TY - JOUR
T1 - CLO
T2 - The cell line ontology
AU - Sarntivijai, Sirarat
AU - Lin, Yu
AU - Xiang, Zuoshuang
AU - Meehan, Terrence F.
AU - Diehl, Alexander D.
AU - Vempati, Uma D.
AU - Schürer, Stephan C.
AU - Pang, Chao
AU - Malone, James
AU - Parkinson, Helen
AU - Liu, Yue
AU - Takatsuki, Terue
AU - Saijo, Kaoru
AU - Masuya, Hiroshi
AU - Nakamura, Yukio
AU - Brush, Matthew H.
AU - Haendel, Melissa A.
AU - Zheng, Jie
AU - Stoeckert, Christian J.
AU - Peters, Bjoern
AU - Mungall, Christopher J.
AU - Carey, Thomas E.
AU - States, David J.
AU - Athey, Brian D.
AU - He, Yongqun
N1 - Funding Information:
The work described is funded in part by the National Institutes of Health (NIH) grants 1R01AI081062 (YH) from the National Institute of Allergy and Infectious Diseases (NIAID), U54 DA021519 for the National Center for Integrative Biomedical Informatics (BDA), 1R24OD011883 from the NIH Office of the Director (MAH and MHB), NIH grant 1R01GM093132-01 (JZ and CJS), NIH contract HHSN272201200010C (BP), U01HL111561 (SCS) as part of the Library of Integrated Network-based Cellular Signatures (LINCS) program, and RC2HG005668 (SCS) supported by the National Human Genome Research Institute (NHGRI), European Molecular Biology Laboratory (EMBL-EBI) core funds (HP, JM), EC FP7 Funds Grant number: 200754 Gen2Phen (CP), and funding from the National Bioscience Database Center (NBDC) of the Japan Science and Technology Agency (JST) for BRC [21]. The content of this paper is solely the responsibility of the author and does not necessarily represent the official views of the NIAID, NHGRI, the NIH or other funding organizations. The article-processing charge for this article was paid by a discretionary fund from Dr. Robert Dysko, the director of the Unit for Laboratory Animal Medicine (ULAM) in the University of Michigan.
Publisher Copyright:
© 2014 Sarntivijai et al.; licensee BioMed Central Ltd.
PY - 2014/8/13
Y1 - 2014/8/13
N2 - Background: Cell lines have been widely used in biomedical research. The community-based Cell Line Ontology (CLO) is a member of the OBO Foundry library that covers the domain of cell lines. Since its publication two years ago, significant updates have been made, including new groups joining the CLO consortium, new cell line cells, upper level alignment with the Cell Ontology (CL) and the Ontology for Biomedical Investigation, and logical extensions. Construction and content: Collaboration among the CLO, CL, and OBI has established consensus definitions of cell line-specific terms such as 'cell line', 'cell line cell', 'cell line culturing', and 'mortal' vs. 'immortal cell line cell'. A cell line is a genetically stable cultured cell population that contains individual cell line cells. The hierarchical structure of the CLO is built based on the hierarchy of the in vivo cell types defined in CL and tissue types (from which cell line cells are derived) defined in the UBERON cross-species anatomy ontology. The new hierarchical structure makes it easier to browse, query, and perform automated classification. We have recently added classes representing more than 2,000 cell line cells from the RIKEN BRC Cell Bank to CLO. Overall, the CLO now contains ~38,000 classes of specific cell line cells derived from over 200 in vivo cell types from various organisms. Utility and discussion: The CLO has been applied to different biomedical research studies. Example case studies include annotation and analysis of EBI ArrayExpress data, bioassays, and host-vaccine/pathogen interaction. CLO's utility goes beyond a catalogue of cell line types. The alignment of the CLO with related ontologies combined with the use of ontological reasoners will support sophisticated inferencing to advance translational informatics development.
AB - Background: Cell lines have been widely used in biomedical research. The community-based Cell Line Ontology (CLO) is a member of the OBO Foundry library that covers the domain of cell lines. Since its publication two years ago, significant updates have been made, including new groups joining the CLO consortium, new cell line cells, upper level alignment with the Cell Ontology (CL) and the Ontology for Biomedical Investigation, and logical extensions. Construction and content: Collaboration among the CLO, CL, and OBI has established consensus definitions of cell line-specific terms such as 'cell line', 'cell line cell', 'cell line culturing', and 'mortal' vs. 'immortal cell line cell'. A cell line is a genetically stable cultured cell population that contains individual cell line cells. The hierarchical structure of the CLO is built based on the hierarchy of the in vivo cell types defined in CL and tissue types (from which cell line cells are derived) defined in the UBERON cross-species anatomy ontology. The new hierarchical structure makes it easier to browse, query, and perform automated classification. We have recently added classes representing more than 2,000 cell line cells from the RIKEN BRC Cell Bank to CLO. Overall, the CLO now contains ~38,000 classes of specific cell line cells derived from over 200 in vivo cell types from various organisms. Utility and discussion: The CLO has been applied to different biomedical research studies. Example case studies include annotation and analysis of EBI ArrayExpress data, bioassays, and host-vaccine/pathogen interaction. CLO's utility goes beyond a catalogue of cell line types. The alignment of the CLO with related ontologies combined with the use of ontological reasoners will support sophisticated inferencing to advance translational informatics development.
KW - Anatomy
KW - Cell line
KW - Cell line cell
KW - Cell line cell culturing
KW - Immortal cell line cell
KW - Mortal cell line cell
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U2 - 10.1186/2041-1480-5-37
DO - 10.1186/2041-1480-5-37
M3 - Article
AN - SCOPUS:84902319909
SN - 2041-1480
VL - 5
JO - Journal of Biomedical Semantics
JF - Journal of Biomedical Semantics
IS - 1
M1 - 37
ER -