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pubmed-literature-retrieval

Name: Pubmed Literature Retrieval
Author: chenpg2

// Use when searching PubMed for literature references, retrieving article metadata or full text, building citation lists for papers or grant proposals, or conducting systematic literature reviews using NCBI E-utilities API

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updated:February 13, 2026 at 03:38

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name	pubmed-literature-retrieval
description	Use when searching PubMed for literature references, retrieving article metadata or full text, building citation lists for papers or grant proposals, or conducting systematic literature reviews using NCBI E-utilities API

PubMed Literature Retrieval

Overview

Search and retrieve biomedical literature from PubMed using NCBI E-utilities REST API. Zero local dependencies — all calls are HTTP GET/POST to eutils.ncbi.nlm.nih.gov. Designed for cloud deployment and LLM tool integration.

When to Use

Writing papers, grant proposals, or literature reviews that need citation support
Searching PubMed by keywords, authors, date ranges, MeSH terms, or publication types
Retrieving structured metadata (title, authors, abstract, DOI, etc.) for a set of articles
Attempting to fetch full-text articles from PubMed Central (PMC)
Building reference lists from search results

Base URL

All E-utility requests use:

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

API Key & Rate Limits

Config	Rate Limit	Notes
No API key	3 requests/sec	Default, sufficient for small searches
With API key	10 requests/sec	Get key from https://www.ncbi.nlm.nih.gov/account/settings/

Include API key in every request: &api_key=YOUR_KEY

Always include &tool=your_tool_name&email=your@email.com in requests for NCBI compliance.

Core Workflow

digraph pubmed_flow {
    rankdir=TB;
    "Build Query" [shape=box];
    "ESearch" [shape=box, label="ESearch\n(get PMIDs)"];
    "Check Count" [shape=diamond];
    "EFetch Metadata" [shape=box, label="EFetch\n(get XML metadata)"];
    "Parse & Format" [shape=box];
    "Need Full Text?" [shape=diamond];
    "ELink to PMC" [shape=box];
    "EFetch PMC" [shape=box, label="EFetch PMC\n(full text XML)"];
    "Return Results" [shape=doublecircle];

    "Build Query" -> "ESearch";
    "ESearch" -> "Check Count";
    "Check Count" -> "EFetch Metadata" [label="≤200 results"];
    "Check Count" -> "ESearch" [label=">200: paginate\nwith retstart"];
    "EFetch Metadata" -> "Parse & Format";
    "Parse & Format" -> "Need Full Text?";
    "Need Full Text?" -> "ELink to PMC" [label="yes"];
    "Need Full Text?" -> "Return Results" [label="no"];
    "ELink to PMC" -> "EFetch PMC";
    "EFetch PMC" -> "Return Results";
}

Step 1: ESearch — Search PubMed

URL Pattern

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=<QUERY>&retmax=<N>&retstart=<OFFSET>&usehistory=y&sort=relevance

Query Syntax — Field Tags

Field Tag	Meaning	Example
`[tiab]`	Title/Abstract	`cancer[tiab]`
`[ti]`	Title only	`CRISPR[ti]`
`[au]`	Author	`Zhang Y[au]`
`[1au]`	First author	`Smith J[1au]`
`[lastau]`	Last author	`Wang L[lastau]`
`[ta]`	Journal abbreviation	`Nature[ta]`
`[dp]`	Date of publication	`2023[dp]` or `2020:2024[dp]`
`[pt]`	Publication type	`Review[pt]`
`[mh]`	MeSH heading	`Neoplasms[mh]`
`[majr]`	MeSH major topic	`Breast Neoplasms[majr]`
`[sh]`	MeSH subheading	`therapy[sh]`
`[la]`	Language	`English[la]`
`[sb]`	Subset	`free full text[sb]`
`[filter]`	Filter	`humans[filter]`

Boolean Operators

Use uppercase: AND, OR, NOT

(breast cancer[tiab] OR breast neoplasms[mh]) AND immunotherapy[tiab] AND 2020:2024[dp] AND Review[pt]

