Tools for loading MEDLINE into a local relational database

Background: Researchers who use MEDLINE for text mining, information extraction, or natural language processing may benefit from having a copy of MEDLINE that they can manage locally. The National Library of Medicine (NLM) distributes MEDLINE in eXtensible Markup Language (XML)formatted text files, but it is difficult to query MEDLINE in that format. We have developed software tools to parse the MEDLINE data files and load their contents into a relational database. Although the task is conceptually straightforward, the size and scope of MEDLINE make the task nontrivial. Given the increasing importance of text analysis in biology and medicine, we believe a local installation of MEDLINE will provide helpful computing infrastructure for researchers. Results: We developed three software packages that parse and load MEDLINE, and ran each package to install separate instances of the MEDLINE database. For each installation, we collected data on loading time and disk-space utilization to prov...

• Type: Journal
• Year: 2004
• Where: BMCBI
• Authors: Diane E. Oliver, Gaurav Bhalotia, Ariel S. Schwartz, Russ B. Altman, Marti A. Hearst
• Keywords: BMCBI 2004, Medline, MEDLINE Data Files, Natural Language Processing