drug-discovery-prompts/upstream/K-Dense-AI-scientific-agent-skills/skills/paper-lookup/references/pubmed.md

title, task, lineage_type, upstream_source, upstream_sha, imported_at, prompt_class, upstream_changes, author, validated

title	task	lineage_type	upstream_source	upstream_sha	imported_at	prompt_class	upstream_changes	author	validated
PubMed (NCBI E-utilities)		import	https://github.com/K-Dense-AI/scientific-agent-skills/blob/9c9bd2e9/skills/paper-lookup/references/pubmed.md	9c9bd2e9	2026-06-27	prompt	accepted	upstream	false

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 protected] 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 <PubmedArticle> with <MedlineCitation> (title, abstract, MeSH terms, authors) and <PubmedData> (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.