Comments on anatomy and temporal ontologies
Pankaj Jaiswal
pj37 at cornell.edu
Wed May 29 16:19:33 EDT 2002
Hi Everyone,
My comments are attached. There are number of growth stage terms that raise
concerns, are defined by MaizeDB for Maize. Leszek, in consultation with
MaizeDB needs to clean that part.
Thanks Leonore and Tanya for clearing some of the doubts, I hope my comments
will make things easier.
Pankaj
Leonore Reiser wrote:
>
> Pankaj et.al.;
> I have attached a text file with responses to some of the points raised in
> this email. Most of my comments are prefixed with ** and where Tanya made
> comments this is noted.
>
> We felt some things needed to be clarified before we go much further with
> changes i.e. that discussing some changes before hand would be helpful.
>
> Thanks for all the constructive comments- it really helps a great deal.
> Leonore
>
> On Sun, 19 May 2002, Pankaj Jaiswal wrote:
>
> > Based on the discussion in the last conference call and subsequent e mails from
> > Leszek and Tanya, here are my comments. The new growth stage ontology files are
> > attached.
> >
> > Tanya Berardini wrote:
> > >
> > > I have summarized specific comments from the TAIR group below. As you will
> > > see, they are quite extensive yet arise from only a partial review of the
> > > ontologies. We find that there are many problems that need to be resolved
> > > before the ontologies can be made public. It would be helpful if we can
> > > discuss the content issues by email: discussions of definitions, what
> > > should be term synonyms, the goal of a generic temporal framework that can
> > > accomodate all plants, etc.
> > >
> > > What should our next step be? What are your opinions on going back to
> > > the basics vs. trying to fix the current ontology?
> > >
> > > Tanya
> > >
> > Thanks Tanya for going through the files I sent earlier. I will work on the
> > anatomy files now.
> >
> > > TEMPORAL FILES:
> > >
> > > (1) We should try to not divide these by monocot and dicot but instead,
> > > like Leonore suggested, by actual stages:
> > >
> > > sporophytic(new)
> > > embryonic
> > > vegetative
> > > reproductive
> > > senesence (new)
> > > gametophytic(which would overlap with sporophytic reproductive stages,
> > > e.g. ovule developmental stages)
> > >
> > > This will help achieve our goal of using single terms to describe common
> > > processes.
> > >
> > > (2) Duplications and definitions (again): There are DBXrefs for terms
> > > like germination PO:0007051 but NO text. So there is germination
> > > PO:0000391 (Arabidopsis- also undefined), PO:0007053 and probably
> > > more. Can we define germination broadly as including imbibition,
> > > through radicle emergence and then make sensu terms. We can have a
> > > generic germination and then stages according to the organism ... but
> > > they should be developmental stages- NOT processes that are being
> > > defined.
> > >
> >
> > In the attached file I have tried to bring all the growth stages from cereals
> > Maize, Sorghum, barley, rice and oat, under higher order terms
> >
> > reproductive stage PO:0007140
> > vegetaive stages PO:0007139
> > embryonic stage PO:0007002
> >
> > I have not placed them under the similar stages defined by arabidopsis, because
> > I want TAIR to have a look at both the vesions and try to bring in the terms
> > defined for arabidopsis, by either moving the instances of
> > reproductive stage PO:0007140
> > vegetaive stages PO:0007139
> > embryonic stage PO:0007002
> > into their version or the vice versa. TAIR has to decide where to place them,
> > because we in cereals definitely do not recognize most of the growth stages they
> > have defined. However, there are some similarities, where Arabidopsis calls
> > "stage 1 flower " is panicle initiation in rice/tassel initiation in Maize.
> > "stage 2 flower " is panicle differentiation is rice
> > Some of the ovule development stages defined by Maize may overlap with that of
> > arabidopsis.
> >
> > My concers were
> >
> > Calling a term(s) "stage 1-18 flower" gives a wrong impression to the user. They
> > are all stages of inflorescence development with the flower as an underlying
> > entity, where the changes are observed. In a generic way it should be called as
> > "inflorescence development stage 1-18" and "stage 1-18 flower" can go as
> > synonym.
