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Open Access Highly Accessed Methodology article

Logical Development of the Cell Ontology

Terrence F Meehan1*, Anna Maria Masci2, Amina Abdulla3, Lindsay G Cowell2, Judith A Blake1, Christopher J Mungall3 and Alexander D Diehl14*

Author Affiliations

1 Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME, USA

2 Dept. of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA

3 Lawrence Berkeley National Laboratory, Berkeley, CA, USA

4 Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY, USA

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BMC Bioinformatics 2011, 12:6  doi:10.1186/1471-2105-12-6

Published: 5 January 2011

Abstract

Background

The Cell Ontology (CL) is an ontology for the representation of in vivo cell types. As biological ontologies such as the CL grow in complexity, they become increasingly difficult to use and maintain. By making the information in the ontology computable, we can use automated reasoners to detect errors and assist with classification. Here we report on the generation of computable definitions for the hematopoietic cell types in the CL.

Results

Computable definitions for over 340 CL classes have been created using a genus-differentia approach. These define cell types according to multiple axes of classification such as the protein complexes found on the surface of a cell type, the biological processes participated in by a cell type, or the phenotypic characteristics associated with a cell type. We employed automated reasoners to verify the ontology and to reveal mistakes in manual curation. The implementation of this process exposed areas in the ontology where new cell type classes were needed to accommodate species-specific expression of cellular markers. Our use of reasoners also inferred new relationships within the CL, and between the CL and the contributing ontologies. This restructured ontology can be used to identify immune cells by flow cytometry, supports sophisticated biological queries involving cells, and helps generate new hypotheses about cell function based on similarities to other cell types.

Conclusion

Use of computable definitions enhances the development of the CL and supports the interoperability of OBO ontologies.