getpapers

getpapers

Get fulltexts or fulltext URLs of papers matching a search query using either the EuropePMC or the IEEE API.

getpapers can fetch article metadata, fulltexts (PDF or XML), and supplementary materials. It's designed for use in content mining, but you may find it useful for quickly acquiring large numbers of papers for reading, or for bibliometrics.

Installation

$ npm install --global getpapers

Usage

Use getpapers --help to see the command-line help:

Usage: getpapers [options]

Options:

  -h, --help              output usage information
  -V, --version           output the version number
  -q, --query <query>     Search query (required)
  -o, --outdir <path>     Output directory (required - will be created if not found)
  --api <name>            API to search [eupmc, ieee] (default: eupmc)
  -x, --xml               Download fulltext XMLs if available
  -p, --pdf               Download fulltext PDFs if available
  -s, --supp              Download supplementary files if available
  -l, --loglevel <level>  amount of information to log (silent, verbose, info*, data, warn, error, or debug)
  -a, --all               search all papers, not just open access

By default, getpapers uses the EuropePMC API.

Screenshot

EuropePMC Query format

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

IEEE Query format

The IEEE query format is loosely documented at IEEE Xplore Gateway. In general, anything that works in the website search will also work in getpapers with the --api ieee option enabled.

Note that IEEE does not provide fulltext XML, and their fulltext PDFs are not easily downloadable (though we're working on it). getpapers will output metadata for the search results, and will attempt to reconstruct the fulltext HTML URLs for any papers that have fulltext HTML.

If you want to actually download the fulltext HTML of papers, you will need this hack-around script. In the future we will incorporate fulltext download into getpapers.

License

Copyright (c) 2014 Shuttleworth Foundation Licensed under the MIT license