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

fno.neeru at yale.edu fno.neeru at yale.edu
Thu Jun 2 16:21:42 EDT 2005 

Hi Katica,
Thanks, so may be I need to go back and look at the GRO ontologies 
again. I will keep writing to you as and when I am stuck. Thanks for 
your all your help.
Regards
Neeru

Quoting Katica Ilic <jitterbug at plantontology.org>:

> 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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