How do I install the Pubmed Search skill?

Run npx skillmds@latest add beita6969/pubmed-search in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Pubmed Search safe to use?

This skill has not completed SkillMD's automated safety review yet. Capability flags: makes network calls, reads secrets. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Pubmed Search?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Pubmed Search free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Pubmed Search?

beita6969 (@beita6969) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Pubmed Search by beita6969 — Agent Skill

Name: Pubmed Search
Rating: 4.2 (5 reviews)
Author: beita6969

Pubmed Search

Search PubMed/MEDLINE for biomedical literature via NCBI E-utilities API. Use when: (1) searching medical/biomedical papers, (2) finding clinical studies, (3) querying with MeSH terms, (4) retrieving abstracts by PMID. NOT for: non-biomedical papers (use arxiv-search or semantic-scholar), full-text access (PubMed provides abstracts), or social science literature.

beita6969 Updated Sep 9, 2026

File contents

PubMed Search

Search PubMed/MEDLINE (36M+ citations) via NCBI E-utilities REST API.

API Endpoints

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

esearch -- Search and get PMIDs

curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=COVID-19+vaccine+efficacy&retmax=10&retmode=json"

Parameters: db=pubmed, term= (URL-encoded query), retmax= (default 20, max 10000), retstart= (pagination), retmode=json, sort=relevance|pub_date, mindate=/maxdate= (YYYY/MM/DD), datetype=pdat.

efetch -- Retrieve records by PMID

curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=39142890,39088712&retmode=xml&rettype=abstract"

einfo -- Database metadata

curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=pubmed&retmode=json"

Query Syntax

Boolean: AND, OR, NOT, parentheses for grouping.

Field tags: [ti] title, [tiab] title/abstract, [au] author, [mesh] MeSH heading, [majr] MeSH major topic, [pt] publication type, [dp] date, [la] language, [jour] journal.

MeSH terms: Standardized vocabulary with automatic explosion to narrower terms. Use [mesh:noexp] for exact heading only. Qualifiers: /therapy, /diagnosis, /epidemiology, /genetics, /prevention and control.

Example: "Breast Neoplasms"[mesh] AND "Drug Therapy"[mesh]

Rate Limiting

Without API key: 3 requests/sec
With NCBI_API_KEY: 10 requests/sec (append &api_key=${NCBI_API_KEY})
Register at: https://www.ncbi.nlm.nih.gov/account/settings/

Two-Step Search Pattern

PMIDS=$(curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=QUERY&retmax=5&retmode=json" \
  | python3 -c "import sys,json; d=json.load(sys.stdin); print(','.join(d['esearchresult']['idlist']))")
curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=${PMIDS}&retmode=xml&rettype=abstract"

Specialty Search Patterns

Oncology: "Neoplasms"[mesh] AND "immunotherapy"[tiab] AND "Clinical Trial"[pt]
Cardiology: "Cardiovascular Diseases"[mesh] AND "meta-analysis"[pt]
Neurology: "Alzheimer Disease"[mesh] AND "biomarkers"[tiab] AND 2020:2024[dp]
Infectious Disease: "Anti-Bacterial Agents"[mesh] AND "Drug Resistance"[mesh]
Genetics: "Genome-Wide Association Study"[pt] AND "Diabetes Mellitus, Type 2"[mesh]
Systematic Reviews: "systematic review"[ti] AND "Randomized Controlled Trial"[pt]

Best Practices

Start broad, narrow with MeSH terms and field tags.
Use retmax=5 for exploration, increase for comprehensive searches.
URL-encode queries (spaces as +, quotes as %22).
Check count in esearch results before paginating.
Document exact query strings for systematic review reproducibility.
For systematic reviews, use "systematic review"[ti] combined with study type filters.

Zero-Hallucination Rule

NEVER fabricate results from training data. Every paper title, author, DOI, PMID, citation count, and metadata detail presented to the user MUST come from an actual API response in this conversation. If the API returns no results or partial data, report exactly what was returned. Do not "fill in" missing details from memory.

