MEDOC: a Python wrapper to load MEDLINE into a local MySQL database

TL;DR

MEDOC is a Python tool that efficiently downloads and loads MEDLINE data into a local MySQL database, enabling complex and rapid queries on a large biomedical literature corpus.

Contribution

It introduces a practical solution for building a local relational database of MEDLINE metadata, facilitating advanced data analysis and querying.

Findings

Loaded 26 million documents in under 5 days

Enables complex, rapid queries on MEDLINE data

Accessible as a free, open-source tool

Abstract

Since the MEDLINE database was released, the number of documents indexed by this entity has risen every year. Several tools have been developed by the National Institutes of Health (NIH) to query this corpus of scientific publications. However, in terms of advances in big data, text-mining and data science, an option to build a local relational database containing all metadata available on MEDLINE would be truly useful to optimally exploit these resources. MEDOC (MEdline DOwnloading Contrivance) is a Python program designed to download data on an FTP and to load all extracted information into a local MySQL database. It took MEDOC 4 days and 17 hours to load the 26 million documents available on this server onto a standard computer. This indexed relational database allows the user to build complex and rapid queries. All fields can thus be searched for desired information, a task that is difficult to accomplish through the PubMed graphical interface. MEDOC is free and publicly available at https://github.com/MrMimic/MEDOC.