pubmed-search-mcp-harness

pubmed-search-mcp-harness is a skill for Claude Code, Codex from u9401066/pharmacy-mcp. It costs 41 tokens per session (372 once invoked), scanned A, original, Apache-2.0.

A set of Cline rules and workflows for the PubMed Search MCP project. It supports literature-search tools, research pipelines, and release checks; a pipeline is a sequence of connected processing steps.

In plain words
What is it for?
Use it for PubMed searches, full-text and pipeline work, skill audits, tool-documentation updates, testing, and release preparation.
Why use it?
It provides repeatable checks for code, documentation, skills, and research-tool behaviour while preserving pipeline state instead of relying only on the agent’s memory.

Skill for Claude CodeCodex

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

Good fit Use it for PubMed searches, full-text and pipeline work, skill audits, tool-documentation updates, testing, and release preparation.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/u9401066/pharmacy-mcp/pubmed-search-mcp-harness
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/pharmacy-mcp --skill pubmed-search-mcp-harness
Clone the repo
git clone --depth 1 https://github.com/u9401066/pharmacy-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/pharmacy-mcp/pubmed-search-mcp-harness/github.svg)](https://agentmods.dev/skills/u9401066/pharmacy-mcp/pubmed-search-mcp-harness)
Your own site
<a href="https://agentmods.dev/skills/u9401066/pharmacy-mcp/pubmed-search-mcp-harness"><img src="https://agentmods.dev/badge/skills/u9401066/pharmacy-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/pharmacy-mcp/pubmed-search-mcp-harness"><img src="https://agentmods.dev/badge/skills/u9401066/pharmacy-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 372 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 original No closer match found 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 $0.00372
Opus 5 $0.00020 $0.00186
Sonnet 5 $0.00008 $0.00074
Haiku 4.5 $0.00004 $0.00037

Measured 12d ago against content hash 5718bca05823, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-12, 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 12d 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

Copies of this mod

1 near-identical copy found in the catalogue:

.cline/skills/pubmed-search-mcp-harness/SKILL.md · 36 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.
  • 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. 12d ago First seen · 36 lines · 41 tokens per session scan A 5718bca05823

Subscribe to this mod's changes

pubmed-search-mcp-harness is a skill published in the GitHub repository u9401066/pharmacy-mcp (3 stars, last pushed 1mo ago), licensed Apache-2.0. It adds 41 tokens to every session and 372 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.

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