Mapping file for maize terms WITH annotation in MaizeGDB

[Pankaj Jaiswal]

Mary Polacco wrote:

> 
> A.  there are a few terms where the mapping was not precise; I have checked
> with Leszek, and would like to propose that we consider adding new terms for
> these cases.
> 
> MaizeGDB: 106161 tillers > PO: axillary shoot ; PO:0006343
> **preferred would be mapping to non-existent term: basal axillary shoot

I was discussing this issue with Toby from Garmene's QTL curation 
perspective earlier. We came up with the following structure

axillary branch
     instance - cauline axillary branch
     instance - basal axillary branch - synonym tiller

cauline axillary branch
Definition:an axillary branch that forms  above ground level, and on an 
elongated internode

basal axillary branch
Definition:an axillary  branch that forms at ground level, generally 
from a non-elongating  internode

Let me know if it works for you.

> 
> MaizeGDB: 15809 pollen > PO: male gametophyte ; PO:0020091
> ** pollen is a parent term for male gametophyte
> 
> MaizeGDB: 45980 leaf cuticle > PO: leaf epidermis ; PO:0006016
> **strictly speaking, leaf cuticle is not a 'cellular' anatomical feature,
> but is considered that way in usage.
> 
> MaizeGDB: 58047 stalk > PO: stem ; PO:0009047
> MaizeGDB: 58047 stalk >> PO: leaf sheath ; PO:0020104
> **while stem is the major component of maize stalk, it also is composed of
> leaf sheath
> 
We are using the term "stalk" at two places as synonyms
  PO:0009047 : stem
  PO:0006341 : primary shoot

I think this term "stalk" is used in a loose sense, though cited quite 
often in the literature. So do you think that it is a valid case of 
creating a new term

shoot  PO:0009006
--p--stalk (new)
----p--stem PO:0009047
----p--leaf sheath  PO:0020104

The term stalk by your suggestion is very much a grass specific term, 
where as stem PO:0009047 is generic. This could create problems with TPR 
violation.






> MaizeGDB: 64474 mid rib > PO: mid vein ; PO:0020139
> **mid rib includes more tissue that just the mid vein, but at this time I am
> only mapping to mid vein
> 

Can we have a definition from MaizeGDB.


Thanks
Pankaj