Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies

Sai Lakshmi Subramanian, Robert R. Kitchen, Roger Alexander, Bob S. Carter, Kei Hoi Cheung, Louise C. Laurent, Alexander Pico, Lewis Rowland Roberts, Matthew E. Roth, Joel S. Rozowsky, Andrew I. Su, Mark B. Gerstein, Aleksandar Milosavljevic

Research output: Contribution to journalArticle

24 Scopus citations

Abstract

The large diversity and volume of extracellularRNA(exRNA) data that will formthe basis of the exRNA Atlas generated by the Extracellular RNA Communication Consortium pose a substantial data integration challenge. We here present the strategy that is being implemented by the exRNA Data Management and Resource Repository, which employs metadata, biomedical ontologies and Linked Data technologies, such as Resource Description Framework to integrate a diverse set of exRNAprofiles into an exRNA Atlas and enable integrative exRNA analysis. We focus on the following three specific data integration tasks: (a) selection of samples from a virtual biorepository for exRNAprofiling and for inclusion in the exRNA Atlas; (b) retrieval of a data slice from the exRNA Atlas for integrative analysis and (c) interpretation of exRNA analysis results in the context of pathways and networks. As exRNAprofiling gains wide adoption in the research community, we anticipate that the strategies discussed here will increasingly be required to enable data reuse and to facilitate integrative analysis of exRNA data.

Original languageEnglish (US)
Article number27497
JournalJournal of Extracellular Vesicles
Volume4
Issue number1
DOIs
StatePublished - Jan 1 2015

    Fingerprint

Keywords

  • DMRR
  • ERC Consortium
  • ExRNA
  • ExRNA Atlas
  • ExRNA Portal

ASJC Scopus subject areas

  • Histology
  • Cell Biology

Cite this

Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies. / Subramanian, Sai Lakshmi; Kitchen, Robert R.; Alexander, Roger; Carter, Bob S.; Cheung, Kei Hoi; Laurent, Louise C.; Pico, Alexander; Roberts, Lewis Rowland; Roth, Matthew E.; Rozowsky, Joel S.; Su, Andrew I.; Gerstein, Mark B.; Milosavljevic, Aleksandar.

In: Journal of Extracellular Vesicles, Vol. 4, No. 1, 27497, 01.01.2015.

Research output: Contribution to journalArticle