pubmed-search-mcp-harness
Manages literature research workflows and PubMed search pipelines for Codex agents.
Install
mkdir -p .claude/skills/pubmed-search-mcp-harness && curl -L -o skill.zip "https://agentskills.codes/api/skills/download/12520" && unzip -o skill.zip -d .claude/skills/pubmed-search-mcp-harness && rm skill.zipInstalls to .claude/skills/pubmed-search-mcp-harness
Activation
This is the description your AI agent reads to decide when to run this skill — the better it matches your request, the more reliably it fires.
Codex harness for PubMed Search MCP. Triggers: pubmed search, literature search, unified_search, pipeline, fulltext, release checklist, Codex.Key capabilities
- →Work with PubMed Search MCP research workflows
- →Manage pipeline state and fulltext access
- →Handle citation exports
- →Perform linting and format checks
- →Run type checks and tests
How it works
The skill acts as a Codex harness for PubMed Search MCP, facilitating research workflows, managing pipeline states, and ensuring adherence to research guardrails like using `unified_search` and preserving session state.
Inputs & outputs
When to use pubmed-search-mcp-harness
- →Performing literature reviews
- →Exporting research citations
- →Managing research pipelines
About this skill
PubMed Search MCP: Codex Harness Skill
Use this skill when working with Codex on PubMed Search MCP research workflows, pipeline state, fulltext access, exports, and release checks.
What To Read First
AGENTS.mdfor Codex workspace instructions..github/agents/research.agent.mdfor research-agent behavior..github/hooks/andscripts/hooks/copilot/for pipeline enforcement assets..claude/skills/pubmed-*and.claude/skills/pipeline-persistencefor user-facing workflows..clinerules/for project/release rules that also apply to Codex.
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:
python scripts/check_cline_skills.py
Research Guardrails
- Prefer
unified_searchas the primary multi-source entrypoint. - For external Python package/API questions, prefer the stable
pubmed_search.apifacade over MCP presentation modules. - Preserve session/pipeline state instead of relying on agent memory.
- Respect NCBI email/API-key policy and institutional access configuration.
- Keep exported citations reproducible with PMIDs, DOI, source, date filters, and query strategy.
When not to use it
- →When not working with Codex on PubMed Search MCP
- →When the task is not related to research workflows or pipeline state
- →When external Python package/API questions do not involve `pubmed_search.api`
Limitations
- →It is a Codex harness specific to PubMed Search MCP
- →It prefers `unified_search` as the primary multi-source entrypoint
- →It requires respecting NCBI email/API-key policy and institutional access configuration
How it compares
This skill provides a specific harness for Codex to interact with PubMed Search MCP, enforcing research guardrails and canonical commands for linting, formatting, and testing, unlike a general search tool.
Compared to similar skills
pubmed-search-mcp-harness side by side with the closest alternatives in the catalog.
| Skill | Installs | Updated | Safety | Difficulty |
|---|---|---|---|---|
| pubmed-search-mcp-harness (this skill) | 0 | 2mo | No flags | Intermediate |
| literature-review | 559 | 2mo | Review | Advanced |
| openalex-database | 48 | 7mo | Review | Intermediate |
| scientific-critical-thinking | 18 | 7mo | Review | Advanced |
Try saying
Example prompts that trigger this skill in your AI assistant.
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