monocot inflorescence development

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This is a sourceforge item to work out terms for monocot inflorescence development. It follows on from [ 877837 ] inflorescence development (+more) https://sourceforge.net/tracker/index.php? func=detail&aid=877837&group_id=36855&atid=440764

Reported by: jenclark

Original Ticket: "geneontology/ontology-requests/1780":https://sourceforge.net/p/geneontology/ontology-requests/1780

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Hi,

I've taken the terms that Pankaj suggested in the preceding sourceforge item and have worked on them a bit and put them into obo format for dag-edit. I have made adjustments to accommodate the differences between dicot and monocot development, and I have cut out the morphogenesis terms completely so we can start with just the development terms and add in the morphogenesis terms later. There are a lot of sensu Eudicotyledon and sensu Poaceae terms which had to be added to accommodate the part_of relationship (http:// www.geneontology.org/GO.usage.html#partof). The Poaceae terms are intended to cover the grasses (http://www.ncbi.nlm.nih.gov/Taxonomy/ Browser/wwwtax.cgi?id=4479) and the Eudicotyledon terms are intended to cover the dicots (http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/ wwwtax.cgi?id=71240).

Can anybody see anything wrong with the structure I have proposed? In the past we have had trouble in plant development discussions because the discussions became so entangled that nothing was ever implemented. To avoid this problem I would be keen also to know which grass terms people think are definately correct, and I can implement those first if other parts prove to be more troublesome. I have not defined the terms because I think the meanings are pretty obvious, but if it helps I can define them as well. The GO:ids are meaningless so please ignore them. They will be replaced with new ideas at the time of implementation.

Thanks for taking the time to look at this. :-)

Jen

Original comment by: jenclark

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monocot file in obo format 12/7/4

Original comment by: jenclark

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Sent e-mail to po-dev to ask for second opinions:

Hi,

Pankaj and I have been working on some terms to cover grass inflorescence and flower development in the Gene Ontology Consortium process ontology. I have just put together a first draft of a proposal for the addtition of terms and I wondered if people with knowledge of grass development could possibly have a look (some time in the next two weeks) and check that it's heading in the right direction?

[ 966600 ] monocot inflorescence development https://sourceforge.net/tracker/index.php? func=detail&aid=966600&group_id=36855&atid=440764

Thank you very much for your help.

Best wishes,

Jennifer

Original comment by: jenclark

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Pankaj:

Hi Jen,

I looked at it yesterday and was hoping to reply today. My immediate concern was do we really have two sensu sections Poaceae and Eudicots. reason being -if we are really on to it then we need sensu liliopsida (monocots) along with Eudicots. -the poaceae flowers which are called as florets do not have sepal/petal/ tepal. -there are two views on looking at a flower in grasses (Poaceae) -the floret is contained in a floret. In this floret the actual flower is missing petal/sepal/tepal. The lemma and palea being part of the floret and flower is also a part of it. -second view which we have adopted in PO is that floret ISA flower. This way lemma and palea from grass floret also becomes PARTOF flower

--flower --i--floret ----i-floret (sensu Poaceae) ------p--lemma ------p--palea generic term because in compositeae the flowers are also called floret

With this it seems that we need to discuss on do we really need instantiations. Which we may have to if we are using the PARTOF relationship in a strict sense. If not, as mentioned in http:// www.geneontology.org/GO.usage.html#partof, then we can have one single term "flower development" without sensu instantiations.

Similarly for inflorescence we have merged all the different types of inflo as synonyms except for the maize ear and tassel

I can foresee some of the problems but I think we need to first come up with a set of queries people would like to make and ofcourse the annotation requirements.

Please let me know your suggestions.

Pankaj

PS: please include Anuradha Pujar <bryonia2000@yahoo.com> in our discussions. She is a new hire at Gramene who will be contributing to the Ontology aspects.

Original comment by: jenclark

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Hi Pankaj,

Thanks ever so much for the swift reply. My replies below have a '*' before them.

1) My immediate concern was do we really have two sensu sections Poaceae and Eudicots.

*Yes this is worrying me too. :-(

2) reason being -if we are really on to it then we need sensu liliopsida (monocots) along with Eudicots.

*Good point.

The sensu designation means 'in the sense of' rather than 'for the annotation of' so we don't need to worry about making the sensu designation broad enough to cover everything that might be annotated to it.

