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Create or update a PubMed database

Source: R/modify_pubmed_db.R
modifyPubmedDb.Rd

This function downloads PubMed/MEDLINE XML files, parses them, and adds the information to the database, then downloads the NIH Open Citation Collection and adds it to the database. Only the most recent version of each PMID is retained. Parsing of XML files will use a parallel backend if one is registered, such as with doParallel::registerDoParallel().

Usage

modifyPubmedDb(
  localDir,
  dbname,
  dbtype = c("postgres", "mariadb", "mysql", "sqlite"),
  nFiles = Inf,
  retry = TRUE,
  nCitations = Inf,
  mode = c("create", "update"),
  ...
)

Arguments

localDir

Directory in which to download the files from PubMed.

dbname

Name of database.

dbtype

Type of database, either 'postgres', 'mariadb', 'mysql', or 'sqlite'. Make sure to install the corresponding DBI driver package first: RPostgres, RMariaDB (for both 'mariadb' and 'mysql'), or RSQLite. Due to the large size of the database, SQLite is recommended only for small-scale testing.

nFiles

Maximum number of xml files to parse that are not already in the database. This should not normally be changed from the default.

retry

Logical indicating whether to retry parsing steps that fail.

nCitations

Maximum number of rows of the citation file to read. This should not normally be changed from the default.

mode

String indicating whether to create the database using the baseline files or to update the database using the update files.

...

Other arguments passed to DBI::dbConnect().

Value

NULL, invisibly. Tab-delimited log files will be created in a logs folder in localDir.

See also

parsePmidStatus(), getCitation(), getPgParams()

Examples

if (FALSE) {
modifyPubmedDb('.', 'pmdb', mode = 'create')
}