Seed & embryo ontology

[Katica Ilic]

Hi Leszek,
Here are my two cents:

1. Embryo sac is not part of the embryo/seed node. This entire node (with
all the children) belongs to the gynoecium node, child of the ovule (or
develops from megaspore). Within this node, you have endosperm (with 4
children terms), which does not belong to the embryo sac node, but it does
to seed node (and you already have it there).

2. Hypodermal nucellar cell should not be in the seed/embryo node either.
Don't get me wrong, the whole node is OK, it just needs to be moved to the
different node. Since none of the terms (please check this out again in
the anatomy ontology) under this node exist in the main ontology, I'll
suggest to Felipe t import the entire node to the megasporocite node (I
would say, as a part of ovary). Similarly, megaspore mother cell should be
deleted too from the seed node, as Pankaj already pointed out (and moved
to the appropriate node in the main ontology). Also, ovule and ovule
primordium are not instances of seed either (true path rule is violated in
all of the cases above).

4. Cotyledon should be under the embryo node (part of).

5. (A minor point): Hypopcotyl-rood axis should have synonym embryo axis
(or vice versa).

6. Please, delete completely following 4 terms: polar nucleus, primary
polar nucleus, sec endosperm nucleus and filiform apparatus (all
subcellular structures).

Also, make sure that no term in your node already exists in the main
anatomy ontology (which will have cell type node in with today's update).
We should avoid duplication. If a term do exist in the mani ont and
deleting it is not an option, my suggestion is to copy and paste exact
definition for that term from the anatomy ont, and then manually change the term ID to
the one from the anatomy ontology. This way, when you import your node
(without choosing the ID stripping option), the two terms will 'merge'
into one. I myself have had a problems when importing a node due to term
duplications.

After trimming all these terms, your seed node will get much shorter (and
it may look to you as incomplete), but don't worry, the other tissue and
cell type terms will be placed in and the final version will be more
comprehensive.

Also, do we need the term parietal cell? I am asking because it should be
in the cell type node too, and so far I did not find any gene annotated or
any publication referring to gene expression in this cell type.

This is all for now.

Cheers,
Katica

On Thu, 15 Apr 2004, Vincent, Leszek wrote:

> 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
> *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*
>

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Katica Ilic             		katica at acoma.stanford.edu
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