Rice profiling project - interest in developing cell type terms (PR#64)

Tue May 31 20:28:30 EDT 2005

Dear Neeru,

Good to hear from you again. I am glad that PO is working for you and that you
are able to find most of the terms that you need. I'll try addressing your
questions, and also, I may have some specific questions for you too:

You asked:
"1) the shoot apical meristem definition includes the axillary meristem and we
were wondering if the two terms could be separated and have an axillary
meristem
and axillary primordium as separate ontological terms."

No, actually, the second part of the definition of SAM refers to the SAMs of
the
axillary shoots: 
PO:0020148 - shoot apical meristem 
Synonyms: apical meristem, primary shoot meristem 
Definition: Meristem formed in the apex of the shoot, including meristems
originating as axillary shoot meristems. 

I think what you are you asking about is 'meristem that is part of the shoot
apex, in the axil of the leaf primordia', right? I think we would need to
change
definitions for some of the existing PO terms, since we already have terms such
as leaf primordium, SAM, shoot apex and axillary bud meristem. I'll get back to
you regarding this once our group discusses it.

These are the terms already in the PO, and I don't think we need to add new
terms, but rather change definitions of the existing:

PO:0020148 - shoot apical meristem 
Synonyms: apical meristem, primary shoot meristem 
Definition: Meristem formed in the apex of the shoot, including meristems
originating as axillary shoot meristems. 

PO:0000037 - shoot apex 
Definition: The topmost part of the shoot, situated at the distal extremity of
the shoot axis, consists of apical meristem the youngest leaf primordia.

PO:0000232 - axillary bud meristem 
Synonyms: axillary meristem 
Definition: Meristems formed in the axil of the leaf. 

PO:0000017 - leaf primordium
Definition: An organized group of cells that will differentiate into leaf that
are emerging as an outgrowth in the shoot apex (flanking the meristem).

Then, you asked:
"2) under the rice growth stages - rice plant growth stages - the child term
germination has no further subdivisions and we have been harvesting cell types
from 0 hr (same as Embryo stage EM10) and 12 and 24 hr post imbibition time
points from a germinating seed. So it would be great if you could possibly add
these two ontologies as child terms under germination."

I am not sure I understand exactly what you are asking, and I don't remember
what Gramene use to have before, but your '0 hours.' should be equivalent of
'dry seed', right?
PO term 'imbibition' covers period up until radicle emergence takes place. Your
'12 and 24 hours post imbibition' does not indicate if radicle emergence stage
was reached at 24 hours post imbibition. Having had some experience (and fun)
growing rice in the lab while I was posdoc, my recollection is that it takes
little longer for radicle emergence in rice, but it also depends on the
temperature. For this very reason, we insist on morphological landmarks for
creating and defining terms and not on less relevant and highly variable
parameters, such as days after anthesis, hours post imbibition, or very
disputable 'hours after germination'. Different rice varieties can reach
different stage (placed under different conditions) at '24 hours post
imbibition'. I agree that term 'imbibition' is a bit stretched, but am not sure
if any new terms would provide adequate granularity that you are asking for.

You also asked:
"3. Also the definition of stomatal complex does not include the subsidiary
cells and from what we have been looking around stomatal complex would be guard
cell surrounding the stomata with the subsidiary cells."

The definition doesn't, but 'subsidiary cell' is a child of 'stomatal complex'
and so is 'guard cell'. Therefore, "guard and subsidiary cells are both a part
of the stomatal complex", even though the definition of the 'stomatal complex'
does not specifically say that. The ontology structure and term relationships
provide such information. That is a benefit of having these terms in the
ontology, a lot of information is provided in the ontology structure itself. 

I hope this helps, please, let me know if you have additional questions, and
I'll get back to you regarding definitions of 'meristem' terms.

