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:
| Example | Description |
|---|---|
| Search and Save PubMed Queries | Search PubMed, parse results, store them using a MySQL or SQLite backend, or export to a citation library |
| Build MeSH-UMLS map | For all MeSH descriptors in a given database, build a table to match them to their UMLS concept |
| Occurrence Matrix | Build an occurrence matrix indicating articles associated with MeSH descriptors of a given UMLS concept |
| Exporting Citations | Export the citation for one or more PMIDs to an Endnote/Bibtex file |
| Loading MEDLINE | Load the MEDLINE baseline files |