An increasingly important source of health-related bibliographic content are preprints - preliminary versions of research articles that have yet to undergo peer review. The two preprint repositories most relevant to health-related sciences are medRxiv and bioRxiv, both of which are operated by the Cold Spring Harbor Laboratory.
The goal of the medrxivr
R package is two-fold. In the
first instance, it provides programmatic access to the Cold Spring Harbour Laboratory (CSHL)
API, allowing users to easily download medRxiv and bioRxiv preprint
metadata (e.g. title, abstract, publication date, author list, etc) into
R. The package also provides access to a maintained static snapshot of
the medRxiv repository (see Data sources).
Secondly, medrxivr
provides functions to search the
downloaded preprint records using regular expressions and Boolean logic,
as well as helper functions that allow users to export their search
results to a .BIB file for easy import to a reference manager and to
download the full-text PDFs of preprints matching their search
criteria.
You can install the stable version of this package using:
medrixvr
provides two ways to access medRxiv data:
mx_api_content(server = "medrxiv")
creates a local copy
of all data available from the medRxiv API at the time the function is
run.mx_snapshot()
provides access to a static snapshot of
the medRxiv database. The snapshot is created each morning at 6am using
mx_api_content()
and is stored as CSV file in the medrxivr-data
repository. This method does not rely on the API (which can become
unavailable during peak usage times) and is usually faster (as it reads
data from a CSV rather than having to re-extract it from the API).
Discrepancies between the most recent static snapshot and the live
database can be assessed using mx_crosscheck()
.The relationship between the two methods for the medRxiv database is summarised in the figure below:
Only one data source exists for the bioRxiv repository:
mx_api_content(server = "biorxiv")
creates a local copy
of all data available from the bioRxiv API endpoint at the time the
function is run. Note: due to it’s size, downloading a
complete copy of the bioRxiv repository in this manner takes a long time
(~ 1 hour).Once you have created a local copy of either the medRxiv or bioRxiv
preprint database, you can pass this object (preprint_data
in the examples above) to mx_search()
to search the
preprint records using an advanced search strategy.
# Perform a simple search
results <- mx_search(data = preprint_data,
query ="dementia")
# Perform an advanced search
topic1 <- c("dementia","vascular","alzheimer's") # Combined with Boolean OR
topic2 <- c("lipids","statins","cholesterol") # Combined with Boolean OR
myquery <- list(topic1, topic2) # Combined with Boolean AND
results <- mx_search(data = preprint_data,
query = myquery)
The dataset (in this case, results
) returned by the
search function above contains 14 variables:
Variable | Description |
---|---|
ID | Unique identifier |
title | Preprint title |
abstract | Preprint abstract |
authors | Author list in the format ‘LastName, InitalOfFirstName.’ (e.g. McGuinness, L.). Authors are seperated by a semi-colon. |
date | Date the preprint was posted, in the format YYYYMMDD. |
category | On submission, medRxiv asks authors to classify their preprint into one of a set number of subject categories. |
doi | Preprint Digital Object Identifier. |
version | Preprint version number. As authors can update their preprint at any time, this indicates which version of a given preprint the record refers to. |
author_corresponding | Corresponding authors name. |
author_corresponding_institution | Corresponding author’s institution. |
link_page | Link to preprint webpage. The “?versioned=TRUE” is required, as otherwise, the URL will resolve to the most recent version of the article (assuming there is >1 version available). |
link_pdf |
Link to preprint PDF. This is used by mx_download() to
download a copy of the PDF for that preprint.
|
license | Preprint license |
published | If the preprint was subsequently published in a peer-reviewed journal, this variable contains the DOI of the published version. |
medrxivr
provides a helper function to export your
search results to a .BIB file so that they can be easily imported into a
reference manager (e.g. Zotero, Mendeley)
Pass the results of your search above (results
) to the
mx_download()
function to download a copy of the PDF for
each record.
Please see the medrxivr website vignette for extended guidance on developing search strategies and for detailed instructions on interacting with the Cold Springs Harbour API for medRxiv and bioRxiv.