Modeling endochondral elements Design Pattern

Representing individual endochondral elements

Status: intermediate draft

Authors and contributors:

• Wasila Dahdul (author)
• Melissa Haendel (author)
• Chris Mungall (author)

Date: 2012

Document Type: ontology_design_pattern

Abstract

TODO Preamble:

Early draft to demonstrate markdown embedded in ontology.

Template

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

• X element
  • X bone
  • X cartilage (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