Seed & embryo ontology

Thu Apr 15 23:12:10 EDT 2004

Hi Katica,

Thanks for the reply. I'll attend to the 'pruning' of terms as you suggest. I'll review definition lengths but let me know if there is a length/character limitation. Sometimes abbreviated defns are virtually useless to a reasonably informed reader let alone an inexperienced user.  Regarding the Dbxrefs - from your explanation you gave me I understood that the PO:LV:ISBN..... format is what was required. The format that I used doesn't imply that I've merged my thoughts in with the published ref. def. My understanding was that the inclusion of the LV was to indicate the author or the definition. Where I did add to the defn I provided a separate Dbxref (PO:LV) to indicate that. So it seems like I should strip out all the "LV" characters just prior to the ISBN.... info. - corrrect? I'll check the recent minutes again & will get back to you if needed.

Regards,
- Leszek

________________________________

From: owner-po-dev at brie4.cshl.org on behalf of Katica Ilic
Sent: Thu 4/15/2004 3:41 PM
To: PO-Developers
Cc: Shuly Avraham
Subject: Re: Seed & embryo ontology

Hi Leszek,

I've just looked at your seed node briefly. It looks good, good job, we
are now getting very close to completing the first draft of anatomy
ontology.

I'll need more time to send you my detailed feedback on the actual
structures and relationships. For now (since I am planning to commit my
cell type node tomorrow), my comments are limited to some 'technical'
issues.

There are sevreal terms that I already have in my cell type node, and we
should avoid duplications. Please see the cell type node (that I
e-mailed sometime ago) and either try using the IDs from there.
Or on the sec thought, wait for me, since I'll be adding all the
cell type terms to the sec nodes as soon as we start merging nodes (see
the April minutes for details). After the annotation demo session, we
talked and aggreed on how to proceed with adding the terms to different nodes). At that time,
you may remember, we also agreed that subcellular structures should not be in the anatomy
ontology. I had a few (polar nucleus, filiform apparatus, etc) in my cell
type node and I deleted them recently. Could you please do the same?

Some definitions are in my opinion, too long (for instance, Aril
PO:0009090 has 93 words and 437 characters in def). This may be a problem
(I need to talk to Shuly), if it turns out that there is a space
limit in the table structure. Even if it's not, it might be a good idea to
keep the definitions short but still informative enough.

And last comment is related to references. When you use a textbook and
then add some of your own words into definition, please use
ISBN:XXXXXXXXXX and then include the second ref as PO:LV. Don't put all
in the same line (PO:LV:ISBN:XXXXXXXXXXX). These are two
reference items, though there is only one reference. I think I already
sent you an e-mail about adding proper dbxrefs sometimes last week.

I'll get back to you later. Please see the minutes I sent out yesterday. I
am also planning to put out the POC curator's style guide (similar to what
GO has), where we can find out all the relevant issues and documentations
related to creating ontologies, so that we don't need to go through our
meeting documenation each time.

All for now. If you want, we can talk over the phone on how to synchronize
adding the cell type terms into your seed node.

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

--------------------------------------------------------------------------
Katica Ilic                             katica at acoma.stanford.edu
The Arabidopsis Information Resource    Tel: (650) 325-1521 ext. 253
Carnegie Institution of Washington      FAX: (650) 325-6857
Department of Plant Biology             URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
U.S.A.
--------------------------------------------------------------------------

-------------- next part --------------
A non-text attachment was scrubbed...
Name: winmail.dat
Type: application/ms-tnef
Size: 8111 bytes
Desc: not available
URL: <http://brie4.cshl.edu/pipermail/po-dev/attachments/20040415/9822cef0/attachment.bin>