Mapping file for maize terms WITH annotation in MaizeGDB

[Vincent, Leszek]

Peter - I don't understand your inclusion of the 2nd half of the
definition ("whether or 
> not on an elongated internode") - Developmentally - when would a
cauline branch ever form/arise from an elongated internode or just an
internode?? Surely such development is restricted/associated with the
node.

The 1st half of the definition would be fine, albeit very brief.

- Leszek

> -----Original Message-----
> From: owner-po-dev at brie4.cshl.org 
> [mailto:owner-po-dev at brie4.cshl.org] On Behalf Of Peter Stevens
> Sent: Thursday, September 16, 2004 6:38 AM
> To: po-dev at plantontology.org; Pankaj Jaiswal
> Subject: Re: Mapping file for maize terms WITH annotation in MaizeGDB
> 
> >Actually, the definition will have to be
> 
> cauline a. b.
> An axillary branch that forms above ground level, whether or 
> not on an elongated internode
> 
> Or I suppose one could remove the second half of the definition...
> 
> P.
> 
> >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
> 
>