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#3 new term for Hull
closed-accepted
nobody
1
2010-06-09
2006-04-18
No
Hi All,
I need a new term to describe 'hull' in cereal plants.
I know experts say that it is nothing different than
lemma and palea, the two parts found in grass floret.
Therefore the options are to put 'hull' as synonyms of
both lemma and palea, which I somehow disagree because
the term 'hull' is never used in florets/grass flowers.
The usage is only in the grass fruits (caryopsis). It
also appears that the same term is used in other
families as well. So we need a species/organ specific
distinction as well.
# dry outer covering of a fruit or seed or nut
# persistent enlarged calyx at base of e.g. a
strawberry or raspberry
-Pankaj
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From Toby (kellogge@msx.umsl.edu)
dated 1/30/2006
Hi Pankaj -
I'd still go with synonym of lemma and palea, probably as
hull sensu Poaceae. I'd prefer to avoid the first defniition
you've listed below, since it doesn't pertain to anything
botanical (or maybe pertains to everything). Following the
second definition, you could have a synonym of calyx being
hull sensu Rosaceae.
From Peter Stevens (peter.stevens@mobot.org)
dated 1/31/2006
I agree with Toby - second would include all sorts of
things, and third is difficult - the K of raspberries barely
is enlarged at all, and is basically marcescent - marcescent
calyces are common, and nobody ever calls then a hull (and I
hope never will).
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From Pankaj 1/31/2006
There is some difficulty on putting hull as synonym. I think
there is a precedence on creating a new term even though a
part is called by different name in a derive parent
structure. e.g. in seed many parts are derived from the
ovule, e.g. chalaza, micropyle, testa etc. These are derived
structures or rather the same structures but sometimes can
be called by different names. Similarly it will be very
difficult to annotate phenotypes and gene expression such
as in case of
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16443696&query_hl=5&itool=pubmed_docsum
to lemma and palea. In this case the actual structure is
called as hull. I think we need hull as a new term, and the
parentage as follows
fruit
---part_of---hull
Also
floret
--part_of--lemma
-----develops_from--hull
--part_of--palea
-----develops_from--hull
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From Toby (2/1/2006)
I've looked at the paper - I still don't see why it can't be
annotated to lemma and palea. Just because the authors use a
non-botanical word does not mean that the databases have to
use the term.
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From Leszek (Leszek@missouri.edu)
dated: 2/1/2006
I support Toby & Peter’s perspective. Furthermore, in a
similar situation Lincoln supported the view that the POC
can also be something of an educator of users in their
understanding & use of internationally recognized botanical
terms. “Hull”, while widely used as a colloquialism, is
rather devoid of good botanical identity & even has varying
lose applications (some even nautical!) therefore requiring
further defining depending on context of use. I support
Toby’s most recent comment & suggest an educational comment
could be provided in the ‘Comments’ area regarding the term
‘hull’ & its compositional affinity with lemma & palea etc.
I think the closest “hull” should get to the PO is via a
synonym as described by Toby earlier. Let’s keep on
maintaining our focus on the use of internationally accepted
botanical terminology in our PO work – clearly there are
researchers out there who need this education.
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From Peter Stevens
dated 2/2/2006
This would seem to be a matter of principle, along the lines
of Leszek's recent comments about the educational side of
the PO. We cannot take account of misuses of terms, nonce
terms, and the like, except by making sure synonymy grows..
After all, many people, inc, botanists of my acquaintance,
call a lamina a leaf and do not blush.
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From Pankaj
dated 2/8/2006
From Pankaj
2/8/2006
Hi Everyone,
As discussed in the ontology conference call here is the
suggested ontology structure for the new term 'hull'.
-PO:0009003 : sporophyte
--part_of--PO:0006342 : infructescence
----part_of--PO:0009001 : fruit
----part_of--PO:NEW : hull
------is_a--PO:NEW : caryopsis hull / hull (sensu Poaceae)
-**---is_a--PO:NEW : Rosaceae hull** / hull (sensu Rosaceae)
** DO WE NEED THIS TERM NOW?
Also add the following parent with develops_from relationship
-PO:0006318 : floret (sensu Poaceae)
--part_of--PO:0009037 : lemma
----develops_from--PO:NEW : caryopsis hull / hull (sensu
Poaceae)
--part_of--PO:0009038 : palea
----develops_from--PO:NEW : caryopsis hull / hull (sensu
Poaceae)
The reason I prefer to call it 'caryopsis hull' is because
having a term with 'sensu Poaceae' as a child of a term that
always belong to that family looks non-sensical.
