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

[fno.neeru at yale.edu]

Hi Katica,

I thought that Gramene and TAIR were using plant structure and GRO 
ontologies developed by POC. But anyways I am browsing on the POC site 
and this site has links to the gramene ontology in itself. So for 
cereals it has link to the Gramene site and I clicked browse and it 
shows me the ontologies for rice. Tim could not make it for the meeting  
and so I attended the ontology workshop on his behalf. 

I was wondering do you have the email i.d of Anu who was also at the 
workshop as I have to get a few good references for rice she had 
mentioned about at the meeting. 

Thanks for your help. 

Regards

Neeru
 


Quoting Katica Ilic <jitterbug at plantontology.org>:

> Hi Neeru,
> 
> Reading back your initial e-mail, it occured to me that you are still
> using
> Gramene Growth Stages Ontology.  We talked about the release of POC
> Growth
> Stages at the meeting in San Diego, and Tim Nelson was invited to
> participate in
> the pre-release ontology reviewing process, so I thought that you
> have seen and
> used the new POC ontology. However, in case you haven't, I just want
> to let you
> know that the Plant Growth Stages Ontology was released about a month
> ago, you
> can browse it on the POC web site: www.plantontology.org. 
> 
> I'll let you know soon about the updates of the definitions for the
> terms in
> question.
> 
> Thanks you for contacting POC, I look forward to hearing from you in
> future.
>  
> Best regards,
> 
> Katica 
> 
> > Hi Katica,
> > I agree with you on changing the definition, because when I was
> looking 
> > on the site for axillary meristem I could not find anything but now
> I 
> > do so as you mentioned changing the definition of some of the
> existing 
> > terms. I hope I have answered your questions. Thanks.
> > Regards
> > Neeru
> > Quoting Katica Ilic <jitterbug at plantontology.org>:
> > 
> >> 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.
> >> >>
> >>
> ---------------------------------------------------------------------
> >> > -----
> >> >>
> >> >>
> >> > 
> >> > 
> >> > 
> >> 
> > 
> > 
> > 
>