title: RDF SKETCH MAPS - KNOWLEDGE COMPLEXITY REDUCTION FOR PRECISION MEDICINE ANALYTICS.
abstract: Realization of precision medicine ideas requires significant research effort to be able to spot subtle differences in complex diseases at the molecular level to develop personalized therapies. It is especially important in many cases of highly heterogeneous cancers. Precision diagnostics and therapeutics of such diseases demands interrogation of vast amounts of biological knowledge coupled with novel analytic methodologies. For instance, pathway-based approaches can shed light on the way tumorigenesis takes place in individual patient cases and pinpoint to novel drug targets. However, comprehensive analysis of hundreds of pathways and thousands of genes creates a combinatorial explosion, that is challenging for medical practitioners to handle at the point of care. Here we extend our previous work on mapping clinical omics data to curated Resource Description Framework (RDF) knowledge bases to derive influence diagrams of interrelationships of biomarker proteins, diseases and signal transduction pathways for personalized theranostics. We present RDF Sketch Maps - a computational method to reduce knowledge complexity for precision medicine analytics. The method of RDF Sketch Maps is inspired by the way a sketch artist conveys only important visual information and discards other unnecessary details. In our case, we compute and retain only so-called RDF Edges - places with highly important diagnostic and therapeutic information. To do this we utilize 35 maps of human signal transduction pathways by transforming 300 KEGG maps into highly processable RDF knowledge base. We have demonstrated potential clinical utility of RDF Sketch Maps in hematopoietic cancers, including analysis of pathways associated with Hairy Cell Leukemia (HCL) and Chronic Myeloid Leukemia (CML) where we achieved up to 20-fold reduction in the number of biological entities to be analyzed, while retaining most likely important entities. In experiments with pathways associated with HCL a generated RDF Sketch Map of the top 30% paths retained important information about signaling cascades leading to activation of proto-oncogene BRAF, which is usually associated with a different cancer, melanoma. Recent reports of successful treatments of HCL patients by the BRAF-targeted drug vemurafenib support the validity of the RDF Sketch Maps findings. We therefore believe that RDF Sketch Maps will be invaluable for hypothesis generation for precision diagnostics and therapeutics as well as drug repurposing studies.
authors.affiliation: Department of Pathology and Anatomical Sciences, USA.
authors.forename: Nattapon
authors.initials: N
authors.lastname: Thanintorn
authors.forename: Juexin
authors.initials: J
authors.lastname: Wang
authors.forename: Ilker
authors.initials: I
authors.lastname: Ersoy
authors.forename: Zainab
authors.initials: Z
authors.lastname: Al-Taie
authors.forename: Yuexu
authors.initials: Y
authors.lastname: Jiang
authors.forename: Duolin
authors.initials: D
authors.lastname: Wang
authors.forename: Megha
authors.initials: M
authors.lastname: Verma
authors.forename: Trupti
authors.initials: T
authors.lastname: Joshi
authors.forename: Richard
authors.initials: R
authors.lastname: Hammer
authors.forename: Dong
authors.initials: D
authors.lastname: Xu
authors.forename: Dmitriy
authors.initials: D
authors.lastname: Shin
mesh_terms: D019295:Computational Biology / Q000379:methods / Q000706:statistics & numerical data; D030541:Databases, Genetic / Q000706:statistics & numerical data; D053263:Gene Regulatory Networks; D006801:Humans; D051188:Knowledge Bases; D007943:Leukemia, Hairy Cell / Q000235:genetics; D015464:Leukemia, Myelogenous, Chronic, BCR-ABL Positive / Q000235:genetics; D009369:Neoplasms / Q000235:genetics; D057285:Precision Medicine / Q000379:methods* / Q000706:statistics & numerical data; D000090063:Proto-Oncogene Mas; D015398:Signal Transduction / Q000235:genetics; D000068936:Theranostic Nanomedicine