Analysis Of Cancer Omics Data In A Semantic Web Framework

TL;DR

This paper enhances cancer omics data analysis by integrating it into a Semantic Web framework, enabling complex querying and reasoning over diverse molecular and functional data sources to better understand therapy responses.

Contribution

It introduces a Semantic Web-based system with a SPARQL endpoint for integrating and reasoning over cancer omics data and knowledge sources, advancing analytical capabilities.

Findings

Successful integration of quantitative and functional data using Semantic Web tools

Ability to answer complex queries on cancer cell resistance to Decitabine

Demonstration of Description Logic reasoning to infer new knowledge

Abstract

Our work concerns the elucidation of the cancer (epi)genome, transcriptome and proteome to better understand the complex interplay between a cancer cell's molecular state and its response to anti-cancer therapy. To study the problem, we have previously focused on data warehousing technologies and statistical data integration. In this paper, we present recent work on extending our analytical capabilities using Semantic Web technology. A key new component presented here is a SPARQL endpoint to our existing data warehouse. This endpoint allows the merging of observed quantitative data with existing data from semantic knowledge sources such as Gene Ontology (GO). We show how such variegated quantitative and functional data can be integrated and accessed in a universal manner using Semantic Web tools. We also demonstrate how Description Logic (DL) reasoning can be used to infer previously unstated conclusions from existing knowledge bases. As proof of concept, we illustrate the ability of our setup to answer complex queries on resistance of cancer cells to Decitabine, a demethylating agent.