---name: pubmed-searchdescription: Search PubMed/MEDLINE for biomedical literature via NCBI E-utilities API. Use when: (1) searching medical/biomedical papers, (2) finding clinical studies, (3) querying with MeSH terms, (4) retrieving abstracts by PMID. NOT for: non-biomedical papers (use arxiv-search or semantic-scholar), full-text access (PubMed provides abstracts), or social science literature.--- # PubMed Search Search PubMed/MEDLINE (36M+ citations) via NCBI E-utilities REST API. ## API Endpoints Base: `https://eutils.ncbi.nlm.nih.gov/entrez/eutils/` ### esearch -- Search and get PMIDs ```bash curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=COVID-19+vaccine+efficacy&retmax=10&retmode=json" ``` Parameters: `db=pubmed`, `term=` (URL-encoded query), `retmax=` (default 20, max 10000), `retstart=` (pagination), `retmode=json`, `sort=relevance|pub_date`, `mindate=`/`maxdate=` (YYYY/MM/DD), `datetype=pdat`. ### efetch -- Retrieve records by PMID ```bash curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=39142890,39088712&retmode=xml&rettype=abstract" ``` ### einfo -- Database metadata ```bash curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=pubmed&retmode=json" ``` ## Query Syntax **Boolean**: `AND`, `OR`, `NOT`, parentheses for grouping. **Field tags**: `[ti]` title, `[tiab]` title/abstract, `[au]` author, `[mesh]` MeSH heading, `[majr]` MeSH major topic, `[pt]` publication type, `[dp]` date, `[la]` language, `[jour]` journal. **MeSH terms**: Standardized vocabulary with automatic explosion to narrower terms. Use `[mesh:noexp]` for exact heading only. Qualifiers: `/therapy`, `/diagnosis`, `/epidemiology`, `/genetics`, `/prevention and control`. Example: `"Breast Neoplasms"[mesh] AND "Drug Therapy"[mesh]` ## Rate Limiting - Without API key: 3 requests/sec - With `NCBI_API_KEY`: 10 requests/sec (append `&api_key=${NCBI_API_KEY}`) - Register at: https://www.ncbi.nlm.nih.gov/account/settings/ ## Two-Step Search Pattern ```bash PMIDS=$(curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=QUERY&retmax=5&retmode=json" \ | python3 -c "import sys,json; d=json.load(sys.stdin); print(','.join(d['esearchresult']['idlist']))") curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=${PMIDS}&retmode=xml&rettype=abstract" ``` ## Specialty Search Patterns - **Oncology**: `"Neoplasms"[mesh] AND "immunotherapy"[tiab] AND "Clinical Trial"[pt]` - **Cardiology**: `"Cardiovascular Diseases"[mesh] AND "meta-analysis"[pt]` - **Neurology**: `"Alzheimer Disease"[mesh] AND "biomarkers"[tiab] AND 2020:2024[dp]` - **Infectious Disease**: `"Anti-Bacterial Agents"[mesh] AND "Drug Resistance"[mesh]` - **Genetics**: `"Genome-Wide Association Study"[pt] AND "Diabetes Mellitus, Type 2"[mesh]` - **Systematic Reviews**: `"systematic review"[ti] AND "Randomized Controlled Trial"[pt]` ## Best Practices 1. Start broad, narrow with MeSH terms and field tags. 2. Use `retmax=5` for exploration, increase for comprehensive searches. 3. URL-encode queries (spaces as `+`, quotes as `%22`). 4. Check `count` in esearch results before paginating. 5. Document exact query strings for systematic review reproducibility. 6. For systematic reviews, use `"systematic review"[ti]` combined with study type filters. ## Zero-Hallucination Rule NEVER fabricate results from training data. Every paper title, author, DOI, PMID, citation count, and metadata detail presented to the user MUST come from an actual API response in this conversation. If the API returns no results or partial data, report exactly what was returned. Do not "fill in" missing details from memory.

Frequently asked questions