Purpose:
Data standards and interoperability are critical for improving care for patients with cancer. Recent efforts by ASCO include the Data Standards and Interoperability Summit in 2016, which led to the Omics and Precision Oncology and Advancing Interoperability workshops. To facilitate improved patient care, several recommendations for data sharing and standardization were made to the community.
Methods:
To address these recommendations, we developed SMART Cancer Navigator, a Web application that uses application programming interfaces to gather clinical and genomic data from 11 public knowledge bases ranging from basic to clinical content coverage; three (CIViC, ClinVar, and OncoKB) explicitly linked genomic variants to clinical factors such as prognosis and treatment selection. We illustrated the utility of this application by selecting one of the monthly case studies presented by the ASCO University Molecular Oncology Tumor Board: Ovarian Cancer (BRCA Mutation). We also performed analyses on information from the three clinico-genomic knowledge bases to corroborate previous work and illustrate the state of data sharing among publicly available resources.
Results:
SMART Cancer Navigator aggregates and contextualizes data from 11 different knowledge bases and stores user queries in a lightweight Web application that can link into Fast Healthcare Interoperability Resources-enabled electronic health records. Potentially relevant clinical trials and/or approved treatments were identified for three mutations found in a hypothetical patient with advanced ovarian cancer. A comparison of the three clinico-genomic knowledge bases indicated substantial differences in coverage at the gene and variant levels.
Conclusion:
SMART Cancer Navigator has immediate relevance to practicing oncologists and others. Additional knowledge bases can be added without undue effort. As a first step toward utility, we generalized and disseminated the resulting implementation (https://smart-cancer-navigator.github.io) and data sets.