POKR: Building a Computable Heterogeneous Knowledge Resource for Precision Oncology

Yanbo Guo, Chen Wang, Raymond Moore, Hongfang Liu, Feichen Shen

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Precision oncology is expected to improve selection of targeted therapies, tailored to individual patients and ultimately improve cancer patients' outcomes. Several cancer genetics knowledge databases have been successfully developed for such purposes, including CIViC and OncoKB, with active community-based curations and scoring of genetic-treatment evidences. Although many studies were conducted based on each knowledge base respectively, the integrative analysis across both knowledge bases remains largely unexplored. Thus, there exists an urgent need for a heterogeneous precision oncology knowledge resource with computational power to support drug repurposing discovery in a timely manner, especially for life-threatening cancer. In this pilot study, we built a heterogeneous precision oncology knowledge resource (POKR) by integrating CIViC and OncoKB, in order to incorporate unique information contained in each knowledge base and make associations amongst biomedical entities (e.g., gene, drug, disease) computable and measurable via training POKR graph embeddings. All the relevant codes, database dump files, and pre-trained POKR embeddings can be accessed through the following URL: https://github.com/shenfc/POKR.

Original languageEnglish (US)
Title of host publicationMEDINFO 2021
Subtitle of host publicationOne World, One Health - Global Partnership for Digital Innovation - Proceedings of the 18th World Congress on Medical and Health Informatics
EditorsPaula Otero, Philip Scott, Susan Z. Martin, Elaine Huesing
PublisherIOS Press BV
Pages243-247
Number of pages5
ISBN (Electronic)9781643682648
DOIs
StatePublished - Jun 6 2022
Event18th World Congress on Medical and Health Informatics: One World, One Health - Global Partnership for Digital Innovation, MEDINFO 2021 - Virtual, Online
Duration: Oct 2 2021Oct 4 2021

Publication series

NameStudies in Health Technology and Informatics
Volume290
ISSN (Print)0926-9630
ISSN (Electronic)1879-8365

Conference

Conference18th World Congress on Medical and Health Informatics: One World, One Health - Global Partnership for Digital Innovation, MEDINFO 2021
CityVirtual, Online
Period10/2/2110/4/21

Keywords

  • Computable Heterogeneous Knowledge Resource
  • Knowledge Graph Embeddings
  • Precision Oncology

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics
  • Health Information Management

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