Modeling endochondral elements Design Pattern

Representing individual endochondral elements

Status: intermediate draft

Authors and contributors:

• Wasila Dahdul (author)
• Melissa Haendel (author)
• Chris Mungall (author)
• Alex Dececci (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 subclass of bone

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

Template

Classes representing individual endochondral elements should typically conform to the following hierarchy:

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

Not all classes need be materialized in the ontology.

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'

The ontology should contain the axiom:

• 'endochondral bone' EquivalentTo bone and develops_from some 'cartilage condensation'

This means that there is no need for assertion under endochondral bone

Equivalence Axioms

TBD. Use PATO? Or directly use composition relation and tissue?

Exceptions

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

Open questions

• Should there be a 4th subclass for elements whose end-state is cartilage; these are past the condensation stage -- see issue 382
  • option 1 : we merge the concepts of cartilage element (sensu TAO-like terms) and cartilage condensation (sensu EMAPA/EHDAA2-like terms)
  • option 2 : we model cartilage element and cartilage condensation as separate classes. Relationships TBD.
• 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