Modeling endochondral elements Design Pattern

Status: intermediate draft

Authors and contributors:

• Wasila Dahdul (author)
• Melissa Haendel (author)
• Chris Mungall (author)
• Alex Dececci (author)
• Paula Mabee (author)

Date: 2013

Document Type: ontology_design_pattern

Abstract

Endochondral elements

Endochondral bones develop from cartilage templates, these cartilage elements are themselves derived from pre-cartilage mesenchymal condensations.

In mature humans the majority of the skeleton is bone, but in other vertebrates the adult skeleton may contain varying amounts of cartilage.

Representation in other ontologies

Ontologies such as the ZFA, TAO typically implement the following subclass hierarchy pattern:

• X element
  • X bone element
  • X cartilage element

With X bone developing from X cartilage

The mammalian embryonic ontologies (EMAPA, EHDAA2) do not implement "element" grouping classes, and instead have the following lineage ([develops_from]) hierarchy :

• X pre-cartilage subclass of pre-cartilage
  • <-- X cartilage(nous) condensation subclass of cartilage condensation
    • <-- X bone subclass of bone element

Typically the last stage is omitted as EMAPA and EHDAA2 do not extend temporally far enough. Note also that the develops_from is not asserted in EMAPA.

When the mature structure is cartilage (e.g. cricoid), this is also represented as a cartilage condensation.

There may be exceptions to the above (e.g. due to fusion/splits during development)

Challenge

integrate these two approaches

Solution

Class hierarchy

We use the following subclass hierarchy template:

• X element
  • X bone element
  • X cartilage element
  • X pre-cartilage condensation

Not all classes need be materialized in the ontology.

Develops from axioms

Where classes are materialized, the following axioms should be created:

• 'X cartilage condensation' SubClassOf develops_from some 'X pre-cartilage condensation'
• 'X bone' SubClassOf develops_from some 'X cartilage condensation'

Equivalence Axioms

We currently use composition as a differentia:

• X element
  • X bone element EquivalentTo 'X element' and composed_primarily_of 'bone tissue'
  • X cartilage element EquivalentTo 'X element' and composed_primarily_of 'cartilage tissue'
  • X pre-cartilage condensation EquivalentTo 'X element' and composed_primarily_of 'pre-cartilage tissue'

The definition of this relation is such that the triad is mutually disjoint. Mixed elements are allowed, they either fall into a single class (if >50% of their tissue is of the requisite type) or they are simply classified under 'element'

Exceptions

• There need not be a 1:1 correspondence between a bone and it's cartilage precursor. cf fusion/merging during development.

Terminological issue

Terms such as 'femur' may be ambiguous w.r.t whether they refer to the element or the bone.

We generally prefer explicit names, but this may not be implemented universally

Primacy of definitions

We would prefer not to repeat text definitions.

One option is to have the bone definition be primary, and define other classes in reference to this.

We are leaning towards moving the core definition to the element, and making the definition for the subclasses trivially follow the parent, directly mirroring the OWL equivalence axiom.

Open questions

• Should we introduce additional subclasses to differentiate embryonic cartilage vs mature? -- see issue 382
• Is develops_from appropriate? Depends how definition relations to cells
• Should classes for ossification centers be materialized? If so, how does this relate to the above
• Mixed endochondral/membrane bones

Tickets

• https://github.com/obophenotype/uberon/issues/382