This tool is used to ingest data from the National Library of Medicine's PubMed publication repository using their EUtils web service. PubMed allows queries to be designed to return very specific record sets based on a range of different attributes such as date added, date modified, number range, affiliation, etc. See their help for using the PubMed search tool and also the advanced search tool, which helps you build your query.
The publications that match the query given to the tool will be fetched as XML data and loaded into the output RecordHandler.
Command Line Arguments
PubmedFetch extends NIHFetch, so it uses the same arguments.
Parameter Value Map
number of records to fetch per batch
your contact email address
maximum records to return – set to ALL in order to retrieve all records without limit
RecordHandler config file path
override the RH_PARAM of output recordhandler using VALUE
term to search against pubmed
As with all the Harvester command-line tools, you can provide all the arguments as parameters is a configuration file (X/-config). Here is a sample configuration for PubmedFetch.
After version 1.2 of the harvester, execution of pubmedfetch has changed. The following refers to 1.1.1 and below:
To execute the PubmedFetch tool from the commandline, there is a convenient environment config file that, when loaded in a bash shell, will allow you to execute PubmedFetch with a simple
$PubmedFetch . For information about that, see ]Environment Config File.
Or you can simply call (paths relative to base harvester folder):