Retrieve articles from PubMed given a Pubmed query

This service retrieves articles from PubMed using NCBI Entrez APIs, and generates an RDF representation thereof. The query string complies with the syntax of the Esearch service and can consist of a sheer list of keywords or a more complex query with types and logical connectors. See the API documentation. The Pubmed query string is provided using property schema:query.

The graph produced contains a maximum of 20 articles. It relies mainly on the Bibiographic Ontology (BIBO) and FRBR-aligned Bibliographic Ontology (FaBiO). An article IRI is preferably based on its DOI, if any, prefixed with http://doi.org/. If no DOI is available, the IRI is PubMed's web page URL prefixed with https://pubmed.ncbi.nlm.nih.gov/. Authors are represented as separate triples with dct:creator, as well as an ordered list with bibo:authorList.

See modeling details.

Canonical URL: https://sparql-micro-services.org/service/pubmed/getArticleByQuery_sd/
Input argument: PubMed query string. Mandatory.
Passed as the object of predicate http://schema.org/query.
Example value: "biomarkers"[MeSH Terms] OR "biomarkers"[All Fields]
Service Description graph: https://sparql-micro-services.org/service/pubmed/getArticleByQuery_sd/ServiceDescription
SHACL shapes graph

Try it out

SPARQL query

prefix schema:   <http://schema.org/>
SELECT ?article ?p ?o WHERE {
    ?search schema:query "'biomarkers'[MeSH Terms] OR 'biomarkers'[All Fields]".
    ?article ?p ?o.
}

Output format

SPARQL response