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The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability - PubMed

  • ️Fri Jan 01 2016

The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability

Alexander D Diehl et al. J Biomed Semantics. 2016.

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.

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Figures

Fig. 1
Fig. 1

High level cell types in CL and related ontologies. The hierarchy of high-level cell types is shown. CL nodes: green, ReO: blue, CLO: orange

Fig. 2
Fig. 2

Logical definition for ‘T-helper 1 cell’ (CL:0000545). The logical definition for the cell type ‘T-helper 1 cell’ as presented by the Protégé ontology editor. The logical definition uses imported classes the Protein Ontology (‘T-box transcription factor TBX21’, PR:000001835; ‘C-X-C chemokine receptor type 3’, PR:000001207; and ‘C-C chemokine receptor type 6’, PR:000001202) and the Gene Ontology (‘interferon-gamma production’, GO:0032609). Note some anonymous ancestor classes are not shown due to space considerations

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References

    1. Bard J, Rhee SY, Ashburner M. An ontology for cell types. Genome biology. 2005;6:R21. doi: 10.1186/gb-2005-6-2-r21. - DOI - PMC - PubMed
    1. Diehl AD, Augustine AD, Blake JA, Cowell LG, Gold ES, Gondre-Lewis TA, Masci AM, Meehan TF, Morel PA, Nijnik A, et al. Hematopoietic cell types: prototype for a revised cell ontology. J Biomed Informat. 2011;44:75–79. doi: 10.1016/j.jbi.2010.01.006. - DOI - PMC - PubMed
    1. Meehan TF, Masci AM, Abdulla A, Cowell LG, Blake JA, Mungall CJ, Diehl AD. Logical development of the cell ontology. BMC Bioinformatics. 2011;12:6. doi: 10.1186/1471-2105-12-6. - DOI - PMC - PubMed
    1. Masci AM, Arighi CN, Diehl AD, Lieberman AE, Mungall C, Scheuermann RH, Smith B, Cowell LG. An improved ontological representation of dendritic cells as a paradigm for all cell types. BMC Bioinformatics. 2009;10:70. doi: 10.1186/1471-2105-10-70. - DOI - PMC - PubMed
    1. Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, et al. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nature Biotechnol. 2007;25:1251–1255. doi: 10.1038/nbt1346. - DOI - PMC - PubMed

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