GO:0010162 : seed dormancy

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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

Reported by: jaiswalp

Original Ticket: "geneontology/ontology-requests/1600":https://sourceforge.net/p/geneontology/ontology-requests/1600

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

Tanya

Original comment by: tberardini

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Original comment by: tberardini

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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

Original comment by: smundodi

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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

Original comment by: jaiswalp

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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.

Original comment by: tberardini

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I agree with your definition.

Pankaj

Original comment by: jaiswalp

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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

Original comment by: jenclark

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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

Original comment by: jaiswalp

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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

Original comment by: tberardini

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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

Original comment by: tberardini

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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.

Original comment by: mah11

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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'.

Original comment by: tberardini

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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

Original comment by: jenclark

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Original comment by: jenclark

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Original comment by: jenclark

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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

Original comment by: jaiswalp

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Original comment by: jenclark

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Original comment by: jenclark

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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.

Original comment by: mah11

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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

Original comment by: jaiswalp

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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

Original comment by: tberardini

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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

Original comment by: tberardini

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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

Original comment by: jenclark

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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

Original comment by: tberardini

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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

Original comment by: jaiswalp

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The processes you describe fit with Jen's proposed definition (see below):

(... from its initial formation to a mature structure.)

As we've defined it in GO, development encompasses morphogenesis AND maturation. Jen has started the documentation that covers this section but I'm not sure it's ready for release yet (Jen?).

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

Tanya

Original comment by: tberardini

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Okay accepted.

Original comment by: jaiswalp

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Original comment by: jenclark

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I have made endosperm development a part_of child of seed development as suggested, and have past on my explanation of part_of to jane so it can be added to the documentation of the part_of relationship.

I will close this item now.

Thanks for all the discussion.

Jen

Original comment by: jenclark