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pubmed-search-mcp-harness

pubmed-search-mcp-harness is a skill for Claude Code, Codex from u9401066/rootcause-mcp. It costs 41 tokens per session (408 once invoked), scanned A, a copy of pubmed-search-mcp-harness, Apache-2.0.

A set of instructions for Cline, a coding agent, to work with PubMed Search MCP, a tool for finding medical research papers. It covers literature-search workflows, saved research state, and release checks.

In plain words
What is it for?
Use it to run unified literature searches, manage research pipelines, keep a lasting research record, audit skills, and run lint, type, test, and release checks.
Why use it?
It gives Cline a consistent way to run searches, preserve progress, and check changes before release. This reduces missed steps when maintaining the PubMed Search MCP project.

Skill for Claude CodeCodex

Which agent this was written for is unclear — built for cline. Also seen: reads .claude/ paths; built for cline.

not rated 0repo 8d ago A scan 41 tokens copy · 91% Apache-2.0

Good fit Use it to run unified literature searches, manage research pipelines, keep a lasting research record, audit skills, and run lint, type, test, and release checks.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/u9401066/rootcause-mcp/pubmed-search-mcp-harness
View source ↗ u9401066/rootcause-mcp
Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent
npx skills add u9401066/rootcause-mcp --skill pubmed-search-mcp-harness
Clone the repo
git clone --depth 1 https://github.com/u9401066/rootcause-mcp

Made for: Claude Code, Codex.

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-search-mcp-harness

README.md
[![agentmods](https://agentmods.dev/badge/skills/u9401066/rootcause-mcp/pubmed-search-mcp-harness/github.svg)](https://agentmods.dev/skills/u9401066/rootcause-mcp/pubmed-search-mcp-harness)
Your own site
<a href="https://agentmods.dev/skills/u9401066/rootcause-mcp/pubmed-search-mcp-harness"><img src="https://agentmods.dev/badge/skills/u9401066/rootcause-mcp/pubmed-search-mcp-harness/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-search-mcp-harness

Your own site · 80×15
<a href="https://agentmods.dev/skills/u9401066/rootcause-mcp/pubmed-search-mcp-harness"><img src="https://agentmods.dev/badge/skills/u9401066/rootcause-mcp/pubmed-search-mcp-harness.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 41 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 408 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 91% 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 $0.00041 $0.00408
Opus 5 $0.00020 $0.00204
Sonnet 5 $0.00008 $0.00082
Haiku 4.5 $0.00004 $0.00041

Measured 11d ago against content hash 5d71d90750a1, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-11, from the pricing page.

Security

Grade A, and why

pubmed-search-mcp-harness 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

91% identical to pubmed-search-mcp-harness — 2 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.

.cline/skills/pubmed-search-mcp-harness/SKILL.md · 38 lines

What it actually says

PubMed Search MCP: Cline Harness Skill

Use this skill when working in the PubMed Search MCP repository with Cline and you need a dependable loop for literature-search tools, pipeline behavior, and release checks.

What To Use First

  • Rules: .clinerules/
  • Workflows: .clinerules/workflows/
    • Run /pubmed-full-check.md for local gates.
    • Run /pubmed-skills-audit.md after changing skills or rules.
    • Run /pubmed-release-publish.md for release prep.
  • User-facing research skills: .claude/skills/pubmed-* and .claude/skills/pipeline-persistence.
    • If a .claude/skills instruction conflicts with current implementation, prefer .clinerules/.

Canonical Commands

  • Lint: uv run ruff check .
  • Format check: uv run ruff format --check .
  • Types: uv run mypy src/ tests/
  • Tests: uv run pytest
  • Tool docs sync: uv run python scripts/count_mcp_tools.py --update-docs
  • Skill audit: python3 scripts/check_cline_skills.py

Research Guardrails

  • Prefer unified_search as the primary multi-source entrypoint.
  • Preserve session/pipeline state instead of relying on agent memory.
  • Use build_research_chronicle and read_research_chronicle for durable research-history artifacts; the former timeline tools are no longer public.
  • Respect NCBI email/API-key policy and institutional access configuration.
  • Keep exported citations reproducible: PMIDs, DOI, source, date filters, and query strategy matter.
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 · 38 lines · 41 tokens per session scan A 5d71d90750a1

Subscribe to this mod's changes

pubmed-search-mcp-harness is a skill published in the GitHub repository u9401066/rootcause-mcp (0 stars, last pushed 8d ago), licensed Apache-2.0. It adds 41 tokens to every session and 408 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it A with 0 findings. It is 91% identical to pubmed-search-mcp-harness, differing in 2 lines, and is treated as a copy.

ResearchScientificai-agentclinicaldddfastmcpfishbone-diagramhealthcare
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