Paper: An Exploration of Mining Gene Expression Mentions and Their Anatomical Locations from Biomedical Text

ACL ID W10-1909
Title An Exploration of Mining Gene Expression Mentions and Their Anatomical Locations from Biomedical Text
Venue Workshop on Biomedical Natural Language Processing
Session
Year 2010
Authors

Here we explore mining data on gene expres- sion from the biomedical literature and present Gene Expression Text Miner (GETM), a tool for extraction of information about the expression of genes and their ana- tomical locations from text. Provided with recognized gene mentions, GETM identifies mentions of anatomical locations and cell lines, and extracts text passages where au- thors discuss the expression of a particular gene in specific anatomical locations or cell lines. This enables the automatic construction of expression profiles for both genes and ana- tomical locations. Evaluated against a ma- nually extended version of the BioNLP '09 corpus, GETM achieved precision and recall levels of 58.8% and 23.8%, respectively. Ap- plication of GETM to MEDLINE and PubMed Central y...