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J Biomed Semantics. 2016 Jul 4;7(1):44. doi: 10.1186/s13326-016-0088-7.

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

Author information

1
Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY, 14203, USA. addiehl@buffalo.edu.
2
European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK.
3
ZFIN, the Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR, 97403, USA.
4
Ontology Development Group, Library, Oregon Health and Science University, Portland, Oregon, 97239, USA.
5
Department of Biology, University of South Dakota, Vermillion, SD, 57069, USA.
6
National Evolutionary Synthesis Center, Durham, NC, 27705, USA.
7
Southwestern Medical Center, University of Texas, Dallas, TX, 75235, USA.
8
Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
9
Oral Diagnostics Sciences, University at Buffalo School of Dental Medicine, Buffalo, NY, 14210, USA.
10
The Jackson Laboratory, Bar Harbor, ME, 04609, USA.
11
Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.

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.

PMID:
27377652
PMCID:
PMC4932724
DOI:
10.1186/s13326-016-0088-7
[Indexed for MEDLINE]
Free PMC Article

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