From feedback_submission at filetta.cshl.edu Tue Jul 4 21:58:07 2006 From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu) Date: Tue, 4 Jul 2006 21:58:07 -0400 Subject: Feedback on POC Message-ID: <200607050158.k651w7UP001218@filetta.cshl.org> *** Feedback from Plant Ontology Live Site *** refer_to_url: http://www.plantontology.org/index.html name: steaven email: steaven at fmail.net organization: send_feedback: Send Clear: Clear comments: steaven http://charresult.com/cigarette.html buy cigarette From pj37 at cornell.edu Thu Jul 6 11:53:47 2006 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Thu, 06 Jul 2006 11:53:47 -0400 Subject: Question GRO term In-Reply-To: <00f501c690e2$da615ba0$b4971a96@NECVA70J> References: <00f501c690e2$da615ba0$b4971a96@NECVA70J> Message-ID: <44AD320B.1070805@cornell.edu> 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: > To: "AUGUSTINE, ALICE CLARA [AG/8042]" > Cc: ; "SATOH, Kouji" ; > "Pankaj Jaiswal" ; "Shoshi Kikuchi" > > 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 (????????) 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; ???? ???? >>>>>>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 From shuly at cshl.edu Thu Jul 6 15:00:55 2006 From: shuly at cshl.edu (Shuly Avraham) Date: Thu, 6 Jul 2006 15:00:55 -0400 Subject: Question GRO term In-Reply-To: <44AD320B.1070805@cornell.edu> References: <00f501c690e2$da615ba0$b4971a96@NECVA70J> <44AD320B.1070805@cornell.edu> Message-ID: <824EEF91-D3C9-4363-8F22-486622ABD27A@cshl.edu> Latest version is loaded to AmiGO-dev: http://dev.plantontology.org/amigo Shuly. On Jul 6, 2006, at 11:53 AM, Pankaj Jaiswal wrote: > 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: >> To: "AUGUSTINE, ALICE CLARA [AG/8042]" >> >> Cc: ; "SATOH, Kouji" >> ; >> "Pankaj Jaiswal" ; "Shoshi Kikuchi" >> >> 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 (????????) 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; ???? ???? >>>>>>> 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 > From pj37 at cornell.edu Wed Jul 12 18:39:33 2006 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Wed, 12 Jul 2006 18:39:33 -0400 Subject: plant ontology editor position: job opportunity Message-ID: <44B57A25.8050606@cornell.edu> Postdoctoral Associate ? 05677 Job Description Description Gramene database (http://www.gramene.org), is seeking applicants for a full time position for a plant biology curator who will participate in the development and maintenance of structured vocabularies for describing plant morphology, anatomy, growth and development stages for its Plant Ontology Consortium (POC) project (http://www.plantontology.org). These vocabularies (ontologies) are necessary to provide the backbone for describing phenotypes and gene expression patterns, and allow database users to perform a set of common queries or searches across different plant databases. The Plant Ontology Consortium is a collaboration among plant genome databases related to rice, Arabidopsis, maize, legumes, Solanaceae, etc. The successful candidate will work with a team of curators, software engineers, and database developers at Gramene and collaborating database projects, such as TAIR (http://www.arabidopsis.org) and MaizeGDB (http://maizegdb.org); contribute to annotation of phenotypes, germplasm and gene products by using the vocabularies developed in the project; participate in development and application of methods to improve consistency and to enhance the quality of annotations; promote the use of ontologies in comparative genomics and biology through active participation in workshops, seminars and scientific meetings. Qualifications Successful candidate will have a Ph.D. degree and training in Plant Biology and related fields (e.g. Systematics, Development, Physiology), a demonstrated ability for independent, critical thinking and excellent communication and teamwork skills. The curator must be able to travel to and attend 2-3 national and international meetings per year. Familiarity with biological data mining, basic UNIX/Linux commands, spreadsheets, and commonly used biological research tools is desired. A working knowledge of SQL would be an asset but not required. Qualified candidates should e-mail a cover letter and resume to Pankaj Jaiswal (pj37 at cornell.edu). From feedback_submission at filetta.cshl.edu Wed Jul 19 15:42:55 2006 From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu) Date: Wed, 19 Jul 2006 15:42:55 -0400 