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

[fno.neeru at yale.edu]

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