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Governance of caBIG Vocabulary Standards and the Vocabulary Review Processes
The VCDE WS has established a number of criteria that every caBIG® “standard” vocabulary should satisfy. Briefly, these are:
- URU (Understandability, Reproducibility, Usability)
- Quality of Documentation
- Maintenance and Extensions (Change Management)
- Accessibility and Distribution
- Intellectual Property Considerations
- Considerations Regarding Mapped Terminologies
- QC and QA
- Concept Definitions
- Community Acceptance
- Reporting Requirements
The VCDE WS engaged in examining the “Best Practices” of what makes a good vocabulary over the years 2005-2006, with the result of a process and list of criteria for evaluation of vocabularies as caBIG Standards. The results have been published as: James J. Cimino, Terry F. Hayamizu, Olivier Bodenreider, Brian Davis , Grace A. Stafford and Martin Ringwald (2009) "The caBIG® terminology review process". Journal of Biomedical Informatics 42: 571–580 and can be accessed https://cabig.nci.nih.gov/workspaces/VCDE/Cimino_et_al%20_2009.pdf. The Vocabulary Standard Review Process is used to evaluate vocabularies as standards within caBIG®.
The following vocabularies have been reviewed and approved as caBIG Vocabulary Standards:
- Gene Ontology(GO) - The GO project has developed three structured controlled vocabularies (ontologies) that describe gene products in terms of their associated biological processes, cellular components and molecular functions in a species-independent manner. There are three separate aspects to this effort: first, the development and maintenance of the ontologies themselves; second, the annotation of gene products, which entails making associations between the ontologies and the genes and gene products in the collaborating databases, and third, development of tools that facilitate the creation, maintenance and use of ontologies.
- NCI Thesaurus (NCIt). The NCI Thesaurus is a cancer-focused terminology that was initially agreed upon to be used as the standard terminology source in caBIG®.
- LOINC (Logical Observation Identifiers Names and Codes). LOINC is a standard for coding medical laboratory observations. It is maintained by the Regenstrief Institute.
- RadLex (Radiology Lexicon). RadLex is a lexicon for the uniform indexing and retrieval of radiological information.
- SNOMED CT (Systematized Nomenclature of Medicine Clinical Terms). SNOMED CT is a medical terminology covering most areas of clinical information such as diseases, findings, procedures, microorganisms, and drugs.
- MedDRA (Medical Dictionary for Regulatory Activities). MedDRA is an international medical terminology required for use in coding, especially around Adverse Events. It is managed by the MSSO (Maintenance and Support Services Organization).
The following vocabularies are under review:
- Nanoparticle Ontology (NPO)
- CTCAE (Common Terminology for Adverse Events)