Definitions:
Hull: The accessory structures present in or attached to the
fruit but are not actually part of the fruit.
Caryopsis hull: A leaf like structure often found enclosing
the grass fruit, caryopsis. It is derived from the lemma
(PO:0009037) and palea (PO:0009038) floral bracts found in
the grass floret (PO:0006318).
Rosaceae hull: please provide the definition if you suggest
the term to be added
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from Toby
dated 2/10/2006
How about the following as an alternative
PO:0006342: infructescence
---part_of--PO:000901: fruit
---part_of--PO:new: dried lemma and palea, syn: hull sensu
Poaceae
---part_of--PO:new: dried calyx, syn hull sensu Rosaceae
---part_of--PO:new: accrescent calyx - comment
"characteristic of some Solanaceae such as Physalis"
The definition "accessory structures present in or attached
to the fruit but are not actually part of the fruit" will
include almost any plant part depending on the species,
including the leaves on a pineapple, the pedicel in some
grasses, etc.
I think by introducing these terms we are addin to the
situation where different developmental stages of the same
organ are given different names. This is common for some
terms, such as integuments, which develop in to tegmen and
testa. The situation with the hull in rice, though, is more
like distinguishing between a young petal and an expanded
petal - the hull is simply a dried out lemma and palea. Once
again, attributes would help here - if we could say young
structure vs. old structure, for example.
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From Pater Stevens
dated 2/10/2006
To add to the jollility surrounding the use of hull, note that
cucurbit people use this term for seed coat variation - thin
hull = thin seed coat, as far as I can work out.
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Pankaj:
I can live with Toby's suggestion but the problem is
-the term name is nothing but the actual definition.
-the users expect to see the term 'hull'.
-we will be using thsi term to create a trait term like
'hull color', which is a composite term and I cannot make
composites based on synonyms.
Also the dried calyx term is in question. It is not always
dried in rosaceae.
In the example suggested by Peter from cucurbits, the
particular instance 'cucurbitaceae hull' will not be a child
of 'hull' under fruit. If required it could be a new is_a
seed coat or just a synonym.
Going by this I would reccommend going by my suggestion.
We can modify the definitions based on Toby's suggestion.
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from Felipe Zapata
dated 4/14/2006
From minutes of conf call on 4/14/2006
Discussion and apparently no agreement. I went over the
problem with Peter again and we thought that this approach
might work.
PO:0006342: infructescence
-----part_of--PO:000901: fruit
-----part_of--PO:new: hull sensu Poaceae
-----part_of--PO:new: hull sensu Rosaceae
-----part_of--PO:new: hull sensu Solanaceae
Do not include a generic Hull.
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#1 for any sensu term there must be a generic term and in
this case the 'hull'. Otherwise I have no problem with this.
I would add the develops from relationships e.g.
-PO:0006318 : floret (sensu Poaceae)
--part_of--PO:0009037 : lemma
----develops_from--hull (sensu Poaceae)
--part_of--PO:0009038 : palea
----develops_from--hull (sensu Poaceae)
#2 the big problem is once we have said that PO:0006318 :
floret (sensu Poaceae), there is no point in this term
carrying the child which also has sensu Poaceae in it. IT is
clear that any thing below PO:0006318 : floret (sensu
Poaceae) is always a poaceae term.
If so my suggestion on having the term 'caryopsis hull'
still stands good.
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Final resolution. New term, PO:0006000 : hull (sensu Poaceae) was created and placed as part of PO:0006342. Other parents with develops_from relationship were , PO:0009038 : palea and PO:0009037 : lemma.
-Pankaj
# Definition: A leaf like structure often found enclosingnthe grass fruit, caryopsis. It is derived from the dried lemma (PO:0009037) and palea (PO:0009038) floral bracts found in the grass floret (PO:0006318).
# PO:0006342 : infructescence
---p--PO:0006000 : hull (sensu Poaceae)
------------------
# PO:0009037 : lemma
-----D--PO:0006000 : hull (sensu Poaceae)
# PO:0009038 : palea
-----D--PO:0006000 : hull (sensu Poaceae)
hull is odd in that it is not a botanical term but rather a vernacular term. So for example the exocarp of many nuts are called hulls. We could restrict it to the grasses as "mature palea and lemma enclosing a caryopsis" The calyx is not the equivalent of the lemma and palea. Also most mebers of the old Dillenid group have a persistent calyx. That group is now known to be highly polyphyetic. So to include that in the definition just makes hull rather meaningless for evo/devo work.