OSCI: standardized stem cell ontology representation and use cases for stem cell investigation.
Publication/Presentation Date
4-25-2019
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.
Volume
20
Issue
Suppl 5
First Page
180
Last Page
180
ISSN
1471-2105
Published In/Presented At
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(Suppl 5), 180. https://doi.org/10.1186/s12859-019-2723-7
Disciplines
Medicine and Health Sciences
PubMedID
31272389
Department(s)
Fellows and Residents
Document Type
Article