Metadata of preprints from both repositories can be accessed via a singular API service hosted on bioRxiv, available at https://api.biorxiv.org. This package,
rbiorxiv, provides a simple interface for interacting with this API service, to allow retrieval of metadata for bioRxiv and medRxiv preprints.
Install development version from Github
The main functions in
rbiorxiv generally conform to the API endpoints outlined in the API documentation (see here).
Retrieve details of either a set of preprints deposited between two dates, or lookup a single preprint by DOI:
# Get details of preprints deposited between 2018-01-01 and 2018-01-10 # By default, only the first 100 records are returned biorxiv_content(from = "2018-01-01", to = "2018-01-10") # Set a limit to return more than 100 records biorxiv_content(from = "2018-01-01", to = "2018-01-10", limit = 200) # Or set limit as "*" to return all records biorxiv_content(from = "2018-01-01", to = "2018-01-10", limit = "*") # Skip the first 100 records biorxiv_content(from = "2018-01-01", to = "2018-01-10", limit = 200, skip = 100) # By default, data is returned in a list. Use the "format" argument to specify # that data should be returned in "json" format or as a data frame ("df"). biorxiv_content(from = "2018-01-01", to = "2018-01-10", format = "df") # Lookup a preprint by DOI biorxiv_content(doi = "10.1101/833400")
The bioRxiv API currently also allows querying of details of medRxiv preprints, by supplying a “server” parameter. This can be specified as follows:
The default server parameter is always “biorxiv”. Note that the following functions documented below are limited to bioRxiv only (at the time of writing).
Retrieve details of published articles associated with bioRxiv preprints that were published between two dates:
Retrieve details of articles published by a specific publisher (specified by their doi prefix) between two dates:
Retrieve summary statistics for bioRxiv content (e.g. number of preprints deposited):