temporal aspects of 'X development' terms

[David Hill]

Hi Everyone,

My thoughts below.

>>
>>
>>> A thought on the temporal scope of 'X development' terms in general:
>>>
>>> If a term like 'vasculature development' is defined to only 
>>> encompass the development of the vasculature from it's formation to 
>>> it's mature state, then wouldn't it be false to say something like 
>>> 'vascular cord development' part_of 'vasculature development' if 
>>> 'vascular cord development' precedes the existence of vasculature in 
>>> time?   (DAVID???)
>>
Yes, the key issue here is whether you consider the vascular cord to be 
an is_a or a part_of the vasculature. In the case of the ureteric bud, 
when this term was created, I/we (I hope) thought that the metanephros 
represented a primordial kidney. It is defined this way in the 
anatomical dictionary, and I think most biologists view it this way. 
Same goes with the mesonephros, even though it is transient. Therefore 
since ureteric bud development is a part_of metanephros development, it 
is also a part_of kidney development. This gets into the sticky issue of 
lineage and when something begins to exist. In general, I think most 
biologists consider primordia to be the beginning of the existence of a 
structure. I think we will continue to be plagued by this question.

I think the really important point to be made here is that in the GO, if 
you say that the development of a structure X is part_of the development 
of a structure Y, then that means that when X is formed, a type of Y 
exists. This question and discussion points out that we think about 
this. The tough job for us is representing what the biologists, or at 
least the consensus of biologists, also think about this. I think Doug's 
point below about what makes sense illustrates this.

So for the above issue Doug has to ask himself, "Does an ichthyologist 
consider the vascular cord to be an is_a or part_of the vasculature?". 
If the answer is yes, then there is a relationship between it and 
vascular development, if the answer is no, then there is not.

Does this make sense?

As for the vascular question, I think that Jen has hit this one 
correctly, since the system development term is new, I think that we 
just haven't moved vasculature development to the right place yet. Can 
you think of components of the vascular system that are not considered 
vasculature?

David

>>> We clearly already have such instances in GO, see 'ureteric bud 
>>> development' for example.
>>>
>>> Biologically, these assertions of part_of make perfect sense...of 
>>> course 'ureteric bud development' is part of 'kidney 
>>> development'...and query results would need to respond that way as 
>>> well.  However, if 'Kidney development' has the scope of 'from it's 
>>> formation to the mature structure', then developmental events that 
>>> occur before the kidney exists can't really be part_of 'kidney 
>>> development' can they?
>>>
>>> I know this isn't a new issue..I'm just trying to figure out what 
>>> the proper course of action is!
>>>
>>> Thoughts?
>>


-- 
David P. Hill, Ph.D.
Senior Scientific Curator
Mouse Genome Informatics
Gene Ontology Consortium
The Jackson Laboratory
600 Main Street
Bar Harbor, ME 04609-1500
tel:207-288-6430
htpp://www.informatics.jax.org
http://www.geneontology.org