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. 2012 Feb 14;3:18.
doi: 10.3389/fgene.2012.00018. eCollection 2012.

The AEO, an Ontology of Anatomical Entities for Classifying Animal Tissues and Organs

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Free PMC article

The AEO, an Ontology of Anatomical Entities for Classifying Animal Tissues and Organs

Jonathan B L Bard. Front Genet. .
Free PMC article

Abstract

This paper describes the AEO, an ontology of anatomical entities that expands the common anatomy reference ontology (CARO) and whose major novel feature is a type hierarchy of ~160 anatomical terms. The breadth of the AEO is wider than CARO as it includes both developmental and gender-specific classes, while the granularity of the AEO terms is at a level adequate to classify simple-tissues (~70 classes) characterized by their containing a predominantly single cell-type. For convenience and to facilitate interoperability, the AEO contains an abbreviated version of the ontology of cell-types (~100 classes) that is linked to these simple-tissue types. The AEO was initially based on an analysis of a broad range of animal anatomy ontologies and then upgraded as it was used to classify the ~2500 concepts in a new version of the ontology of human developmental anatomy (www.obofoundry.org/), a process that led to significant improvements in its structure and content, albeit with a possible focus on mammalian embryos. The AEO is intended to provide the formal classification expected in contemporary ontologies as well as capturing knowledge about anatomical structures not currently included in anatomical ontologies. The AEO may thus be useful in increasing the amount of tissue and cell-type knowledge in other anatomy ontologies, facilitating annotation of tissues that share common features, and enabling interoperability across anatomy ontologies. The AEO can be downloaded from http://www.obofoundry.org/.

Keywords: anatomical hierarchy; cell-type assignations; ontology; tissue classification.

Figures

Figure 1
Figure 1
The AEO shown in the COBrA browser. Here, the hierarchies for immaterial anatomical entities (blue arrow) and gender-specific anatomical entities (red arrow) are expanded.
Figure 2
Figure 2
The AEO shown in the in the COBrA browser. Here, the hierarchies for anatomical group (blue arrow) and developing anatomical structure (red arrow) are expanded.
Figure 3
Figure 3
The simple-tissue hierarchy of the AEO shown in the COBrA browser. All top and secondary levels terms are shown together with some tertiary level ones.
Figure 4
Figure 4
The use of the AEO in classifying the ontology of human developmental anatomy (EHDAA2). The ontology is opened in the OBO-Edit browser to demonstrate (i) those tissues classed (is_a relationship) within the gender-specific anatomical structure hierarchy (red arrow), and (ii) the head category of organism subdivision with its constituent organ groups (part_of relationship).
Figure 5
Figure 5
The cell-type hierarchy of the AEO shown in the COBrA browser. This subset of the full cell-type ontology includes about 90 classes in all but only the epithelial cell class is expanded (red arrow). The editor uses the has_part relationship to show those anatomical entities (simple-tissues) which include the various epithelial cell-types.

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References

    1. Aitken S., Korf R., Webber B., Bard J. (2005). COBrA: a bio-ontology editor. Bioinformatics 21, 825–82610.1093/bioinformatics/bti097 - DOI - PubMed
    1. Bard J. B. L. (2008). “Anatomical ontologies for model animals,” in Anatomy Ontologies for Bioinformatics, eds Burger A., Davidson D., Baldock R., editors. (Springer: ), 3–25
    1. Burger A., Davidson D., Baldock R. (eds). (2008). Anatomy Ontologies for Bioinformatics. New York: Springer
    1. Day-Richter J., Harris M. A., Haendel M., The Gene Ontology OBO-Edit Working Group. Lewis S. (2007). Obo-Edit – an ontology editor for biologists. Bioinformatics 23, 2198–220010.1093/bioinformatics/btm112 - DOI - PubMed
    1. Haendel M. A., Neuhaus F., Osumi-Sutherland D., Mabee P., Mejino J. L. V., Mungall C., Smith B. (2008). “CARO, the common anatomy reference ontology,” in Anatomy Ontologies for Bioinformatics, eds Burger A., Davidson D., Baldock R., editors. (New York: Springer; ), 327–349

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