Subject: Feedback on POC Message-ID: <200607191942.k6JJgtH1019733@filetta.cshl.org> *** Feedback from Plant Ontology Live Site *** refer_to_url: http://www.plantontology.org/index.html comments: http://www.plantontology.org/amigo/go.cgi?open_0=PO:0004709&open_1=all&open_1=PO:0004709&open_1=PO:0009006&open_1=PO:0004713 With reference to above URL, loosk like there are a couple of issues with the terms that have 'bud' as part of the term name. Various children of PO:0004709 : axillary bud PO:0004713 : terminal bud should have IS_A relationship instead of the PART_OF. The following children terms must have PART_OF relationships to other parent terms like inflorescence and shoot apex. e.g. terminal floral bud PART_OF inflorescence, terminal inflorescence bud PART_OF stem / PART_OF shootapex, etc. # PO:0004714 : terminal floral bud # PO:0004715 : terminal inflorescence bud # PO:0004716 : terminal vegetative bud # PO:0004710 : axillary floral bud # PO:0004711 : axillary inflorescence bud # PO:0004712 : axillary vegetative bud Also we need a new generic term 'BUD' so that both the following can become instances of it. PO:0004709 : axillary bud PO:0004713 : terminal bud The suggested definition of the 'bud' : It is an undeveloped shoot that may develop vegetative or reproductive shoot parts and normally occurs in the axil of a leaf or at the tip of the stem. Depending on the environmental and physiological conditions a bud may remain in a dormant condition for some time or it may form a shoot immediately. name: Pankaj email: pj37 at cornell.edu organization: cu send_feedback: Send your feedback From feedback_submission at filetta.cshl.edu Wed Jul 19 16:18:56 2006 From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu) Date: Wed, 19 Jul 2006 16:18:56 -0400 Subject: Feedback on POC Message-ID: <200607192018.k6JKIuq6020043@filetta.cshl.org> *** Feedback from Plant Ontology Live Site *** refer_to_url: http://www.plantontology.org/download/download.html comments: Hello, I am looking for terms to refer to the initials for the endodermis and cortex in the root of Arabidopsis (the initial for endodermis and cortex, and its daughter cells). I do not find the terms, are they there and I do not see them? If not, are you planning to incorporate them? Thanks, Juliette name: Juliette Colinas email: jhc16 at duke.edu organization: Duke University/ Benfey lab send_feedback: Send your feedback From feedback_submission at filetta.cshl.edu Wed Jul 19 16:45:03 2006 From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu) Date: Wed, 19 Jul 2006 16:45:03 -0400 Subject: Feedback on POC Message-ID: <200607192045.k6JKj3AH020253@filetta.cshl.org> *** Feedback from Plant Ontology Live Site *** refer_to_url: http://www.plantontology.org/index.html comments: http://www.plantontology.org/amigo/go.cgi?view=details&show_associations=terms&search_constraint=terms&depth=0&query=PO:0000030 The definition of the term 'septum' says A thin partition or membrane that divides a cavity or a mass of tissue, e.g., in anther, ovary or fruit. The term we have is very generic and is a child of anther and carpel as well. We need to add various instances where it is found as separate terms because even called by the same name ontogenically its development in anther and carpel is different. name: Pankaj email: pj37 at cornell.edu organization: cu send_feedback: Send your feedback From felipe.zapata at umsl.edu Wed Jul 19 17:02:10 2006 From: felipe.zapata at umsl.edu (Felipe Zapata) Date: Wed, 19 Jul 2006 16:02:10 -0500 Subject: Feedback on POC In-Reply-To: <200607192045.k6JKj3AH020253@filetta.cshl.org> References: <200607192045.k6JKj3AH020253@filetta.cshl.org> Message-ID: <9FD8BC5C-4A2B-4636-B255-9F3586427F8D@umsl.edu> welcome back to the INFINITE problem of instantiation.... On Jul 19, 2006, at 3:45 PM, feedback_submission at filetta.cshl.edu wrote: > *** Feedback from Plant Ontology Live Site *** > > refer_to_url: http://www.plantontology.org/index.html > > comments: http://www.plantontology.org/amigo/go.cgi? > view=details&show_associations=terms&search_constraint=terms&depth=0&q > uery=PO:0000030 > > The definition of the term 'septum' says > A thin partition or membrane that divides a cavity or a mass of > tissue, e.g., in anther, ovary or fruit. > > The term we have is very generic and is a child of anther and > carpel as well. We need to add various instances where it is found > as separate terms because even called by the same name > ontogenically