Tools created for the Cb GRITS Project:
Understanding the functional relationship between genes remains to be a
major challenge in interpretation of genomic data. Bioinformatics tools
to automate extraction and utilization of gene information from the
biological databases and the scientific literature are being developed.
We present a new software environment called Semantic Gene Organizer
© (SGO) which utilizes Latent Semantic Indexing (LSI), a
concept-based vector space model, to automatically extract gene
relationships from titles and abstracts in MEDLINE citations.
FAUN: We have develop a Web-based bioinformatics tool called Feature Annotation Using Nonnegative matrix factorization (FAUN) to facilitate both the discovery and classification of functional relationships among genes. Both the computational complexity and parameterization of nonnegative matrix factorization (NMF) for processing gene sets are currently being investigated. FAUN has been tested on several manually constructed gene collections (size ranging from 50 to 800 genes) and has been particularly engineered to analyze several microarray-derived gene sets obtained from studies of the developing cerebellum in normal and mutant mice. FAUN provides utilities for collaborative knowledge discovery and identification of new gene relationships from text streams and repositories (e.g., MEDLINE). It is particularly useful for the validation and analysis of gene associations suggested by microarray experimentation. Click here for a video about NIMBioS with Elina Tjioe demonstrating FAUN. This project is supported by the Gene Regulation in Time & Space project (funded by the NIH).
GST Retreat Poster (March 14, 2008, 4.7MB ppt) UT-ORNL-KBRIN Poster (March 28-30, 2008); published in BMC Bioinformatics July 8, 2008