Question GRO term
Pankaj Jaiswal
pj37 at cornell.edu
Thu Jul 6 11:53:47 EDT 2006
In the version 1.25 of the po_anatomy.obo file the following new terms
were added. The same will be available for browsing in the next release
of the ontology soon.
-Pankaj
[Term]
id: PO:0006090
name: organogenic callus
namespace: plant_structure
def: "A type of cultured callus that has competence to form any organ
such as root\, leaf\, shoot\, leafless\nshoot/bare stem\, etc."
[POC:curators]
synonym: "meristematic callus" []
is_a: PO:0000009 ! cultured callus
[Term]
id: PO:0006091
name: embryogenic callus
namespace: plant_structure
def: "A type of cultured callus that form embryo-like structures such as
somatic embryos." [POC:curators]
is_a: PO:0000009 ! cultured callus
Added additonal parent for somatic embryo PO:0000011
embryogenic callus PO:0006091
--developsfrom--somatic embryo PO:0000011
---------------------------------------------------------------------------
Shoshi Kikuchi wrote:
> Dear Katica and all
>
>
>>Dr. Kikuchi (and others), please let me know if this would work for
>>annotation purposes.
>
>
> Thank you very much for your discusiion and very quick arrangement.
>
> We agree the annotation and it will work.
>
> Sincerely yours,
>
> Shoshi Kikuchi
>
> ***********************************
> Shoshi Kikuchi Ph.D
> Plant Genome Research Unit
> Division of Genome and Biodiversity Research
> National Institute of Agrobilogical Sciences (NIAS)
> Kan'non dai 2-1-2
> Tsukuba Ibaraki 305-8602 Japan
> TEL/FAX +81-29-838-7007
> Email: skikuchi at nias.affrc.go.jp
> WEB: ?(RMOS) http://microarray.rice.dna.affrc.go.jp
> (KOME) http://cdna01.dna.affrc.go.jp/cDNA/
> ************************************
>
> ----- Original Message -----
> From: <katica at acoma.Stanford.EDU>
> To: "AUGUSTINE, ALICE CLARA [AG/8042]" <alice.clara.augustine at monsanto.com>
> Cc: <po-dev at plantontology.org>; "SATOH, Kouji" <ksatoh at nias.affrc.go.jp>;
> "Pankaj Jaiswal" <pj37 at cornell.edu>; "Shoshi Kikuchi"
> <skikuchi at nias.affrc.go.jp>
> Sent: Friday, June 16, 2006 3:19 AM
> Subject: RE: Question GRO term
>
>
>
>>Hi Clare,
>>
>>Thanks for explanation.
>>
>>Based on the responses we got so far, my suggestion would be to add two
>>terms, 'embryogenic callus' and 'organogenic callus':
>>
>>PO:0000004 : in vitro cultured cell, tissue and organ
>> (i) PO:0000009 : cultured callus
>> (i) embryogenic callus
>> (i) organogenic callus (syn. meristematic callus)
>>
>>I need to double check about the synonym for the latter term.
>>
>>Since both callus types can originate (be induced) from a variety of
>>tissues, I would ignore this aspect, it can get really complicated,
>>(triggering large proliferation of terms).
>>Also, at this point, I would suggest not to propagate term 'meristemoid'
>>under 'in vitro cultured cell, tissue and organ' node. This term is
>
> already
>
>>in the PSO,
>>
>>PO:meristemoid, PO:0000070,
>>
>>Def: A cell or a group of cells constituting an active locus of
>>meristematic activity in a tissue composed of somewhat older,
>
> differentiating
>
>>cells.
>>
>>The definition describes all meristemoid cell, regardless of location.
>>However, if 'in vitro meristemoid cell' is required for accurate
>>annotations (in cases where term' meristemoid' is not sufficiently
>>granular), we will add it to PSO.
>>
>>Dr. Kikuchi (and others), please let me know if this would work for
>>annotation purposes.
>>
>>Best regards,
>>
>>Katica
>>
>>On Wed, 14 Jun 2006, AUGUSTINE, ALICE CLARA [AG/8042] wrote:
>>
>>
>>>Katica and all,
>>>
>>>There is a clear distinction between embryogenic callus and organogenic
>>>callus and the usage is pretty consistent amidst the tissue culture
>>>community.
