#1600 GO:0010162 : seed dormancy

TermGenie
closed-fixed
5
2014-08-26
2004-03-15
No

I think following parent term is not required for
GO:0010162

GO:0009793 : embryonic development (sensu Magnoliophyta)

Based on my understanding Embryo is already developed
before it goes under dormancy.

Pankaj

Discussion

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  • Tanya Berardini

    Tanya Berardini - 2004-03-16

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    I think you're right, Pankaj. Jen can probably fix this quite
    quickly.

    Tanya

     
  • Tanya Berardini

    Tanya Berardini - 2004-03-16
    • assigned_to: nobody --> jenclark
     
  • Suparna Mundodi

    Suparna Mundodi - 2004-03-16

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    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

     
  • Pankaj Jaiswal

    Pankaj Jaiswal - 2004-03-16

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    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

     
  • Tanya Berardini

    Tanya Berardini - 2004-03-16

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    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.

     
  • Pankaj Jaiswal

    Pankaj Jaiswal - 2004-03-16

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    I agree with your definition.

    Pankaj

     
  • Jennifer Deegan

    Jennifer Deegan - 2004-03-24

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    How about if I make a new term 'seed development' with 'embryonic
    development (sensu Magnoliophyta)' and 'seed dormancy' both being
    part_of children?

    Jen

     
  • Pankaj Jaiswal

    Pankaj Jaiswal - 2004-03-24

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    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

     
  • Tanya Berardini

    Tanya Berardini - 2004-03-24

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    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

     
  • Tanya Berardini

    Tanya Berardini - 2004-03-24

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    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

     
  • Midori Harris

    Midori Harris - 2004-03-24

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    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.

     
  • Tanya Berardini

    Tanya Berardini - 2004-03-24

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    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'.

     
  • Jennifer Deegan

    Jennifer Deegan - 2004-03-25

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    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

     
  • Jennifer Deegan

    Jennifer Deegan - 2004-04-05
    • status: open --> closed
     
  • Jennifer Deegan

    Jennifer Deegan - 2004-04-05
    • status: closed --> closed-fixed
     
  • Pankaj Jaiswal

    Pankaj Jaiswal - 2004-04-05

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    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

     
  • Jennifer Deegan

    Jennifer Deegan - 2004-04-06
    • status: closed-fixed --> pending-fixed
     
  • Jennifer Deegan

    Jennifer Deegan - 2004-04-06
    • status: pending-fixed --> open-fixed
     
  • Midori Harris

    Midori Harris - 2004-04-06

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    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.

     
  • Pankaj Jaiswal

    Pankaj Jaiswal - 2004-04-06

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    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

     
  • Tanya Berardini

    Tanya Berardini - 2004-04-06

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    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

     
  • Tanya Berardini

    Tanya Berardini - 2004-04-06

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    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

     
  • Jennifer Deegan

    Jennifer Deegan - 2004-04-07

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    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

     
  • Tanya Berardini

    Tanya Berardini - 2004-04-07

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    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

     
  • Pankaj Jaiswal

    Pankaj Jaiswal - 2004-04-07

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    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

     
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