Seed & embryo ontology

[Pankaj Jaiswal]

Hi Leszek,

Thanks for the seed node, it looks great. This helped me a lot in refining
the tissue node. I will send the tissue node structure by weekend.

Here are some of my comments, though I agree with you that since many of
the terms from tissue and cell nodes were not there you crested those to
cover the big picture.

I believe some of the terms will come from the ovule node. So they may be
replaced in the final version. e.g. integument, micropyle etc.
The same goes for cell and tissue types. However the structure presented
by you will definitely help us filling those nodes.

megaspore mother cell LV:0019032
this is not a part of seed

ovule LV:0019045
is not an instance of seed. It's a part of ovary.
I think you wanted to have a develops_from relationship here. Seed
develops from ovule.

I am not sure if we want to populate the POC with the phenotypes /
attributes of ovule type instances. Do you think a generic term "ovule"
will work right now.

ovule primordium LV:0019045
again is not an instance of seed. correct structure is seed develops from
ovule. Ovule develps from ovule primordium.


cotyledon PO:0020030
by definition cotyledon is a part_of embryo atleast in dicots. I am not
sure if it is true for monocots where scutellum is considered as an
equivalent of dicot cotyledon.

There are several other instances like
obturator LV:0019021, transmitting tissue LV:0019027 etc. that seems to be
part of ovule.


Vincent, Leszek said:
> Dear PO colleagues,
>
> Attached is my seed & embryo ontology for your perusal & evaluation. I
> look forward to your feedback. You will note that I included some
> cellular detail in places. This happened just because their inclusion
> helped me to work with concepts (from coarsely granular to finely
> granular). We can move/obsolete them as & when necessary. While some of
> the fine grained terms are probably appropriate for inclusion in GO they
> are NOT there yet. One way or another these terms need to be provided in
> the PO. These present gaps provided further motivation to 'paint' the
> 'full canvas' in this draft version. For the ID range I used 19000 -
> 20000.
>
> - Leszek
>
> *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*
> P. Leszek D. Vincent Ph.D., FLS
> Plant Science Unit
> Dept. of Agronomy
> 215 Curtis Hall
> University of Missouri-Columbia
> Columbia
> MO 65211-7020
> USA.
> Ph: (573) 884-3716 (Agronomy)
> Fax:(573) 884-7850
> Ph/Fax (Home): (573) 441-1228
> Email: Leszek at missouri.edu
> Yahoo! Messenger: leszekvincent
> Plant Systematist on The Plant Ontology Consortium - NSF award 0321666
> Associate Curator, Dunn-Palmer Herbarium (UMO)
> Research Associate, Missouri Botanical Garden (MO), USA
> CEO - PhytoSynergy, LLC
> *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*
>


-- 
Pankaj Jaiswal
Gramene Database
www.gramene.org