Plant gametogenesis

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This is a continuation of [ 798477 ] plant gametogenesis cont.

Reported by: jenclark

Original Ticket: "geneontology/ontology-requests/1092":https://sourceforge.net/p/geneontology/ontology-requests/1092

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Hi Jen,

Was there supposed to be an attachment for this?

Tanya

Original comment by: tberardini

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Hi Tanya,

No it's just here as a reminder to me that I haven't finished this yet. I'll put text in as soon as I get a chance to straighten my plan out.

Thanks,

Jen

Original comment by: jenclark

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Hi,

I've expanded the plant gametogenesis terms as suggested in one of the predecessors of this sourceforge item. I constructed all the new terms in DAG-Edit so I've put the term and definition files on the file download section on this page. Please could the folks in the GO office have a look and tell me if I'm heading the right direction with these new terms? You can tell the new ones because they're numbered between GO:0000000 and GO:0000100.

Thanks,

Jen

Original comment by: jenclark

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From Jane:

Jen - comments on gametogenesis...there's a problem with all those part of relations...we can discuss if u like,

j

Ontology

- shouldn't fertilization, gametogenesis, gametophyte development be part_of rather than is_a sexual reproduction?

- spore development (sensu Magnoliophyta) - from the def it sounds like this should be part_of gametophyte development?

- the terms that involve the development/differentiation of some type of cell e.g. antipodal cell differentiation need to be given extra parents under 'cell differentiation'. Look for other extra parents too e.g. spore development (don't know if this is a term?), mitosis terms etc.

- Redundant relationship - pollen formation under microsporogenesis and its parent spore development (sensu Mag) - remove from one of these places.

- GO:0009564/GO:0048157 what's the difference between formation here and development/differentiation elsewhere?

- I think there may be a problem with some of the part_of relationships...remember when we were talking at the meeting about the different part_of relationships? Well the one we're supposed to use, 'necessarily part_of' means (in process) 'whenever this process occurs, it occurs as part of this larger process'. This means that you can't have the same term as part_of more than one parent process. Having more than one part_of parent also causes problems with the true path. the terms I've noticed that cause a problem are GO:0009557, GO:0009558, GO:0009560, GO:0009561, GO:0009562, GO:0009563, GO:0009564...actually loads.

- GO:0009560 - redundant relationship under GO:0009560.

Defs

- define antopodal cell in 'antipodal cell disintegration'.

- typo in GO:0000009 - 'endosprem'

- GO:0000001 - define mycropyle.

- GO:0000013 - define synergid cell.

- GO:0000062 - define ovule primordium.

- GO:0000062/GO:0000061 formation v/s development - what's the difference? Add to def.

On Mon, 13 Oct 2003, Jennifer I Clark wrote:

>> Hi, >> >> Would it be possible for you to have a look at the >> gametogenesis section of ontology that I've >> uploaded onto this sourceforge page? >> [ 800444 ] Plant gametogenesis >> https://sourceforge.net/tracker/index.php?func=detail&aid= 800444&group_id=36855&atid=440764 >> >> I've added a lot of new terms to the plant >> gametogenesis section and I know the biology is >> good, but I'd just like to check that they way >> I've constrcted it corresponds to what you'd >> expect for the ontology. >> >> Thanks, >> >> Jen >> >> >> -- >> EMBL - European Bioinformatics Institute >> and Wolfson College, Cambridge. >> http://www.ebi.ac.uk/~jenclark/ >> >> >>

Original comment by: jenclark

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Not done yet:

- the terms that involve the development/differentiation of some type of cell e.g. antipodal cell differentiation need to be given extra parents under 'cell differentiation'. Look for other extra parents too e.g. spore development (don't know if this is a term?), mitosis terms etc.

- GO:0009564/GO:0048157 what's the difference between formation here and development/differentiation elsewhere?

Defs

- define antopodal cell in 'antipodal cell disintegration'.

- GO:0000001 - define mycropyle.

- GO:0000013 - define synergid cell.

- GO:0000062 - define ovule primordium.

- GO:0000062/GO:0000061 formation v/s development - what's the difference? Add to def.

Original comment by: jenclark

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The latest version is attached below with the date: 14/10/03

Original comment by: jenclark

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not done yet:

- the terms that involve the development/differentiation of some type of cell e.g. antipodal cell differentiation need to be given extra parents under 'cell differentiation'. Look for other extra parents too e.g. spore development (don't know if this is a term?), mitosis terms etc.

- GO:0009564/GO:0048157 what's the difference between formation here and development/differentiation elsewhere?

Defs

- GO:0000062/GO:0000061 formation v/s development - what's the difference? Add to def.

Original comment by: jenclark

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Hi Jen,

I finally had a chance to look at this. Sorry for the delay.

Some comments:

1. I don't think 'male gametophyte development' should be a part of 'gamete generation (s.M.)'.

2. 'male gametophyte development' and '...formation' are not related to each other. I think they should be. Perhaps as suggested in the 'development terms' discussion:

% X development --<X formation

3. Could we leave the main name of (in your file) GO:0000018 as 'female gametophyte development' and have 'mature embryo sac development' as the synonym?

That's all for now. You could also run the whole defs file through a spell checker as I ran across a few typos along the way.

Good job! I'll look at this again next week.

Tanya

Original comment by: tberardini

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Original comment by: jenclark

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Original comment by: jenclark

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Hi Tanya, Thanks for looking at that. I think there might be a bit of a delay while I find out all about development v morphogenesis v formation and things but by the end of that I should be able to fix this up much better. I 've attached the latest files at the bottom.

