Overview and utilization of the NCI thesaurus.

The NCI Thesaurus is a reference terminology covering areas of basic and clinical science, built with the goal of facilitating translational research in cancer. It contains nearly 110 000 terms in approximately 36000 concepts, partitioned in 20 subdomains, which include diseases, drugs, anatomy, genes, gene products, techniques, and biological processes, among others, all with a cancer-centric focus in content, and originally designed to support coding activities across the National Cancer Institute. Each concept represents a unit of meaning and contains a number of annotations, such as synonyms and preferred name, as well as annotations such as textual definitions and optional references to external authorities.

Representing the NCI Thesaurus in OWL DL: Modeling tools help modeling languages.

The National Cancer Institute's (NCI) Thesaurus is a biomedical reference ontology. The NCI Thesaurus is represented using Description Logic, more specifically Ontylog, a Description logic implemented by Apelon, Inc. We are exploring the use of the DL species of the Web Ontology Language (OWL DL)-a W3C recommended standard for ontology representation-instead of Ontylog for representing the NCI Thesaurus.

NCI Thesaurus: a semantic model integrating cancer-related clinical and molecular information.

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.

Modeling a description logic vocabulary for cancer research.

The National Cancer Institute has developed the NCI Thesaurus, a biomedical vocabulary for cancer research, covering terminology across a wide range of cancer research domains. A major design goal of the NCI Thesaurus is to facilitate translational research. We describe: the features of Ontylog, a description logic used to build NCI Thesaurus; our methodology for enhancing the terminology through collaboration between ontologists and domain experts, and for addressing certain real world challenges arising in modeling the Thesaurus; and finally, we describe the conversion of NCI Thesaurus from Ontylog into Web Ontology Language Lite.

caCORE: a common infrastructure for cancer informatics.

Motivation: Sites with substantive bioinformatics operations are challenged to build data processing and delivery infrastructure that provides reliable access and enables data integration. Locally generated data must be processed and stored such that relationships to external data sources can be presented. Consistency and comparability across data sets requires annotation with controlled vocabularies and, further, metadata standards for data representation.