Belated comments from Leszek (05/30-31/'02) indicated via the following format in margin:

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**Leszek:
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My comments are marked with

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$$$ Pankaj: comments 
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Pankaj:I hope now TAIR will work on this file to organize rest of the
part. I am freezing the work on this file from my side. I have not
touched the TAIR part since its them who will have to work on
it. Please make the necessary corrections or updates.

** Tanya has made some of the changes already and we are working on
others
to try and integrate better. But rather than make global changes- we
thought we'd try to come to an understanding about some basics first and
make sure we understood the non-arabidopisis terms better.**

Pankaj: Another thing, I am not willing to accept this ontology as a
"plant
temporal ontology"... best is to call it a "plant growth stage
ontology" PO:0007040

** I think there is agreement on that- at least in terms
of getting rid of the temporal term- how about plant developmental
stages?**
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**Leszek: my take is that the terms 'growth' & 'development' are virtually synonymous in the literature I've consulted - being phenotypic expression(s) of the process of ONTOGENY. The OMD defs support this. Seems like developmental biologists focus a lot on the process of ontogeny, while breeders focus more on 'trait stages' which are colloquially called 'growth stages' (I'm generalizing but let's debate this if necessary & I may have overlooked some aspect). I too recommend 'plant growth stage ontology' & would provide the synonym 'plant developmental stages'. Suggest we mention that plant growth stages are phenotypic expressions (~Trait stages) of the 'ontogenetic process'.
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$$$ Pankaj: I guess here we have to be clear about clarifying the difference between development and growth

Growth: (Websters Dictionary)- A progressive development of an organism
Development: (Websters Dictionary)- The act , process or result of developing or state of being developed
Growth: (online medical dictionary)- <biology> The series of changes which animal and vegetable organisms undergo in their passage from the embryonic state to maturity, from a lower to a higher state of organization.
Development: (online medical dictionary)- The process of growing; the gradual increase of an animal or a vegetable body; the development from a seed, germ, or root, to full size or maturity; increase in size, number, frequency, strength, etc.

Given the definitions, I would rather suggest to call it simply "Plant growth stage". reason Vegetative/reproductive/embryonic are the main growth stages and underlying these are their instances of developmental stages (they are overlapping stages and does not occur in a series as defined for growth in the definition from OMD)  that lead to a full organization of a plant. Once again these are the milestones that are recorded and not the actual development process (which are part of GO-process)

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**Leszek: See my comment above - growth/development are synonyms of the well established term ONTOGENY which covers the concept dealing with growth/development from zygote formation thru to seed/propagule formation & probably up to & including senescence (from beginning to end)!
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GENERAL COMMENTS:

(1) General terminology questions: crop species related?

** We did have some questions about some of the terminology- it likely
reflects the perspective of crop species that later developmental stages
seem to be defined in terms of seed characteristics. Should there be
seed
developmental stages (which includes embryo stages as well as endosperm
developmental stages)? I noticed on your site (Gramene) the following
link (http://www.riceweb.org/Plant.htm#morph) describes three phases,
vegetative, reproductive and ripening. I am sure that fruit ripening
stages would be very highly desireable to include for tomato- but they
dont (to my knowledge) define whole plant stages in terms of fruit
ripening. Perhaps we need to further divide whole plant stages from
organ specific stages (e.g. leaf plastochrons, flower developmental stages,
fruit ripening stages)?**
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$$$ Pankaj: How about 
 %vegetative stage
 %reproductive stage
 %ripening stage 
  %fruit ripening stage
  %embryonic stage syn: seed development stage (from post fertilization to germination)
   %endosperm development stage
   %embryo development stage

For the suggested organ specific stages (e.g. leaf plastochrons, flower developmental stages,
fruit ripening stages), you can decide where to have this, but things to be considered is that how much granularity do we expect to find in the curation and are these terms really valid growth stages accepted by community.
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**Leszek: I'm wrestling with why we are not considering vegetative stage, reproductive stage & ripening stage (above) to be 'part of' relationships (i.e. each a component of a larger whole (ontogeny a.k.a. plant growth stages), rather than being a subset i.e. 'is a' relationship - I'm prejudiced by my understanding that these stages are part of the larger process of ontogeny.

