Understanding the Systems Biology of Pathogen Virulence Using Semantic Methodologies

David Rhee, Kevin Shieh, Julie Sullivan, Gos Micklem, Kami Kim, Aaron Golden

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

Abstract

Systems biology approaches to the integrative study of cells, organs and organisms offer the best means of understanding in a holistic manner the diversity of molecular assays that can be now be implemented in a high throughput manner. Such assays can sample the genome, epigenome, proteome, metabolome and microbiome contemporaneously, allowing us for the first time to perform a complete analysis of physiological activity. The central problem remains empowering the scientific community to actually implement such an integration, across seemingly diverse data types and measurements. One promising solution is to apply semantic techniques on a self-consistent and implicitly correct ontological representation of these data types. In this paper we describe how we have applied one such solution, based around the InterMine data warehouse platform which uses as its basis the Sequence Ontology, to facilitate a systems biology analysis of virulence in the apicomplexan pathogen Toxoplasma gondii, a common parasite that infects up to half the worlds population, with acute pathogenic risks for immuno-compromised individuals or pregnant mothers. Our solution, which we named 'toxoMine', has provided both a platform for our collaborators to perform such integrative analyses and also opportunities for such cyberinfrastructure to be further developed, particularly to take advantage of possible semantic similarities of value to knowledge discovery in the Omics enterprise. We discuss these opportunities in the context of further enhancing the capabilities of this powerful integrative platform.

Original languageEnglish (US)
Title of host publicationProceedings - 2016 IEEE 10th International Conference on Semantic Computing, ICSC 2016
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages314-320
Number of pages7
ISBN (Print)9781509006618
DOIs
StatePublished - Mar 22 2016
Event10th IEEE International Conference on Semantic Computing, ICSC 2016 - Laguna Hills, United States
Duration: Feb 3 2016Feb 5 2016

Other

Other10th IEEE International Conference on Semantic Computing, ICSC 2016
CountryUnited States
CityLaguna Hills
Period2/3/162/5/16

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Keywords

  • data warehouse
  • epigenomics
  • genomics
  • integrative analysis
  • InterMine
  • metabolomics
  • pathogen
  • proteomics
  • sequence ontology
  • systems biology
  • toxoplasma gondii

ASJC Scopus subject areas

  • Artificial Intelligence
  • Computer Networks and Communications
  • Information Systems

Cite this

Rhee, D., Shieh, K., Sullivan, J., Micklem, G., Kim, K., & Golden, A. (2016). Understanding the Systems Biology of Pathogen Virulence Using Semantic Methodologies. In Proceedings - 2016 IEEE 10th International Conference on Semantic Computing, ICSC 2016 (pp. 314-320). [7439354] Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/ICSC.2016.33