jackwener--opencli/docs/adapters/browser/pubmed.md

PubMed

Mode: 🌐 Public · Domain: pubmed.ncbi.nlm.nih.gov

Commands

Command	Description
opencli pubmed search	Search PubMed articles with filters
opencli pubmed article	Get article metadata and abstract by PMID
opencli pubmed author	Search articles by author and affiliation
opencli pubmed citations	List cited-by or reference relationships
opencli pubmed related	Find related PubMed articles
opencli pubmed clinical-trial	Search PubMed clinical trials with a preset query profile
opencli pubmed review	Search PubMed review articles with a preset query profile
opencli pubmed mesh	Search articles by MeSH term
opencli pubmed journal	Search articles by journal name

Usage Examples

# Search articles
opencli pubmed search "machine learning cancer" --year-from 2023 --has-abstract --limit 10

# Search by author
opencli pubmed author "Smith J" --position first --affiliation Harvard

# Read one article by PMID
opencli pubmed article 37780221 --full-abstract

# Citation relationships
opencli pubmed citations 37780221 --direction citedby --limit 20
opencli pubmed citations 37780221 --direction references --limit 20

# Related articles with scores
opencli pubmed related 37780221 --score

# Clinical trial preset
opencli pubmed clinical-trial "breast cancer" --year-from 2020 --free-full-text --limit 10

# Review preset
opencli pubmed review "immunotherapy" --year-from 2021 --has-abstract --limit 10

# Search by MeSH term
opencli pubmed mesh "Neoplasms" --major --limit 10

# Search by journal
opencli pubmed journal "Nature" --year-from 2020 --sort date --limit 10

Output

Listing commands return pmid, title, authors, journal, year, article_type, doi, and url where available. The pmid column is the stable identifier for opencli pubmed article <pmid>.

article now returns a single structured row: pmid, title, authors, journal, year, date, article_type, language, doi, pmc, affiliations, grants, mesh_terms, keywords, abstract, and url. By default the abstract is truncated for readability; pass --full-abstract when you need the complete abstract text.

clinical-trial is a preset over the same E-utilities search path. It always adds the PubMed Clinical Trial[PT] and humans[mesh] filters, and optionally adds free full text[sb].

review is the parallel preset for literature overviews. It always adds the PubMed Review[PT] filter, and can optionally require abstracts with --has-abstract.

Prerequisites

• No browser required. Commands use the NCBI E-utilities public API.
• Optional: set NCBI_API_KEY for the higher NCBI rate limit.
• Optional: set NCBI_EMAIL so NCBI can identify your tool usage.

export NCBI_API_KEY=YOUR_API_KEY
export NCBI_EMAIL=you@example.com

Failure Semantics

• Invalid pmid, limit, year, sort, position, direction, MeSH term, journal, clinical-trial query, or review query values fail before network access with ArgumentError.
• HTTP errors, fetch failures, invalid JSON, E-utilities error envelopes, and partial summary payloads fail with CommandExecutionError.
• Valid no-result searches and missing relationships fail with EmptyResultError.