The repository contains an examples folder with scripts demonstrating how to use BioMedQuery's pre-assembled high-level processes and workflows.

The following examples are available:

Search and Save PubMed QueriesSearch PubMed, parse results, store them using a MySQL or SQLite backend, or export to a citation library
UMLS-MeSH Mapping and FilteringFor all MeSH descriptors in a given data disease_occurances, build a table to match them to their UMLS concept, and filter them by UMLS concepts
Exporting CitationsExport the citation for one or more PMIDs to an Endnote/Bibtex file
Loading MEDLINELoad the MEDLINE baseline files