The reason I added this term under GO:0009793 is because of
the definition of the term which states
"The embryonic development that ends with seed dormancy,
as in, but not restricted to, the flowering plants
(Magnoliophyta, ncbi_taxonomy_id:3398). "
ends with seed dormancy makes me think seed dormancy is
included in the process.Should the definition of 9793 change
then?
Suparna
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
We may state this "from start to the physiological
maturity stage of the embryo development but does not
involve the physiological process of seed dormancy"
pankaj
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Or maybe even just this for embryonic development (s.M.)
"The embryonic development that ends WHEN seed dormancy
BEGINS, as in, but not restricted to, the flowering plants
(Magnoliophyta, ncbi_taxonomy_id:3398). "
This definition implies that seed dormancy is NOT included
within embryonic development.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
I think GO uses PART_OF relationship in a very strict sense
and we all know that sed dormancy is not always a part of
seed development. Therefore I would rather defer from doing
this relationship.
Also at some point you might have to move sensu
Magnoliophyta to sensu viridiplantae or create a second term
because embryo is not always a part of seed.
However I like your idea of bringing in 'seed development'
term.
Pankaj
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
I agree with Pankaj. Though the concept 'seed development'
is a good one, the children are not always necessarily part_of
the process, depending on which plant you're looking at.
Maybe the general term can go in for now (but let's have a
clear definition) and then children can be added when we
have the ability to handle the additional types of part-of
relationships that we've talked about at the GO meetings.
Tanya
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
I agree with Pankaj. Though the concept 'seed development'
is a good one, the children are not always necessarily part_of
the process, depending on which plant you're looking at.
Maybe the general term can go in for now (but let's have a
clear definition) and then children can be added when we
have the ability to handle the additional types of part-of
relationships that we've talked about at the GO meetings.
Tanya
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
There seems to be some confusion about the sense in which GO uses
'part_of' --
> I think GO uses PART_OF relationship in a very strict sense
> and we all know that seed dormancy is not always a part of
> seed development.
It would be OK to make seed dormancy part_of seed development in GO
(assuming the plant biology is correct - I don't know enough to comment
on that!), because GO is using part_of to mean 'necessarily is part', not
'necessarily has part'. So as long as the child never appears in any context
other than as part of the parent, it's OK to include the relationship.
Thanks for the clarification. In this case, the biology dictates
that we should not have 'seed dormancy' as a necessarily is
part of 'seed development'.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
seed morphogenesis is also an is _a child of morphogenesis
term: seed development
goid: GO:0048316
definition: Biological processes specifically aimed at the progression of the
seed over time, from its initial formation to a mature structure. A seed is
a propagating organ formed in the sexual reproductive cycle of
gymnosperms and angiosperms, consisting of a protective coat enclosing
an embryo and food reserves.
definition_reference: GO:jic
definition_reference: http://cancerweb.ncl.ac.uk
term: seed dormancy
goid: GO:0010162
definition: The processes by which a dormant state is induced and
maintained in a seed. Dormancy is characterized by a suspension of
physiological activity that can be reactivated once dormancy is broken.
definition_reference: TAIR:lr
term: seed morphogenesis
goid: GO:0048317
definition: Developmental processes by which the seed is generated and
organized.
definition_reference: GO:jic
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Can you add a sentence to teh definition/comment
suggesting that seed dormancy is not always a part of seed
development.
It relationship type is not apparent from the [p]/< icons for
the user.
Also I am still confude with the seed development and seed
morphogenesis definitions, they make the same meaning, only
the wording is different. I think morphogeneis is more related
to acquiring shapes and forms http://www.google.com/search?q=define:Morphogenesis
Pankaj
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
We do not normally add that sort of comment to terms or their part_of
parents -- there is no precedent for adding anything about the
relationships to either definitions or comments. At present there is only one
part_of relationship in GO, which is explained in the documentation (see http://www.geneontology.org/GO.usage.html#partof\).
It would be redundant, and an enormous amount of work for little gain, to
add text eplaining the meaning of 'part_of' to each definition or comment,
and inconsistent to do it for only one term.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
I am not sure how many people have a tendency to read the
help documents.
In any case as Tanya suggested the term, seed dormancy
goid: GO:0010162 is only an instance of a physiological
process and not 'seed development". Seed development is
independent of the dormancy.
