Modeling a description logic vocabulary for cancer research

Abstract

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. Ontylog has proven well suited for constructing big biomedical vocabularies. We have capitalized on the Ontylog constructs Kind and Role in the collaboration process described in this paper to facilitate communication between ontologists and domain experts. The artifacts and processes developed by NCI for collaboration may be useful in other biomedical terminology development efforts.

Federated ontology-based queries over cancer data

“…The NCIt ontology is very large, as it provides a common vocabulary for the whole cancer domain [7]. Each caGrid data service is, in general, concerned with data pertaining to more specific domains than the whole NCIt ontology.…”

“…Each data source is represented as an information model [5] in the Unified Modeling Language (UML) [6], and it is exposed as a data service. Semantic interoperability is achieved by using a metadata registry, which maintains the information models annotated with concepts from a domain ontology, namely the NCI thesaurus (NCIt) [7]. The data services also expose a common query interface based on the caGrid query language (CQL).…”

“…Each UML model is associated with semantic metadata, which indicates the meaning of the objects and associations between them. The semantic annotations come mainly from the NCIt ontology [7], which can be accessed via the LexEVS API [15]. NCIt is the primary terminology used in caBIG ® , but other well-structured ontologies should be suitable for the annotations.…”

What Are Ontologies Good For?

“…Applications of OWL are particularly prevalent in the life sciences, where it has been used by the developers of several large biomedical ontologies, including the Biological Pathways Exchange (BioPAX) ontology [21], the GALEN ontology [20], the Foundational Model of Anatomy (FMA) [7], and the National Cancer Institute thesaurus [10].…”

Using Semantic Web Technologies to Build a Community-Driven Knowledge Curation Platform for the Skeletal Dysplasia Domain

“…To overcome these issues, and to extend the existing common terminology used by the community, we developed the Bone Dysplasia ontology (that defines more than 1200 concepts) to capture all the relevant knowledge by integrating and re-using well known ontologies, such as NCI Thesaurus [5], Human Phenotype Ontology (HP) [6] or the REAMS ontology 10 -describing radiographic features. the root Bone Dysplasia class (further sub-classed by 40 bone dysplasia groups and then by specific skeletal dysplasias) and the Gene Mutation and Phenotypic Characteristic classes.…”