1. What is the CBO?
The CBO is a semantically structured controlled vocabulary for clinical molecular diagnostics. The CBO addresses the need for consistent representation of clinically relevant molecular biological and cytogenetic entities in a standardized and machine-readable format. It combines the attributes of a controlled vocabulary by providing standardized naming conventions and coded values, as well as the attributes of an ontology. Structuring the CBO in an ontology format provides a platform for advanced queries, inference logic, correlation, making assertions and managing the complex data of current clinical practice.
Content that meets the criteria for inclusion in the CBO is curated using public domain resources. The CBO naming conventions utilize existing standards when possible and alternative methods when necessary to ensure consistently reproducible and traceable content. Quality assurance processes are used to verify new concepts prior to inclusion in the CBO. The standardized content is represented in codified values and structured in the CBO ontology.
2. What is an ontology?
An ontology is a "specification of a conceptualization" or "a set of definitions of a relational and formal vocabulary." Ontologies are useful for representing and sharing knowledge of a specified domain among people and computers. In the case of the CBO, the formal vocabulary describes clinically relevant molecular biological entities, in which these definitions are semantically structured or networked. For more information about ontologies, visit http://www-ksl.stanford.edu/kst/what-is-an-ontology.html
3. Why is there a need for the CBO?
Existing medical terminologies do not sufficiently support the description of molecular diagnostic and cytogenetic findings due to significant gaps and inaccuracies. The CBO addresses the need for consistent descriptions and representations of molecular entities performed in clinical diagnostics in a standardized and machine-readable format. Other notable ontologies of interest in molecular biology are oriented toward research and focus primarily on functional attributes, which do not meet the requirements for clinical use. The scope of the CBO focuses on this gap to meet the needs of clinical molecular diagnostics and cytogenetics.
4. What is the scope of the CBO?
Targets of current diagnostic analysis are considered clinically significant and are therefore included in the CBO. However, the CBO also includes place holders for some domains primarily of research interest that are not currently a part of clinical diagnostic practice.
5. How can I use the CBO?
The CBO can be used for:
Codification of clinical reports
Data mining
Interfaces between clinical information systems
6. How do I gain access to the CBO?
A set of demonstration files is available to any visitor to the Web site. Registered users can download the entire CBO and detailed documentation, including the white paper describing the methodology used to add new content.
7. Why is the CBO publicly available?
The goal of making the CBO publicly available is to encourage its widespread use and consideration. We hope to receive feedback on the design and growth of the ontology from the larger scientific community.
8. What are future plans for the CBO?
The continued growth of the CBO will include development of concepts for cytogenetics, infectious disease and continued growth of the content related to clinical genetics and molecular pathology. As proteomic and transcriptomic technologies become more widely adopted, concepts necessary to describe these findings will be added.
9. What naming conventions are used in the CBO?
The CBO applies existing standards when possible. However, alternative naming conventions are applied when necessary. A complete guide to the CBO naming conventions can be found in the CBO white paper.
10. Will there be additional CBO content available in the future?
Yes, continuous content additions will be made to the CBO. All content additions will be publicly available through the CBO web site. For this reason, it is important to utilize the most current version of the CBO.
11. Is the scope of the CBO limited to human concepts?
Human and nonhuman molecular biological entities are represented in the CBO. The CBO includes nonhuman species that are clinically significant to humans, such as pathogenic viruses and bacteria. Of these, only concepts needed to accurately and clearly document diagnostic results are included.
12. How much information is in the CBO?
There are currently 13,520 Concepts, 28,962 Relationships, 6,133 Facets and 7,703 Terms in the CBO.