A semantic cross-species derived data management application

David B. Keator, Jinran Chen, Nolan Nichols, Fariba Fana, Hal Stern, Tallie Z. Baram, Steven L. Small

Research output: Contribution to journalArticle

1 Scopus citations

Abstract

Managing dynamic information in large multi-site, multi-species, and multi-discipline consortia is a challenging task for data management applications. Often in academic research studies the goals for informatics teams are to build applications that provide extract-transform-load (ETL) functionality to archive and catalog source data that has been collected by the research teams. In consortia that cross species and methodological or scientific domains, building interfaces which supply data in a usable fashion and make intuitive sense to scientists from dramatically different backgrounds increases the complexity for developers. Further, reusing source data from outside one’s scientific domain is fraught with ambiguities in understanding the data types, analysis methodologies, and how to combine the data with those from other research teams. We report on the design, implementation, and performance of a semantic data management application to support the NIMH funded Conte Center at the University of California, Irvine. The Center is testing a theory of the consequences of “fragmented” (unpredictable, high entropy) early-life experiences on adolescent cognitive and emotional outcomes in both humans and rodents. It employs cross-species neuroimaging, epigenomic, molecular, and neuroanatomical approaches in humans and rodents to assess the potential consequences of fragmented unpredictable experience on brain structure and circuitry. To address this multi-technology, multi-species approach, the system uses semantic web techniques based on the Neuroimaging Data Model (NIDM) to facilitate data ETL functionality. We find this approach enables a low-cost, easy to maintain, and semantically meaningful information management system, enabling the diverse research teams to access and use the data.

Original languageEnglish (US)
Article number45
JournalData Science Journal
Volume16
DOIs
StatePublished - Sep 20 2017
Externally publishedYes

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Keywords

  • Database
  • MRI
  • Neuroscience
  • NIDM
  • RDF
  • Semantic web

ASJC Scopus subject areas

  • Computer Science (miscellaneous)
  • Computer Science Applications

Cite this

Keator, D. B., Chen, J., Nichols, N., Fana, F., Stern, H., Baram, T. Z., & Small, S. L. (2017). A semantic cross-species derived data management application. Data Science Journal, 16, [45]. https://doi.org/10.5334/dsj-2017-045