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

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 (), 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 .

A new ontology (structured hierarchy) of human developmental anatomy for the first 7 weeks (Carnegie stages 1–20)

“…However, the relatively few terms that CARO includes are of limited use if one wishes to capture something of the richness of anatomy. The solution adopted here has been to use the Anatomical Entity Ontology or AEO (Bard, ), a substantial expansion of CARO that includes, for example, ~ 80 simple tissues (those containing a single cell type) and a wide variety of immaterial AEs (e.g. pits, rows, lumens, cavities) rather than the four (based on dimension: point, line, etc.)…”

NETME: on-the-fly knowledge network construction from biomedical literature

“… 2010 ), ProteinOntology(PRO) (Natale et al. 2016 ), Anatomical Entity Ontology (AEO) (Bard 2012 ), Phenotype And Trait Ontology (PATO) ( http://obofoundry.org/ontology/pato.html ), Cell Ontology (CL) (Diehl et al. 2016 ), Cell Line Ontology (CLO) (Sarntivijai et al.…”

“…( 2010 ) is a structured controlled vocabulary for the source of an enzyme comprising tissues, cell lines, cell types and cell cultures. Anatomical Entity Ontology (AEO) Bard ( 2012 ) is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology, to about 160 classes using the is_a relationship; it thus provides a detailed type classification for tissues. The AEO is useful in increasing the amount of knowledge in anatomy ontology, facilitating annotation and enabling interoperability across anatomy ontology.…”

COMICS: Cartoon Visualization of Omics Data in Spatial Context Using Anatomical Ontologies

“…Many such ontologies already exist, including the model-system specific C. elegans gross anatomy (WBBT), 7 the Drosophila gross anatomy (FBbt and FBdv), also referred to as the Drosophila anatomy ontology (DAO), 8 the Mouse Adult Gross Anatomy (MA), 9 Xenopus anatomy and development (XAO), 10 and Zebrafish anatomy and development (ZFA and ZFS). 11 There are also the more general Anatomical Entity Ontology (AEO), 12 Biological Spatial Ontology (BSPO), 13 and the general vertebrate “Uber-anatomy” ontology (UBERON) 14 currently (20170415) containing 15 036 anatomical terms. The zebrafish ZFA and ZFS ontologies contain 3175 anatomical terms (20170627 release) and the mouse MA 3257 terms (20170207 version).…”