Skillintermediate

PubMed (NCBI E-utilities)

PubMed provides citations, abstracts, and metadata for 37M+ biomedical and life science articles. It does NOT contain full text -- for that, use PMC.

Claude Code Knowledge Pack7/10/2026

Overview

PubMed (NCBI E-utilities)

PubMed provides citations, abstracts, and metadata for 37M+ biomedical and life science articles. It does NOT contain full text -- for that, use PMC.

Base URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/

Authentication

API key optional but recommended. Without: 3 req/sec. With: 10 req/sec.
Pass as: &api_key=YOUR_KEY
Also include &tool=your_app_name&email=your@email.com on all requests.

Key Endpoints

1. eSearch -- Search and get PMIDs

GET /esearch.fcgi?db=pubmed&term={query}&retmode=json

Parameter	Required	Default	Description
`db`	Yes	--	`pubmed`
`term`	Yes	--	Search query. Supports PubMed syntax: field tags `[AU]`, `[TI]`, `[TA]`, `[MH]` (MeSH), boolean AND/OR/NOT
`retmax`	No	20	Max PMIDs returned (max 10,000)
`retstart`	No	0	Pagination offset
`retmode`	No	`xml`	`json` or `xml`
`rettype`	No	`uilist`	`uilist` (IDs) or `count` (count only)
`sort`	No	`relevance`	`relevance`, `pub_date`, `Author`, `JournalName`
`datetype`	No	--	`pdat` (publication), `mdat` (modification), `edat` (entrez)
`mindate` / `maxdate`	No	--	Date range `YYYY/MM/DD`
`reldate`	No	--	Items from last N days
`usehistory`	No	--	`y` to store on History Server for large result sets

Example:

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=CRISPR+gene+therapy&retmode=json&retmax=5&sort=pub_date

Response:

{
  "esearchresult": {
    "count": "224107",
    "retmax": "5",
    "retstart": "0",
    "idlist": ["39984857", "39984678", "39984543", "39984210", "39983901"]
  }
}

2. eSummary -- Get document summaries

GET /esummary.fcgi?db=pubmed&id={pmids}&retmode=json

Parameter	Required	Description
`db`	Yes	`pubmed`
`id`	Yes	Comma-separated PMIDs (max 10,000)
`retmode`	No	`json` or `xml`

Example:

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=39984857,39984678&retmode=json

Response fields: uid, pubdate, source (journal), authors, title, volume, issue, pages, fulljournalname, elocationid (DOI), articleids (PMC, DOI, etc.), pubtype, pmcrefcount

3. eFetch -- Retrieve full records (abstracts, MEDLINE)

GET /efetch.fcgi?db=pubmed&id={pmids}&rettype={type}&retmode={mode}

rettype	retmode	Returns
(omit)	`xml`	Full PubMed XML (citation + abstract)
`medline`	`text`	MEDLINE format
`abstract`	`text`	Plain text abstract
`uilist`	`text`	PMID list

Example -- get abstracts as XML:

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=39984857&retmode=xml

The XML contains with (title, abstract, MeSH terms, authors) and `` (article IDs, publication history).

4. eLink -- Find related articles

GET /elink.fcgi?dbfrom=pubmed&db=pubmed&id={pmid}&cmd=neighbor_score&retmode=json

Returns related PMIDs with relevance scores.

Search Syntax Tips

Field tags: aspirin[TI] (title), Smith J[AU] (author), Nature[TA] (journal), neoplasms[MH] (MeSH heading)
Boolean: CRISPR AND (therapy OR treatment)
Date range: 2020/01/01:2024/12/31[PDAT]
Publication type: review[PT], clinical trial[PT]
Organism: humans[MH], mice[MH]

Rate Limits

3 requests/second without API key
10 requests/second with API key
Include tool and email parameters on every request
Large batch jobs should run outside peak hours (Mon-Fri 5AM-9PM ET)

Error Format

{"error": "API rate limit exceeded", "count": "11"}

HTTP 400 for bad requests, 429 for rate limiting.