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

Wed Jun 1 10:20:27 EDT 2005

Hi Katica,

>From Neeru's mail i gather she is using gramene ontology for anatomy and
growth stages. There is a possibility that she is not aware that PO has a
different version of growth stages than the one avaible on gramene.
Maybe we could send her a follow-up mail with the link?

anu

> 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.
>>> ---------------------------------------------------------------------
>> -----
>>>
>>>
>>
>>
>>
>
>