pubmed-cli

name	pubmed-cli
description	Search PubMed, fetch article metadata, traverse citation graphs, and look up MeSH terms from the command line. Use when: (1) Searching PubMed with Boolean/MeSH queries, (2) Fetching article details by PMID (abstract, authors, DOI, MeSH terms), (3) Finding papers that cite a given article (cited-by), (4) Finding papers cited by a given article (references), (5) Finding related articles with relevance scores, (6) Looking up MeSH vocabulary (tree numbers, scope notes), (7) Exporting citations in RIS format for Zotero/EndNote, (8) Building reproducible literature review workflows, (9) Verifying document references against PubMed for accuracy and detecting fabricated citations.
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pubmed-cli

PubMed from your terminal. Search, fetch, cite, traverse — built for humans and AI agents. Zero dependencies, structured JSON, agent-ready.

Install

brew install drpedapati/tools/pubmed-cli

Binary: /opt/homebrew/bin/pubmed

Verify: pubmed --help

Configuration

Set your NCBI API key for higher rate limits (recommended):

export NCBI_API_KEY="your-key"

• Without key: 3 requests/second
• With key: 10 requests/second
• Get a key at: https://www.ncbi.nlm.nih.gov/account/settings/

Commands

search — Query PubMed

pubmed search "fragile x syndrome" --json --limit 10
pubmed search "autism AND EEG" --json --limit 20 --sort date
pubmed search "ALS" --json --year 2023-2025 --type review
pubmed search "CRISPR" --json --sort cited --limit 5

Returns: count (total hits), ids (PMIDs), query_translation (how NCBI interpreted the query).

Supports: Boolean operators (AND, OR, NOT), MeSH terms ([MeSH Terms]), field tags ([Title/Abstract], [Author]), wildcards (neoplas*), phrase search ("exact phrase").

fetch — Get article details

pubmed fetch 38000001 --json
pubmed fetch 38000001 38000002 38000003 --json
pubmed fetch "38000001,38000002" --json

Returns per article: pmid, title, abstract, abstract_sections (structured), authors (with affiliations), journal, volume, issue, pages, year, doi, pmcid, mesh_terms (with major topic flags), publication_types.

cited-by — Papers that cite this article

pubmed cited-by 38000001 --json --limit 10

Returns: source_id, links (PMIDs of citing papers).

references — Papers cited by this article

pubmed references 38000001 --json --limit 10

Returns: source_id, links (PMIDs of referenced papers).

related — Similar articles with relevance scores

pubmed related 38000001 --json --limit 10

Returns: source_id, links (PMIDs with score — higher = more similar).

mesh — MeSH vocabulary lookup

pubmed mesh "depression" --json
pubmed mesh "autism spectrum disorder" --json

Returns: ui (MeSH ID), name, scope_note, tree_numbers, entry_terms (synonyms), annotation.

refcheck — Verify document references

pubmed refcheck manuscript.docx --json
pubmed refcheck manuscript.docx --human
pubmed refcheck manuscript.docx --audit-text --json
pubmed refcheck manuscript.docx --audit-text --csv-out report.csv --ris-out verified.ris

Requires: docx-review installed and on PATH.

Extracts references from a .docx document, verifies each against PubMed using a tiered query strategy (PMID → DOI → title → author+year → relaxed), and reports verification status.

Verification statuses:

• VERIFIED_EXACT — reference matches PubMed record exactly
• VERIFIED_WITH_CORRECTION — matched but with metadata differences (wrong DOI, year, pages)
• VERIFIED_BY_TITLE — matched by title but lower confidence
• NOT_IN_PUBMED — no matching PubMed record found
• POSSIBLY_FABRICATED — hallucination signals detected (known author but no matching paper)

Flags:

• --audit-text — audit in-text citations against reference list (finds uncited refs, orphan markers)
• --csv-out FILE — export verification report to CSV
• --ris-out FILE — export verified references as RIS citations

Output Formats

Flag	Format	Use case
--json	Structured JSON	Agent parsing, programmatic use
--human / -H	Rich terminal tables	Interactive exploration
--csv FILE	CSV export	Spreadsheet import, data analysis
--ris FILE	RIS citations	Zotero, EndNote, Mendeley import

Always use --json for agent workflows. The other formats are for human review and export.

Search Modifiers

Flag	Values	Example
--limit N	Any positive integer (default 20)	--limit 50
--sort	relevance, date, cited	--sort cited
--year	YYYY or YYYY-YYYY	--year 2020-2025
--type	review, trial, meta-analysis, randomized, case-report, or custom	--type review

Workflow: Systematic Literature Search

# 1. Search with filters
pubmed search "ALS AND biomarkers" --json --limit 50 --year 2020-2025 --type review > search.json

# 2. Fetch full details for top results
cat search.json | jq -r '.ids[:10] | join(" ")' | xargs pubmed fetch --json > articles.json

# 3. Check what each key paper cites
pubmed references 38000001 --json --limit 20 > refs.json

# 4. Find related work
pubmed related 38000001 --json --limit 20 > related.json

# 5. Export for reference manager
pubmed fetch 38000001 38000002 38000003 --ris bibliography.ris

Workflow: Citation Network Traversal

# Start with a seed paper
pubmed fetch 38000001 --json

# Forward citations (who cited this?)
pubmed cited-by 38000001 --json --limit 20

# Backward citations (what did this cite?)
pubmed references 38000001 --json --limit 20

# Similar papers (NCBI's relevance algorithm)
pubmed related 38000001 --json --limit 20

# Chain: fetch details of citing papers
pubmed cited-by 38000001 --json | jq -r '.links[].id' | head -5 | xargs pubmed fetch --json

Workflow: Document Reference Verification

# 1. Quick check — see verification summary
pubmed refcheck paper.docx --human

# 2. Full audit with in-text citation check
pubmed refcheck paper.docx --audit-text --human

# 3. Export for records
pubmed refcheck paper.docx --audit-text --json > report.json
pubmed refcheck paper.docx --csv-out report.csv --ris-out verified.ris

Workflow: MeSH-Guided Search

# 1. Look up the correct MeSH term
pubmed mesh "fragile x" --json

# 2. Use the official MeSH term in search
pubmed search '"Fragile X Syndrome"[MeSH Terms]' --json --limit 20

# 3. Combine with other terms
pubmed search '"Fragile X Syndrome"[MeSH] AND EEG[Title/Abstract]' --json --year 2020-2025

Exit Codes

• 0 — success
• 1 — user error (invalid flags, bad PMID) or API failure

Error messages are written to stderr with actionable descriptions.

Rate Limiting

Built-in rate limiter respects NCBI guidelines:

• 3 req/s without API key, 10 req/s with key
• Automatic retry on HTTP 429 with exponential backoff
• Respects Retry-After headers