Table 1.
Vertebrate anatomy ontologies and others formally related to VSAO (*applicable to multiple species).
Figure 1.
Four high-level classes of skeletal anatomy (‘cell’, ‘skeletal tissue’, ‘skeletal element’, ‘skeletal subdivision’) and their children based on anatomical granularity.
Cell terms (CL) are shown in yellow fill, tissue terms in grey fill, skeletal element terms in blue fill, and skeletal subdivision terms in green fill. Parent classes from CARO in red font. Alligator mississippiensis sectioned maxilla (∼day 27 in ovo; Ferguson stage 19) stained with Mallory's trichrome (A); midsagittally sectioned embryonic head (day 45 in ovo; Ferguson stage 23) in lateral (B) and saggital (C) view, double stained whole-mount (alizarin red and alcian blue).
Figure 2.
Some skeletogenic cells and their relationships to other cells and skeletal tissues.
CL terms are shown in yellow fill, VSAO tissue terms in grey fill.
Figure 3.
Some skeletal tissues in the VSAO and selected relationships to other tissues, cells, and skeletal elements.
CL terms are shown in yellow fill, tissue terms in grey fill, skeletal element terms in blue fill, and skeletal subdivision terms in green fill.
Figure 4.
Representation of the skeleton in vertebrate anatomy ontologies.
The vertebrate skeleton can be partitioned according to many different criteria – and it had been by the different groups (Table 1) that developed anatomy ontologies. For example (A), ‘bone’ had been treated as a type of tissue by all except the MA, who also related it to the concept of ‘bone organ’. In the VSAO (B), the concepts of bone tissue and bone element were disentangled, named and defined. Individual bone elements were related to their tissue and cell components as well as developmental processes. From these links one can reason that, e.g., the ‘femur’ is part_of ‘endoskeleton’, develops_from ‘cartilage element’, and participates_in the process of ‘endochondral ossification’, whereas the ‘frontal bone’ is part_of ‘dermal skeleton’ and participates_in the process of ‘direct ossification’. Image on left shows chondrocytes embedded in a bone matrix developed from periosteum of fractured chick dermal bone. Image on right shows a late gestational stage mouse embryo stained with alcian blue and alizarin red. CL term is shown in yellow fill, tissue terms in grey fill, skeletal element terms in blue fill, and skeletal subdivision terms in green fill. Parent classes from CARO are in red font, GO terms in green font, TAO terms in blue font, and VSAO terms in black font.
Figure 5.
Some skeletal subdivisions and their relationships in the VSAO.
CARO parent term is in red font and VSAO terms in black font.
Figure 6.
Representation of a skeletal element with multiple classification criteria.
The ‘tripus’ is directly asserted (solid lines) to be a type of ‘endochondral bone’, part_of the ‘Weberian ossicle set’, part_of ‘vertebra 3′ and to form through the process of (‘participates_in’) ‘intramembranous ossification’. The reasoner infers (dotted lines) the tripus to be a type of ‘membrane bone’ and a ‘Weberian ossicle’, and infers it to participate in ‘endochondral ossification’. Skeletal element terms are shown in blue fill, skeletal subdivision term in green fill, TAO terms in blue font, VSAO terms in black font, and GO process terms in green font.