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obophenotype / mouse-anatomy-ontology

Ontologies for mouse anatomy and development
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request clarification: pouch and pouch endoderm #2

Open cmungall opened 10 years ago

cmungall commented 10 years ago

Example:

[Term]
id: EMAPA:16124
name: 1st branchial pouch
namespace: anatomical_structure
comment: order=8 for EMAPA:16118
relationship: ends_at TS19 ! TS19
relationship: part_of EMAPA:16118 ! 1st branchial arch
relationship: starts_at TS12 ! TS12

[Term]
id: EMAPA:16125
name: 1st branchial pouch endoderm
namespace: anatomical_structure
comment: order=0 for EMAPA:16124
relationship: ends_at TS19 ! TS19
relationship: part_of EMAPA:16124 ! 1st branchial pouch
relationship: starts_at TS12 ! TS12

The pharyngeal pouches are often defined to be the part of the endoderm that is pocketed between the arches, touching the ectoderm (cleft) on the other side.

If so, what is the difference between the two classes above? Does the former one extend into the mesodermal portion of the arch itself?

tfhayamizu commented 10 years ago

Sorry for the delayed response. The ontological organization of the branchial arches, as with many parts of the EMAPA, is a legacy from its original uniparental, strictly partonomic structure. This should no doubt be revisited in a major way.

Kaufman and Bard (1999) state "Subjacent to the endodermal lining of the pouch, this tissue is supported by branchial arch mesenchyme." My interpretation of this is that the class "branchial pouch" is intended to represent the entire structure, similar to the way brain ventricles are represented. This should be further investigated.

A related issue is whether there is actually a distinction between "branchial pouch endoderm" and "branchial membrane endoderm."