Authors and contributors:

• Chris Mungall (author)

Date: 2012

Document Type: ontology_design_pattern

In common usage the terms skeletal system and skeleton may be used interchangeably, but they have different meanings in this ontology

Uberon follows the FMA in using the terms 'skeletal system' and 'skeleton' very precisely, as the following partonomic view shows:

• skeletal system -- skeleton plus all joints
  • skeleton -- set of all skeletal elements in an organism
  • articular system -- set of all joints in an organism

Note that we generalize the FMA notion of skeleton, to include cartilage elements, but the basic division remains the same: joints are NOT part of skeleton, they are part of the articular system (and by transitivity, part of the skeletal system).

Note the above partonomy is not pairwise part-disjoint - joints can be a part of bone parts.

This is carried through for individual structures, the following template is followed:

• X skeletal system -- all skeletal elements plus joints in X
  • X skeleton -- set of all skeletal elements in an X
  • X articular system -- set of all joints in an X

There are a number of issues with the above scheme.

1. It can lead to class inflation if we include two cuts of every skeletal subdivision. This can be managed somewhat automatically.

2. It can be confusing for users and editors. Users may accidentally select the wrong term as the labels sound similar, and not everyone reads definitions closely. Editors may classify things wrongly.

3. It leads to some curious unintuitive situations. For example, by the above definition, cranial sutures are not part of the skull, assuming the skull is part of the skeleton. However, cranial sutures would be part of the cranial skeletal system.

It is not clear if the above system should be maintained or if the skeleton terms should be merged into the skeletal system ones. More user input is required.