Thanks again,

Jen

Original comment by: jenclark

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Yes, I think we should sort out the generic defs/organization first. Hopefully, that will be quite soon. As far as I'm concerned, we should be ready to use the new and improved layout as David last suggested it.

Tanya

Original comment by: tberardini

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terms for plant gametogenesis

Original comment by: jenclark

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I have talked with David Hill and lots of other people, about how to deal with the formation and development terms. As a result of this discussion I have changed the terms that cover 'formation' of a particular cell to 'differentiation' of that cell. i.e. 'formation of the synergid cell' becomes 'differentiation of the synergid cell'. I have also used this for small groups of cells with the same identity e.g. 'formation of the eight-nucleate embryo sac' is now 'differentation of the eight-nucleate embryo sac'. I think that should solve all the remaining problems and so this work is ready to commit. I will do that next wednesday, 25/2/04 unless anybody suggests anything else that needs changing. I will upload the new copies of the files at the bottom of this page. They are the ones with the latest dates on the file names.

Thanks,

Jen

Original comment by: jenclark

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term definitions

Original comment by: jenclark

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Some responses from David Hill on e-mail:

I'm not sure this will work. Sorry! This comes back to the when does development/differentiation occur. I think that formation of the synergid cell is actually part of the differentiation of the cell that is the precursor to the synergid cell. Differentiation of the synergid cell would be the synregid cell turning into something else. Does this make sense?

David

I would think in this context, formation is better, but I think what I said below is confusing. I think the distinction, which is a hard/subtle one is: Is the "formation of a synergid cell" reflective of an unspecialized cell becoming a synergid cell, or is the formation of a synergid cell the conversion of another cell type into a synergid cell. If it is the former, then it is differentiation, if it is the latter, then it is formation (part of this formation would be differentiation). I don't know enough about the cell types to determine which is correct. I think below I should have said the synergid cell maturing rather than turning into something else.

David

So as I sit here and think about this I think I have a way to sum it up. Cell differentiation is cell autonomous. It can be influenced by outside events, but it all occurs within the cell that is differentiating. Is this the case with synergid cells and eight-nucleate embryos? Does it represent a cell turning into another kind of cell?

David

Original comment by: jenclark

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my response to david on e-mail:

Hi David,

Thanks for taking the time to help me with this. The synergid cell is made by conversion from a more generic kind of cell. There are 8 of these generic cells and once they are formed they shuffle around to different places within the embryo sac. Once each generic cell has arrived in it's proper place it changes identity. The synergid cell is defined by its location near the interior side of the micropyle of the embryo sac of an angiosperm. The generic cells are called embryo sac cells.

Thanks,

Jen

Then his next response:

In this case it sounds like differentiation, where the synergid cell differentiates based on its position in the embryo.

David

Then me:

Hi,

Cool

In that case can I just check what you meant by this bit:

---

>>>>> I'm not sure this will work. Sorry! This comes back to the when >>>>> does development/differentiation occur. I think that formation of >>>>> the synergid cell is actually part of the differentiation of the >>>>> cell that is the precursor to the synergid cell. Differentiation of >>>>> the synergid cell would be the synregid cell turning into something >>>>> else. Does this make sense? >>>>> David

I just looked at some other differentiation cells in the ontologies and I see:

glial cell differentiation ; GO:0010001 def: The process whereby a relatively unspecialized cell acquires the specialized features of a glial cell.

does that mean that my synergid cell term should be:

synergid cell differentiation ; GO:new def: The process whereby a relatively unspecialized cell acquires the specialized features of a synergid cell.

or do you disagree with this use of differentiation and think that we should be saying 'differentiation to form a synergid cell'.

Thanks,

Jen

Original comment by: jenclark

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David's response:

synergid cell differentiation ; GO:new def: The process whereby a relatively unspecialized cell acquires the specialized features of a synergid cell.

I think the above will work because from you last e-mail, this is exactly what you describe. Unspecialized cells take on this characteristic based on where they are in the embryo.I was confused by your original e-mail because I thought it was referring to more than one cell type. I think my original e-mail to you was misleading based on a misconception on my part.

David

Original comment by: jenclark

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I have incorporated the standard definition for differentiation into the differentiation terms. The new files are uploaded below. (18_2_pm)

Jen

Original comment by: jenclark

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defs

Original comment by: jenclark

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terms for plant gametogenesis

Original comment by: jenclark

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Another e-mail discussion:

Hi David,

Can I ask another question please?

I have a process:

eight nucleate embryo sac differentiation ; GO:0000017 def: Mitosis of all four nuclei of the four-nucleate embryo sac to give rise to the eight-nucleate embryo sac.

Would you be happy with the idea that having 8 nuclei instead of 4 is enough of a change to merit the name of differentiation?

Thanks,

Jen

If you folks consider this a cellular process, then I think it is o.k. For example in animals, we have the formation of multinucleate myotubes, but I'm not sure I would consider this cell differentiation instead I would be tempted to call it muscle formation.

David

Hi,

I see, yes, that sounds similar. In that case would you be happy for me to call it 'eight-nucleate embryo sac formation'? That's what I would have done in the first place really since the only change is the number of nuclei.

Thanks,

Jen

Original comment by: jenclark

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This discussion will now move to [ 899726 ] plant gametogenesis 2 https://sourceforge.net/tracker/index.php? func=detail&aid=899726&group_id=36855&atid=440764 since the current page is getting very long.

Jen

Original comment by: jenclark

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closing, since there's an open one for continuation

Original comment by: mah11

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• status: open --> closed

Original comment by: mah11