> >
> > definitions for "flower development TAIR?PO: 0000004" such as "stages of flower
> > development in Arabidopsis" should be changed.
> >
> > DBXref like "principal growth stage-1.0" should be replaced with "Arabidopsis
> > growth stage-1.0"
> >
> > Terms like
> > "12 rosette stage" PO?TAIR: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 1mm
> > length.
> > replaced by saying
> > Comment: For arabidopsis: stage at which the first 12 leaves have reached more
> > than 1mm length.
> >
> > The reason for asking this is because if we agree to do something like this then
> > a person from Maize can also use the same term with a comment for maize.
> >
> >
> > Same has been done for all the similar terms from cereals. The terms like
> > booting stage
> > milk stage
> > dough stage
> > heading stage
> >
> > Example:
> > term: booting stage (sensu Poaceae)
> > goid: PO:0007148
> > definition: This stage is characterized by a swelling of the flag leaf sheath,
> > caused by an increase in the size of the panicle/tassel as it grows up the leaf
> > sheath.
> > definition_reference: GR:pj37
> > definition_reference: web:http
> > //www.uaex.edu/Other_Areas/publications/HTML/MP192/1_Rice_Growth_and_Development_Reproductive.asp
> > comment: For Barley, Wheat and Oat: Zadok scale-40.
> > For Sorghum, leaf collars of all leaves are now visible. Sorghum head is
> > enclosed in the flag leaf sheath. Peduncle (stalk supporting the head) is
> > beginning to elongate
> >
> > (I have not included DBXref from MaizeDB, since Leszek needs to work on this)
> >
> > With the comments from respective crops which may suggest how they identify the
> > stage or when does this stage appears in teh particular crop. Mean how many days
> > after pollination, or after days to heading. There is no difference in
> > definition of these stages with one exception of when this stage appears in
> > different crops/plants, and if there are any other underlying events, then they
> > all go as commets from that crop/plant.
> >
> >
> > 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.
> >
> > 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.
> >
> > Vs
> > reproductive: TAIR/PO: 0000306
> > stages of development that between flowering and death of the plant. (TAIR:lr)
> >
> > In most of the cereal crops, the plant does not die. Its harvested for forage
> > (on e may call it an unnatural death). However in some of maize and rice
> > varieties (atleast I know about these two), there is a new growth cycle
> > "ratooning stage PO:0007145", which "Produces new tillers from nodes after
> > harvest". There is no question of plant dyeing. There are stay green varieties
> > of sorghum which does not follow the pattern of undergoing natural death.
> >
> > I am afraid of using the word death in the definition "stages of development
> > that occur between flowering and death of the plant. (TAIR:lr)". since the plant
> > may be perennial (ratooning variety of rice/maize or the tree species)
> >
> > I would rather say "Stages from inflorescence initiation or formation of
> > inflorescence primordia or flower initial (in cases of plants having solitary
> > flower) to flowering. Includes fertilization (GR:pj37)". and in the comments I
> > will say
> > "The mid vegetative and vegetative lag phase may overalp with the reproductive
> > stage".
> >
> > 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".
> >
> > 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?
> >
> >
> > Leszek, Could you please look at the following and try to fix it.
> >
> > linear grain-filling (sensu Zea) PO:0007029. and its instances
> > blister stage PO:0007030 its instances
> > coleoptilar stage PO:0007031
> > embryo-1 PO:0007032
> > early dough stage (sensu Zea)PO:0007034
> > late dough stage (sensu Zea)PO:0007035
> > milk stage (sensu Zea)PO:0007033
> >
> > I believe, except
> > linear grain-filling (sensu Zea) PO:0007029. and its instance
> > blister stage PO:0007030
> >
> > rest all can go in as general for sensu Poaceae.
> > I already have similar terms
> > dough stage (sensu Poaceae)PO:0007042
> > hard dough stage PO:0007154
> > soft dough stage PO:0007152
> > milk stage (sensu Poaceae)PO:0007046
> >
> >
> >
> > 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.