What about: 

 <vegetative stage
 <reproductive stage
  %seed development stage (from post fertilization to germination) (syn.: ovule development stage)
   %embryo development stage
   %endosperm development stage     (will sometime need to include %developement of perisperm)
   %seed-coat development stage
 <ripening stage 
  %fruit ripening stage (syn.: ovule ripening stage; seed development stage)
   %embryo development stage
   %endosperm development stage
   %seed-coat development stage

You will note that I've rearranged & re-described the contents of Pankaj's proposal to reflect the relationships as I currently perceive them. What do the rest of you think of this?? 'Embryonic stage' doesn't work for me (at present). Am I missing something of the dialogue?

Regarding the question of granularity: I suggest we be proactive by providing granularity to a level that is finer than is currently practised (if this is possible & where this could be 'relatively easily' done). I don't have a problem with generating terms in an ontology which are not widely used. Let's consider being proactive like Michael's Sequence Ontology - it seems to cover the gamut of terms that are out there.  
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(2) confusion about terms

a. flowering stages : I'm a little confused. Can we step back and say it
does not include floral induction and floral transition? The definition
of
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$$$ Pankaj: accepted. 
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PO:0007151 (flowering stages) refers to anthesis and includes
fertilization. I think of fertilization and pollination as
events/processes- rather than developmental stages, and anthesis as a
particlular event that marks a stage of flower development (e.g. stage
13 in Arabidopsis).

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**Leszek: I'm wary of lumping events with processes. To me a process is very different from an event. Process has the distinct perspective of biological process. Event is much more of an anthropocentric concept. Anthesis, pollination & fertilization are all processes - part of the big scheme of ontogeny. I does seem that anthesis is cast by some into a trait event but fundamentally I consider it a process. If we refer to the recordable growth aspect of these events, as used as traits, then perhaps we would be wise to refer to these as 'anthesis event', 'pollination event' & 'fertilization event'. This could enable us to keep the current growth stage (developmental stage) designations, as used for maize, in our plant growth stage ontology - without conflicting with the processes of anthesis, pollination & fertilization which need to be in GO...process.
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$$$ Pankaj: Well first of all except maize (MaizeDB), I haven't see any other cereal crop mentioning about the pollination/fertilization/anthesis as growth stages. Leszek please confirm this. Secondly I agree with TAIR that these terms are defined in GO -process and should not be there, but since MaizeDB has defined them , they need to work on this. The reason I am suggesting this is because we need to work in close coordination with the respective databases to define the correct structure. 
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**Leszek: Pankaj, I may be misunderstanding your text above. Yes, I also agree that anthesis, pollination & fertilization should be included in GO process, and as process terms & concepts, should not be represented as such in maizeDB as developmental stages. I need to wrestle more with how to bring about this change to maizeDB. Clearly none of these 3 processes can be considered as growth stages. I think this is just a historical situation which needs to be upgraded - somehow - so as to be consistent & correct with the growing of our ontology structure....
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		Actually, I have alot of confusion about some of
the synonyms for many things here- but can only address the terms I
recognize. For example, I don't think that embryo sac development is
synonymous with megasporogenesis (making spores !=making
gametophytes).
		Also flowering stage PO:0007151 has as a synonym
anthesis and also a instance-child anthesis PO:0007021.

