scapula classes

[wdahdul]

There are three classes for 'scapula':
scapula
pectoral fin scapula
pectoral limb scapula

Perhaps this is an artifact of the merge process, but for Phenoscape, we would like these to be merged into a single class since these are homologous. We are currently annotating to 'scapula' UBERON:0006849.

Is there a way to retain the taxonomically variable relationships (e.g., pectoral fin scapula develops_from scapulocoracoid in actinopterygians)?

[cmungall]

You're correct, this was deliberate, in order to have named classes for the different taxon-specific relationships.

We can merge these and make the axioms taxon GCIs

For example, (scapula and part_of some tetrapoda) part_of some shoulder

It may be the case that some of the existing taxon-specific relationships are artefactual

On the limb side we have the following ontogeny:

• UBERON:0006210 ! body-wall mesenchyme
  • UBERON:0006291 ! scapula pre-cartilage condensation
    • UBERON:0006290 ! scapula cartilage condensation
      • UBERON:0001124 ! pectoral limb scapula

I think there is a case that this is true by definition for any scapula

On the fin side, we have a lineage taken from ZFA, with the scapula developing from the scapulocoracoid (cartilage), consistent with the TAO textual def. It shares this lineage with the coracoid:

• ZFA:0001455 ! scapulocoracoid
• ZFA:0000332 ! coracoid
• ZFA:0000583 ! scapula

Does it make sense to identify some homolog or analog of the scapulocoracoid in limbed vertebrates? Here it gets trickier, the appendicular skeleton is in good shape in uberon thanks to the efforts of phenoscape and others, but the exception is the coracoid which needs a bit of work.

My inclination is to merge the two lineages, we would have scapula (bone) developing from scapula cartilage, and coracoid (bone) developing from coracoid cattilage. The coracoid cartilage and scapula cartilage would together as a mereological sum form the scapulocoracoid (cartilage). Now this grouping may be considered odd in some tetrapods(?) but I think logically it is fine.

What do you think?

[cmungall]

The current def for (generic) scapula is

def: "Endochondral bone that is dorsoventrally compressed and provides attachment site for muscles of the pectoral appendage." [VSAO:0000157]

Are there no other endochondral bones that are DV compressed and have muscle attachments to the forelimb?

[ANiknejad]

Hi Wasila,

I wonder how to consider this assertion regarding homology of the 'scapula' through Vertebrates?

"The scapula is the main skeletal element of the pectoral girdle allowing muscular fixation of the forelimb to the axial skeleton. The vertebrate limb skeleton has traditionally been considered to develop from the lateral plate mesoderm, whereas the musculature originates from the axial somites. However, in birds, the scapular blade has been shown to develop from the somites. We investigated whether a somitic contribution was also present in the mammalian scapula. Using genetic lineage-tracing techniques, we show that the medial border of the mammalian scapula develops from somitic cells. (...) Our results establish the avian scapular blade and medial border of the mammalian scapula as homologous structures as they share the same developmental origin."

PMID:20136669 "Valasek P, Theis S, Krejci E, Grim M, Maina F, Shwartz Y, Otto A, Huang R, Patel K, Somitic origin of the medial border of the mammalian scapula and its homology to the avian scapula blade. J Anat (2010)"

What do you think about?
Thank you very much in advance.

Anne

Anne Niknejad
Bgee curator

[cmungall]

I made some changes based on Anne's comments. I think we will want to add df relationshops for the scapular blade.

But getting back to the original question, I can make the merge any time, it would be great to have some additional comments on coracoid, but we can come back to this later? Shall I go ahead and do the merge now?

[wdahdul]

Yes, the proposed merge looks fine to me. Sorry for the delay - I'll review the rest of the request with Alex and Nizar tomorrow.

[cmungall]

I'm closing this but we shouldn't forget the coracoid..

[cmungall]

btw the fix is in releases/2013-11-08 which should be visible now