BioText Team Experiments for the TREC 2004 Genomics Track

The BioText group participated in the two main tasks of the TREC 2004 Genomics track. Our approach to the ad hoc task was similar to the one used in the 2003 Genomics track, but due to the lack of training data, we did not achieve the high scores of the previous year. The most novel aspect of our submission for the categorization task centers around our method for assigning Gene Ontology (GO) codes to articles marked for curation. This approach compares the text surrounding a target gene to text that has been found to be associated with GO codes assigned to homologous genes for organisms with genomes similar to mice (namely, humans and rats). We applied the same method to GO codes that have been assigned to MGI entries in years prior to the test set. In addition, we filtered out proposed GO codes based on their previously observed likelihood to co-occur with one another.