Comments on anatomy and temporal ontologies
Vincent, Leszek
Leszek at missouri.edu
Fri May 31 14:04:39 EDT 2002
Leonore, Tanya, Pankaj (& other colleagues),
I've gone through the file of notes which you folk have been building & have added my comments (attached).
We're covering some very important groundwork & I encourage all of us directly involved with this maybe sometimes painful task of sorting out/refining of the basics that it is an invaluable & an essential foundation. The reality is that this teasing out/refining will be ongoing for quite some time... We have good company with many GO developers who appreciate this.
Regards,
- Leszek
> -----Original Message-----
> From: Leonore Reiser [mailto:lreiser at acoma.Stanford.EDU]
> Sent: Wednesday, May 22, 2002 3:15 PM
> To: Pankaj Jaiswal
> Cc: Tanya Berardini; Vincent, Leszek; Curators At TAIR
> (E-mail); Doreen
> Ware (E-mail); Coe, Edward H.; Gramene developers; Lincoln Stein
> (E-mail); Mary Polacco (E-mail); Richard Bruskiewich (E-mail); Susan
> McCouch (E-mail); Victor Ulat (E-mail); Michael Ashburner (E-mail);
> SPRIG-CVO_Development (E-mail)
> Subject: Re: Comments on anatomy and temporal ontologies
>
>
>
> Pankaj et.al.;
> I have attached a text file with responses to some of the
> points raised in
> this email. Most of my comments are prefixed with ** and
> where Tanya made
> comments this is noted.
>
> We felt some things needed to be clarified before we go much
> further with
> changes i.e. that discussing some changes before hand would
> be helpful.
>
> Thanks for all the constructive comments- it really helps a
> great deal.
> Leonore
>
>
> On Sun, 19 May 2002, Pankaj Jaiswal wrote:
>
> > Based on the discussion in the last conference call and
> subsequent e mails from
> > Leszek and Tanya, here are my comments. The new growth
> stage ontology files are
> > attached.
> >
> > Tanya Berardini wrote:
> > >
> > > I have summarized specific comments from the TAIR group
> below. As you will
> > > see, they are quite extensive yet arise from only a
> partial review of the
> > > ontologies. We find that there are many problems that
> need to be resolved
> > > before the ontologies can be made public. It would be
> helpful if we can
> > > discuss the content issues by email: discussions of
> definitions, what
> > > should be term synonyms, the goal of a generic temporal
> framework that can
> > > accomodate all plants, etc.
> > >
> > > What should our next step be? What are your opinions on
> going back to
> > > the basics vs. trying to fix the current ontology?
> > >
> > > Tanya
> > >
> > Thanks Tanya for going through the files I sent earlier. I
> will work on the
> > anatomy files now.
> >
> > > TEMPORAL FILES:
> > >
> > > (1) We should try to not divide these by monocot and
> dicot but instead,
> > > like Leonore suggested, by actual stages:
> > >
> > > sporophytic(new)
> > > embryonic
> > > vegetative
> > > reproductive
> > > senesence (new)
> > > gametophytic(which would overlap with sporophytic
> reproductive stages,
> > > e.g. ovule developmental stages)
> > >
> > > This will help achieve our goal of using single terms to
> describe common
> > > processes.
> > >
> > > (2) Duplications and definitions (again): There are
> DBXrefs for terms
> > > like germination PO:0007051 but NO text. So there is germination
> > > PO:0000391 (Arabidopsis- also undefined), PO:0007053 and probably
> > > more. Can we define germination broadly as including imbibition,
> > > through radicle emergence and then make sensu terms. We can have a
> > > generic germination and then stages according to the
> organism ... but
> > > they should be developmental stages- NOT processes that are being
> > > defined.
