    • section headings
    • figure/table captions (if present)
    • page separators (if present)

The paper is very long

Fix:

  • Still ingest the full text.
  • If you must split, keep output/PAPER.md as the concatenated master file.

Recommended Agent Skills

Expand your agent's capabilities with these related and highly-rated skills.

WILLOSCAR/research-units-pipeline-skills

thesis-compile-review

对中文毕业论文进行编译、warning 分级、模板模式检查、数据与引用复查，并把问题回写成可继续迭代的 review checklist。 **Trigger**: 毕业论文编译检查, thesis compile review, warning 分级, 终稿复查, main.pdf 检查. **Use when**: 论文已经回写到 TeX 交付层，需要确认是否真正达到“可提交”的质量，而不是只做到能编译。 **Skip if**: 还处于中间层重构阶段，`chapters/*.tex` 尚未形成稳定交付稿。 **Network**: none. **Guardrail**: 不在这里重构章节主线；如果发现结构问题，明确回退到上游修复。

377 25
Explore
WILLOSCAR/research-units-pipeline-skills

front-matter-writer

Write the survey's front matter files (Abstract, Introduction, Related Work, Discussion, Conclusion) in paper voice, with high citation density and a single evidence-policy paragraph. **Trigger**: front matter writer, introduction writer, related work writer, abstract writer, discussion writer, conclusion writer, 引言, 相关工作, 摘要, 讨论, 结论. **Use when**: you are in C5 (prose allowed) and need the paper-like shell to stop the draft reading like stitched subsections. **Skip if**: `Approve C2` is missing in `DECISIONS.md`, or `citations/ref.bib` is missing. **Network**: none. **Guardrail**: no invented facts/citations; no pipeline jargon in final prose; no repeated evidence disclaimers; only use keys present in `citations/ref.bib`.

377 25
Explore
WILLOSCAR/research-units-pipeline-skills

thesis-question-list

维护中文毕业论文的 `codex_md/question_list.md`：把本轮问题、边界、优先级、协作方案和验收口径结构化，作为整条 thesis pipeline 的控制面。 **Trigger**: 毕业论文问题清单, thesis question list, 论文修改清单, 本轮目标, 结构问题梳理, review问题整理. **Use when**: 你已经有一批材料或上一轮 review 结果，需要明确这一轮到底修什么、不修什么，并给后续重构与编译复查提供统一入口。 **Skip if**: 当前只是在做一次性局部措辞修改，且没有形成新一轮结构/证据/编译问题。 **Network**: none. **Guardrail**: 不在这里写正文；不把问题单写成长篇散文；每条问题必须可执行、可验收。

377 25
Explore
WILLOSCAR/research-units-pipeline-skills

novelty-matrix

Create a novelty/prior-work matrix comparing the submission’s contributions against related work (overlaps vs deltas). **Trigger**: novelty matrix, prior-work matrix, overlap/delta, 相关工作对比, 新颖性矩阵. **Use when**: peer review 中评估 novelty/positioning，需要把贡献与相关工作逐项对齐并写出差异点证据。 **Skip if**: 缺少 claims（先跑 `claims-extractor`）或你不打算做新颖性定位分析。 **Network**: none (retrieval of additional related work is out-of-scope unless provided). **Guardrail**: 明确 overlap 与 delta；尽量给出可追溯证据来源（来自稿件/引用/作者陈述）。

377 25
Explore
WILLOSCAR/research-units-pipeline-skills

protocol-writer

Write a systematic review protocol into `output/PROTOCOL.md` (databases, queries, inclusion/exclusion, time window, extraction fields). **Trigger**: protocol, PRISMA, systematic review, inclusion/exclusion, 检索式, 纳入排除. **Use when**: systematic review pipeline 的起点（C1），需要先锁定 protocol 再开始 screening/extraction。 **Skip if**: 不是做 systematic review（或 protocol 已经锁定且不允许修改）。 **Network**: none. **Guardrail**: protocol 必须包含可执行的检索与筛选规则；需要 HUMAN 签字后才能进入 screening。

377 25
Explore
WILLOSCAR/research-units-pipeline-skills

rubric-writer

Write a rubric-based peer review report (`output/REVIEW.md`) using extracted claims and evidence gaps (novelty/soundness/clarity/impact). **Trigger**: rubric review, referee report, peer review write-up, 审稿报告, REVIEW.md. **Use when**: peer-review pipeline 的最后阶段（C3），已有 `output/CLAIMS.md` + `output/MISSING_EVIDENCE.md`（以及可选 novelty matrix）。 **Skip if**: 上游产物未就绪（claims/evidence gaps 缺失）或你不打算输出完整审稿报告。 **Network**: none. **Guardrail**: 给可执行建议（actionable feedback），并覆盖 novelty/soundness/clarity/impact；避免泛泛而谈。

377 25
Explore

Didn't find tool you were looking for?

Be as detailed as possible for better results