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BMC Bioinformatics. 2019 Apr 25;20(Suppl 5):180. doi: 10.1186/s12859-019-2723-7.

OSCI: standardized stem cell ontology representation and use cases for stem cell investigation.

Author information

1
University of Michigan Medical School, Ann Arbor, MI, USA. yongqunh@med.umich.edu.
2
Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.
3
University of Miami, Miami, FL, USA.
4
Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
5
SBCNY, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
6
University of Michigan Medical School, Ann Arbor, MI, USA.
7
John Hopkins Unversity, Baltimore, MD, USA.
8
DataSmith LLC, Detroit, MI, USA.
9
Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.
10
University of Pennsylvania, Philadelphia, PA, USA.
11
ELIXIR, Wellcome Genome Campus, Hinxton, Cambridge, UK.
12
Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA. addiehl@buffalo.edu.

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.

KEYWORDS:

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

PMID:
31272389
PMCID:
PMC6509805
DOI:
10.1186/s12859-019-2723-7
[Indexed for MEDLINE]
Free PMC Article

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