Pankaj
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Yes, as I suggested in my comment from 3-24-04, please do
not make 'seed dormancy' a part-of child of 'seed
development' as there are plants (many agricultural crop
species) where 'seed dormancy' is never a part of 'seed
development'.
One could possibly have 'seed dormancy (sensu whatever this
applies to - eudicotyledons? - need an expert here)' as a part-
of child of 'seed development' but not the parent 'seed
dormancy' term.
Tanya
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Yes, as I suggested in my comment from 3-24-04, please do
not make 'seed dormancy' a part-of child of 'seed
development' as there are plants (many agricultural crop
species) where 'seed dormancy' is never a part of 'seed
development'.
One could possibly have 'seed dormancy (sensu whatever this
applies to - eudicotyledons? - need an expert here)' as a part-
of child of 'seed development' but not the parent 'seed
dormancy' term.
Tanya
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Please could you possibly reread Midori's comment
below in which she explained the part_of
relationship? From what you are saying it seems
that you may be misunderstanding it.
Just to reiterate, there are several types of
part_of relationship. The GO consortium only
uses the version that is called
'necessarily is part', which means that wherever
the child exists, it is as part of the parent. So
in the case we are discussing it would be
appropriate to make seed dormancy a part_of child
of seed development if the following criteria hold:
1) seed dormancy can exist as part of seed
development.
2) in some species seed development does
not include a seed dormancy phase.
3) under no circumstance may seed dormancy
exist without having arisen as part of seed development.
The other part_of relationship type that
you seem to be thinking of is called
'necessarily has part'. This is the exact
inverse; wherever the parent exists,
it has the child as a part, but the child is
not necessarily part of the parent. This means that
seed dormancy would have 'necessarily has part'
relationship to seed development if the following
criteria hold:
1) seed development always includes a seed
dormancy phase regardless of the species.
2) seed dormancy can occur even if seed
development is not taking place.
Did you find that documentation on this
was hard to follow? If so then is there
anything we could do to make it better?
I know what you mean about it being a bit
unapproachable but the GO is really too technical
to work in isolation and without accompanying
documentation. Also there are really too many
rules to consider trying to have them all in
the comments so that the GO would work entirely
without separate documentation.
On a separate note, I'm not completely sure
that we have the same idea of when seed development
ends. My understanding is that seed development
ends after seed dormancy. Do you have a different
view that seed development ends
before seed dormancy? If so then please would it
be possible for you to find a published
reference that makes this point clear
because I have been unable to find anything
that clearly states that seed development
ends before the onset of seed dormancy and my
references seem to suggest the opposite.
Thanks for considering this.
Jen
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
So if some species don't have seed dormancy then the point
is moot. Finally, a light bulb went off in my head.
Unless Pankaj can come up with an example of seed dormancy
outside of seed development, I drop all my objections. Since
the definition of seed development does NOT explicitly say
that seed dormancy is involved, there is no need for
confusion.
Maybe in addition to the examples from the component
ontology in the 'part-of' documentation, we could have
examples from the process ontology? Something like what
you wrote below would be good.
Sorry it took me so long to figure this out.
Tanya
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Seed dormancy phase starts after the embryo development has
gone through the torpedo stage and somewhat in a growth
phase where it fills the embryo sac. As sson as this
development stage is reached, ALL THE DEVELOPMENT ACTIVITIES
ARE CEASED and starts the onset of dormancy phase. There is
no development/growth (cell division) going on at the time
seed is undergoing a physiological state of dromancy.
Therefore basically seed dormancy is not a part of seed
development but a part of "seed maturation process" (new GO
term), which is a physiological state/process.
Embryo can continue to develop after the dormancy is broken.
Logged In: YES
user_id=579762
I think you're right, Pankaj. Jen can probably fix this quite
quickly.
Tanya
Logged In: YES
user_id=614564
The reason I added this term under GO:0009793 is because of
the definition of the term which states
"The embryonic development that ends with seed dormancy,
as in, but not restricted to, the flowering plants
(Magnoliophyta, ncbi_taxonomy_id:3398). "
ends with seed dormancy makes me think seed dormancy is
included in the process.Should the definition of 9793 change
then?
Suparna
Logged In: YES
user_id=561361
I think so.
We may state this "from start to the physiological
maturity stage of the embryo development but does not
involve the physiological process of seed dormancy"
pankaj
Logged In: YES
user_id=579762
Or maybe even just this for embryonic development (s.M.)
