BioText: Software

BioText Software for Download

Abbreviation Definition Recognition Software

The ExtractAbbrev class implements a simple algorithm for extraction of abbreviations and their definitions from biomedical text. Abbreviations (short forms) are extracted from the input file, and those abbreviations for which a definition (long form) is found are printed out, along with that definition, one per line. A file consisting of short-form/long-form pairs (tab separated) can be specified in tandem with the -testlist option for the purposes of evaluating the algorithm.

Downloading is free, but please acknowledge us by citing this paper if you use the code in research:

A Simple Algorithm for Identifying Abbreviation Definitions in Biomedical Text, Ariel Schwartz and Marti Hearst, in the proceedings of the Pacific Symposium on Biocomputing (PSB 2003) Kauai, Jan 2003. pdf

Java sourcecode	ExtractAbbrev.java
Java Documentation	ExtractAbbrev.html
Sample input file	test.txt
Sample testing file	pairs.txt

Software to parse and load MEDLINE into a RDBMS

Downloading is free, but please acknowledge us by citing this paper if you use the code:

Tools for loading Medline into a local relational database Diane E. Oliver, Gaurav Bhalotia, Ariel S. Schwartz, Russ B. Altman, Marti A. Hearst, BMC Bioinformatics 2004, (7Oct2004) Available at BioMedCentral

MedlineParser java code. Applicable to MEDLINE 2004. gzipped tar file zip file

MedlineParser perl code. Applicable to MEDLINE 2003. parsemedline.pl medline-schema-perl-oracle.sql