ToxoMine

An integrated omics data warehouse for Toxoplasma gondii systems biology research

David B. Rhee, Matthew McKnight Croken, Kevin R. Shieh, Julie Sullivan, Gos Micklem, Kami Kim, Aaron Golden

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Toxoplasma gondii (T. gondii) is an obligate intracellular parasite that must monitor for changes in the host environment and respond accordingly; however, it is still not fully known which genetic or epigenetic factors are involved in regulating virulence traits of T. gondii. There are on-going efforts to elucidate the mechanisms regulating the stage transition process via the application of high-throughput epigenomics, genomics and proteomics techniques. Given the range of experimental conditions and the typical yield from such high-throughput techniques, a new challenge arises: How to effectively collect, organize and disseminate the generated data for subsequent data analysis. Here, we describe toxoMine, which provides a powerful interface to support sophisticated integrative exploration of high-throughput experimental data and metadata, providing researchers with a more tractable means toward understanding how genetic and/or epigenetic factors play a coordinated role in determining pathogenicity of T. gondii. As a data warehouse, toxoMine allows integration of high-throughput data sets with public T. gondii data. toxoMine is also able to execute complex queries involving multiple data sets with straightforward user interaction. Furthermore, toxoMine allows users to define their own parameters during the search process that gives users near-limitless search and query capabilities. The interoperability feature also allows users to query and examine data available in other InterMine systems, which would effectively augment the search scope beyond what is available to toxoMine. toxoMine complements the major community database ToxoDB by providing a data warehouse that enables more extensive integrative studies for T. gondii. Given all these factors, we believe it will become an indispensable resource to the greater infectious disease research community.

Original languageEnglish (US)
Article numberbav066
JournalDatabase
Volume2015
DOIs
StatePublished - 2015

Fingerprint

Systems Biology
Data warehouses
Toxoplasma
Toxoplasma gondii
Throughput
Biological Sciences
Epigenomics
epigenetics
Research
Virulence
Metadata
Interoperability
Genomics
Proteomics
proteomics
infectious diseases
Communicable Diseases
data analysis
complement
Parasites

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Information Systems

Cite this

Rhee, D. B., Croken, M. M., Shieh, K. R., Sullivan, J., Micklem, G., Kim, K., & Golden, A. (2015). ToxoMine: An integrated omics data warehouse for Toxoplasma gondii systems biology research. Database, 2015, [bav066]. https://doi.org/10.1093/database/bav066

ToxoMine : An integrated omics data warehouse for Toxoplasma gondii systems biology research. / Rhee, David B.; Croken, Matthew McKnight; Shieh, Kevin R.; Sullivan, Julie; Micklem, Gos; Kim, Kami; Golden, Aaron.

In: Database, Vol. 2015, bav066, 2015.

Research output: Contribution to journalArticle

Rhee, DB, Croken, MM, Shieh, KR, Sullivan, J, Micklem, G, Kim, K & Golden, A 2015, 'ToxoMine: An integrated omics data warehouse for Toxoplasma gondii systems biology research', Database, vol. 2015, bav066. https://doi.org/10.1093/database/bav066
Rhee, David B. ; Croken, Matthew McKnight ; Shieh, Kevin R. ; Sullivan, Julie ; Micklem, Gos ; Kim, Kami ; Golden, Aaron. / ToxoMine : An integrated omics data warehouse for Toxoplasma gondii systems biology research. In: Database. 2015 ; Vol. 2015.
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