We could do what we did before and tailor it to the species being annotated. e.g. just have:

sensu Arabidopsis sensu Poaceae (or several more specific taxa if there are further specific annotation needs within this group.)

We probably need to be quite specific here since there is so much diversity in flower development, and so many species being studied. It might be better to use smaller taxonomic groups that are already being annotated and where we are absolutely sure about what we are saying. Then in future we will not have to further split out the taxa specific terms.

3) -the poaceae flowers which are called as florets do not have sepal/petal/tepal.

*Great. I haven't put those in as children of floret development (sensu Poaceae) so does that mean that the children of that term are correct?

4) -there are two views on looking at a flower in grasses (Poaceae) -the floret is contained in a floret. In this floret the actual flower is missing petal/sepal/tepal. The lemma and palea being part of the floret and flower is also a part of it. -second view which we have adopted in PO is that floret ISA flower. This way lemma and palea from grass floret also becomes PARTOF flower

* Thanks for telling me about that. Good to know you've already discussed it. In fact the lemma and palea terms are already indirect children of flower development via floral bract development so I think that's fine.

5)

--flower --i--floret ----i-floret (sensu Poaceae) ------p--lemma ------p--palea

floret should be a generic term because in compositeae the flowers are also called floret

*I could make 'floret development' a synonym of 'flower development' and make the two floret development sensu terms children of 'flower development'. I'm pretty certain that wouldn't cause mayhem but we could rethink if it does. It would also make good logical sense to me, since they are types of flowers.

6) With this it seems that we need to discuss on do we really need instantiations. Which we may have to if we are using the PARTOF relationship in a strict sense. If not, as mentioned in http:// www.geneontology.org/GO.usage.html#partof, then we can have one single term "flower development" without sensu instantiations.

* This is what puzzles me too. I'd be really keen to know what people think.

Here's how I've been thinking of it:

In plant developmental biology we look at different kinds of plants and try to see what's the same. e.g. we see flowers in grasses and trees and small weedy dicots and say 'look those structures are all basically the same thing'. This research mindset has lead to many really fairly different things being described using the same words. This is why I have ended up adding so many sensu terms. (The whole point of sensu terms is that if two different concepts have the same name we can distinguish them using the sensu modifier. For example a compositae flower and an arabidopsis flower are both called 'flowers' but are really quite different, as one is technically an inflorescence.)

It seems to me that to allow annotators the proper scope to annotate to the greatest possible granularty we will need to provide terms for the different types of flower and floral organ. The shortage of distinguishing language within the research community is a problem for us here, and means that we will need to fall back on the use of sensu quite a lot to do this. However, I think that it's more important to be able to capture the information and developmental concepts, than to be bound by the lack of distinguishing vocabulary.

The questions is, how many of the different types of flower do we consider to be different enough to have their own term? In the case of the Poaceae floret I consider that it is different from an arabidopsis flower on the basis that it has the palea and a lemma.

7) Similarly for inflorescences we have merged all the different types of inflo as synonyms except for the maize ear and tassel

*Really? Okay. I think that's the same kind of thing as above. If you feel you need new child terms of inflorescence to allow you to annotate to the maximum granularity then I can add as many as you need. I guess the inflorescences would be distinguished on the basis of their architecture.

8) I can foresee some of the problems but I think we need to first come up with a set of queries people would like to make and of course the annotation requirements.

*That seems like an excellent plan. Let me know what you think.

(Anuradha, if you want to ask millions of questions then go ahead. This is pretty hard stuff to get used to when you're new and it's worth asking. My e-mail address is jclark@ebi.ac.uk if you prefer to ask offlist.)

Jen

Original comment by: jenclark

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e-mail from toby (Elizabeth Kellogg):

Hi Jennifer - Looks fine, although I'm not quite sure what the development ontology is designed to do. It seems as though you could have a development term for every term that's in the PO, which would make for quite a few terms. Toby

my reply:

Hi Toby,

Thanks for looking at that. In the long term the development node of the process ontology will probably move to cross-products which means that we'll take 'development' from the process ontology, and all the plant bits like 'leaf' and 'root' and 'carpel' from the anatomy ontology and put them together to get all the development terms. We can't do that yet though so I have to make all the terms individually right now.