> > >
> >
> > In the attached file I have tried to bring all the growth
> stages from cereals
> > Maize, Sorghum, barley, rice and oat, under higher order terms
> >
> > reproductive stage PO:0007140
> > vegetaive stages PO:0007139
> > embryonic stage PO:0007002
> >
> > I have not placed them under the similar stages defined by
> arabidopsis, because
> > I want TAIR to have a look at both the vesions and try to
> bring in the terms
> > defined for arabidopsis, by either moving the instances of
> > reproductive stage PO:0007140
> > vegetaive stages PO:0007139
> > embryonic stage PO:0007002
> > into their version or the vice versa. TAIR has to decide
> where to place them,
> > because we in cereals definitely do not recognize most of
> the growth stages they
> > have defined. However, there are some similarities, where
> Arabidopsis calls
> > "stage 1 flower " is panicle initiation in rice/tassel
> initiation in Maize.
> > "stage 2 flower " is panicle differentiation is rice
> > Some of the ovule development stages defined by Maize may
> overlap with that of
> > arabidopsis.
> >
> > My concers were
> >
> > Calling a term(s) "stage 1-18 flower" gives a wrong
> impression to the user. They
> > are all stages of inflorescence development with the flower
> as an underlying
> > entity, where the changes are observed. In a generic way it
> should be called as
> > "inflorescence development stage 1-18" and "stage 1-18
> flower" can go as
> > synonym.
> >
> > definitions for "flower development TAIR?PO: 0000004" such
> as "stages of flower
> > development in Arabidopsis" should be changed.
> >
> > DBXref like "principal growth stage-1.0" should be replaced
> with "Arabidopsis
> > growth stage-1.0"
> >
> > Terms like
> > "12 rosette stage" PO?TAIR:0000415, can be replaced with
> > "12 leaf stage" as a generic one with
> > "12 rosette stage" and "Arabidopsis growth stage 1.12" as synonyms
> > followed by definition part from existing term "12 rosette stage"
> > PO?TAIR:0000415
> > definition: stage at which the first 12 leaves have reached
> more than 1mm
> > length.
> > replaced by saying
> > Comment: For arabidopsis: stage at which the first 12
> leaves have reached more
> > than 1mm length.
> >
> > The reason for asking this is because if we agree to do
> something like this then
> > a person from Maize can also use the same term with a
> comment for maize.
> >
> >
> > Same has been done for all the similar terms from cereals.
> The terms like
> > booting stage
> > milk stage
> > dough stage
> > heading stage
> >
> > Example:
> > term: booting stage (sensu Poaceae)
> > goid: PO:0007148
> > definition: This stage is characterized by a swelling of
> the flag leaf sheath,
> > caused by an increase in the size of the panicle/tassel as
> it grows up the leaf
> > sheath.
> > definition_reference: GR:pj37
> > definition_reference: web:http
> >
> //www.uaex.edu/Other_Areas/publications/HTML/MP192/1_Rice_Grow
> th_and_Development_Reproductive.asp
> > comment: For Barley, Wheat and Oat: Zadok scale-40.
> > For Sorghum, leaf collars of all leaves are now visible.
> Sorghum head is
> > enclosed in the flag leaf sheath. Peduncle (stalk
> supporting the head) is
> > beginning to elongate
> >
> > (I have not included DBXref from MaizeDB, since Leszek
> needs to work on this)
> >
> > With the comments from respective crops which may suggest
> how they identify the
> > stage or when does this stage appears in teh particular
> crop. Mean how many days
> > after pollination, or after days to heading. There is no
> difference in
> > definition of these stages with one exception of when this
> stage appears in
> > different crops/plants, and if there are any other
> underlying events, then they
> > all go as commets from that crop/plant.
> >
> >
> > conflicts with
> >
> > reproductive stage PO:0007140
> > Stages from inflorescence initiation or formation of
> inflorescence primordia to
> > flowering (GR:pj37).
> > Comment: A greater part of vegetative stage in Poaceae
> overlap the reprdutive
> > stage.
> >
> > Everyone knows that the stage should be defined by the time
> reproduction is
> > occurring which includes the development of gametes. In
> case of the Poaceae
> > family members, this stage of development starts almost at
> the same time stem
> > elongation stage begins (this is about the same time when
> 5th leaf has emerged).
> > So its not only temporal but also spatial.
