plant gametogenesis cont.

[gocentral]

This sourceforge item is opened as a continuation of [ 780468 ] megagametogenesis/oogenesis/spore development which is getting very long.

Reported by: jenclark

Original Ticket: "geneontology/ontology-requests/1081":https://sourceforge.net/p/geneontology/ontology-requests/1081

[gocentral]

Logged In: YES user_id=735846

Hi Tanya,

Here's the latest draft:

%sexual reproduction -%gametophyte development ; GO:new, synonym:gametogenesis (sensu Magnoliophyta) --%female gametophyte development, synonym: megagametogenesis
(and children) --%male gametophyte development, synonym: microgametogenesis
(and children) -%gametogenesis ; GO:0007276 --%ovum generation, synonym: female gamete generation, synonym: oogenesis ; GO:0007292 ---%megasporogenesis, synonym: female gamete generation (sensu Magnoliophyta) ; GO:0009554 ----%female gametophyte egg cell differentiation ; GO:new
---%oogenesis (sensu Insecta) --%male gamete generation ; GO:new def: Generation of the haploid male gamete. ---%spermatogenesis ; GO:0007283 ---%microsporogenesis, synonym: male gamete generation (sensu Magnoliophyta) ; GO:0009556 ----%male gametophyte sperm cell differentiation ; GO:new --%gamete generation (sensu Magnoliophyta) ; GO:0009552 was Gametogenesis (sensu Magnoliophyta) ---%megasporogenesis, synonym: female gamete generation (sensu Magnoliophyta) ; GO:0009554 ----%female gametophyte egg cell differentiation ; GO:new
---%microsporogenesis, synonym: male gamete generation (sensu Magnoliophyta) ; GO:0009556 ----%male gametophyte sperm cell differentiation ; GO:new -%spore development (sensu Magnoliophyta) ; GO:new
--%microsporogenesis ; GO:0009556 --%megasporogenesis ; GO:0009554

Does that work okay with the formatting? I can construct it in DAG-edit if that's easier. I think it should be okay though since I've fixed all the formatting to be one hyphen per indentation.

Jen

Original comment by: jenclark

[gocentral]

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Hi Tanya,

This name change

--%gamete generation (sensu Magnoliophyta) ; GO:0009552 was Gametogenesis (sensu Magnoliophyta)

is going to affect about 50 annotations. I've been very careful to keep the term because it will affect annotations. I would just like to check that the annotations will still be correct after the name change. The term currently has the definition sting for generation of gametes but the term name for gametophyte development. As long as the annotations have been made to the definition then they will remain correct after the term name changes. Do you think that this is the case?

Thanks,

Jen

Original comment by: jenclark

[gocentral]

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Hi Jen,

We had yesterday off (Labor Day) so I'm just catching up now. I like most of the latest draft quite a bit. The only quibble I (still) have is that the term 'ovum development' is a parent of 'megasporogenesis.' Can't we just call it 'female gamete development' and leave it at that? We can put the 'ovum development' in as a synonym for the 'oogenesis sensu' terms but the curators over here would really prefer it if 'megasporogenesis' did not fall under such a 'animal-specific' term.

Is there a pressing need to have these be synonyms of the grouping node?

As for the annotations, there are no direct annotations to GO:0009552, all the ones that I can see in the GO database are to its children terms. I also don't see any in our local curation database so I think we're ok with making this change.

I will, though, look over the annotations to micro- and mega- gametogenesis to make sure that they belong to the gametophyte development and not to gamete generation (micro-and megasporogenesis).

Thanks,

Tanya

Original comment by: tberardini

[gocentral]

Logged In: YES user_id=579762

Hi Jen,

We had yesterday off (Labor Day) so I'm just catching up now. I like most of the latest draft quite a bit. The only quibble I (still) have is that the term 'ovum development' is a parent of 'megasporogenesis.' Can't we just call it 'female gamete development' and leave it at that? We can put the 'ovum development' in as a synonym for the 'oogenesis sensu' terms but the curators over here would really prefer it if 'megasporogenesis' did not fall under such a 'animal-specific' term.

Is there a pressing need to have these be synonyms of the grouping node?

As for the annotations, there are no direct annotations to GO:0009552, all the ones that I can see in the GO database are to its children terms. I also don't see any in our local curation database so I think we're ok with making this change.

I will, though, look over the annotations to micro- and mega- gametogenesis to make sure that they belong to the gametophyte development and not to gamete generation (micro-and megasporogenesis).

Thanks,

Tanya

Original comment by: tberardini

[gocentral]

Logged In: YES user_id=579762

Hi Jen,

We had yesterday off (Labor Day) so I'm just catching up now. I like most of the latest draft quite a bit. The only quibble I (still) have is that the term 'ovum development' is a parent of 'megasporogenesis.' Can't we just call it 'female gamete development' and leave it at that? We can put the 'ovum development' in as a synonym for the 'oogenesis sensu' terms but the curators over here would really prefer it if 'megasporogenesis' did not fall under such a 'animal-specific' term.