Jen

Original comment by: jenclark

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Hi,

At this time,

I would suggest not to instantiate to monocot/dicot divide. We can just have generic flower development and as you said floret sensu Poaceae can become its instance.

I wrote to Chris Mungal on the aspect of searching annotations by clade and not just the species and his reply was that he can make it available. When ? That I don't know.

If that's available (I would very much like to), the following query can work.

-show me all the proteins that contribute to MONOCOT flower and not to DICOT flower development.

If we go with this then we can avoid populating instantiated terms like flower development sensu monocots/dicots and their children sepal/tepal/petal/stamen/carpel development.

Thus allowing us to annotate to the generic term. However once we have the floret sensu Poaceae the only instantiations we need is for parts of androecium and gynoecium. We struggled with this in PO anatomy also because once the sensu term is there nothing generic can go underneath.

This is the same argument Toby is referring to. Try to limit the instantiations. I haven't looked at it, w which we should to see how many reports are there that suggest, parts of different flower types develop differently.

My suggestion is all based on the anatomy organization we have agreed for PO. We tried not to instantiate even for species unless absolutely necessary. The places where we had to was because of the current state of ontology design and the DB query mechanism.

You may want to have a look at the most recent version of anatomy.ontology file at http://brebiou.cshl.edu/viewcvs/Poc/anatomy/anatomy.ontology?rev=1.26&content-type=text/vnd.viewcvs-markup

---

Here is my updated version on inflo and flower development

inflorescence development; synonym: panicle dev, spike dev, raceme dev etc -i-ear dev (sensu Zea) -i-tassel dev (sensu Zea) -p-inflorescence bract dev ---i-glume dev -p-spikelet development ---p-glume dev ---i-spikelet development (sensu Zea) -----p--sessile spikelet dev -----p--pedicellate spikelet dev

flower development -p-androecium dev ---p-stamen dev -p-gynoecium dev ---p-carpel dev -p-corolla dev ---p-petal dev -p-calyx ---p-sepal dev -p-tepal dev -p-floral bract dev ---p-lemma dev ---p-palea dev -i-floret dev (sensu Poaceae) ---p-lemma dev -----i-fertile lemma dev -----i-sterile lemma dev ---p-palea dev ---p-androecium dev(sensu Poaceae) -----p-stamen dev (sensu Poaceae) ---p-gynoecium dev(sensu Poaceae) -----p-carpel dev (sensu Poaceae)

After having the top level structure we can fill in the finer terms.

Will see if I can come up with a set of queries in the next couple of days.

Original comment by: jaiswalp

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Hi Pankaj,

Yes that does sound rather sensible. I'll mess around with the dag today and think through what happens if I do not use sensu terms. :-)

Jen

Original comment by: jenclark

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I just remembered that Tanya recommended this paper too so I'm reading that:

A floret by any other name: control of meristem identity in maize. McSteen P, Laudencia-Chingcuanco D, Colasanti J. PMID: 10664615

Jen

Original comment by: jenclark

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Hi Pankaj,

I tried thinking about having very few sensu terms and I think you might be right. I think if we try it we'll find out.

I have looked at your terms and I include my comments. I've also got all the sensu eudicot flower development terms removed from the ontology so it is ready to receive whatever we decide is needed. I think it's fairly clear from the current status of our discussions that whatever is needed, it probably isn't eudicot terms.

Here are my thoughts on your dags:

A)

inflorescence development; syn: panicle dev, spike dev, raceme dev etc -i-ear dev (sensu Zea) -i-tassel dev (sensu Zea) -p-inflorescence bract dev ---i-glume dev -p-spikelet development ---p-glume dev ---i-spikelet development (sensu Zea) -----p--sessile spikelet dev -----p--pedicellate spikelet dev

1) Are you sure you want panicle dev, spike dev, raceme dev as synonyms instead of is_a children?

I notice that in the in the anatomy ontology you have e.g.

%inflorescence -<raceme inflorescence --<panicle

2) What is the other sensu version of ear dev, tassel dev, spikelet dev that you would like in the process ontology?

