Plant development terms, page 2

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This entry is a continuation of the earlier plant development terms entry [721338] (which has become too large to handle easily).

Please read through item 721338 in full before commenting on this one! Item 711107 is also relevant.

Midori

Reported by: mah11

Original Ticket: "geneontology/ontology-requests/783":https://sourceforge.net/p/geneontology/ontology-requests/783

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Sorry about the scatter-brained ness of this Sourceforge item. Reconciling monocot and dicot flower morphogenesis is proving to be much more complicated that I had (naively) hoped. I'm even wondering whether we should split them out:

flower morphogenesis (sensu Eudicot) flower morphogenesis (sensu Poaceae)

What do you think? I'll let you ponder this before I send out another ontology to look at.

Also, should we think of a way to group the existing meristem terms under a super term? Maybe 'meristem development' as Jen suggested?

Currently:

%development ---%meristem organization ------%meristem initiation ---%meristem specification ---%meristem maintenance

We were thinking of obsoleting 'meristem organization' and suggestion 'meristem maintenance' as a substitute and moving 'meristem initiation' up one node, like this.

%development ---%meristem development ------<meristem initiation ------<meristem specification ------<meristem maintenance

Another term to ponder:

specification of organ position/phyllotactic patterning/phyllotactic pattern specification (isa pattern specification, part of organogenesis) gene: FFO1 (fused floral organs 1)

Original comment by: tberardini

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[ 877837 ] inflorescence development (+more) is also connected.

Jen

Original comment by: jenclark

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I just checked with Tanya if I can take this over since she is busy and this coincides with one of my other items. She says that's fine. Also she said

'As far as making 'xxx morphogenesis' and 'xxx development' terms synonymous, as is the proposed case for xxx = inflorescence, I don't think this should be done. As you've just done for 'seed development' and 'seed morphogenesis,' I think that the development group has come up with standard definitions and usage for these two types of terms.
I know that I made the mistake of making shoot morphogenesis = shoot development and root morphogenesis = root development and this should be cleaned up. I just didn't want to perpetuate this mistake with new terms to be added.'

Jen

Original comment by: jenclark

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Original comment by: jenclark

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I have just read through both of these sourceforge items. They are about trying to capture plant development and to accommodate both monocots and dicots. It's quite a big problem to try to deal with and there a lot of ideas in here to consider.

Although no firm conclusions have been reached here, I think a good job has been done of identifying the kinds of problems that need to be addressed.

This might be one to include in the content meeting later in the year, but in the meantime I think the best thing would be if I read through this about two dozen times and write a clear summary of what's happened so far and what the current questions are.

(This comment is partly a note to me so next time I come back I can remember what the plan is.)

Jen

Original comment by: jenclark

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Yes! A summary would be wonderful!

Original comment by: tberardini

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Rightio. I'll have shot. :-)

Ta for the encouragement.

Jen

Original comment by: jenclark

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This is Tanya's plan from the previous page now in obo format. It is this file that is being discussed in this item.

Original comment by: nobody

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These are the defs. Previously in .doc format, now in .txt format.

Original comment by: jenclark

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Sent this e-mail to Tanya and Pankaj:

I took the plant development sourceforge item and tried to make sense of the comments:

http://www.ebi.ac.uk/~jclark/GOwebsite/plants\_dev/plant.dev.html

It seems to me that it might make sense to split this into several separate sourceforge items. Below were the individual threads covered. Those with an x were resolved. The remaining ones could probably be further subdivided in future into more manageable chunks as well.

Germination parentage x
Terms to cover floral organs and whorls of organs.
Preference for development terms over morphogenesis terms. x
Use of 'embryo' or 'embryonic' x
cotyledons v. prophylls.
cotyledon/leaf relationship
flowering v. flower development x
parentage of flowering x
order of terms in graph x

It seemed to me that the main problems that Tanya was trying to address were reconciling monocot and dicot flowering patterns and dealing with the floral whorl issues. These issues got buried in a series of more minor concerns.

It might be good if those of us contributing agreed in principle that we should just think a bit about how to deal with the big ideas without getting sidetracked by many small details. We could also try to work out what high level processes we need to capture and then deal with them one at a time.

e.g. monocot flower development dicot flower development floral organ development floral whorls development

Does that seem like a reasonable starting place?

Thanks,

Jen

Original comment by: jenclark

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Hi Pankaj and Tanya,

I'd like to split this item so we have separate sourceforge items for monocot and dicot flowering terms. Would that seem okay? It seems as if the dicot flowering terms are much closer to being ready to go than the monocot ones, and they are also very urgently needed by Tanya for annotation. I think that if we work on smaller sections of ontology then we will have a better chance of getting to the implementation stage. If the monocot terms turn out not to fit exactly into the dicot structure then we can always move things around a bit once we get to that stage.

What would you think about this? It seems to me that we've been biting off more than we can chew up to now and have consequently failed to get anything at all to the implementation stage.

Jen

Original comment by: jenclark

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This item has now been split into several other items for further work. These are 966600 monocot inflorescence development 966599 Monocot flower development terms 951331 Dicot Flower development

There are several other threads that can come out of this work, so for now I would like this item to remain open until have made sure that all the individual threads are being carried on in new sourceforge items.

If you're coming to this item new I would recomend not trying to read through it at first, but instead visiting the follow in threads. This item is also summarized in full at http://www.ebi.ac.uk/~jclark/GOwebsite/ plants_dev/plant.dev.html

Thanks,

Jen

Original comment by: jenclark

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I will close this now. The information will still be there. Jen

Original comment by: jenclark

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• milestone: 257750 --> TermGenie
• status: open --> closed-fixed

Original comment by: jenclark