The cell ontology 2016: Enhanced content, modularization, and ontology interoperability

Alexander D. Diehl, Terrence F. Meehan, Yvonne M. Bradford, Matthew H. Brush, Wasila M. Dahdul, David S. Dougall, Yongqun He, David Osumi-Sutherland, Alan Ruttenberg, Sirarat Sarntivijai, Ceri E. Van Slyke, Nicole A. Vasilevsky, Melissa Haendel, Judith A. Blake, Christopher J. Mungall

Research output: Contribution to journalArticle

32 Citations (Scopus)

Abstract

Background: The Cell Ontology (CL) is an OBO Foundry candidate ontology covering the domain of canonical, natural biological cell types. Since its inception in 2005, the CL has undergone multiple rounds of revision and expansion, most notably in its representation of hematopoietic cells. For in vivo cells, the CL focuses on vertebrates but provides general classes that can be used for other metazoans, which can be subtyped in species-specific ontologies. Construction and content: Recent work on the CL has focused on extending the representation of various cell types, and developing new modules in the CL itself, and in related ontologies in coordination with the CL. For example, the Kidney and Urinary Pathway Ontology was used as a template to populate the CL with additional cell types. In addition, subtypes of the class 'cell in vitro' have received improved definitions and labels to provide for modularity with the representation of cells in the Cell Line Ontology and Reagent Ontology. Recent changes in the ontology development methodology for CL include a switch from OBO to OWL for the primary encoding of the ontology, and an increasing reliance on logical definitions for improved reasoning. Utility and discussion: The CL is now mandated as a metadata standard for large functional genomics and transcriptomics projects, and is used extensively for annotation, querying, and analyses of cell type specific data in sequencing consortia such as FANTOM5 and ENCODE, as well as for the NIAID ImmPort database and the Cell Image Library. The CL is also a vital component used in the modular construction of other biomedical ontologies-for example, the Gene Ontology and the cross-species anatomy ontology, Uberon, use CL to support the consistent representation of cell types across different levels of anatomical granularity, such as tissues and organs. Conclusions: The ongoing improvements to the CL make it a valuable resource to both the OBO Foundry community and the wider scientific community, and we continue to experience increased interest in the CL both among developers and within the user community.

Original languageEnglish (US)
Article number44
JournalJournal of Animal Science and Biotechnology
Volume7
Issue number1
DOIs
StatePublished - 2016

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Interoperability
Ontology
cells
Foundries
Biological Ontologies
National Institute of Allergy and Infectious Diseases (U.S.)
Modular construction
Gene Ontology

ASJC Scopus subject areas

  • Biotechnology
  • Food Science
  • Biochemistry
  • Animal Science and Zoology

Cite this

Diehl, A. D., Meehan, T. F., Bradford, Y. M., Brush, M. H., Dahdul, W. M., Dougall, D. S., ... Mungall, C. J. (2016). The cell ontology 2016: Enhanced content, modularization, and ontology interoperability. Journal of Animal Science and Biotechnology, 7(1), [44]. https://doi.org/10.1186/s13326-016-0088-7

The cell ontology 2016 : Enhanced content, modularization, and ontology interoperability. / Diehl, Alexander D.; Meehan, Terrence F.; Bradford, Yvonne M.; Brush, Matthew H.; Dahdul, Wasila M.; Dougall, David S.; He, Yongqun; Osumi-Sutherland, David; Ruttenberg, Alan; Sarntivijai, Sirarat; Van Slyke, Ceri E.; Vasilevsky, Nicole A.; Haendel, Melissa; Blake, Judith A.; Mungall, Christopher J.

In: Journal of Animal Science and Biotechnology, Vol. 7, No. 1, 44, 2016.

Research output: Contribution to journalArticle

Diehl, AD, Meehan, TF, Bradford, YM, Brush, MH, Dahdul, WM, Dougall, DS, He, Y, Osumi-Sutherland, D, Ruttenberg, A, Sarntivijai, S, Van Slyke, CE, Vasilevsky, NA, Haendel, M, Blake, JA & Mungall, CJ 2016, 'The cell ontology 2016: Enhanced content, modularization, and ontology interoperability', Journal of Animal Science and Biotechnology, vol. 7, no. 1, 44. https://doi.org/10.1186/s13326-016-0088-7
Diehl, Alexander D. ; Meehan, Terrence F. ; Bradford, Yvonne M. ; Brush, Matthew H. ; Dahdul, Wasila M. ; Dougall, David S. ; He, Yongqun ; Osumi-Sutherland, David ; Ruttenberg, Alan ; Sarntivijai, Sirarat ; Van Slyke, Ceri E. ; Vasilevsky, Nicole A. ; Haendel, Melissa ; Blake, Judith A. ; Mungall, Christopher J. / The cell ontology 2016 : Enhanced content, modularization, and ontology interoperability. In: Journal of Animal Science and Biotechnology. 2016 ; Vol. 7, No. 1.
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