With the rapid advancements in cancer research, the information that is useful for characterizing disease, staging tumors, and creating treatment and survivorship plans has been changing at a pace that creates challenges when physicians try to remain current. One example involves increasing usage of biomarkers when characterizing the pathologic prognostic stage of a breast tumor. We present our semantic technology approach to support cancer characterization and demonstrate it in our end-to-end prototype system that collects the newest breast cancer staging criteria from authoritative oncology manuals to construct an ontology for breast cancer. Using a tool we developed that utilizes this ontology, physician-facing applications can be used to quickly stage a new patient to support identifying risks, treatment options, and monitoring plans based on authoritative and best practice guidelines. Physicians can also re-stage existing patients or patient populations, allowing them to find patients whose stage has changed in a given patient cohort. As new guidelines emerge, using our proposed mechanism, which is grounded by semantic technologies for ingesting new data from staging manuals, we have created an enriched cancer staging ontology that integrates relevant data from several sources with very little human intervention.
Furthermore, in addition to including classes for all cancer stages for the respective guideline, we also map the breast cancer terms to community-accepted terms from the National Cancer Institute thesaurus (NCIt) @cite_10 , and incorporate recommended tests and treatment plans from the openly reusable Clinical Interpretations of Variants in Cancer (CIViC) @cite_22 data that can be used to provide stage specific recommendations. Furthermore, our ontology includes terms that are not included in NCIt or AJCC, such as more specific subclasses of tumor characteristics (, , , , etc.) that are available in the Surveillance, Epidemiology, and End Results (SEER) dataset @cite_1 .
@cite_1 @cite_10 @cite_22
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The NCI Thysaurus is a public domain description logic-based terminology produced by the National Cancer Institute, and distributed as a component of the NCI Center for Bioinformatics caCORE distribution. It is deep and complex compared to most broad clinical vocabularies, implementing rich semantic interrelationships between the nodes of its taxonomies. The semantic relationships in the Thysaurus are intended to facilitate translational research and to support the bioinformatics infrastructure of the Institute. CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer