Cell line ontology: Redesigning the cell line knowledgebase to aid integrative translational informatics

Sirarat Sarntivijai; Zuoshuang Xiang; Terrence F. Meehan; Alexander D. Diehl; Uma Vempati; Stephan Schurer; Chao Pang; James Malone; Helen Parkinson; Brian D. Athey; Yongqun He

Cell line ontology: Redesigning the cell line knowledgebase to aid integrative translational informatics

Sirarat Sarntivijai, Zuoshuang Xiang, Terrence F. Meehan, Alexander D. Diehl, Uma Vempati, Stephan Schurer, Chao Pang, James Malone, Helen Parkinson, Brian D. Athey, Yongqun He

Molecular and Cellular Pharmacology

Research output: Contribution to journal › Conference article

Abstract

The Cell Line Ontology (CLO) is a community-based ontology in the domain of biological cell lines with a focus on permanent cell lines from culture collections. Upper ontology structures that frame the skeleton of CLO include the Basic Formal Ontology and Relation Ontology. Cell lines contained in CLO are associated with terms from other ontologies such as Cell Type Ontology, NCBI Taxonomy, and Ontology for Biomedical Investigation. A common design pattern for the cell line is used to model cell lines and their attributes, with the Jurkat cell line as an example. Currently CLO contains over 36.000 cell line entries obtained from ATCC, HyperCLDB, Coriell, and by manual curation. The cell lines are derived from 194 cell types, 656 anatomical entries, and 217 organisms. The OWL-based CLO is machine-readable and can be used in various applications.

Original language	English (US)
Pages (from-to)	25-32
Number of pages	8
Journal	CEUR Workshop Proceedings
Volume	833
State	Published - Dec 1 2011
Event	2nd International Conference on Biomedical Ontology, ICBO 2011 - Buffalo, NY, United States Duration: Jul 26 2011 → Jul 30 2011

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Keywords

Cell line
Cell line ontology
CLO

ASJC Scopus subject areas

Computer Science(all)

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Sarntivijai, S., Xiang, Z., Meehan, T. F., Diehl, A. D., Vempati, U., Schurer, S., Pang, C., Malone, J., Parkinson, H., Athey, B. D., & He, Y. (2011). Cell line ontology: Redesigning the cell line knowledgebase to aid integrative translational informatics. CEUR Workshop Proceedings, 833, 25-32.

Cell line ontology : Redesigning the cell line knowledgebase to aid integrative translational informatics. / Sarntivijai, Sirarat; Xiang, Zuoshuang; Meehan, Terrence F.; Diehl, Alexander D.; Vempati, Uma; Schurer, Stephan; Pang, Chao; Malone, James; Parkinson, Helen; Athey, Brian D.; He, Yongqun.

In: CEUR Workshop Proceedings, Vol. 833, 01.12.2011, p. 25-32.

Research output: Contribution to journal › Conference article

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abstract = "The Cell Line Ontology (CLO) is a community-based ontology in the domain of biological cell lines with a focus on permanent cell lines from culture collections. Upper ontology structures that frame the skeleton of CLO include the Basic Formal Ontology and Relation Ontology. Cell lines contained in CLO are associated with terms from other ontologies such as Cell Type Ontology, NCBI Taxonomy, and Ontology for Biomedical Investigation. A common design pattern for the cell line is used to model cell lines and their attributes, with the Jurkat cell line as an example. Currently CLO contains over 36.000 cell line entries obtained from ATCC, HyperCLDB, Coriell, and by manual curation. The cell lines are derived from 194 cell types, 656 anatomical entries, and 217 organisms. The OWL-based CLO is machine-readable and can be used in various applications.",

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AU - Diehl, Alexander D.

AU - Vempati, Uma

AU - Schurer, Stephan

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AU - Malone, James

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Cell line ontology: Redesigning the cell line knowledgebase to aid integrative translational informatics

Abstract

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Keywords

ASJC Scopus subject areas

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