Publication Type Filters

Type	Tag
Review	`Review[pt]`
Systematic Review	`Systematic Review[pt]`
Meta-Analysis	`Meta-Analysis[pt]`
Clinical Trial	`Clinical Trial[pt]`
Randomized Controlled Trial	`Randomized Controlled Trial[pt]`
Case Reports	`Case Reports[pt]`
Editorial	`Editorial[pt]`
Letter	`Letter[pt]`

Sort Options

Value	Meaning
`relevance`	Best match (default)
`pub_date`	Most recent first
`Author`	By first author
`JournalName`	By journal

ESearch Parameters

Parameter	Required	Description
`db`	Yes	Always `pubmed`
`term`	Yes	Search query with field tags
`retmax`	No	Max UIDs returned (default 20, max 10000)
`retstart`	No	Index offset for pagination (default 0)
`usehistory`	No	Set `y` to store results on History Server
`sort`	No	Sort order (see above)
`datetype`	No	`pdat` (pub date), `edat` (Entrez date)
`mindate`	No	Start date (YYYY/MM/DD or YYYY)
`maxdate`	No	End date (YYYY/MM/DD or YYYY)
`api_key`	No	NCBI API key

Example ESearch Call

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=CRISPR+AND+cancer[tiab]+AND+2023:2024[dp]+AND+Review[pt]&retmax=50&sort=pub_date&usehistory=y

ESearch Response (XML)

Key fields to extract:

<Count> — total matching records
<IdList><Id> — list of PMIDs
<QueryKey> and <WebEnv> — for History Server (when usehistory=y)

Step 2: EFetch — Retrieve Article Metadata

URL Pattern (by PMID list)

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=PMID1,PMID2,PMID3&rettype=xml&retmode=xml

URL Pattern (by History Server)

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=KEY&WebEnv=WEBENV&rettype=xml&retmode=xml&retstart=0&retmax=100

EFetch Parameters

Parameter	Required	Description
`db`	Yes	Always `pubmed`
`id`	Yes*	Comma-separated PMIDs (*or use query_key+WebEnv)
`query_key`	Yes*	From ESearch with usehistory=y
`WebEnv`	Yes*	From ESearch with usehistory=y
`rettype`	Yes	`xml` for structured data, `abstract` for text
`retmode`	Yes	`xml` or `text`
`retmax`	No	Max records per request (default 20, recommend ≤200)
`retstart`	No	Offset for pagination

Parsing EFetch XML — Key XPaths

Extract these fields from each <PubmedArticle>:

Field	XPath
PMID	`MedlineCitation/PMID`
Title	`MedlineCitation/Article/ArticleTitle`
Abstract	`MedlineCitation/Article/Abstract/AbstractText`
Authors	`MedlineCitation/Article/AuthorList/Author` (LastName + Initials)
Journal	`MedlineCitation/Article/Journal/Title`
Journal Abbrev	`MedlineCitation/Article/Journal/ISOAbbreviation`
Year	`MedlineCitation/Article/Journal/JournalIssue/PubDate/Year`
Month	`MedlineCitation/Article/Journal/JournalIssue/PubDate/Month`
Volume	`MedlineCitation/Article/Journal/JournalIssue/Volume`
Issue	`MedlineCitation/Article/Journal/JournalIssue/Issue`
Pages	`MedlineCitation/Article/Pagination/MedlinePgn`
DOI	`PubmedData/ArticleIdList/ArticleId[@IdType='doi']`
PMC ID	`PubmedData/ArticleIdList/ArticleId[@IdType='pmc']`
MeSH Terms	`MedlineCitation/MeshHeadingList/MeshHeading/DescriptorName`
Pub Types	`MedlineCitation/Article/PublicationTypeList/PublicationType`
Keywords	`MedlineCitation/KeywordList/Keyword`

Step 3 (Optional): Full-Text Retrieval via PMC

Tier 1: Check PMC availability from EFetch

If the EFetch XML contains <ArticleId IdType="pmc">PMCxxxxxxx</ArticleId>, the full text is available in PMC.

