دورية أكاديمية
OSCI: standardized stem cell ontology representation and use cases for stem cell investigation
| العنوان: | OSCI: standardized stem cell ontology representation and use cases for stem cell investigation |
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| المؤلفون: | 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 |
| المصدر: | BMC Bioinformatics, Vol 20, Iss S5, Pp 237-247 (2019) |
| بيانات النشر: | BMC, 2019. |
| سنة النشر: | 2019 |
| المجموعة: | LCC:Computer applications to medicine. Medical informatics LCC:Biology (General) |
| مصطلحات موضوعية: | Stem cell, Cell ontology, Cell line ontology, OSCI, iPSC, hPSC, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5 |
| الوصف: | 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. |
| نوع الوثيقة: | article |
| وصف الملف: | electronic resource |
| اللغة: | English |
| تدمد: | 1471-2105 |
| Relation: | http://link.springer.com/article/10.1186/s12859-019-2723-7; https://doaj.org/toc/1471-2105 |
| DOI: | 10.1186/s12859-019-2723-7 |
| URL الوصول: | https://doaj.org/article/17a11f05b62841618ea4c7ca553c05cf |
| رقم الأكسشن: | edsdoj.17a11f05b62841618ea4c7ca553c05cf |
| قاعدة البيانات: | Directory of Open Access Journals |
Find this article in full text from Springer Verlag. 
Full Text Finder | تدمد: | 14712105 |
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| DOI: | 10.1186/s12859-019-2723-7 |