children of organogenesis

[J Clark]

Hi David,

> 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.

Sorry if I was unclear. This is actually one of the two 
options that I was suggesting. I'm happy to undertake this 
work if the annotators feel that they have been using the 
'organX development' terms for annotation of 'development' 
as stated in the name, rather than 'morphogenesis' as sated 
by the position in the graph.

> The huge issue for curators here is that many authors use morphogenesis 
> and development interchangeably.

Yes that is a concern to me too. I think it's really 
imporant that we're all absolutely clear about what we mean 
by the difference between morphogenesis and development 
before we start changing things.

  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.

Yes I can see that that is going to be a very complicated 
situation. It's going to make the graph very confusing if we 
have those kinds of synonyms isn't it? It will be necessary 
though to make the system useful for the users.

Do you think we should be opening this up to the annotation 
mailing list or will all the annotators who have to deal 
with development terms be on this list?


Thanks,

Jen





-- 
EMBL - European Bioinformatics Institute,
Gene Ontology Consortium,
and Wolfson College, Cambridge.
http://www.ebi.ac.uk/~jclark/