An improved ontological representation of dendritic cells as a paradigm for all cell types - PubMed (original) (raw)

An improved ontological representation of dendritic cells as a paradigm for all cell types

Anna Maria Masci et al. BMC Bioinformatics. 2009.

Abstract

Background: Recent increases in the volume and diversity of life science data and information and an increasing emphasis on data sharing and interoperability have resulted in the creation of a large number of biological ontologies, including the Cell Ontology (CL), designed to provide a standardized representation of cell types for data annotation. Ontologies have been shown to have significant benefits for computational analyses of large data sets and for automated reasoning applications, leading to organized attempts to improve the structure and formal rigor of ontologies to better support computation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL's utility for computation and for cross-species data integration.

Results: To enhance the CL's utility for computational analyses, we developed a method for the ontological representation of cells and applied this method to develop a dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. We avoid multiple uses of is_a by linking DC-CL terms to terms in other ontologies via additional, formally defined relations such as has_function.

Conclusion: This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. Accordingly, we propose our method as a general strategy for the ontological representation of cells. DC-CL is available from http://www.obofoundry.org.

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Figures

Figure 1

Figure 1

The representation of Langerhans cells in the Cell Ontology. A portion of the Cell Ontology is shown with ovals corresponding to cell types defined in the ontology and arrows corresponding to relations between those cell types. Langerhans cell is represented by a yellow oval; blue arrows correspond to is_a relations, and orange arrows correspond to develops_from relations. Only a subset of Langerhans cell parent types are included in the figure.

Figure 2

Figure 2

The representation of dendritic cell types in the Dendritic Cell Ontology (DC-CL). Rectangles correspond to the terms for dendritic cell types represented in DC-CL, and the lines connecting the rectangles correspond to the is_a relations between these cell types. Black lines connect the highest-level terms in DC-CL to the Cell Ontology term leukocyte. Blue lines connect the DC-CL term conventional dendritic cell to the terms for its subtypes, while red lines connect these terms to the respective subtype terms. The green lines connect the terms _CD11c_- plasmacytoid dendritic cell and CD11c low plasmacytoid dendritic cell to the terms for their respective subtypes. Abbreviations used in the figure are: DC, dendritic cell; PDC, plasmacytoid dendritic cell; and LC, Langerhans Cell.

Figure 3

Figure 3

The ontologies and relations referred to in the Dendritic Cell Ontology (DC-CL). The rectangles and ovals represent ontologies, and the arrows represent relations joining terms in the ontologies. Abbreviations for the ontology names are shown in normal font, and the relations used to link DC-CL to each ontology are shown in italics. The black arrow indicates relations used to join DC-CL terms to other DC-CL terms, while the blue arrows indicate trans-ontological relations. Ontologies and relations shown in rectangles are used to define DC-CL types, while the ontologies and relations shown in ovals are used to make non-classificatory assertions about DC-CL types. Abbreviations used in the figure are: GO CC, Gene Ontology Cellular Component Ontology; PRO, Protein Ontology; IO, Immunology Ontology; FMA, Foundational Model of Anatomy; and GO BP, Gene Ontology Biological Process Ontology.

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