B)

flower development -p-androecium dev ---p-stamen dev -p-gynoecium dev ---p-carpel dev -p-corolla dev ---p-petal dev -p-calyx ---p-sepal dev -p-tepal dev -p-floral bract dev ---p-lemma dev ---p-palea dev -i-floret dev (sensu Poaceae) ---p-lemma dev -----i-fertile lemma dev -----i-sterile lemma dev ---p-palea dev ---p-androecium dev(sensu Poaceae) -----p-stamen dev (sensu Poaceae) ---p-gynoecium dev(sensu Poaceae) -----p-carpel dev (sensu Poaceae)

1) Is there any way in which the Poaceae floret is significantly different from the generic flower, other than the possession of extra bits? According to the argument you gave before I don't think there is. The part of rule states that wherever the child exists, it is as part of the parent, but it doesn't necessarily have to exist in every instance of the parent. So this structure above could maybe be:

flower development (syn. floret dev, ray floret dev.) -p-androecium dev ---p-stamen dev -p-gynoecium dev ---p-carpel dev -p-corolla dev ---p-petal dev -p-calyx ---p-sepal dev -p-tepal dev -p-floral bract dev ---p-lemma dev -----i-fertile lemma dev -----i-sterile lemma dev ---p-palea dev

With this we are assuming that the arabidopsis flower and the poaceae flower and the asteraceae ray floret are all basically the same thing but that they are composed of different selections of the structures listed as part of children of 'flower development' above.

(By the way, do you represent dags like this in PO? In GO we generally show them like this:

%grass -%green grass -<grass blade --%green grass blade.

% equals is_a < equals part_of

with a standard number of hyphens to show that a term is the child of the term above. If the method you've used above is your preferred method then that's fine though, I can just get used to it. It's very clear and I see that you have spaced the child terms very carefully relative to the parent terms which is really helpful.)

Thanks,

Jen

Original comment by: jenclark

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Please see my comments following Pankaj:

Jen:A)

inflorescence development; syn: panicle dev, spike dev, raceme dev etc -i-ear dev (sensu Zea) -i-tassel dev (sensu Zea) -p-inflorescence bract dev ---i-glume dev -p-spikelet development ---p-glume dev ---i-spikelet development (sensu Zea) -----p--sessile spikelet dev -----p--pedicellate spikelet dev

1) Are you sure you want panicle dev, spike dev, raceme dev as synonyms instead of is_a children?

Pankaj: Yes. As of now. I would suggest to have them as synonyms. the idea is unless somebody finds a gene or a group of genes responsible for the development of raceme/cyme kind of inflorescence. we can have them as synonyms. At least consistent with the POC.

Jen: I notice that in the in the anatomy ontology you have e.g.

%inflorescence -<raceme inflorescence --<panicle

Pankaj: Did you get it from an old version. The new version says http://brie.cshl.org:8086/go.cgi?open\_0=PO:0009049&open\_1=PO:0009075

$plant ontology ; PO:0009075 %plant growth and development ; PO:0009012 %plant structure ; PO:0009011 %sporophyte ; PO:0009003 <shoot ; PO:0009006 <inflorescence ; PO:0009049 ; synonym:cob (sensu sorghum) ; synonym:corymb ; synonym:cyme ; synonym:dichasium ; synonym:drepanium ; synonym:helicoid cyme ; synonym:monochasium ; synonym:panicle ; synonym:PO:0009048 ; synonym:PO:0009050 ; synonym:PO:0020088 ; synonym:PO:0020111 ; synonym:PO:0020112 ; synonym:PO:0020113 ; synonym:PO:0020114 ; synonym:PO:0020115 ; synonym:PO:0020116 ; synonym:PO:0020117 ; synonym:PO:0020118 ; synonym:PO:0020119 ; synonym:PO:0020120 ; synonym:raceme ; synonym:rhipidium ; synonym:scorpioid cyme ; synonym:spike (sensu Triticeae) ; synonym:umbel ; synonym:verticillaster

Jen: 2) What is the other sensu version of ear dev, tassel dev, spikelet dev that you would like in the process ontology?

Pankaj: Actually, there are some people working on Triticeae that use this term "ear" for their inflorescence. That's the reason we have this. We did not create the other sensu. On the other hand you can avoid adding sensu Zea and can add it later on when there is a requirement from other species. All you have to make it clear is that this ear is different than the "ear development/morphogenesis" in mammals.