>>>
>>>Organogenic - has competence to form any organ (root, leaf, shoot,
>
> leafless
>
>>>shoot/bare stem etc). In the embryogenic callus type, embryo-like
>
> structures
>
>>>develop, called somatic embryos, that then simultaneously develop shoots
>
> and
>
>>>roots.
>>>
>>>Then there is also the question of "meristematic callus". This type of
>>>callus that produces meristemoids (meristematic cell masses)
>>>Meristemoid: A localized group of callus cells, characterized by their
>>>accumulation of starch, RNA and protein, and giving rise to adventitious
>>>shoots or roots.
>>>Would it make sense to put organogenic callus and meristematic callus as
>>>synonyms?
>>>
>>>Another point to note is Meristemoids occur in 2 contexts:
>>>One as progenitors of stomata and the other as defined above.
>>>
>>>Cheers
>>>Regards,
>>>Alice Clara Augustine
>>>
>>>-----Original Message-----
>>>From: owner-po-dev at plantontology.org
>
> [mailto:owner-po-dev at plantontology.org]
>
>>>On Behalf Of katica at acoma.Stanford.EDU
>>>Sent: Wednesday, June 14, 2006 11:26 PM
>>>To: POC-dev; katica at acoma.Stanford.EDU
>>>Cc: SATOH, Kouji; Pankaj Jaiswal; Shoshi Kikuchi
>>>Subject: RE: Question GRO term
>>>
>>>Satoh,
>>>
>>>Sorry I wasn't specific enough regardng embryogenic callus,
>>>'embryogenic callus' should describe callus with demonstrable competence
>>>to form somatic embryos. 'organogenic callus' has competence to form
>
> roots
>
>>>and/or shoots.
>>>
>>>I vaguely remember that some people referred to embryogenic callus even
>>>though regeneration of shoots/roots took place from such callus. My
>>>recollection goes back to literature that was published some 12 or more
>>>years ago.
>>>
>>>Is there a clear distinction in plant tissue culture community regarding
>>>proper use of this terminology, 'embryogenic callus' and 'organogenic
>>>callus'?
>>>
>>>Katica
>>>
>>>
>>>On Wed, 14 Jun 2006 katica at acoma.stanford.edu wrote:
>>>
>>>
>>>>Dear Satoh,
>>>>
>>>>On Wed, 14 Jun 2006, SATOH, Kouji wrote:
>>>>....
>>>>
>>>>>I have question for you: you described the callus as embryogenic, does
>>>>>
>>>>>>this refer to callus that will give rise to somatic embryos, or
>>>>>>to the callus
>>>>>>induced from embryo tissue within seed, or both? I don't know
>>>>>>enough about
>>>>>>callus induction from rice seeds, some clarification would help with
>>>>>>defining parent terms for the new term 'embryogenic callus'.
>>>>>
>>>>>"Embryogenic callus" is the callus is able to generate somatic embryo,
>>>
>>>does
>>>
>>>>>not indicate the callus derived from embryo tissue.
>>>>
>>>>OK, 'embryogenic calus' refers to callus with demonstrable
>
> morphogenetic
>
>>>>competence (either organogenesis or embryogenesis). Coincidentally, in
>
> the
>
>>>>particular case of the callus induced from rice seeds, it originated
>
> from
>
>>>>embryonic tissue too (which is relevant for placing the new term under
>>>
>>>proper
>>>
>>>>parent term).
>>>>
>>>>
>>>>>And I think "Embryogenic callus" is one of organogenic callus.
>>>>>Three type of tissues are generated from callus.They are adventitious
>>>>>shoot,
>>>>>root, and embryo(same as soamtic embryo).
>>>>>Because plant call has "totipotency".
>>>>>Therefore the methods of re-diffrerentiation of plant from callus are
>>>
>>>two.
>>>
>>>>>One is direct induced somatic embryo from callus.
>>>>>This callus is embryogenic callus
>>>>>
>>>>>Other is two step method, at first, the induction of adventitious
>
> shoot
>
>>>(or
>>>
>>>>>root), and after that, induced root (or shoot).
>>>>>This callus is "organogenic callus"
>>>>>
>>>>>Can I answer the your question?
>>>>
>>>>Yes, you did. Thank you very much for clarification.