Tier 2: EFetch from PMC

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=PMC_ID&rettype=xml

This returns JATS XML with the complete article body, including sections, figures, tables, and references.

Tier 3: PMC Open Access PDF

https://www.ncbi.nlm.nih.gov/pmc/articles/PMCxxxxxxx/pdf/

Tier 4: Fallback via DOI

If not in PMC, construct: https://doi.org/<DOI> — may lead to publisher paywall.

ELink Alternative (batch PMC lookup)

To find PMC IDs for multiple PMIDs at once:

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&db=pmc&id=PMID1&id=PMID2&id=PMID3

LLM-Friendly Output Format

After parsing XML, format results as structured text:

--- Article 1 of N ---
PMID: 12345678
Title: Example Article Title Here
Authors: Smith J, Zhang Y, Wang L, et al.
Journal: Nature Medicine (Nat Med)
Date: 2024 Jan
Volume: 30, Issue: 1, Pages: 45-52
DOI: 10.1038/s41591-024-xxxxx
Abstract: [Full abstract text here...]
MeSH: Neoplasms; Immunotherapy; CRISPR-Cas Systems
Type: Review
PMC: PMC9876543 (full text available)
URL: https://pubmed.ncbi.nlm.nih.gov/12345678/
---

Pagination for Large Result Sets

When <Count> exceeds retmax:

Use usehistory=y in ESearch to get WebEnv and query_key
Loop EFetch with incrementing retstart:
- Batch 1: retstart=0&retmax=200
- Batch 2: retstart=200&retmax=200
- Continue until retstart >= Count
Respect rate limits between requests

Common Search Patterns

Find recent reviews on a topic

<TOPIC>[tiab] AND Review[pt] AND 2020:2024[dp] AND English[la]

Find clinical trials by intervention

<INTERVENTION>[tiab] AND Randomized Controlled Trial[pt] AND humans[filter]

Find articles by specific author in a journal

<AUTHOR>[au] AND <JOURNAL>[ta] AND 2020:2024[dp]

Find free full-text articles

<TOPIC>[tiab] AND free full text[sb]

Find systematic reviews and meta-analyses

<TOPIC>[tiab] AND (Systematic Review[pt] OR Meta-Analysis[pt])

MeSH-based precise search

<MESH_TERM>[majr] AND <SUBHEADING>[sh] AND 2020:2024[dp]

Common Mistakes

Mistake	Fix
Sending >10000 IDs in URL	Use History Server (WebEnv + query_key)
Not URL-encoding special chars	Encode spaces as `+`, `"` as `%22`, `#` as `%23`
Exceeding rate limit	Add delay: 0.34s without key, 0.1s with key
Using lowercase boolean	Must be uppercase: `AND`, `OR`, `NOT`
Missing `db=pubmed` parameter	Always include `db=pubmed`
Fetching too many at once	Keep `retmax` ≤ 200 for EFetch
Not checking `<Count>` before fetch	Always check total results first

Quick Reference

Task	E-utility	Key Parameters
Search by query	ESearch	`db=pubmed&term=<query>`
Get metadata by PMID	EFetch	`db=pubmed&id=<pmids>&rettype=xml`
Get metadata from search	EFetch	`db=pubmed&query_key=K&WebEnv=W&rettype=xml`
Find PMC full text	ELink	`dbfrom=pubmed&db=pmc&id=<pmids>`
Get PMC full text	EFetch	`db=pmc&id=<pmcid>&rettype=xml`
Batch upload PMIDs	EPost	`db=pubmed&id=<pmid_list>`
Check spelling	ESpell	`db=pubmed&term=<query>`
Citation match	ECitMatch	`db=pubmed&bdata=<citation_strings>`

name	pubmed-literature-retrieval
description	Use when searching PubMed for literature references, retrieving article metadata or full text, building citation lists for papers or grant proposals, or conducting systematic literature reviews using NCBI E-utilities API