query format - petermr/pygetpapers GitHub Wiki

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