pubmed-api

Imported from wentorai/research-plugins (skills/literature/search/pubmed-api/SKILL.md). Install upstream with npx skills add wentorai/research-plugins --skill pubmed-api. Copyright stays with the author.

PubMed E-utilities API Guide

Overview

PubMed is the premier biomedical literature database maintained by the National Center for Biotechnology Information (NCBI) at the US National Library of Medicine. It indexes over 36 million citations and abstracts from MEDLINE, life science journals, and online books. The Entrez Programming Utilities (E-utilities) provide programmatic access to the entire PubMed database and other NCBI databases.

E-utilities consist of a suite of server-side programs that accept URL-based requests and return structured data. These tools are essential for biomedical researchers, systematic reviewers, and developers building health informatics applications. The API supports complex search queries using MeSH (Medical Subject Headings) terms, boolean operators, and field-specific searches.

The API is free and does not require authentication for basic usage. Registering for an NCBI API key raises the rate limit from 3 to 10 requests per second, which is recommended for any automated workflow.

Authentication

No authentication required for basic usage (3 requests/second). For higher rate limits (10 requests/second), register for a free API key at https://www.ncbi.nlm.nih.gov/account/ and include it in requests:

&api_key=YOUR_API_KEY

Including tool and email parameters in requests helps NCBI contact you if there are issues with your application.

Core Endpoints

ESearch: Search and Retrieve PMIDs

• URL: GET https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi
• Parameters:

  Param	Type	Required	Description
  db	string	Yes	Database name (e.g., pubmed, pmc)
  term	string	Yes	Search query (supports boolean operators and field tags)
  retmax	integer	No	Maximum number of IDs returned (default: 20, max: 10000)
  retstart	integer	No	Index of first ID to retrieve (for pagination)
  retmode	string	No	Response format: xml (default) or json
  sort	string	No	Sort order: relevance, pub_date, author, journal
  datetype	string	No	Date type for range filter: pdat, mdat, edat
  mindate	string	No	Start date (YYYY/MM/DD)
  maxdate	string	No	End date (YYYY/MM/DD)
  usehistory	string	No	Set to "y" to store results on server for subsequent retrieval

• Example:

  curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=CRISPR+AND+cancer[Title]&retmax=10&retmode=json&sort=pub_date"

• Response: JSON/XML with esearchresult containing count (total hits), idlist (array of PMIDs), and optionally webenv and querykey for history server.

EFetch: Retrieve Full Records

• URL: GET https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi
• Parameters:

  Param	Type	Required	Description
  db	string	Yes	Database name
  id	string	Yes	Comma-separated list of PMIDs (or use WebEnv/query_key)
  rettype	string	No	Return type: abstract, medline, full, xml
  retmode	string	No	Format: xml, text
  WebEnv	string	No	Web environment from ESearch with usehistory=y
  query_key	string	No	Query key from ESearch

• Example:

  curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=33116299,34735795&rettype=abstract&retmode=xml"

• Response: XML with complete PubMed records including MedlineCitation with Article (title, abstract, authors, journal), MeSHHeadingList, and PubmedData (DOI, publication status).

ESummary: Retrieve Document Summaries

• URL: GET https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi
• Parameters:

  Param	Type	Required	Description
  db	string	Yes	Database name
  id	string	Yes	Comma-separated PMIDs
  retmode	string	No	Response format: xml or json
  version	string	No	Set to "2.0" for enhanced XML format

• Example:

  curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=33116299&retmode=json&version=2.0"

• Response: JSON with document summary including uid, title, authors, source (journal), pubdate, doi, and pmcid.

Rate Limits

Without API key: 3 requests per second. With API key: 10 requests per second. Exceeding limits results in temporary IP blocking. For large-scale data mining, use the NCBI FTP site for bulk downloads. Always include a delay of at least 334ms (or 100ms with API key) between requests. Weekend and evening hours (US Eastern time) are less congested.

Common Patterns

Systematic Literature Search

Perform a structured search using MeSH terms and field qualifiers:

# Search for clinical trials on diabetes treatment from the last 2 years
curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=diabetes[MeSH]+AND+treatment[Title]+AND+clinical+trial[Publication+Type]&mindate=2024/01/01&maxdate=2026/03/09&datetype=pdat&retmax=100&retmode=json"

Pipeline: Search then Fetch

Use the history server to efficiently search and then retrieve records:

# Step 1: Search and store results
curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=machine+learning+AND+radiology&retmax=0&usehistory=y&retmode=json"

# Step 2: Fetch records using WebEnv and query_key from step 1
curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&WebEnv=WEBENV_VALUE&query_key=1&retmax=50&rettype=abstract&retmode=xml"

Retrieve Structured Metadata for Citation Management

Get JSON summaries for a batch of known PMIDs:

curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=33116299,34735795,35363452&retmode=json&version=2.0"

References

• Official documentation: https://www.ncbi.nlm.nih.gov/books/NBK25501/
• E-utilities quick start: https://www.ncbi.nlm.nih.gov/books/NBK25500/
• PubMed search help: https://pubmed.ncbi.nlm.nih.gov/help/