rootcause-mcp: Skill for Claude Code

.claude/skills/pubmed-paper-exploration/SKILL.md

pubmed-paper-exploration is a skill for Claude Code from u9401066/rootcause-mcp. It costs 56 tokens per session (1,244 once invoked), scanned A, a copy of pubmed-paper-exploration, Apache-2.0.

A workflow for exploring the research around one key paper. It can find similar papers, the papers cited by it, and later papers that cite it, then organize those links into a citation tree or research timeline.

In plain words
What is it for?
Use it to trace a paper’s background, find related research, identify later work, assess citation metrics, or map a research area.
Why use it?
It removes the need to follow references and citations manually from one paper at a time. A citation tree shows how papers connect, while a research timeline shows how a topic developed.

Skill for Claude Code

Written for Claude Code: installed under .claude/.

This is u9401066/rootcause-mcp's own configuration. It tells Claude Code how to work on rootcause-mcp itself, so it is not a mod to install elsewhere. Copy it as a starting point and replace the rules that are about this project. Everything rootcause-mcp configures →

Reuse

Borrowing it

Nothing to install: this file belongs to u9401066/rootcause-mcp. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.

Copy the file
curl -O https://raw.githubusercontent.com/u9401066/rootcause-mcp/master/.claude/skills/pubmed-paper-exploration/SKILL.md
Clone the repo
git clone --depth 1 https://github.com/u9401066/rootcause-mcp

Made for: Claude Code.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for pubmed-paper-exploration

README.md
[![agentmods](https://agentmods.dev/badge/skills/u9401066/rootcause-mcp/pubmed-paper-exploration/github.svg)](https://agentmods.dev/skills/u9401066/rootcause-mcp/pubmed-paper-exploration)
Your own site
<a href="https://agentmods.dev/skills/u9401066/rootcause-mcp/pubmed-paper-exploration"><img src="https://agentmods.dev/badge/skills/u9401066/rootcause-mcp/pubmed-paper-exploration/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for pubmed-paper-exploration

Your own site · 80×15
<a href="https://agentmods.dev/skills/u9401066/rootcause-mcp/pubmed-paper-exploration"><img src="https://agentmods.dev/badge/skills/u9401066/rootcause-mcp/pubmed-paper-exploration.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 56 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 1,244 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin 86% copy Near-identical to another mod in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00056 $0.01244
Opus 5 $0.00028 $0.00622
Sonnet 5 $0.00011 $0.00249
Haiku 4.5 $0.00006 $0.00124

Measured 11d ago against content hash 471ec261ec97, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-12, from the pricing page.

Security

Grade A, and why

pubmed-paper-exploration scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 11d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

Origin

This is a copy

86% identical to pubmed-paper-exploration — 34 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.

.claude/skills/pubmed-paper-exploration/SKILL.md · 198 lines

How it starts

The opening of the file, as written. The whole thing — 198 lines — stays where its author put it; the contents beside it link to each section on GitHub.

論文深度探索

描述

這個 workflow 用在「已經有一篇關鍵論文」之後的深挖。你可以沿三個方向展開:相似文獻、這篇引用了誰、誰又引用了它,再進一步建立 citation tree 或研究時間軸。

觸發條件

  • 「這篇論文的相關研究」
  • 「誰引用這篇?」
  • 「這篇建立在誰的研究上?」
  • 「幫我畫這篇論文的 citation tree」
  • 已提供 PMID 或明確的種子論文標題

如果還沒有 PMID

先用 unified_search 找到種子論文:

unified_search(
    query="remimazolam randomized controlled trial",
    limit=5,
    ranking="quality"
)

拿到 PMID 後,再進入下面 workflow。


核心探索方向

工具 作用 方向
fetch_article_details 取得文章完整資訊 當前論文
find_related_articles 找主題相近文章 橫向
get_article_references 找這篇引用了誰 往過去
find_citing_articles 找誰引用這篇 往未來
get_citation_metrics 看引用影響力 評估重要性
build_citation_tree 建立引用網路 視覺化
build_research_chronicle 建立研究編年史 演化脈絡

最常用範例

1. 先拿文章細節

fetch_article_details(pmids="30217674")

2. 找相似文章

find_related_articles(pmid="30217674", limit=10)

3. 找這篇引用了誰

get_article_references(pmid="30217674", limit=30)

4. 找誰引用了這篇

find_citing_articles(pmid="30217674", limit=20)

5. 看哪幾篇最有影響力

get_citation_metrics(
    pmids="30217674,35678901,34567890",
    sort_by="relative_citation_ratio"
)

6. 直接建 citation tree

build_citation_tree(
    pmid="30217674",
    depth=2,
    direction="both",
    output_format="mermaid"
)

建議工作流程

情境:從一篇關鍵 RCT 往外展開

# Step 1: 當前論文
fetch_article_details(pmids="30217674")

# Step 2: 三個方向同時展開
find_related_articles(pmid="30217674", limit=10)
get_article_references(pmid="30217674", limit=20)
find_citing_articles(pmid="30217674", limit=20)

# Step 3: 對重要 PMIDs 做引用影響力排序
get_citation_metrics(
    pmids="35678901,34567890,33456789",
    sort_by="citation_count"
)

# Step 4: 視覺化引用網路
build_citation_tree(
    pmid="30217674",
    depth=2,
    direction="both",
    output_format="cytoscape"
)

如果想看時間演化

以單篇或一組 PMID 建編年史

build_research_chronicle(
    pmids="30217674,35678901,34567890",
    topic="Remimazolam Clinical Development",
    output="mermaid"
)

Read the full file on GitHub · 198 lines

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 11d ago First seen · 198 lines · 56 tokens per session scan A 471ec261ec97

Subscribe to this mod's changes

pubmed-paper-exploration is a skill published in the GitHub repository u9401066/rootcause-mcp (0 stars, last pushed 9d ago), licensed Apache-2.0. It adds 56 tokens to every session and 1,244 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 0 findings. It is 86% identical to pubmed-paper-exploration, differing in 34 lines, and is treated as a copy.

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