children of organogenesis

[David Hill]

Hi Jen,

Here is what I think. It is more complex than this. If they just get 
moved to under organogenesis, then they will still be morphogenesis no 
matter what the def says, because organogenesis is a  type of 
morphogenesis. Here is my proposal (lots of work). Create a term called 
organ development under development. This term will have at least two 
part_of children, organogenesis (also a is_a morphogenesis) and (organ 
maturation, do we want to create a maturation term?). Then, every organ 
that is in the GO (as defined by an anatomical organ) should have an 
organ development, and organ morphogenesis (such as 
cardiogenesis-synonym heart morphogenesis), and an organ maturation term 
(such as heart maturation-synonym cardiac maturation). The next step 
would be to move all of the organ development terms that currently exist 
to be under the new organ development term. THEN, we would have to go an 
look at all of the children of the current organ development terms and 
decide if they should go directly under development or be moved to be 
under morphogenesis or maturation. This is a pretty big job, but I think 
it would work. It also would not create errors in annotation because all 
the gene products currently annotated to "organX" development would 
still be accurate, although not as precise as they maybe could be.

The huge issue for curators here is that many authors use morphogenesis 
and development interchangeably. One example is in the mammalian eye. 
The eye forms and takes shape during embryonic development. Shortly 
after birth, the cells in the retina differentiate into the 
characteristic neural retinal layers. Many authors call this retinal 
morphogenesis even though there is really no shape change or creation of 
form happenning here. Things like this maybe should be handled by the 
clever use of synonyms, while the original graph remains true. So, in 
dveloping the GO, I may define this process as retinal maturation, but I 
would make a synonym for it called retinal morphogenesis so that what is 
used a get at  what is used in the literature. Sorry for the long e-mail.

David




Jennifer I Clark wrote:

> Hi,
>
> Would it be possible for everybody to take a quick look at
>
>
>    [ 1065289 ] organ morphogenesis terms 2
>
> https://sourceforge.net/tracker/index.php?func=detail&aid=1065289&group_id=36855&atid=440764 
>
>
> It's about the children of organogenesis. Organogenesis is about the 
> morphogenesis of an organ and it has children called 'x development' 
> and 'x morphogenesis'. The impression that I get about these child 
> terms was that the initial designation of 'development' or 
> 'morphogenesis' was basically interchangeable since the terms were 
> made before any clear distinction between these ideas had been worked 
> out. A few months ago I redefined the development ones with the 
> standard definition of development, with a view to moving them out of 
> under 'organogenesis'. This is how we would have done things according 
> to the old rules. However, now I have been told that if it doesn't 
> affect annotation then it's okay to adjust the terms called 'x 
> development' to make them into 'x morphogenesis' terms. So I'm now 
> wondering the following:
>
> If there are terms called 'x development' under 'organogenesis', 
> should I move these terms out to be children of 'organ development' or 
> should I get the annotators to check the annotations, and where 
> appropriate just change the 'x development' terms into 'x 
> morphogenesis' terms.
>
> Does anybody have any views on this?
>
> Thanks,
>
> Jen
>
>


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