Search biomedical literature in PubMed, build queries with standardized subject terms and filters, and retrieve abstracts and publication details. Record search methods for repeatable reviews and use NCBI APIs to monitor literature.
Direct PubMed and NCBI E-utilities search workflows for biomedical literature, MeSH queries, PMID lookup, citation retrieval, and API-backed literature monitoring. Use when a task needs biomedical literature from PubMed rather than general web search.
Review the instructions the agent will receive before you install.
Use this skill when a task needs biomedical literature from PubMed rather than general web search.
Start with the research question, split it into concepts, then combine concepts with Boolean operators.
concept_1 AND concept_2 AND filter
synonym_a OR synonym_b
NOT exclusion_term
Useful PubMed field tags:
[ti]: title[ab]: abstract[tiab]: title or abstract[au]: author[ta]: journal title abbreviation[mh]: MeSH term[majr]: major MeSH topic[pt]: publication type[dp]: date of publication[la]: languageExamples:
diabetes mellitus[mh] AND treatment[tiab] AND systematic review[pt] AND 2023:2026[dp]
(metformin[nm] OR insulin[nm]) AND diabetes mellitus, type 2[mh] AND randomized controlled trial[pt]
smith ja[au] AND cancer[tiab] AND 2026[dp] AND english[la]
Prefer MeSH when the concept has a stable controlled-vocabulary term. Combine MeSH with title/abstract terms when the topic is new or terminology varies.
Correct subheading syntax puts the subheading before the field tag:
diabetes mellitus, type 2/drug therapy[mh]
cardiovascular diseases/prevention & control[mh]
Use [majr] only when the topic must be central to the paper. It can improve
precision but may miss relevant work.
Publication types:
clinical trial[pt]meta-analysis[pt]randomized controlled trial[pt]review[pt]systematic review[pt]guideline[pt]Date filters:
2026[dp]
2020:2026[dp]
2026/03/15[dp]
Availability filters:
free full text[sb]
hasabstract[text]
NCBI E-utilities supports repeatable API workflows:
esearch.fcgi: search and return PMIDs.esummary.fcgi: return lightweight article metadata.efetch.fcgi: fetch abstracts or full records in XML, MEDLINE, or text.elink.fcgi: find related articles and linked resources.Use an email and API key for production scripts. Store API keys in environment variables, never in committed files or command history.
import os
import time
import requests
BASE = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils"
def esearch(query: str, retmax: int = 20) -> list[str]:
params = {
"db": "pubmed",
"term": query,
"retmode": "json",
"retmax": retmax,
"tool": "ecc-pubmed-search",
"email": os.environ.get("NCBI_EMAIL", ""),
}
api_key = os.environ.get("NCBI_API_KEY")
if api_key:
params["api_key"] = api_key
response = requests.get(f"{BASE}/esearch.fcgi", params=params, timeout=30)
response.raise_for_status()
time.sleep(0.35)
return response.json()["esearchresult"]["idlist"]
pmids = esearch("hypertension[mh] AND randomized controlled trial[pt] AND 2024:2026[dp]")
print(pmids)
For batches, prefer NCBI history server parameters (usehistory=y,
WebEnv, query_key) instead of passing very long PMID lists through URLs.
For each search pass, record:
Example:
| Database | Date searched | Query | Filters | Results |
| --- | --- | --- | --- | ---: |
| PubMed | 2026-05-11 | `sickle cell disease[mh] AND CRISPR[tiab]` | 2020:2026[dp], English | 42 |
raise_for_status() or otherwise handle non-200
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