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$$$ Pankaj:
I am sorry I will correct the problem with flowering stage PO:0007151 and its synonym. Consider anthesis as a separate term and Ath stage 13 flower as its synonym
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**Leszek: Regarding the megasporogenesis matter - the genaral international understanding is as follows:

Megasporogenesis comprises: megaspore mother cell -> 4 megaspores (via RD) -> 1 megaspore (3 usually abort) -> 8 nucleate embryo-sac (typically) via mitosis - the embryo-sac being a megagametophyte.
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		Also- the definition of fertilization (again- something
that is a developmental process) refers only to fertilization of egg by
sperm
yet has double fertilization as a synonym. I'd prefer to leave this in
the GO process ontology as double fertilization (sensu Magnoliopsida)-
OR
is this a bona fide plant developmental stage ?
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$$$ Pankaj:MaizeDB has to work on this. I agree with the TAIR's suggestion, it is a GO process
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**Leszek: Regarding the representation of this in maizeDB - answered above - I'll work on this. 'Is this a bona fide plant growth stage'? I'd say NO.
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b. terms that seem to be charateristics of populations
rather than descriptions of stages of development of an individual.

Some
examples are: flowering stage PO:0007151 (when 50% of the plants in the
field are in some stage of bloom?) and late heading stage PO:0007090 (is
that 50-100 percent of the individual inflorescences or of the
population)?

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$$$ Pankaj:These are actual growth stages recorded in Poaceae. Yes it is a growth stage defined by population. ( i will see if we can change it for individual plant since until now these stages have been recorded for trait analyses and not the functional genomics studies)

late heading stage is the 50-100 percent inflorescence emerged in grasses, where it does not mean that the flowers have opened as yet. (they may or may not). and underlying the flowering stage events occurring in this stage are: (a). The tips of the lemma and palea (hulls) open. #(b) The filaments elongate.# (c). The anthers exsert from the lemma and palea. #(d). As the lemma and palea open further, the tips of the feathery stigma become visible. #(e). The filaments elongate past the tips of lemma and palea. #(f). The spikelet closes, leaving the anther outside. Anther dehiscence (pollen shed) usually occurs just prior to or at the time the lemma and palea open (step a). This whole process takes just a few hours in grasses. May be we should say 
  
   %flowering stage (new term)
    %flowering stage (sensu Poaceae) PO:0007151
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**Leszek: Again, to me these are 'phenotypes' that are recorded as observation of 'events'. I go along with Pankaj's structure except I think it would be appropriate to make it 'stages' rather than 'stage' i.e. %flowering stages (sensu Poaceae) PO:0007151

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c.  terms that sound like phenotypes:

secondary dormancy induced
PO:0007122; secondary dormancy lost PO:0007123, seed not dormant
PO:0007121, viable seed germination PO:0007120, kernel loosening in
daytime PO:0007117

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$$$ Pankaj: I agree these are not growth stages, but for this I will have to ask the barley/wheat/oat community to consider changing or getting rid off.
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**Leszek: certainly appear to be phenotypes to me too.
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d.  just plain don't know.

e.g. ratooning- sounds like axillary shoot
development (like what happens when you release apical dominance).

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$$$ Pankaj:True I agree with your thoughts, but some people consider it as a growth stage since it begins a new life cycle in cereals (minus germination and seedling). At the worst I can make it a synonym of tillering.
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**Leszek: "A ratoon is a shoot growing from the root of a plant (especially sugar cane) that has been cut down. v.i. to grow new shoots, or grow as a new shoot, from the root of a plant that has been cut down." (from Webster's). Also a common phenomenon in Pineapple (Ananas comosus, Bromeliaceae)  cultivation. 

I think making this a synonym of tillering would not be such a good choice as tillers usually arise from the lower region of the culm - from branch buds which occur in some of the lowermost leaf axils in Zea mays & other members of the Poaceae - clearly a form of vegetative reproduction (i.e. technically a form of APOMIXIS). Tillering is also a term used by horticulturalists whereby sections of grass culm are buried, giving rise to new growth of certain species of turf (this really confuses the application of the term 'tillering'). So I'd say it should be placed in an 'area' which is representing reproduction, specifically vegetative reproduction (one of the forms of apomixis) - But I don't think it's appropriately placed in a 'plant growth stages' ontology. 
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Should
we include events that are not part of the normal life history (for an
annual plant- senesence/death is normal, though I agree that using this
as the part of the reproductive stage is not good). Maybe there needs to be
another option for perennial, biennials etc...but lets stick to the
annuals we know and love for the moment (when someone sequencing poplar
or loblolly pine joins they can have some fun too).**