> >
> > Another thing, I am not willing to accept this ontology as a "plant temporal
> > ontology", because its not based on time frames. There is an element of spatial
> > variation in it because of overlapping vegetative and reproductive stages. The
> > best is to call it a "plant growth stage ontology" PO:0007040
> >
> >
> > I might be worong in interpreting some of the concepts, so please correct me.
> >
> > Pankaj
>
> -------------------------------------------------------------------------------
> Leonore Reiser, Ph.D. lreiser at acoma.stanford.edu
> The Arabidopsis Information Resource FAX: (650) 325-6857
> Carnegie Institution of Washington Tel: (650) 325-1521 ext. 311
> Department of Plant Biology URL: http://arabidopsis.org/
> 260 Panama St.
> Stanford, CA 94305
> -------------------------------------------------------------------------------
>
> --------------------------------------------------------------------------------
> Name: topankaj
> topankaj Type: Plain Text (TEXT/PLAIN)
> Encoding: BASE64
--
******************************************
Pankaj Jaiswal, Ph.D.
Postdoctoral Associate
Dept. of Plant Breeding
Cornell University
Ithaca, NY-14853, USA
Tel:+1-607-255-3103 / Fax:+1-607-255-6683
E mail: pj37 at cornell.edu
http://www.gramene.org
******************************************
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My comments are marked with
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$$$ Pankaj: comments
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Pankaj:I hope now TAIR will work on this file to organize rest of the
part. I am freezing the work on this file from my side. I have not
touched the TAIR part since its them who will have to work on
it. Please make the necessary corrections or updates.
** Tanya has made some of the changes already and we are working on
others
to try and integrate better. But rather than make global changes- we
thought we'd try to come to an understanding about some basics first and
make sure we understood the non-arabidopisis terms better.**
Pankaj: Another thing, I am not willing to accept this ontology as a
"plant
temporal ontology"... best is to call it a "plant growth stage
ontology" PO:0007040
** I think there is agreement on that- at least in terms
of getting rid of the temporal term- how about plant developmental
stages?**
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$$$ 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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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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$$$ Pankaj: How about
%vegetative stage
%reproductive stage
%ripening stage
%fruit ripening stage
%embryonic stage syn: seed development stage (from post fertilization to germination)
%endosperm development stage
%embryo development stage
For the suggested organ specific stages (e.g. leaf plastochrons, flower developmental stages,
fruit ripening stages), you can decide where to have this, but things to be considered is that how much granularity do we expect to find in the curation and are these terms really valid growth stages accepted by community.
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(2) confusion about terms
a. flowering stages : I'm a little confused. Can we step back and say it
does not include floral induction and floral transition? The definition
of
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$$$ 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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$$$ Pankaj: Well first of all except maize (MaizeDB), I haven't see any other cereal crop mentioning about the pollination/fertilization/anthesis as growth stages. Leszek please confirm this. Secondly I agree with TAIR that these terms are defined in GO -process and should not be there, but since MaizeDB has defined them , they need to work on this. The reason I am suggesting this is because we need to work in close coordination with the respective databases to define the correct structure.
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Actually, I have alot of confusion about some of
the synonyms for many things here- but can only address the terms I
recognize. For example, I don't think that embryo sac development is
synonymous with megasporogenesis (making spores !=making
gametophytes).
Also flowering stage PO:0007151 has as a synonym
anthesis and also a instance-child anthesis PO:0007021.
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$$$ 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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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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$$$ Pankaj:MaizeDB has to work on this. I agree with the TAIR's suggestion, it is a GO process
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b. terms that seem to be charateristics of populations
rather than descriptions of stages of development of an individual.
Some
examples are: flowering stage PO:0007151 (when 50% of the plants in the
field are in some stage of bloom?) and late heading stage PO:0007090 (is
that 50-100 percent of the individual inflorescences or of the
population)?
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$$$ 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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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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$$$ Pankaj: I agree these are not growth stages, but for this I will have to ask the barley/wheat/oat community to consider changing or getting rid off.
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d. just plain don't know.
e.g. ratooning- sounds like axillary shoot
development (like what happens when you release apical dominance).