>>>>Best regards,
>>>>
>>>>Katica
>>>>
>>>>>best regards
>>>>>Satoh
>>>>>
>>>>>++++++++++++++++++++++++++++++++++++
>>>>>SATOH, Kouji (º´Æ£¹ÀÆó) Ph. D
>>>>>Unit of Plant Genome Research
>>>>>National Institute of Agrobiological Sciences
>>>>>Mail: ksatoh at nias.affrc.go.jp
>>>>>Tel: 029-838-7007
>>>>>++++++++++++++++++++++++++++++++++++
>>>>>
>>>>>
>>>>>>-----Original Message-----
>>>>>>From: katica at acoma.stanford.edu [mailto:katica at acoma.stanford.edu]
>>>>>>Sent: Wednesday, June 14, 2006 2:27 AM
>>>>>>To: POC-dev; Pankaj Jaiswal
>>>>>>Cc: Shoshi Kikuchi; º´Æ£ ¹ÀÆó
>>>>>>Subject: Re: Question GRO term
>>>>>>
>>>>>>
>>>>>>Dear Kikuchi,
>>>>>>
>>>>>>Pankaj Jaiswal forwarded your request to POC. Currently, we only
>>>>>>have term
>>>>>>'cultured callus' and 'cultured embryo' in Plant structure ontology
>>>
>>>(PSO).
>>>
>>>>>>New term, embryogenic callus, would need to be introduced to PSO.
>>>>>>
>>>>>>I have question for you: you described the callus as embryogenic,
>
> does
>
>>>>>>this refer to callus that will give rise to somatic embryos, or
>>>>>>to the callus
>>>>>>induced from embryo tissue within seed, or both? I don't know
>>>>>>enough about
>>>>>>callus induction from rice seeds, some clarification would help with
>>>>>>defining parent terms for the new term 'embryogenic callus'.
>>>>>>
>>>>>>Also, there are no Growth stage terms for in vitro cultures. Since
>
> Plant
>
>>>>>>Growth Stages are pertinent to a whole plant, we intentionally
>>>>>>ommitted dealing with staging for tissue culture entities.
>>>>>>
>>>>>>Best Regards,
>>>>>>
>>>>>>Katica
>>>>>>
>>>>>>
>>>>>>>Shoshi Kikuchi wrote:
>>>>>>>
>>>>>>>>Dear Pankaj
>>>>>>>>
>>>>>>>>We are now preparing for the ontology-based description of our
>>>>>>
>>>>>>full-length
>>>>>>
>>>>>>>>cDNA clones.
>>>>>>>>
>>>>>>>>I have a question. What is the appropriate description of
>
> embryogenic
>
>>>>>>>>callus. Many of our full-length cDNA libraries are originated from
>>>
>>>rice
>>>
>>>>>>>>callus induced from mature seed.
>>>>>>>>
>>>>>>>>21 day-old callus after induction on the medium containing
>>>>>>
>>>>>>2,4-D as auxin
>>>>>>
>>>>>>>>from a mature seed.
>>>>>>>>
>>>>>>>>What kind of GRO term is the most appropriate one?
>>>>>>>>
>>>>>>>>Sincerely yours,
>>>>>>>>
>>>>>>>>Shoshi
>>>>>>>>***********************************
>>>>>>>>Shoshi Kikuchi Ph.D
>>>>>>>>Plant Genome Research Unit
>>>>>>>>Division of Genome and Biodiversity Research
>>>>>>>>National Institute of Agrobilogical Sciences (NIAS)
>>>>>>>>Kan'non dai 2-1-2
>>>>>>>>Tsukuba Ibaraki 305-8602 Japan
>>>>>>>>TEL/FAX +81-29-838-7007
>>>>>>>>Email: skikuchi at nias.affrc.go.jp
>>>>>>>>WEB: ¡£¡£(RMOS) http://microarray.rice.dna.affrc.go.jp
>>>>>>>> (KOME) http://cdna01.dna.affrc.go.jp/cDNA/
>>>>>>>>************************************
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>--
>>>>>>
>>
>>--------------------------------------------------------------------------
>>
>>>>>>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.
>>>>>>
>>
>>--------------------------------------------------------------------------
>>
>>>>
>>>
>>--
>>--------------------------------------------------------------------------
>>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.
>>--------------------------------------------------------------------------
>>
>
>
>
--
Pankaj Jaiswal
G-15, Bradfield Hall
Dept. of Plant Breeding and Genetics
Cornell University
Ithaca, NY-14853, USA
Ph. +1-607-255-3103 / 4199
fax: +1-607-255-6683
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