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query format

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Ayush Garg edited this page Apr 15, 2021 · 3 revisions

Queries are processed by EuropePMC. In their simplest form, they can be free text, like this:

--query "brain tumour rnaseq"

But they can also be much more detailed, using the EuropePMC webservice's query language (see Appendix 1 of the EuropePMC reference PDF).

For example, we can restrict our search to only papers that mention "transcriptome assembly" in the methods:

--query "METHODS:'transcriptome assembly'"

Or to only papers with a CC-BY license:

--query "LICENSE:'cc by' OR LICENSE:'cc-by'"

Note that in this case, we combine two restrictions using the logical OR keyword. We can also use AND, and can group operations using brackets:

--query "(LICENSE:'cc by' OR LICENSE:'cc-by') AND METHODS:'transcriptome assembly'"

A selection of the most commonly useful search fields are explained below...

Restrict search by bibliographic metadata

Field Description Example
PMCID: Search for a publication by its PubMed Central ID, where applicable (i.e. available as full text) PMCID:PMC1287967
TITLE: Search for a term or terms in publication titles TITLE:aspirin, TITLE:”protein knowledgebase”
ABSTRACT: Search for a term or terms in publication abstracts ABSTRACT:malaria, ABSTRACT:”chicken pox”
AUTH: Search for a surname and (optionally) initial(s) in publication author lists AUTH:einstein, AUTH:”Smith AB”
JOURNAL: Journal title – searchable either in full or abbreviated form JOURNAL:”biology letters”, JOURNAL:”biol lett”
LICENSE: Search for content according to the assigned Creative Commons license (where provided). LICENSE:"cc by" OR LICENSE:"cc-by", LICENSE:cc

Restrict by article metadata

Field Description Example
DISEASE: Search for mined diseases DISEASE:dysthymias
GENE_PROTEIN: Search for records that have GENE_PROTEINS mined GENE_PROTEIN:gng11
GOTERM: Search for records that have GOTERM mined GOTERM:apoptosis
CHEM: Limit your search by MeSH substance CHEM:propantheline, CHEM:”protein kinases”
ORGANISM: Search for mined organisms ORGANISM:terebratulide
PUB_TYPE: Limit your search by publication type PUB_TYPE:review, PUB_TYPE:”retraction of publication”

Section-level search

Field Description Example
INTRO: Find articles with a phrase in the Introduction & Background section INTRO:“protein interactions”
METHODS: Find articles with a phrase in the Materials & Methods section METHODS:“yeast two-hybrid”
RESULTS: Find articles with a phrase in the Results section RESULTS:"in vivo"
DISCUSS: Find articles with a phrase in the Discussion seciton DISCUSS:cardivascular

Credits: Rik Smith-Unna

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