UniGene Library annotation --Question

[Katica Ilic]

Pankaj,

On Tue, 7 Dec 2004, Pankaj Jaiswal wrote:


> Can somebody help me identify which plant structure terms I shall use
> for the following as described for the EXT library in GenBank records.
> --------------------------------------
>
>
> <http://www.ncbi.nlm.nih.gov/UniGene/library.cgi?ORG=Os&LID=16310>
> Organism: 	Oryza sativa subsp. japonica
> Developmental stage: 	3-5 leaves plantlets
> Sex: 	hermaphrodite
> Cultivar: 	Nipponbare
> Tissue: 	shoot apex
> Organ: 	shoot apex
>
> Do you think that annotating to the following will be acceptable.
>
> term: shoot apical meristem
> Accession: PO:0020148

I am not sure about this, since you are suggesting a more granular term
than what they provided. It seems that having the term 'shoot apex' would
be useful, there are many publications where people use it.
> ___________________________________
>
> For the following
> http://www.ncbi.nlm.nih.gov/UniGene/library.cgi?ORG=Os&LID=10901
>
> Organism: 	Oryza sativa (japonica cultivar-group)
> Developmental stage: 	two weeks old seedling
> Cultivar: 	Lansheng
> Organ: 	all plant
>
> According to the recent suggestion, should this be annotated to
> "whole plant" term or to the "sporophyte".
>
> Personally I would like to annotate it to term "sporophyte" with an
> additional annotation to the appropriate growth stage.
>
Either one is fine, and since we should encourage people to use the most
appropriate term, sporophyte should be the one (in my humble opinion).

> --------------------------------
>
> Similar situation is for the following
>
> http://www.ncbi.nlm.nih.gov/UniGene/library.cgi?ORG=Os&LID=11046
>
> Organism: 	Oryza sativa
> Developmental stage: 	Two-week-old rice seeding infested by brown
> planthopper
> Strain: 	B5 resistant variety to brown planthopper
> Vector: 	pT-Ad


I am not sure here either, you can't pull out the proper dev stage
term, and they did't specify if they used the whole plant or not, and even
term sporophyte may not work out, since they didn't specify anything.

I don't thing that there is any term outh there taht I would be
entirely comfortable using in this particular case.

Katica




>
>
> ************************
> Pankaj Jaiswal, PhD
> G15-Bradfield Hall
> Dept. of Plant Breeding
> Cornell University
> Ithaca, NY-14853, USA
>
> Tel: +1-607-255-3103
>       +1-607-255-4109
> Fax: +1-607-255-6683
> http://www.gramene.org
> ************************
>

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Katica Ilic             		katica at acoma.stanford.edu
The Arabidopsis Information Resource 	Tel: (650) 325-1521 ext. 253
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