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$$$ Pankaj:
can we exclude this for the moment.
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**Leszek: Are we being 'chicken'?? - just joking!
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SPECIFIC COMMENTS:

(1) issue: basal nodes:

**What about sporophytic and gametophytic nodes? Definitely gametophytic
developmental stages are concurrent with sporophytic stages but
shouldn't
they have their own parent node?

e.g. (something like)

%reproductive stages
 %ovule developmental stages
  %anatropous ovule developmental stages
   %ovule initiation stage (synonym: Arabidopsis ovule stage 1-I)
   %ovule elongation stage (synonym: Arabidopsis ovule stage 1-II)
   %nucellar differentiation stage ?? (synonym: Arabidopsis ovule stage
2-I)
   %integument initiation stage (synonym: Arabidopsis ovule stage 2-II)
    <megaspore mother cell meiosis I
 %megasporogenesis stages
  %monosporic megasporogenesis stages
   %megaspore mother cell meiosis I
   %megaspore meosis II

## so are ovule developmental stages and megasporogenesis stages each
others'
siblings and both children of reproductive stages? I'm not sure if I'm
reading the spacing right.##
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$$$ Pankaj:I believe these are all GO-process-development terms and are not the growth stages. MaizeDB has some of these terms like . 
gametophyte development PO:0007017 and its instances
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**Leszek: 'Ovule developmental stages' & 'megasporogenesis' should be siblings. They're certainly not 'growth stages'. I'll need to 'root out' the problems in maizeDB (somehow...). Megasporogenesis starts off being 2n (sporophytic) but end up n (gametophytic). So in the mist I see multiple parentage too. I suggest that both sporophytic & gametophytic nodes will need to represent these concepts.
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at least in the case of arabidopsis which is an anatropous ovule with
monosporic megasporogenesis.

It would be very difficult to really make extensive overlaps in the
developmental stages of different plants- because their developmental
programs are so diverse. For simplicity- maybe just working with
angiosperms-and in particular, the organisms of concern to us (Brassicas
and Poeaceae) is enough of a challenge. If we can work it out for these-
the rest will (hopefully) be simpler. It is very likely that
diversification will happen quicky (i.e. rapidly moving to 'sensu'
terms)
but the broader categories (e.g. vegetative, reproductive, embryogenic,
seed developmental stages, leaf developmental stages etc... would be
grouped. **

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$$$ Pankaj:I know that's why i sent you the first shared version is a very crude form because I was really confused.
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**Leszek: I suggest we go for coarser granularity so as to accommodate a generic structure (in the non-taxonomic sense) & use taxon-specific (i.e. sensu....) for finer granularity, at quite an early stage. From this trial run I think there's enough writing 'on the wall' to indicate that producing a structure that will accommodate just the Poaceae, let alone A. thaliana, necessitates a coarse granularity. Or am I out of the loop?? I don't think reaching the goal of developing a generic structure is because we're just newbies/easily confused - but rather the information content is VERY COMPLEX & trying to represent it in a relatively fine-grained structure is seemingly not possible because the biology we're trying to represent in the ontology is too complex/diverse to enable this.
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(2) issue:  	proposed terms "inflorescence development stage 1-18"
		vs.
		existing terms "stage 1-18 flower"

**Like maize and rice, Arabidopsis has some canonical terms used to
define stages of development. And this is a likely place of departure. What
could possibly be the analogous maize stage to stage 5 flower in Arabidopsis
(stage of flower development when the petal and sepal primordia arise)? It's a
question people are trying to answer but I don't think that the answer
is known. A person would certainly describe an expression pattern in terms
of these stages in Arabidopsis (gene X is expressed throughout the sepals
from stages 4-11). Since we are using morphogical landmarks, rather than
temporal landmarks, there will more often be divergences here).**

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$$$ Pankaj: I agree at some point there has to be a divergence. In this particular instance of primordia development, the grasses don't have a defined granularity 
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Pankaj:definitions for "flower development TAIR?PO: 0000004" such as "stages of
flower
development in Arabidopsis" should be changed.

