Growth&Dev Curation ATTN Anu, Katica, Leszek

Tue Apr 25 12:20:46 EDT 2006

We might consider introducing some more terms here. If terms based strictly
on numbers of leaves are not truly informative about life stage  inter- and
intra-species, the challenge seems to find a better set of terms, at least
in some cases. The stage should be the thing, and not the numbers of leaves
in the species or cultivar. Leaf number might better be a comment or some
species/cultivar-specific synonym rather than the main term. I suspect that
Marty's point about Gaspe Flint life cycle and leaf number may well play out
in other plants than maize.

Pankaj, thanks for the point about higher term annotation when the stages is
not well-described in literature, eg for a cDNA library. RE leaf numbers vs
stage, If I know the inbred line or cultivar, then I could make an informed
guess at more granular term (right Marty), but in general, it is easier on
to let the user make that leap from comments about the library, etc.

   mary

> From: Marty Sachs <msachs at uiuc.edu>
> Reply-To: po-dev at plantontology.org, Marty Sachs <msachs at uiuc.edu>
> Date: Tue, 25 Apr 2006 09:45:51 -0500
> To: po-dev at plantontology.org
> Subject: Re: Growth&Dev Curation ATTN Anu, Katica, Leszek
> 
> Anu,
> 
> For the terms LP.06 thru LP.08 a synonym of 'ear initiation in maize'
> is given.  That's fine and shows the flexibility.  However, depending
> on the accession the same synonym can also be given for LP.05 or
> LP.20.  In fact, for Gaspe Flint, ear initiation occurs during embryo
> development.
> 
> The same can be said for the synonym 'tassel initiation'.
> 
> However, for 3-4 week leaf primordium
>   PO:0007123 LP.06 six leaves visible
> 
> This again is very line dependent.  E.g., Gaspe Flint never has 'six
> leaves visible' and is pretty much done flowering by 4 weeks.
> 
> -Marty
> 
> At 10:13 AM -0400 4/25/06, Anuradha Pujar wrote:
>> Hi Mary, Marty,
>> 
>> Maize mappings provided by Leszek gives considerable flexibility to
>> accomodate different varieties described by Marty.
>> 
>> The list below are the maize synonyms (growth stage) that came up for
>> Mary's terms: I would map to the PO term that has the synonym that comes
>> closest to the description in the paper being curated. If not, we could
>> ask for the addition of a more suitable synonym. Which after a round of
>> discussion, has to be added to the maize-mapping file first and then to
>> the ontology file.
>> 
>> However, literature describing  plant growth stages in weeks or days will
>> remain a problem. And will depend on cuators knowledge about the plant. At
>> gramene-rice curators choose a higher level term such as vegetative growth
>> or reproductive growth.
>> 
>> 
>> 1. For immature ear
>>>    PO:0007046   IL.01 1/4 inflorescence length reached
>> 
>> PO:0007123: LP.06 six leaves visible
>> Syn: 3.01-ear initiation in maize, 3.1 ear initiation/mid-whorl stage in
>> maize, ear initiation in maize, early whorl stage in maize
>> 
>> PO:0007063 : LP.07 seven leaves visible
>> Syn; 3.01-ear initiation, 3.1 ear initiation/mid-whorl stage in maize, ear
>> initiation in maize
>> 
>> PO:0007095: LP.08 eight leaves visible
>> Syn: 3.01-ear initiation in Maize, 3.1 ear initiation/mid-whorl stage in
>> maize, ear initiation in maize
>> 
>> 2. For Immature tassel
>>>    same as for immature ear.
>> 
>> PO:0007115: LP.04 four leaves visible
>> Syn: 2 tassel initiation/early whorl stage in maize, early whorl stage in
>> maize
>> 
>> LP.05 five leaves visible
>> Syn: tassel initiation/early whorl stage in maize, early whorl stage in maize
>> 
>> PO:0007025: IE.00 inflorescence tip just visible above flag leaf sheath
>> Syn: beginning of tassel emergence in maize
>> 
>> PO:0007041: PO:0007041 : inflorescence emergence from flag leaf sheath
>> Syn:tasseling
>> 
>> 3. >For immature seek or kernel
>>>     PO:0007001   early stage of fruit ripening
>> 
>> PO:0007001   early stage of fruit ripening
>> Syn: 7 linear grain-filling in maize, 7.03-early dough in maize, 7.3 early
>> dough stage/embryo 3 in maize, R4 in maize, early dough, kernel content
>> soft, about 45% dry matter
>> 
>> 4. >For 3-4 week leaf primordium
>>>     PO:0007123 LP.06 six leaves visible
>>  I am not sure if this goes to a whole plant growth stage term..
>> 
>> 
>> Thanks
>> anu
>> 
>> 
>>>  Mary,
>>> 
>>>  The problem is trying to relate developmental programs that aren't
>>>  necessarily related.  We've discussed this many times before.  The
>>>  number of leaves a plant has doesn't give an indication of where that
>>>  plant is in terms of floral development.  Gaspe Flint is fully mature
>>>  and has flowered with only 5 leaves.  Tropical varieties won't flower
>>>  until the plant has more than 20 leaves.
>>> 
>>>  The fact that corn-belt hybrids flower with a certain number of
>>>  leaves only reflects their particular background.  Nothing general
>>>  can be said about this.
>>> 
>>> -Marty
>>> 
>>>  At 3:24 PM -0500 4/24/06, Mary (Polacco) Schaeffer wrote:
>>>> Anu and I have discussed the vagueness some folks use in describing
>>>> developmental stages as presenting a major curation challenge.  I am
>>>>  asking
>>>> for some insight into making the calls in matching a precise PO term,
>>>>  with a
>>>> vague literature or GenBank description, just to be sure I am not out in
>>>> left field with the intentions of this group. Some example calls are
>>>>  below.
>>>> 
>>>> In all cases, each gets also a plant anatomy term. Basically I am trying
>>>> to
>>>> make a statement that would not be wrong, eg at least 6 leaves (maybe
>>>>  more)
>>>> should be visible in most 3-4 week maize plants. An immature ear might be
>>>> considered to be smaller or bigger that 1/4 inflorescence length, etc.
>>>> 
>>>> So is there a better call for the below?
>>>> 
>>>> For immature ear
>>>>    PO:0007046   IL.01 1/4 inflorescence length reached
>>>> For Immature tassel
>>>>    same as for immature ear.
>>>> For immature seek or kernel
>>>>     PO:0007001   early stage of fruit ripening
>>>> For 3-4 week leaf primordium
>>>>     PO:0007123 LP.06 six leaves visible
>>>> For juvenile shoot
>>>>     PO:0006339  juvenile leaf
>>>> 
>>>> 
>>>> 
>>>> Thanks,
>>>>   mary
>>>> 
>>>> 
>>> 
>>> 
> 
> 