Gene Expression Text Miner (GETM)

GETM is a tool which is capable of extracting information about the expression of genes from biomedical literature. Using the data extracted by GETM, it is possible to get an overview of the cell types that are discussed in context with gene expression of a particular gene (example), and vice versa (example).

GETM is the subject of the following paper: Gerner M., Nenadic, G. and Bergman, C. M. (2010) An exploration of mining gene expression mentions and their anatomical locations from biomedical text. BioNLP '10 Proceedings of the 2010 Workshop on Biomedical Natural Language Processing.

For questions, suggestions or bug reports, please contact Martin Gerner or Casey Bergman.
For more information about the developers of this project see: Martin Gerner's personal page, the Nenadic group or the Bergman lab.
The files on this webpage can also accessed from this project's SourceForge project page.

GETM dataset query interface

The dataset extracted by GETM can be queried using the form below. Enter either an anatomical location or a gene name and click submit.


GETM tool and evaluation corpus availability

Last updated: December 18th, 2013.