Jen B)

flower development -p-androecium dev ---p-stamen dev -p-gynoecium dev ---p-carpel dev -p-corolla dev ---p-petal dev -p-calyx ---p-sepal dev -p-tepal dev -p-floral bract dev ---p-lemma dev ---p-palea dev -i-floret dev (sensu Poaceae) ---p-lemma dev -----i-fertile lemma dev -----i-sterile lemma dev ---p-palea dev ---p-androecium dev(sensu Poaceae) -----p-stamen dev (sensu Poaceae) ---p-gynoecium dev(sensu Poaceae) -----p-carpel dev (sensu Poaceae)

Jen 1) Is there any way in which the Poaceae floret is significantly different from the generic flower, other than the possession of extra bits? According to the argument you gave before I don't think there is. The part of rule states that wherever the child exists, it is as part of the parent, but it doesn't necessarily have to exist in every instance of the parent. So this structure above could maybe be:

flower development (syn. floret dev, ray floret dev.) -p-androecium dev ---p-stamen dev -p-gynoecium dev ---p-carpel dev -p-corolla dev ---p-petal dev -p-calyx ---p-sepal dev -p-tepal dev -p-floral bract dev ---p-lemma dev -----i-fertile lemma dev -----i-sterile lemma dev ---p-palea dev

With this we are assuming that the arabidopsis flower and the poaceae flower and the asteraceae ray floret are all basically the same thing but that they are composed of different selections of the structures listed as part of children of 'flower development' above.

Pankaj: I agree with you and was very much thinking on the similar lines for POC, but the problem is how about if someone likes to search on "show me all the genes that are responsible for the development of floret or its parts?". Right now this structure will not be able to support this kind of a query, because the petal/sepal/tepal annotations will also appear in his/her query result if floret is a synonym of flower and not instance.

I also agree that this is very much a sticky point and creates problems by compelling us to create sensu instantiations.

Though this can be avoided by a query that involves (see below) relationship_type "NOT always a PARTOF as a subtype of PARTOF" and combining with the synonym. Which I doubt if its possible with the current state of relationship type usage (PARTOF is part of no matter how we interpret it) and use of synonyms.

Show me all the genes that are responsible for development of Floret (a synonym) and its PARTs that are NOT ALWAYS a PARTOF generic flower.

Jen: (By the way, do you represent dags like this in PO? In GO we generally show them like this:

%grass -%green grass -<grass blade --%green grass blade.

% equals is_a < equals part_of

with a standard number of hyphens to show that a term is the child of the term above. If the method you've used above is your preferred method then that's fine though, I can just get used to it. It's very clear and I see that you have spaced the child terms very carefully relative to the parent terms which is really helpful.)

Pankaj: Yes we do. We try to be as consistent as possible with the GO.

e.g.

-<flower ; PO:0009046 --%floret ; PO:0009082 ---%floret (sensu Poaceae) ; PO:0006318 ----<gynoecium (sensu Poaceae) ; PO:0006384 -----%gynoecium of ear floret ; PO:0006365 -----%gynoecium of tassel floret ; PO:0006317 ----%tassel floret ; PO:0006310 -----<gynoecium of tassel floret ; PO:0006317 ----%ear floret ; PO:0006354 -----<gynoecium of ear floret ; PO:0006365

Thanks Pankaj

Original comment by: jaiswalp

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Hi Pankaj,

I have interspersed my comments below.

1) Are you sure you want panicle dev, spike dev, raceme dev as synonyms instead of is_a children?

Pankaj: Yes. As of now. I would suggest to have them as synonyms. the idea is unless somebody finds a gene or a group of genes responsible for the development of raceme/cyme kind of inflorescence. we can have them as synonyms. At least consistent with the POC.

Jen: Good point. Okay I can leave them as synonyms.

b)

Pankaj: Did you get it from an old version. The new version says http://brie.cshl.org:8086/go.cgi?open\_0=PO:0009049&open\_1=PO:0009 075

Jen: Ah! That's very nice. Shall I treat the Amigo/PO site as the most up to date from now on then?

2) Jen: What is the other sensu version of ear dev, tassel dev, spikelet dev that you would like in the process ontology?

