Video Tip of the Week: eGIFT, extracting gene information from text


eGIFT, as the tag line says, is a tool to extract gene information from text. It’s a tool that allows you to search for and explore terms  and documents related to a gene or set of genes. There are many ways to search and explore eGIFT, find genes given a specific term, find terms related to a set of genes and more. How does the tool do this? You can check out the user guide to find out more, but here is a brief summary from the site:

We look at PubMed references (titles and abstracts), gather those references which focus on the given gene, and automatically identify terms which are statistically more likely to be relevant to this gene than to genes in general. In order to understand the relationship between a specific iTerm and the given gene, we allow the users to see all sentences mentioning the iTerm, as well as the abstracts from which these sentences were extracted.

To learn more about how this tool was put together and the calculations involved, you can check out the BMC Bioinformatics publication about it from 2010, eGIFT: Mining Gene Information from the Literature.

But, for today, take a tour of the site and some of the things you can do in today’s Tip of the Week.

Relevant Links:
eGIFT
PubMed (tutorial)
XplorMed (tutorial)
Literature & Text Mining Resource Tutorials

Tudor, C., Schmidt, C., & Vijay-Shanker, K. (2010). eGIFT: Mining Gene Information from the Literature BMC Bioinformatics, 11 (1) DOI: 10.1186/1471-2105-11-418