opinions needed on germination

[J Clark]

(Forwarded to po-dev from the go list.)

Hi all,

We (at SGD) have been working on revising the 'germination' 
area of the
process ontology.  There are a couple of major problems with it:

- 'spore germination' currently has 'post-embryonic 
development'
parentage and so cannot be used for Dicty, bacteria, and other
organisms without embryos.

- 'spore germination (sensu Fungi)' has completely different 
parentage;
its direct parent is 'sporulation' (which is pretty much the 
opposite
of germination!).

In making a revised tree it would be helpful to have 
opinions  on a few
specific questions from other folks whose organisms germinate.

1) we're wondering about obsoleting this term:

germination (GO:0009844):  The physiological and 
developmental changes
by a seed, spore, pollen grain (microspore), or zygote that 
occur after
release from dormancy, and encompassing events prior to and 
including
the first visible indications of growth.

Is there really that much in common between these different 
types of
germination that a grouping term is useful?


2) 'pollen germination' currently has 'post-embryonic 
development'
parentage. Should it?  My botany is rusty, but it seems to 
me that this
takes place before an embryo exists.


3) all the germination terms except the 'sensu Fungi' one 
currently
have 'cell differentiation' parentage.  This sounds 
reasonable for seed
or pollen germination, but isn't spore germination really 
just a
resumption of growth, after breakdown of the spore wall and 
protective
structures?


Once I get some feedback on these issues, I'll submit a 
proposal on the
details to SF.

Thanks!
Maria




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