Pankaj: Actually, there are some people working on Triticeae that use this term "ear" for their inflorescence. That's the reason we have this. We did not create the other sensu. On the other hand you can avoid adding sensu Zea and can add it later on when there is a requirement from other species. All you have to make it clear is that this ear is different than the "ear development/morphogenesis" in mammals.

jen: Cool. We can have ear development sensu terms and leave the others as generic then. :-)

B) flower development (syn. floret dev, ray floret dev.) -p-androecium dev ---p-stamen dev -p-gynoecium dev ---p-carpel dev -p-corolla dev ---p-petal dev -p-calyx ---p-sepal dev -p-tepal dev -p-floral bract dev ---p-lemma dev -----i-fertile lemma dev -----i-sterile lemma dev ---p-palea dev

Pankaj: I agree with you and was very much thinking on the similar lines for POC, but the problem is how about if someone likes to search on "show me all the genes that are responsible for the development of floret or its parts?". Right now this structure will not be able to support this kind of a query, because the petal/sepal/tepal annotations will also appear in his/her query result if floret is a synonym of flower and not instance.

Jen: But surely that can be solved by using the species specific query that you suggested before. If you search for the genes annotated to the children of flower development that belong to a poaceae species then you automatically get those genes responsible for the development of a floret or it's parts.

Thanks for all the discussion. This is really helping. I hope we can get some terms in really quickly to help the annotators get a head start.

Best wishes,

Jen

Original comment by: jenclark

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For 2A section, I have opened a discussion on po mailing list. Lets see what we get.

The poc ontology browser can be accessed at http://amigo.plantontology.org/go.cgi At least for now. I will let yu know when the link is stable.

Pankaj

Original comment by: jaiswalp

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sorry it was 2B section -pankaj

Original comment by: jaiswalp

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Pankaj wrote to the list and this was the only reply we got:

A flower is most certainly NOT a floret. This is a common misconception, but it isn't so.

A floret is a flower PLUS 1) lemma, 2) palea, 3) the axis on which the flower and these two bracts are borne, and 4) lodicules, depending on interpretation. Many or most people interpret the lodicules as perianth parts, in which case they are part of the flower, but if they are interpreted as additional structures, rather than as part of the flower, they are an additional component of the floret.

Now, you can find some literature in which the lemma and palea are interpreted as modified floral parts, in which case the flower and floret would become identical or nearly identical in meaning, but this is an extremely unconventional interpretation.

Jerry

Original comment by: jenclark

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Hi Pankaj,

I'm not sure that the PO list people have helped make this any clearer for us. Do you have any thoughts on what to do next? Jerry doesn't seem keen to accept the PO view of the floret being like the flower and that contradicts the paper that Tanya mentioned. Maybe we need to think of a way to deal with this that will accommodate both possible views until the researchers reach an agreement?

Jen

Original comment by: jenclark

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Hi Pankaj,

I asked David Hill about our monocot problems and he had an idea. What do you think about this?

My question:

we have three flower-ish things that are not really quite the same (dicots, grasses and maize flower-ish things). One is a flower, the next is a floret (which is a flower plus a stem and two bracts) and the third is another slightly different thing also called a floret. Then all three of these things have anthers (male sexual organs) which are really exactly the same.

I'm just not sure how to make the development terms for these. Especially since the anther development term can't have the part_of relationship to three separate kinds of flower-ish thing. It would make lots of sensu terms which would be a bit crazy since the anthers are all actually the same:

-%reproductive structure development --%flower development ---<anther development (sensu dicot) --%floret development ---%floret development (sensu grass) ----<anther development (sensu grass) ---%floret development (sensu maize) ----<anther development (sensu maize)

Do you know if there's a simple fix for this that I just haven't noticed?

David:

How about?

-%reproductive structure development synonyms flower development, floret development --<anther development --<flower part that is specific to dicot development (e.g. dicot petal development) --<flower part the is specific to grass development --<bract development --<floret stem development --<flower part the is specific to maize development

Since I don't know the anatomy, you will have to put the right terms in for the above.

Original comment by: jenclark

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Hi,

This item has been open for a long time. Please comment to let us know whether you would like it to remain assigned to you, or would prefer it to be reassigned. (You don't necessarily have to work on it immediately if you keep it; we just need to know whether it's still on your list.)

Thanks, Midori & David Ontology development group managers

Original comment by: mah11

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• status: open --> closed-out-of-date

Original comment by: jenclark