HP_0009815 Aplasia/hypoplasia of the extremities and HP_0045060 Aplasia/hypoplasia involving bones of the extremities are inferred to be equiv classes.

[nicolevasilevsky]

HP_0009815 Aplasia/hypoplasia of the extremities and HP_0045060 Aplasia/hypoplasia involving bones of the extremities are inferred to be equiv classes.

These two classes have the same logical def:
HP_0009815 Aplasia/hypoplasia of the extremities
Logical def:
'has part' some
(aplastic/hypoplastic and ('inheres in part of' some 'appendicular skeleton') and ('has modifier' some abnormal))

Text def:
Absence (due to failure to form) or underdevelopment of the extremities.

HP_0045060 Aplasia/hypoplasia involving bones of the extremities
Logical def:
'has part' some
(aplastic/hypoplastic and ('inheres in part of' some 'appendicular skeleton') and ('has modifier' some abnormal))

No text def.

I think the logical def of HP_0045060 Aplasia/hypoplasia involving bones of the extremities should be revised.

Related to #149

@cmungall @pnrobinson

[drseb]

@pnrobinson can you clarify what the difference is? Can the extremities be aplastic/hypoplastic without having a bone-involvement?

[pnrobinson]

Clearly if you have aplasia of all bones of an arm, then you would not have an entire bone-less arm but rather a stump. You can have aplasia of an individual bone without having limb aplasia. Of course the concepts are highly related. Both of the classes are grouping classes and probably would never be used for a specific annotation. At some point we need to revisit the structure of the ontology here. I believe also that the muscle section of the ontology is going to need a lot of work, and this would be a good opportunity to revise this section.

[drseb]

Clearly if you have aplasia of all bones of an arm, then you would not have an entire bone-less arm but rather a stump. You can have aplasia of an individual bone without having limb aplasia.

But all these examples involve some bone, right? The question is if you can have a hypoplastic extremity where no bone is involved?

[drseb]

Would you say that "Hypoplastic biceps" is a subclass of "Aplasia/hypoplasia of the extremities"?

[pnrobinson]

This is a good point, and we have not yet committed ontologically to one or other interpretation. I think that it is probably better to build out the muscle section of the ontology to better group items like hypoplastic biceps.
Given the way we have been definining things to date, I would asnwer your question with YES, this is true. I am not sure that we want to keep it that way though. I think we need a F2F workshop to deal with issues like this though -- it would be a lot of work to restructure everything and we should not do it term for term!

[nicolevasilevsky]

@pnrobinson for now, do you mind if I remove the logical def for HP_0045060 Aplasia/hypoplasia involving bones of the extremities?