> >
> > Vs
> > reproductive: TAIR/PO: 0000306
> > stages of development that between flowering and death of
> the plant. (TAIR:lr)
> >
> > In most of the cereal crops, the plant does not die. Its
> harvested for forage
> > (on e may call it an unnatural death). However in some of
> maize and rice
> > varieties (atleast I know about these two), there is a new
> growth cycle
> > "ratooning stage PO:0007145", which "Produces new tillers
> from nodes after
> > harvest". There is no question of plant dyeing. There are
> stay green varieties
> > of sorghum which does not follow the pattern of undergoing
> natural death.
> >
> > I am afraid of using the word death in the definition
> "stages of development
> > that occur between flowering and death of the plant.
> (TAIR:lr)". since the plant
> > may be perennial (ratooning variety of rice/maize or the
> tree species)
> >
> > I would rather say "Stages from inflorescence initiation or
> formation of
> > inflorescence primordia or flower initial (in cases of
> plants having solitary
> > flower) to flowering. Includes fertilization (GR:pj37)".
> and in the comments I
> > will say
> > "The mid vegetative and vegetative lag phase may overalp
> with the reproductive
> > stage".
> >
> > I believe, we need to redefine the definitions for
> > "vegetaive stages"PO/TAIR:0000305 and PO:0007139 (chose either)
> > "stages of development that occur from seed germination up
> to flowering" from
> > PO/TAIR:0000305
> > or
> > "Stages from germination to inflorescence initiation or
> formation of flower
> > initial in plants with solitary flowers (without
> inflorescence)." from
> > PO:0007139
> >
> > with comments saying "The mid vegetative and vegetative lag
> phase may overalp
> > with the reproductive stage".
> >
> > Conflict with the term germination.
> >
> > Although its the same process but the type of gerination
> differ, epigeal Vs
> > hypogeal. I have not said anything about in the present
> file. However a person
> > can understand from looking at the terms
> > hypocotyl and cotyledon emergence PO?TAIR:0000396
> > and
> > coleoptile emergence from seed (sensu Poaceae) PO:0007006
> >
> > Do we need to mention about the germination types?
> >
> >
> > Leszek, Could you please look at the following and try to fix it.
> >
> > linear grain-filling (sensu Zea) PO:0007029. and its instances
> > blister stage PO:0007030 its instances
> > coleoptilar stage PO:0007031
> > embryo-1 PO:0007032
> > early dough stage (sensu Zea)PO:0007034
> > late dough stage (sensu Zea)PO:0007035
> > milk stage (sensu Zea)PO:0007033
> >
> > I believe, except
> > linear grain-filling (sensu Zea) PO:0007029. and its instance
> > blister stage PO:0007030
> >
> > rest all can go in as general for sensu Poaceae.
> > I already have similar terms
> > dough stage (sensu Poaceae)PO:0007042
> > hard dough stage PO:0007154
> > soft dough stage PO:0007152
> > milk stage (sensu Poaceae)PO:0007046
> >
> >
> >
> > I hope now TAIR will work on this file to organize rest of
> the part. I am
> > freezing the work on this file from my side. I have not
> touched the TAIR part
> > since its them who will have to work on it. Please make the
> necessary
> > corrections or updates.
> >
> > Another thing, I am not willing to accept this ontology as
> a "plant temporal
> > ontology", because its not based on time frames. There is
> an element of spatial
> > variation in it because of overlapping vegetative and
> reproductive stages. The
> > best is to call it a "plant growth stage ontology" PO:0007040
> >
> >
> > I might be worong in interpreting some of the concepts, so
> please correct me.
> >
> > Pankaj
>
> --------------------------------------------------------------
> -----------------
> Leonore Reiser, Ph.D. lreiser at acoma.stanford.edu
> The Arabidopsis Information Resource FAX: (650) 325-6857
> Carnegie Institution of Washington Tel: (650) 325-1521 ext. 311
> Department of Plant Biology URL: http://arabidopsis.org/
> 260 Panama St.
> Stanford, CA 94305
> --------------------------------------------------------------
> -----------------
>
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