CLO: The cell line ontology

Sirarat Sarntivijai, Yu Lin, Zuoshuang Xiang, Terrence F. Meehan, Alexander D. Diehl, Uma D. Vempati, Stephan C Schuerer, Chao Pang, James Malone, Helen Parkinson, Yue Liu, Terue Takatsuki, Kaoru Saijo, Hiroshi Masuya, Yukio Nakamura, Matthew H. Brush, Melissa A. Haendel, Jie Zheng, Christian J. Stoeckert, Bjoern PetersChristopher J. Mungall, Thomas E. Carey, David J. States, Brian D. Athey, Yongqun He

Research output: Contribution to journalArticle

42 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Article number37
JournalJournal of Biomedical Semantics
Volume5
Issue number1
DOIs
StatePublished - Aug 13 2014

Fingerprint

Ontology
Cells
Cell Line
Biomedical Research
Vaccines
Biological Ontologies
Bioassay
Pathogens
Foundries
Joining
Host-Pathogen Interactions
Informatics

Keywords

  • Anatomy
  • Cell line
  • Cell line cell
  • Cell line cell culturing
  • Immortal cell line cell
  • Mortal cell line cell

ASJC Scopus subject areas

  • Information Systems
  • Computer Science Applications
  • Computer Networks and Communications
  • Health Informatics

Cite this

Sarntivijai, S., Lin, Y., Xiang, Z., Meehan, T. F., Diehl, A. D., Vempati, U. D., ... He, Y. (2014). CLO: The cell line ontology. Journal of Biomedical Semantics, 5(1), [37]. https://doi.org/10.1186/2041-1480-5-37

CLO : The cell line ontology. / Sarntivijai, Sirarat; Lin, Yu; Xiang, Zuoshuang; Meehan, Terrence F.; Diehl, Alexander D.; Vempati, Uma D.; Schuerer, Stephan C; Pang, Chao; Malone, James; Parkinson, Helen; Liu, Yue; Takatsuki, Terue; Saijo, Kaoru; Masuya, Hiroshi; Nakamura, Yukio; Brush, Matthew H.; Haendel, Melissa A.; Zheng, Jie; Stoeckert, Christian J.; Peters, Bjoern; Mungall, Christopher J.; Carey, Thomas E.; States, David J.; Athey, Brian D.; He, Yongqun.

In: Journal of Biomedical Semantics, Vol. 5, No. 1, 37, 13.08.2014.

Research output: Contribution to journalArticle

Sarntivijai, S, Lin, Y, Xiang, Z, Meehan, TF, Diehl, AD, Vempati, UD, Schuerer, SC, Pang, C, Malone, J, Parkinson, H, Liu, Y, Takatsuki, T, Saijo, K, Masuya, H, Nakamura, Y, Brush, MH, Haendel, MA, Zheng, J, Stoeckert, CJ, Peters, B, Mungall, CJ, Carey, TE, States, DJ, Athey, BD & He, Y 2014, 'CLO: The cell line ontology', Journal of Biomedical Semantics, vol. 5, no. 1, 37. https://doi.org/10.1186/2041-1480-5-37
Sarntivijai S, Lin Y, Xiang Z, Meehan TF, Diehl AD, Vempati UD et al. CLO: The cell line ontology. Journal of Biomedical Semantics. 2014 Aug 13;5(1). 37. https://doi.org/10.1186/2041-1480-5-37
Sarntivijai, Sirarat ; Lin, Yu ; Xiang, Zuoshuang ; Meehan, Terrence F. ; Diehl, Alexander D. ; Vempati, Uma D. ; Schuerer, Stephan C ; Pang, Chao ; Malone, James ; Parkinson, Helen ; Liu, Yue ; Takatsuki, Terue ; Saijo, Kaoru ; Masuya, Hiroshi ; Nakamura, Yukio ; Brush, Matthew H. ; Haendel, Melissa A. ; Zheng, Jie ; Stoeckert, Christian J. ; Peters, Bjoern ; Mungall, Christopher J. ; Carey, Thomas E. ; States, David J. ; Athey, Brian D. ; He, Yongqun. / CLO : The cell line ontology. In: Journal of Biomedical Semantics. 2014 ; Vol. 5, No. 1.
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AU - Diehl, Alexander D.

AU - Vempati, Uma D.

AU - Schuerer, 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.

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AU - Zheng, Jie

AU - Stoeckert, Christian J.

AU - Peters, Bjoern

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