Name
Abstract | ||
|---|---|---|
The Stanford Tissue Microarray Database (TMAD) is a repository of data amassed by a consortium of pathologists and biomedical researchers. The TMAD data are annotated with multiple free-text fields, specifying the pathological diagnoses for each tissue sample. These annotations are spread out over multiple text fields and are not structured according to any ontology, making it difficult to integrate this resource with other biological and clinical data. We developed methods to map these annotations to the NCI thesaurus and the SNOMED-CT ontologies. Using these two ontologies we can effectively represent about 80% of the annotations in a structured manner. This mapping offers the ability to perform ontology driven querying of the TMAD data. We also found that 40% of annotations can be mapped to terms from both ontologies, providing the potential to align the two ontologies based on experimental data. Our approach provides the basis for a data-driven ontology alignment by mapping annotations of experimental data. Introduction and Background Tissue Microarrays allow for the immunohistochemical analysis of large numbers of tissue samples and are used for confirmation of microarray gene-expression results as well as for predictive pathology (1) . A single tissue microarray (TMA) paraffin block can contain as many as 500 different tumors, enabling the screening of thousands of tumor samples for protein expression using a few array sections (2) . Commercial digital-imaging systems can rapidly store thousands of images resulting from such sections. The Stanford Tissue Microarray Database (TMAD) provides a central repository for data from TMA's akin to the Stanford Microarray Database (SMD) for gene expression arrays. |
Year | Venue | Keywords |
|---|---|---|
2006 | AMIA | digital image,protein expression,gene expression,ontology alignment,tissue microarray,snomed ct |
Field | DocType | Citations |
Ontology (information science),Ontology alignment,Ontology-based data integration,Ontology,Annotation,Information retrieval,Computer science,Open Biomedical Ontologies,Systematized Nomenclature of Medicine,Microarray databases | Conference | 15 |
PageRank | References | Authors |
2.56 | 3 | 4 |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Nigam Shah | 1 | 1380 | 107.49 |
| Daniel L. Rubin | 2 | 1645 | 145.14 |
| Kaustubh S. Supekar | 3 | 41 | 4.26 |
| Mark A Musen | 4 | 7141 | 766.74 |