Query Tissue Microarray Samples
The Stanford Tissue Microarray Database (TMAD) is a repository of data serving a consortium of pathologists and biomedical researchers. The tissue samples in TMAD are annotated with multiple free-text fields, specifying the pathological diagnoses for each sample. These text annotations are not structured according to any ontology, making future integration of this resource with other biological and clinical data difficult.
We have developed methods to map these annotations to the NCI thesaurus. Using the NCI-T we can effectively represent annotations for about 86% of the samples.This mapping enables ontology driven integration and querying of tissue microarray data. We have deployed the mapping and ontology driven querying tools at the TMAD site for general use.
Reference Paper #1 - Ontology-based Annotation and Query of Tissue Microarray Data. N. H. Shah, D. L. Rubin, K. S. Supekar, M. A. Musen. AMIA Annual Symposium, Washington DC, AMIA, 709-713. Published 2006.
Reference Paper #2 - Annotation and query of tissue microarray data using the NCI Thesaurus. N. H. Shah, D. L. Rubin, I. Espinosa, K. Montgomery, M. A. Musen. BMC Bioinformatics, 8, 296. Published 2007.