pubmed-search

name	pubmed-search
description	Search PubMed biomedical literature for a topic, gene, drug, disease, or clinical question and retrieve article details. Use when the user wants peer-reviewed biomedical or clinical references. Uses the plugin's built-in read-only PubMed MCP tool for discovery — no credential or install needed.
license	Apache-2.0

PubMed Literature Search (Codex-native)

Codex-native biomedical literature search wired to this plugin's built-in read-only MCP tool. Inspired by Google DeepMind's pubmed-database (science-skills, Apache-2.0); the MCP integration is Codex Science's own.

How to run

1. Search with the plugin MCP tool science_search_pubmed:
   • arguments: query (topic/gene/drug/disease terms, ≤500 chars), limit (1–10, default 5).
   • returns a JSON list of {id, title, url} where id is the PMID and url is the PubMed entry. Note: this discovery tool returns PMIDs and links only — no abstract.
2. Fetch details for the PMIDs you keep: open each url with a fetch tool, or use NCBI E-utilities efetch/esummary (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=<PMID>&retmode=xml) to get title, authors, journal, year, and abstract. Ask before large batch fetches; stay within NCBI rate limits.
3. Refine with focused terms, MeSH-style phrasing, or a date/keyword narrow when results are too broad.
4. Report each kept article with title, PMID, journal/year, one-line relevance, and the URL.
5. Provenance & review: record queries, tool, and cited PMIDs with $science-provenance; check claims with $science-review before presenting.

Boundaries

• Cite only PMIDs actually returned by the tool; never invent PMIDs, journals, or abstracts. Verify the abstract before quoting it.
• Search results are references, not clinical advice; do not infer diagnosis, dosing, or treatment from them.
• Prefer primary studies and systematic reviews over secondary summaries when the user needs evidence strength.