"The embryonic development that ends WHEN seed dormancy
BEGINS, as in, but not restricted to, the flowering plants
(Magnoliophyta, ncbi_taxonomy_id:3398). "
This definition implies that seed dormancy is NOT included
within embryonic development.
Logged In: YES
user_id=561361
I agree with your definition.
Pankaj
Logged In: YES
user_id=735846
How about if I make a new term 'seed development' with 'embryonic
development (sensu Magnoliophyta)' and 'seed dormancy' both being
part_of children?
Jen
Logged In: YES
user_id=561361
I think GO uses PART_OF relationship in a very strict sense
and we all know that sed dormancy is not always a part of
seed development. Therefore I would rather defer from doing
this relationship.
Also at some point you might have to move sensu
Magnoliophyta to sensu viridiplantae or create a second term
because embryo is not always a part of seed.
However I like your idea of bringing in 'seed development'
term.
Pankaj
Logged In: YES
user_id=579762
I agree with Pankaj. Though the concept 'seed development'
is a good one, the children are not always necessarily part_of
the process, depending on which plant you're looking at.
Maybe the general term can go in for now (but let's have a
clear definition) and then children can be added when we
have the ability to handle the additional types of part-of
relationships that we've talked about at the GO meetings.
Tanya
Logged In: YES
user_id=579762
I agree with Pankaj. Though the concept 'seed development'
is a good one, the children are not always necessarily part_of
the process, depending on which plant you're looking at.
Maybe the general term can go in for now (but let's have a
clear definition) and then children can be added when we
have the ability to handle the additional types of part-of
relationships that we've talked about at the GO meetings.
Tanya
Logged In: YES
user_id=436423
There seems to be some confusion about the sense in which GO uses
'part_of' --
> I think GO uses PART_OF relationship in a very strict sense
> and we all know that seed dormancy is not always a part of
> seed development.
It would be OK to make seed dormancy part_of seed development in GO
(assuming the plant biology is correct - I don't know enough to comment
on that!), because GO is using part_of to mean 'necessarily is part', not
'necessarily has part'. So as long as the child never appears in any context
other than as part of the parent, it's OK to include the relationship.
See http://www.geneontology.org/GO.usage.html#partof
for the gory details.
Logged In: YES
user_id=579762
Thanks for the clarification. In this case, the biology dictates
that we should not have 'seed dormancy' as a necessarily is
part of 'seed development'.
Logged In: YES
user_id=735846
I have done this:
-%development ; GO:0007275
--%seed development ; GO:0048316
---<embryonic development (sensu Magnoliophyta) ; GO:0009793
---<seed dormancy ; GO:0010162
---<seed morphogenesis ; GO:0048317
seed morphogenesis is also an is _a child of morphogenesis
term: seed development
goid: GO:0048316
definition: Biological processes specifically aimed at the progression of the
seed over time, from its initial formation to a mature structure. A seed is
a propagating organ formed in the sexual reproductive cycle of
gymnosperms and angiosperms, consisting of a protective coat enclosing
an embryo and food reserves.
definition_reference: GO:jic
definition_reference: http://cancerweb.ncl.ac.uk
term: seed dormancy
goid: GO:0010162
definition: The processes by which a dormant state is induced and
maintained in a seed. Dormancy is characterized by a suspension of
physiological activity that can be reactivated once dormancy is broken.
definition_reference: TAIR:lr
term: seed morphogenesis
goid: GO:0048317
definition: Developmental processes by which the seed is generated and
organized.
definition_reference: GO:jic
Logged In: YES
user_id=561361
Can you add a sentence to teh definition/comment
suggesting that seed dormancy is not always a part of seed
development.
It relationship type is not apparent from the [p]/< icons for
the user.
Also I am still confude with the seed development and seed
morphogenesis definitions, they make the same meaning, only
the wording is different. I think morphogeneis is more related
to acquiring shapes and forms
http://www.google.com/search?q=define:Morphogenesis
Pankaj
Logged In: YES
user_id=436423
We do not normally add that sort of comment to terms or their part_of
parents -- there is no precedent for adding anything about the
relationships to either definitions or comments. At present there is only one
part_of relationship in GO, which is explained in the documentation (see
http://www.geneontology.org/GO.usage.html#partof\).
It would be redundant, and an enormous amount of work for little gain, to
add text eplaining the meaning of 'part_of' to each definition or comment,
and inconsistent to do it for only one term.
Logged In: YES
user_id=561361
I am not sure how many people have a tendency to read the
help documents.
