Ontology-Mediated Query Answering with Data-Tractable Description Logics

Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.

Over the last 8 years, the National Cancer Institute (NCI) has launched a major effort to integrate molecular and clinical cancer-related information within a unified biomedical informatics framework, with controlled terminology as its foundational layer. The NCI Thesaurus is the reference terminology underpinning these efforts. It is designed to meet the growing need for accurate, comprehensive, and shared terminology, covering topics including: cancers, findings, drugs, therapies, anatomy, genes, pathways, cellular and subcellular processes, proteins, and experimental organisms. The NCI Thesaurus provides a partial model of how these things relate to each other, responding to actual user needs and implemented in a deductive logic framework that can help maintain the integrity and extend the informational power of what is provided. This paper presents the semantic model for cancer diseases and its uses in integrating clinical and molecular knowledge, more briefly examines the models and uses for drug, biochemical pathway, and mouse terminology, and discusses limits of the current approach and directions for future work.