Tanya:flower development PO:0000004 could be changed to flower development
(sensu Arabidopsis/Brassicaseae), same PO id , can create new term,
flower development for generic use##

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$$$ Pankaj: Sure
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Pankaj:DBXref like "principal growth stage-1.0" should be replaced with
"Arabidopsis
growth stage-1.0"

Tanya:ok. trivial fix 

(3) issue:  Terms like
		"12 rosette stage" PO:0000415, can be replaced with
		"12 leaf stage" as a generic one with "12 rosette stage"

		and "Arabidopsis growth stage 1.12" as synonyms followed
by		definition part from existing term "12 rosette stage"
		PO?TAIR:0000415
	definition: stage at which the first 12 leaves have reached more
than 1 mm length.
	replaced by saying
	Comment: For arabidopsis: stage at which the first 12 leaves
have reached more than 1mm length.

** I don't think that would work-a maize plant with 12 leaves is not the
same as an Arabidopsis plant with 12 leaves.

Tanya:This raises the issue of the proper use of the comment field.  Jane
Lomax has just put out a nice description of the proper uses of the
field
in the GO.  We might want to adopt similar standards.
 If the definitions have to be qualified with comments, as has been
done above, then it seems that one of two things needs to be
done. Either use two different terms, "12 leaf stage" and use that for
maize and "12 rosette stage" and use that for Arabidopsis.  If
the actual string should be the same then the term should be qualified
with the sensu addition, i.e.  12 leaf stage (sensu Zea) and 12 leaf
stage (sensu Arabidopsis) with different definitions. ##
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$$$ Pankaj: I will consider using teh second option (sensu)
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**Leszek: I think this is further evidence that we won't be able to obtain more than coarse granularity because of needing to represent taxon-specific terms (which might be the same but have different definitions!). It's is interesting watching this hypothesis being tested... 

What do you folk 'feel' about using the 'sensu....' format relatively early on in the ontology (i.e. probably 'high up' in the DAG structure) rather than much later as I think you might have been hoping for???
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   We have the same question about booting stages... is it defined the
exact
same way in rice, barley, oat, wheat, maize or is the same term used
with
different meanings? For example- the term import can mean 1) to bear or
convey as meaning or portent OR 2) to bring from a foreign or external
source. The string is the same but the meaning is different. **

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$$$ Pankaj: The definition is same everywhere, Only difference is the time of appearance depending on crop and cultivar
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**Leszek: Further need for the 'sensu....' format with appropriate & taxon-specific definitions.
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Pankaj:(4) conflicts with

reproductive stage PO:0007140
Stages from inflorescence initiation or formation of inflorescence
primordia to
flowering (GR:pj37).
Comment: A greater part of vegetative stage in Poaceae overlap the
reprdutive
stage.
 Vs
reproductive: TAIR/PO: 0000306
stages of development that between flowering and death of the plant.
(TAIR:lr)


Everyone knows that the stage should be defined by the time reproduction
is occurring which includes the development of gametes. In case of the
Poaceae family members, this stage of development starts almost at the same time
stem elongation stage begins (this is about the same time when 5th leaf has
emerged).
So its not only temporal but also spatial.

