name: pubmed-lookup description: | Find and read biomedical literature through NCBI E-utilities and Europe PMC (no key): search PubMed for papers on a target, antibody or method, read titles, journals, years and abstracts, and fetch open-access full text. Use this instead of web_search for any question about published structures, epitopes, affinities or protocols. homepage: https://www.ncbi.nlm.nih.gov/books/NBK25501/ metadata: version: "1.0.0"

PubMed lookup

Fixed, keyless endpoints. Fetch them with web_fetch. NCBI allows about three requests per second without a key; a search plus a summary is enough for most questions.

Search

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=PD-1+nanobody+crystal+structure&retmode=json&retmax=10&sort=relevance

Returns esearchresult.idlist (PMIDs) and count. Field tags narrow a term: PD-1[Title], Zak KM[Author], 2020:2026[dp] (date published), "Nature Communications"[Journal].

Titles, journals, years

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=26602187,28280600&retmode=json

Read result[<pmid>].title, .source (journal), .pubdate, .authors[].name, .elocationid (DOI).

Abstract

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=26602187&rettype=abstract&retmode=text

Plain text, several PMIDs at once with commas.

Open-access full text (Europe PMC)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PD-1+nanobody+structure+AND+OPEN_ACCESS:y&format=json&pageSize=10&resultType=lite

OPEN_ACCESS:y keeps the search to articles whose full text may be fetched; a PMCID alone does not mean that. For each result with isOpenAccess = Y, the full text is https://www.ebi.ac.uk/europepmc/webservices/rest/<pmcid>/fullTextXML with the pmcid value verbatim (it already carries the PMC prefix). For anything else, the PubMed abstract above is what is available.