In any case as Tanya suggested the term, seed dormancy
goid: GO:0010162 is only an instance of a physiological
process and not 'seed development". Seed development is
independent of the dormancy.
Pankaj
Logged In: YES
user_id=579762
Yes, as I suggested in my comment from 3-24-04, please do
not make 'seed dormancy' a part-of child of 'seed
development' as there are plants (many agricultural crop
species) where 'seed dormancy' is never a part of 'seed
development'.
One could possibly have 'seed dormancy (sensu whatever this
applies to - eudicotyledons? - need an expert here)' as a part-
of child of 'seed development' but not the parent 'seed
dormancy' term.
Tanya
Logged In: YES
user_id=579762
Yes, as I suggested in my comment from 3-24-04, please do
not make 'seed dormancy' a part-of child of 'seed
development' as there are plants (many agricultural crop
species) where 'seed dormancy' is never a part of 'seed
development'.
One could possibly have 'seed dormancy (sensu whatever this
applies to - eudicotyledons? - need an expert here)' as a part-
of child of 'seed development' but not the parent 'seed
dormancy' term.
Tanya
Logged In: YES
user_id=735846
Hi,
Please could you possibly reread Midori's comment
below in which she explained the part_of
relationship? From what you are saying it seems
that you may be misunderstanding it.
Just to reiterate, there are several types of
part_of relationship. The GO consortium only
uses the version that is called
'necessarily is part', which means that wherever
the child exists, it is as part of the parent. So
in the case we are discussing it would be
appropriate to make seed dormancy a part_of child
of seed development if the following criteria hold:
1) seed dormancy can exist as part of seed
development.
2) in some species seed development does
not include a seed dormancy phase.
3) under no circumstance may seed dormancy
exist without having arisen as part of seed development.
The other part_of relationship type that
you seem to be thinking of is called
'necessarily has part'. This is the exact
inverse; wherever the parent exists,
it has the child as a part, but the child is
not necessarily part of the parent. This means that
seed dormancy would have 'necessarily has part'
relationship to seed development if the following
criteria hold:
1) seed development always includes a seed
dormancy phase regardless of the species.
2) seed dormancy can occur even if seed
development is not taking place.
Did you find that documentation on this
was hard to follow? If so then is there
anything we could do to make it better?
I know what you mean about it being a bit
unapproachable but the GO is really too technical
to work in isolation and without accompanying
documentation. Also there are really too many
rules to consider trying to have them all in
the comments so that the GO would work entirely
without separate documentation.
On a separate note, I'm not completely sure
that we have the same idea of when seed development
ends. My understanding is that seed development
ends after seed dormancy. Do you have a different
view that seed development ends
before seed dormancy? If so then please would it
be possible for you to find a published
reference that makes this point clear
because I have been unable to find anything
that clearly states that seed development
ends before the onset of seed dormancy and my
references seem to suggest the opposite.
Thanks for considering this.
Jen
Logged In: YES
user_id=579762
Hi Jen,
So if some species don't have seed dormancy then the point
is moot. Finally, a light bulb went off in my head.
Unless Pankaj can come up with an example of seed dormancy
outside of seed development, I drop all my objections. Since
the definition of seed development does NOT explicitly say
that seed dormancy is involved, there is no need for
confusion.
Maybe in addition to the examples from the component
ontology in the 'part-of' documentation, we could have
examples from the process ontology? Something like what
you wrote below would be good.
Sorry it took me so long to figure this out.
Tanya
Logged In: YES
user_id=561361
Here is my 2c on it.
Seed dormancy phase starts after the embryo development has
gone through the torpedo stage and somewhat in a growth
phase where it fills the embryo sac. As sson as this
development stage is reached, ALL THE DEVELOPMENT ACTIVITIES
ARE CEASED and starts the onset of dormancy phase. There is
no development/growth (cell division) going on at the time
seed is undergoing a physiological state of dromancy.
Therefore basically seed dormancy is not a part of seed
development but a part of "seed maturation process" (new GO
term), which is a physiological state/process.
Embryo can continue to develop after the dormancy is broken.
Ref:
http://trc.ucdavis.edu/egsutter/plb171/lecturespdf4/5-Seed%20dormancy02.pdf
PMID: 14676287
PMID: 11124119
That's the farthest I can go on this and thanks for making
some of the things clear.
Also if you are compiling the seed development tree then
consider bringing in the endosperm development term in it.
Pankaj