Best regards,

Katica

> ---------- Forwarded message ----------
> Date: Thu, 26 May 2005 19:35:44 -0400
> From: fno.neeru at yale.edu
> To: Katica Ilic <katica at acoma.Stanford.EDU>
> Subject: Re: Fwd: rice profiling project  interest in developing cell type
>     terms
> 
> Hi Katica,
> This is from Neeru at Tim Nelson lab, Yale. We had met at the ontology
> workshop at PAG meeting. Sorry for the long silence. How are you doing.
> Over here we were wondering if you could help us out with some of the
> ontologies. Most of the ontologies that we are using are from the
> gramene website and  fit really very well in defining our cell types
> and growth stages. There are few we have questions about...
> 1) the shoot apical meristem definition includes the axillary meristem
> and we were wondering if the two terms could be separated and have an
> axillary meristem and axillary primordium as separate ontological
> terms.
> 2) under the rice growth stages- rice plant growth stages- the child
> term germination has no furhter subdivisions and we have been
> harvesting cell types from 0 hr ( same as Embryo stage EM10) and 12 and
> 24 hr post imbibition time points from a germinating seed. So it would
> be great if you could possibly add these two ontologies as child terms
> under germination.
> 3) Also the definition of stomatal complex does not include the
> subsidiary cells and from what we have been looking around stomatal
> complex would be guard cell surrounding the stomata with the subsidiary
> cells.
> 
> Please let us know what you think. Thanks
> Best Regards
> Neeru
> 
> Quoting Katica Ilic <katica at acoma.Stanford.EDU>:
> 
>>
>> Dear Tim,
>>
>> Thank you for your message. I am glad to see that you are using
>> Plant
>> Ontologies, and I agree we need to work together to make it better.
>>
>> For the Plant Structure Ontology, this is a very good point you made,
>> we
>> haven't done any instantiation yet, that is, we have not propagated
>> each cell type
>> under every tissue of every organ, for the following reasons:
>>
>> 1. It would be to redundant, and ontology would end up be too large
>> and
>> difficult to search through since each cell type in each tissue of
>> the each organ would be a separate term, resulting in dozens of terms
>> that
>> would refer to for example, parenchyma cell type. This is the major
>> problem of our ontology (in a way, we inherited it from GO, but I
>> can
>> explain this some other time), and we are currently exploring
>> several
>> options.
>>
>> What we want to avoid, is to have several thousand terms in the
>> plant structure ontology, while the sum total of the plant anatomy
>> terms
>> is in fact less that thousand (by my rough estimate).
>>
>> 2. Even if we do end up instantiating terms and propagating plant
>> ontology, there is a fundamental conceptual problem here, that is,
>> this instatiation and term multiplication is against the modular
>> nature
>> that underlines the plant structure, for example, xylem element
>> is xylem element, regardless of its location,
>> therefore having several terms refering to the exact position of the
>> xylem
>> element wouldn't add up much, if there is only a better way to
>> indicate
>> this posiotional information, that is to use several terms in
>> conjuction
>> to describe cell type, it's location and dev stage. This so far is
>> not
>> possible and we are trying to figure out how to tackle this
>> computationaly.
>>
>> Lincoln Stain and toby Kellogg, two PIs on the POC project wrote a
>> document last summer, called 'Multiplicative chrisis" in which they
>> explianed this very problem. If you want to take a look, I can send
>> it to
>> you.
>>
>> For the developmental stages ontology, I understand this problem
>> too,
>> and I'll pass your question to the POC members in charge of this
>> aspect of
>> the ontology. It might be a couple of week before we get back to
>> you,
>> since soon we are all leaving for the PAG meeting in San Diego.
>>
>> I already check the PAG web site out, you are not registered, but if
>> you have
>> anyone from your group who is coming to this meeting, I would like to
>> arrange
>> for a meeting. I fact, I would suggest the Ontology workshop on
>> Monday Jan 17,
>> where all the POC members will be present.
>>
>> We also have our annual POC in-person meeting on Jan 18 and minutes
>> will
>> be posted on the POC web site. The "Multiplicative chrisis" document
>> is on
>> the agenda.
>>
>> Best regards,
>>
>> Katica
>>
>>
>> On Mon, 10 Jan 2005, Timothy Nelson wrote:
>>
>> > Dear Katica,
>> > We are finally at the point of needing to interface with the POC
>> to
>> > assure that our rice cell profiling data is tagged with a
>> > community-standard vocabulary. We have been pleased to see that
>> much
>> > new vocabulary has been added for rice at the Ontology website in
>> > recent weeks. We would like to work with you on several issues:
>> >
>> > 1. We will need to describe our data with greater precision than
>> is
>> > currently available. We find it difficult to distinguish between
>> > "plant" ontological terms and other terms. For example, how does
>> one
>> > tag data that needs info not just as to cell type, but for a
>> > particular cell type, within a particular organ, at a particular
>> zone
>> > within the organ, and all at a particular developmental stage?
>> >
>> > 2. What is the appropriate syntax for adding sub-descriptors? For
>> > example, there currently exist developmental stages described as
>> > "seedling", "1-4 leaf stage", "germination", etc., but our data
>> comes
>> > from much narrower windows than described with those terms.
>> >
>> > We realize it will be an ongoing process to refine the
>> vocabulary,
>> > and we look forward to being part of the process.
>> >
>> > Best regards,
>> >
>> > Tim Nelson
>> > Professor, Dept MCDB, Yale University
>> >
>> > >From: "Ware, Doreen" <ware at cshl.edu>
>> > >To: "'timothy.nelson at yale.edu'" <timothy.nelson at yale.edu>
>> > >Cc: "'Katica Ilic'" <katica at acoma.Stanford.EDU>,
>> > >         "Pankaj Jaiswal (E-mail)"
>> > >	 <pj37 at cornell.edu>
>> > >Subject: rice profiling project  interest in developing cell type
>> terms
>> > >Date: Wed, 29 Sep 2004 09:58:43 -0400
>> > >X-YaleITSMailFilter: Version 1.1e (attachment(s) not renamed)
>> > >Status: RO
>> > >
>> > >Dear Dr. Nelson,
>> > >
>> > >Thank you for introducing yourself and your project "Virtual
>> center for
>> > >cellular expression profiling of rice" last week.  I wanted to
>> follow-up and
>> > >introduce you to Katica Ilic the project coordinator for POC and
>> will be the
>> > >best contact person to discuss working within the POC framework to
>> develop
>> > >the correct terms and relationships for you project.  Please feel
>> free to
>> > >email Katica with your specific questions or to use contact link
>> on the POC
>> > >website  for po at plantontology.org.
>> > >
>> > >Doreen
>> > >
>> > >
>> > >Doreen Ware USDA ARS
>> > >Research Investigator
>> > >Cold Spring Harbor Laboratory
>> > >1 Bungtown Rd.
>> > >Cold Spring Harbor, NY 11724
>> > >Phone: 516 367-6979
>> > >Fax: 516 367-6851
>> > >E-mail: ware at cshl.edu
>> >
>>
>> ---------------------------------------------------------------------
> -----
>> 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.
>> ---------------------------------------------------------------------
> -----
>>
>>
> 
> 
> 