Growth&Dev Curation ATTN Anu, Katica, Leszek

[Pankaj Jaiswal]

Just to add to this thread. One can assign multiple terms mapped to a 
single description given by the author. The annotations are not restrictive.


Pankaj

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
>>>
>