Is there a pressing need to have these be synonyms of the grouping node?

As for the annotations, there are no direct annotations to GO:0009552, all the ones that I can see in the GO database are to its children terms. I also don't see any in our local curation database so I think we're ok with making this change.

I will, though, look over the annotations to micro- and mega- gametogenesis to make sure that they belong to the gametophyte development and not to gamete generation (micro-and megasporogenesis).

Thanks,

Tanya

Original comment by: tberardini

[gocentral]

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Yes that's a good lot of points. I'll change the term names as you suggest:

-%gametogenesis ; GO:0007276 --%female gamete generation ; GO:0007292 ---%megasporogenesis, synonym: female gamete generation (sensu Magnoliophyta) ; GO:0009554 ----%female gametophyte egg cell differentiation ; GO:new
---%oogenesis (sensu Insecta)

Thanks for checking those annotations. If you could let me know when you've done that then I'll implement the planned changes.

Thanks,

Jen

Original comment by: jenclark

[gocentral]

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Hi Jen,

I've been giving this yet more thought and realized that we should probably change the structure some more. This is because the individual '%sporogenesis' terms are not equivalent to the whole gamete generation process but are part of it. Note the changes in parentage and the addition of two new terms.

How about:

%sexual reproduction -%gametophyte development ; GO:new, synonym:gametogenesis (sensu Magnoliophyta) --%female gametophyte development, synonym: megagametogenesis
(and children) --%male gametophyte development, synonym: microgametogenesis
(and children) -%gametogenesis ; GO:0007276 --%female gamete generation ; GO:0007292 ---%female gamete generation (sensu Magnoliophyta) ; GO: new -----<megasporogenesis ; GO:0009554 -----<female gametophyte egg cell differentiation ; GO:new
---%oogenesis (sensu Insecta) --%male gamete generation ; GO:new def: Generation of the haploid male gamete. ---%spermatogenesis ; GO:0007283 ---%male gamete generation (sensu Mag.), synonym: pollen development ; GO:new ----<microsporogenesis ; GO:0009556 ----<male gametophyte sperm cell differentiation ; GO:new --%gamete generation (sensu Magnoliophyta) ; GO:0009552 was Gametogenesis (sensu Magnoliophyta) ---%female gamete generation (sensu Magnoliophyta) ; GO:new (and children) ---%male gamete generation (sensu Magnoliophyta), synonym: pollen development; GO:new (and children) -%spore development (sensu Magnoliophyta) ; GO:new
--%microsporogenesis ; GO:0009556 --%megasporogenesis ; GO:0009554

What do you think?

Thanks,

Tanya

BTW: TIGR has 12 gene products annotated to microgametogenesis GO:000955. You might want to contact Linda Hannick (lhannick@tigr.org) to have her check on these. I'm still going through TAIR's annotations.

Original comment by: tberardini

[gocentral]

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Hi again,

More thinking (dangerous). You can go ahead and implement the changes we've discussed (if you agree with my latest suggestion, or we can talk some more) before I finish looking at all our annotations. If I have to move some annotations to the new 'female/male gamete generation' terms then I'll need the new terms to be in place before I can do the transfer.

Thanks,

Tanya

Original comment by: tberardini

[gocentral]

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Hi Tanya,

That's great. I'll commit that.

Thanks,

Jen

Original comment by: jenclark

[gocentral]

• status: open --> closed-fixed

Original comment by: jenclark

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Hi Jen,

I just noticed something! You created new terms for female gametophyte development and male gametophyte development with synonyms mega and microgametogenesis but there were already EXISTING terms micro and megagametogenesis that I had added a while back. I thought that you were going to change the main string to be the gametophyte development and move the gametogenesis string to be the synonyms. I did not notice that there were GO:new terms beside these. My fault! The upshot is that now there are two megagametogenesis terms and two microgametogenesis terms in the GO! I'd say get rid of the new ones, maybe not even move them to the obsolete node, just straight deletion so we can reuse the ids. It was just a mix-up.

I could do this now but I want you to have a chance to read this message.

Whoops.

Tanya

I fixed the definition of megasporogenesis so that the wording was right. It was a copy-paste error from when I first entered this. I also fixed the children of gamete generation so that megagametogenesis and microgametogenesis were no longer children of this. Also changed the relationship types of the sporogenesis terms under spore development (sensu Mag.) to be isa instead of part of.

Original comment by: tberardini

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The stuff after my signature were changes I was going to make to the structure/relationship types before I realized the duplication error so I haven't done any of these. The definition updates stand.

Original comment by: tberardini

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Hi Tanya,

Thanks for pointing that out. I'll merge the terms and change the name. It's a pretty complicated juggling of words isn't it?

I've opened a new sourceforge item for this now since it will soon be too long to generate the e-mail. It's [ 800444 ] Plant gametogenesis

Thanks,

Jen

Original comment by: jenclark