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

[Katica Ilic]

Hi Neeru,

I thought that it would confuse people who are using POC and Gramene site
interchangeably. The reason is, Gramene (and TAIR) already switched to using
Plant Structure Ontology, so if you go to the Gramene site (ontology view) or to
TAIR Keword Browser, you would find PO terms from the Plant Structure Ontology,
however, you would also come across Gramene and TAIR temporal ontologies, since
both databases are still maintaining their species-specific Growth and
Development Stages. Therefore, GRO terms in temporal ontology at Gramene site
are not the same as the PO Plant Growth Stages terms.

Plant Growth Stages can be browsed only at the POC web site, until both
databases switch to PO temporal ontology. Here at TAIR, we plan to completely
switch to PO by the end of the year, the latest. 

You will be hearing from Anu soon.

Best regards,

Katica

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