OSCI: standardized stem cell ontology representation and use cases for stem cell investigation
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 st...
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doaj-17a11f05b62841618ea4c7ca553c05cf2020-11-25T03:49:39ZengBMCBMC Bioinformatics1471-21052019-04-0120S523724710.1186/s12859-019-2723-7OSCI: standardized stem cell ontology representation and use cases for stem cell investigationYongqun He0William D. Duncan1Daniel J. Cooper2Jens Hansen3Ravi Iyengar4Edison Ong5Kendal Walker6Omar Tibi7Sam Smith8Lucas M. Serra9Jie Zheng10Sirarat Sarntivijai11Stephan Schürer12K. Sue O’Shea13Alexander D. Diehl14University of Michigan Medical SchoolRoswell Park Comprehensive Cancer CenterUniversity of MiamiPharmacological Sciences, Icahn School of Medicine at Mount SinaiPharmacological Sciences, Icahn School of Medicine at Mount SinaiUniversity of Michigan Medical SchoolUniversity of Michigan Medical SchoolJohn Hopkins UnversityDataSmith LLCDepartment of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at BuffaloUniversity of PennsylvaniaELIXIR, Wellcome Genome CampusUniversity of MiamiUniversity of Michigan Medical SchoolDepartment of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at BuffaloAbstract 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.http://link.springer.com/article/10.1186/s12859-019-2723-7Stem cellCell ontologyCell line ontologyOSCIiPSChPSC |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
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 |
spellingShingle |
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 OSCI: standardized stem cell ontology representation and use cases for stem cell investigation BMC Bioinformatics Stem cell Cell ontology Cell line ontology OSCI iPSC hPSC |
author_facet |
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 |
author_sort |
Yongqun He |
title |
OSCI: standardized stem cell ontology representation and use cases for stem cell investigation |
title_short |
OSCI: standardized stem cell ontology representation and use cases for stem cell investigation |
title_full |
OSCI: standardized stem cell ontology representation and use cases for stem cell investigation |
title_fullStr |
OSCI: standardized stem cell ontology representation and use cases for stem cell investigation |
title_full_unstemmed |
OSCI: standardized stem cell ontology representation and use cases for stem cell investigation |
title_sort |
osci: standardized stem cell ontology representation and use cases for stem cell investigation |
publisher |
BMC |
series |
BMC Bioinformatics |
issn |
1471-2105 |
publishDate |
2019-04-01 |
description |
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. |
topic |
Stem cell Cell ontology Cell line ontology OSCI iPSC hPSC |
url |
http://link.springer.com/article/10.1186/s12859-019-2723-7 |
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