pubmed-database
Programmatic PubMed access via NCBI E-utilities REST API. Covers Boolean/MeSH queries, field-tagged search, endpoints (ESearch, EFetch, ESummary, EPost, ELink), history server for batches, citation matching, systematic review strategies. Use for biomedical literature search or automated pipelines.
npx skills add BioTender-max/awesome-bio-agent-skills --skill pubmed-database --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# PubMed Database ## Overview PubMed is the U.S. National Library of Medicine's database providing free access to 36M+ biomedical citations from MEDLINE and life sciences journals. This skill covers programmatic access via the E-utilities REST API and advanced search query construction using Boolean operators, MeSH terms, and field tags. ## When to Use - Searching biomedical literature with structured Boolean/MeSH queries - Building automated literature monitoring or extraction pipelines - Conducting systematic literature reviews or meta-analyses - Retrieving article metadata, abstracts, or citation information by PMID/DOI - Finding related articles or exploring citation networks programmatically - Batch processing large sets of PubMed records - For Python-native PubMed access, prefer BioPython (`Bio.Entrez`) — this skill covers direct REST API usage - For broader academic search (non-biomedical), use OpenAlex or Semantic Scholar APIs ## Prerequisites ```bash pip install requests # HTTP client for E-utilities API # Optional: pip install biopython — Bio.Entrez wrapper (higher-level API) ``` **API Rate Limits**: - Without API key: **3 requests/second** - With API key: **10 requests/s
- Overview
- When to Use
- Prerequisites
- Quick Start
- Core API
- 1. Search Query Construction
- 2. ESearch — Search and Retrieve PMIDs
- 3. EFetch — Download Full Records
- 4. ESummary and ELink — Summaries and Related Articles
- 5. Citation Matching and Identifier Lookup
- 6. Publication Filtering
- Key Concepts
- E-utilities Endpoint Summary
- History Server Pattern
pip install requests # HTTP client for E-utilities API
What does the pubmed-database skill do?
Programmatic PubMed access via NCBI E-utilities REST API. Covers Boolean/MeSH queries, field-tagged search, endpoints (ESearch, EFetch, ESummary, EPost, ELink), history server for batches, citation matching, systematic review strategies. Use for biomedical literature search or automated pipelines.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill pubmed-database --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.