Agent-Skills.md

Agent Skills: PubMed Database

Direct REST API access to PubMed. Advanced Boolean/MeSH queries, E-utilities API, batch processing, citation management. For Python workflows, prefer biopython (Bio.Entrez). Use this for direct HTTP/REST work or custom API implementations.

UncategorizedID: drshailesh88/integrated_content_OS/pubmed-database
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Install this agent skill to your local

pnpm dlx add-skill https://github.com/drshailesh88/integrated_content_OS/tree/HEAD/skills/cardiology/pubmed-database

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skills/cardiology/pubmed-database/SKILL.md

PubMed Database

Direct REST API access to the National Library of Medicine's biomedical literature repository for systematic reviews and research analysis.

Triggers

  • User asks to search for medical/scientific literature
  • User needs to find research papers on a cardiology topic
  • User wants to build a literature review
  • User requests evidence for a clinical claim
  • User needs citations for an article or newsletter

Core Capabilities

Search Construction

Build sophisticated queries combining:

  • Boolean operators (AND, OR, NOT)
  • Field tags: [mh] for MeSH terms, [au] for author, [ti] for title, [tiab] for title/abstract
  • Publication filters by date, type, and availability

E-utilities API Endpoints

| Endpoint | Purpose | |----------|---------| | ESearch | Search and retrieve PMIDs | | EFetch | Retrieve full records | | ESummary | Get document summaries | | EPost | Upload ID lists | | ELink | Find related articles |

Rate limits: 3 requests/second (10 with API key)

Filtering Options

  • Publication type (clinical trials, systematic reviews, meta-analyses)
  • Date ranges
  • Text availability (free full text, abstracts)
  • Species (human studies)

Citation Export Formats

  • NBIB (for reference managers)
  • AMA, MLA, APA, Vancouver styles
  • BibTeX for LaTeX

Example Queries

Cardiology-Specific Searches

# Recent SGLT2 inhibitor trials in heart failure
"SGLT2 inhibitors"[mh] AND "heart failure"[mh] AND "clinical trial"[pt] AND "2023"[dp]:present[dp]

# Interventional cardiology systematic reviews
"percutaneous coronary intervention"[mh] AND "systematic review"[pt]

# TAVR outcomes
"transcatheter aortic valve replacement"[tiab] AND (outcomes[tiab] OR mortality[tiab])

Building Evidence for Content

  1. Start with MeSH terms for precision
  2. Add free-text synonyms for coverage
  3. Filter by publication type and recency
  4. Review abstracts for relevance
  5. Extract key findings with PMIDs for citation

Workflow Integration

When writing cardiology content:

  1. Use this skill to find supporting evidence
  2. Document PMIDs for all factual claims
  3. Prefer systematic reviews and meta-analyses
  4. Include recent trials (last 2-3 years) for currency
  5. Cross-reference with citation-management skill for formatting

Best Practices

  • Always verify claims with primary sources
  • Note study limitations when citing
  • Distinguish between observational and RCT evidence
  • Use MeSH terms for reproducible searches
  • Document search strategy for transparency