OSCI: Standardized stem cell ontology representation and use cases for stem cell investigation

Yongqun He, William D. Duncan, Daniel J. Cooper, Jens Hansen, Ravi Iyengar, Edison Ong, Kendal Walker, Omar Tibi, Sam Smith, Lucas M. Serra, Jie Zheng, Sirarat Sarntivijai, Stephan Schürer, K. Sue O'shea, Alexander D. Diehl

Research output: Contribution to journalArticle

2 Scopus citations

Abstract

Background: Stem cells and stem cell lines are widely used in biomedical research. The Cell Ontology (CL) and Cell Line Ontology (CLO) are two community-based OBO Foundry ontologies in the domains of in vivo cells and in vitro cell line cells, respectively. Results: To support standardized stem cell investigations, we have developed an Ontology for Stem Cell Investigations (OSCI). OSCI imports stem cell and cell line terms from CL and CLO, and investigation-related terms from existing ontologies. A novel focus of OSCI is its application in representing metadata types associated with various stem cell investigations. We also applied OSCI to systematically categorize experimental variables in an induced pluripotent stem cell line cell study related to bipolar disorder. In addition, we used a semi-automated literature mining approach to identify over 200 stem cell gene markers. The relations between these genes and stem cells are modeled and represented in OSCI. Conclusions: OSCI standardizes stem cells found in vivo and in vitro and in various stem cell investigation processes and entities. The presented use cases demonstrate the utility of OSCI in iPSC studies and literature mining related to bipolar disorder.

Original languageEnglish (US)
Article number180
JournalBMC Bioinformatics
Volume20
DOIs
StatePublished - Apr 25 2019

Keywords

  • Bipolar disorder
  • Cell line ontology
  • Cell ontology
  • OSCI
  • Stem cell
  • hPSC
  • iPSC

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics

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    He, Y., Duncan, W. D., Cooper, D. J., Hansen, J., Iyengar, R., Ong, E., Walker, K., Tibi, O., Smith, S., Serra, L. M., Zheng, J., Sarntivijai, S., Schürer, S., O'shea, K. S., & Diehl, A. D. (2019). OSCI: Standardized stem cell ontology representation and use cases for stem cell investigation. BMC Bioinformatics, 20, [180]. https://doi.org/10.1186/s12859-019-2723-7