My Cancer Genome: Coevolution of Precision Oncology and a Molecular Oncology Knowledgebase. (2021)

• Record Type: Journal Article
• Authors: Holt, Marilyn E.; Mittendorf, Kathleen F.; LeNoue-Newton, Michele; Jain, Neha M.; Anderson, Ingrid; Lovly, Christine M.; Osterman, Travis; Micheel, Christine; Levy, Mia
• Is Part Of: JCO Clinical Cancer Informatics. Volume 5(2021)
• Publication Date: 2021
• Subjects: 616.994
• DOI: 10.1200/CCI.21.00084
• Languages: English
• ISSNs: 2473-4276

Abstract

Abstract : PURPOSE: The My Cancer Genome (MCG) knowledgebase and resulting website were launched in 2011 with the purpose of guiding clinicians in the application of genomic testing results for treatment of patients with cancer. Both knowledgebase and website were originally developed using a wiki-style approach that relied on manual evidence curation and synthesis of that evidence into cancer-related biomarker, disease, and pathway pages on the website that summarized the literature for a clinical audience. This approach required significant time investment for each page, which limited website scalability as the field advanced. To address this challenge, we designed and used an assertion-based data model that allows the knowledgebase and website to expand with the field of precision oncology. METHODS: Assertions, or computationally accessible cause and effect statements, are both manually curated from primary sources and imported from external databases and stored in a knowledge management system. To generate pages for the MCG website, reusable templates transform assertions into reconfigurable text and visualizations that form the building blocks for automatically updating disease, biomarker, drug, and clinical trial pages. RESULTS: Combining text and graph templates with assertions in our knowledgebase allows generation of web pages that automatically update with our knowledgebase. Automated page generation empowers rapid scaling of the website as assertions with new biomarkers and drugs are added to the knowledgebase. This process has generated more than 9, 100 clinical trial pages, 18, 100 gene and alteration pages, 900 disease pages, and 2, 700 drug pages to date. CONCLUSION: Leveraging both computational and manual curation processes in combination with reusable templates empowers automation and scalability for both the MCG knowledgebase and MCG website.