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Overview

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

Note: When working with the notebooks, a corresponding julia script is generated automatically on every save. For this feature to work properly, make sure you have nbconvert installed.

The following examples are available:

Example	Description
Search and Save PubMed Queries	Search pubmed, parse results and store using 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 a occurrence matrix indicating papers associated with MeSH descriptors of a given UMLS concept
Exporting Citations	Export the citation for one or more PMIDs to a Endnote/Bibtex file