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$$$ 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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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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$$$ Pankaj:
can we exclude this for the moment.
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SPECIFIC COMMENTS:
(1) issue: basal nodes:
**What about sporophytic and gametophytic nodes? Definitely gametophytic
developmental stages are concurrent with sporophytic stages but
shouldn't
they have their own parent node?
e.g. (something like)
%reproductive stages
%ovule developmental stages
%anatropous ovule developmental stages
%ovule initiation stage (synonym: Arabidopsis ovule stage 1-I)
%ovule elongation stage (synonym: Arabidopsis ovule stage 1-II)
%nucellar differentiation stage ?? (synonym: Arabidopsis ovule stage
2-I)
%integument initiation stage (synonym: Arabidopsis ovule stage 2-II)
<megaspore mother cell meiosis I
%megasporogenesis stages
%monosporic megasporogenesis stages
%megaspore mother cell meiosis I
%megaspore meosis II
## so are ovule developmental stages and megasporogenesis stages each
others'
siblings and both children of reproductive stages? I'm not sure if I'm
reading the spacing right.##
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$$$ 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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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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$$$ Pankaj:I know that's why i sent you the first shared version is a very crude form because I was really confused.
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(2) issue: proposed terms "inflorescence development stage 1-18"
vs.
existing terms "stage 1-18 flower"
**Like maize and rice, Arabidopsis has some canonical terms used to
define stages of development. And this is a likely place of departure. What
could possibly be the analogous maize stage to stage 5 flower in Arabidopsis
(stage of flower development when the petal and sepal primordia arise)? It's a
question people are trying to answer but I don't think that the answer
is known. A person would certainly describe an expression pattern in terms
of these stages in Arabidopsis (gene X is expressed throughout the sepals
from stages 4-11). Since we are using morphogical landmarks, rather than
temporal landmarks, there will more often be divergences here).**
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$$$ 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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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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$$$ Pankaj: The definition is same everywhere, Only difference is the time of appearance depending on crop and cultivar
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Pankaj:(4) conflicts with
reproductive stage PO:0007140
Stages from inflorescence initiation or formation of inflorescence
primordia to
flowering (GR:pj37).
Comment: A greater part of vegetative stage in Poaceae overlap the
reprdutive
stage.
Vs
reproductive: TAIR/PO: 0000306
stages of development that between flowering and death of the plant.
(TAIR:lr)
Everyone knows that the stage should be defined by the time reproduction
is occurring which includes the development of gametes. In case of the
Poaceae family members, this stage of development starts almost at the same time
stem elongation stage begins (this is about the same time when 5th leaf has
emerged).
So its not only temporal but also spatial.
**First- I agree that using temporal here in the ontology is bad- the
only reason that was used was when it went into the GO CVS and Chris wanted
the same name for all' developmental stage ontologies'. I'd be very happy to
change this back to developmental stages (which is what it was).
Second- what about changing the definition of reproductive stages to
include stages from floral induction/transition (regardless of if there
is an infloresence or single flower formed) through seed
maturation/dormancy?**
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$$$ 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)
(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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$$$ Pankaj: Actually this makes sense, I will consider making the stem elongation stage (sensu Poaceae)PO:0007048 as part of vegetative as well as reproductive and still leave the comment there.
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(6) Conflict with the term germination.
Although its the same process but the type of gerination differ, epigeal
Vs
hypogeal. I have not said anything about in the present file. However a
person can understand from looking at the terms
hypocotyl and cotyledon emergence PO?TAIR:0000396
and coleoptile emergence from seed (sensu Poaceae) PO:0007006
Do we need to mention about the germination types?
** I dont think that is a bad thing - to classify according to epigeal
and hypogeal...But I don't think though that is what was meant by emergence
in PO:0000396. It could be better defined as emergence from the seed coat
(maybe epicotyl and hypocotyl emergence from seed coat) as distinct from
emerging from the ground.That would be more like the term seedling
emergence which you have (though the description is based on grass
morphology- it could be more generalized and the epigeal and hypogeal
instances created for this)**
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$$$ Pankaj: Agreed can you do that.
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