**First- I agree that using temporal here in the ontology is bad- the
only reason that was used was when it went into the GO CVS and Chris wanted
the same name for all' developmental stage ontologies'. I'd be very happy to
change this back to developmental stages (which is what it was).
Second- what about changing the definition of reproductive stages to
include stages from floral induction/transition (regardless of if there
is an infloresence or single flower formed) through seed
maturation/dormancy?**

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$$$ Pankaj:cant include dormancy and senescence and reproductive consider this
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they are part of maturation/ripening process, which is post reproductive (post fertilization) except for leaf senescence (vegetative lag phase)

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**Leszek: I suggest that we're running into the 'wall' of compartmentalization of biological processes which really are a continuum. Besides including 'floral induction/transition... thru to 'maturation/dormancy' in the definition of 'reproductive stages' we should not overlook the need to include asexual means of reproduction (i.e. the various forms of apomixis & facultative & obligate apomixis). Also, I would argue that the 'maturation/ripening process' should be a child of reproduction & not equivalent to a 'sibling'. 'Maturation/ripening' are part of the continuum of reproduction & I consider dormancy & senescence to be different end-points for different organs in the process of reproduction e.g. the occurrence/formation of an abscission layer in the pedicel (peduncle) of a fruit is a part of senescence. Associated with this could be the onset of dormancy in the seed. To me these components are still clearly a part of the reproduction processes. I would further argue that leaf senescence should be included in a subcomponent of reproduction, that being associated with asexual reproduction. I recognize that some of this might be difficult to appreciate for the Poaceae taxa but I still suspect it is probably appropriate. It is easier to see the above being more appropriate for A. thaliana - although you may think I'm stretching a point here. All in all I'm challenged to get as close as possible to the 'truth' of what comprises the reproduction process/continuum even if some of this involves a paradigm shift. I'm waxing philosophical here so I'd better stop!
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(5) I believe, we need to redefine the definitions for
"vegetaive stages"PO/TAIR:0000305 and PO:0007139 (chose either)
"stages of development that occur  from seed germination up to
flowering" from
PO/TAIR:0000305
or
"Stages from germination to inflorescence initiation or formation of
flower initial in plants with solitary flowers (without inflorescence)." from
PO:0007139

with comments saying "The mid vegetative and vegetative lag phase may
overalp with the reproductive stage".

** again- I dont think that having comments to define differences rather
than seperate terms is necessarily the way to go (see above). If a stage
is a part of both reproductive and vegetative stages (sensu whatever) why not allow
this multiple parentage- this is acceptible in a DAG structure right?**

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$$$ Pankaj: Actually this makes sense, I will consider making the stem elongation stage (sensu Poaceae)PO:0007048 as part of vegetative as well as reproductive and still leave the comment there.
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**Leszek: Great. This overlapping/networked complexity is quite something. Who says plants are 'straight-forward/simple'??
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(6) Conflict with the term germination.

Although its the same process but the type of gerination differ, epigeal
Vs
hypogeal. I have not said anything about in the present file. However a
person can understand from looking at the terms
hypocotyl and cotyledon emergence PO?TAIR:0000396
and coleoptile emergence from seed (sensu Poaceae) PO:0007006

Do we need to mention about the germination types?

** I dont think that is a bad thing - to classify according to epigeal
and hypogeal...But I don't think though that is what was meant by emergence
in PO:0000396. It could be better defined as emergence from the seed coat
(maybe epicotyl and hypocotyl emergence from seed coat) as distinct from
emerging from the ground.That would be more like the term seedling
emergence which you have (though the description is based on grass
morphology- it could be more generalized and the epigeal and hypogeal
instances created for this)**

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$$$ Pankaj: Agreed can you do that.
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**Leszek: I don't think we'd be stretching a point if we placed Poaceae germination under 'hypogeal germination' as a parent. Something like: %hypogeal germination (sensu Poaceae) with an appropriate definition for the specifics of emergence of radicle (primary root) ensheathed by coleorhiza from pericarp & emergence of plumule, ensheathed by coleoptile, from pericarp. I don't think epicotyl & hypocotyl emergence would be appropriate (epicotyl maybe at a push, definitely not hypocotyl).
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