its development in anther and carpel is different. > > > > name: Pankaj > > email: pj37 at cornell.edu > > organization: cu > > send_feedback: Send your feedback > .............. Felipe Zapata Department of Biology University of Missouri St. Louis One University Boulevard St. Louis, MO 63121 USA p.314.516.7997 f.314.516.6233 -------------- next part -------------- An HTML attachment was scrubbed... URL: From feedback_submission at filetta.cshl.edu Wed Jul 19 19:08:08 2006 From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu) Date: Wed, 19 Jul 2006 19:08:08 -0400 Subject: Feedback on POC Message-ID: <200607192308.k6JN88bn020930@filetta.cshl.org> *** Feedback from Plant Ontology Live Site *** refer_to_url: http://www.plantontology.org/index.html name: career email: career at gmail.com organization: send_feedback: Send Clear: Clear comments: good day! 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name: Juliette Colinas email: jhc16 at duke.edu organization: Duke University/ Benfey lab send_feedback: Send your feedback From feedback_submission at filetta.cshl.edu Thu Jul 27 14:17:11 2006 From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu) Date: Thu, 27 Jul 2006 14:17:11 -0400 Subject: Feedback on POC Message-ID: <200607271817.k6RIHBSV001790@filetta.cshl.org> *** Feedback from Plant Ontology Live Site *** refer_to_url: http://www.plantontology.org/index.html comments: Hello, I asked this question earlier but I might have mistaken your answer for spam. I am looking for terms describing the endodermis/cortex initial and its daughter cells, are there any, if not will you make some? Thank you, Juliette name: Juliette Colinas email: jhc16 at duke.edu organization: Duke University/ Benfey lab send_feedback: Send your feedback From pj37 at cornell.edu Thu Jul 27 14:12:23 2006 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Thu, 27 Jul 2006 14:12:23 -0400 Subject: Feedback on POC [problem loading the files in OBO-Edit] In-Reply-To: <200607271753.k6RHrX87001565@filetta.cshl.org> References: <200607271753.k6RHrX87001565@filetta.cshl.org> Message-ID: <44C90207.6060907@cornell.edu> feedback_submission at filetta.cshl.edu wrote: > *** Feedback from Plant Ontology Live Site *** > > refer_to_url: http://www.plantontology.org/index.html > > comments: Hello, > > when I load the ontology in OBO-Edit, I do not get the full ontology loaded anymore, it used to work in the past, maybe it is a new version of the ontology file that has some problem? > > name: Juliette Colinas > > email: jhc16 at duke.edu > > organization: Duke University/ Benfey lab > > send_feedback: Send your feedback > Dear Juliette, I just now tried loading the po_anatomy.obo (ver 1.27) and po_temporal.obo (ver 1.27), in the OBO-Edit version 1.000-beta17 It worked for me. Just make sure when you load the ontology select the OBO-flat file adapter. Let me know the version number of the files and OBO-Edit if it still doesn't work. Pankaj From feedback_submission at filetta.cshl.edu Thu Jul 27 15:07:55 2006 From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu) Date: Thu, 27 Jul 2006 15:07:55 -0400 Subject: Feedback on POC Message-ID: <200607271907.k6RJ7tg3002402@filetta.cshl.org> *** Feedback from Plant Ontology Live Site *** refer_to_url: http://www.plantontology.org/index.html comments: Hello, a question about your ontology of root developmental stages in the plant growth ontology. The terms 'establishment of tissue systems', 'root elongation', and 'root hair formation' are defined to correspond to Benfey developmental stages 1 to 3. Something is not clear to me: is this ontology supposed to describe different *time points* in development? If so, then these definitions are wrong, because Benfey's developmental stages 1 to 3 refer to different portions of the root at a *single* time point. If not, then I find it a little confusing to mix spatial and temporal 'growth' in one ontology. Here is the experimental description of stages 1 to 3: 1: where the root tip reaches its full diameter (about 0.15 mm from the root tip) 2:where cells transition from being optically dense to a more transparent appearance as they begin longitudinal expansion (about 0.30 mm from the root tip) 3:where root hairs are fully elongated (about 0.45 to 2 mm from the root tip) Would you agree that the plant structure terms 'primary root tip', 'primary root elongation zone', and 'primary root differentiation zone' can be used to describe these stages? Thanks, Juliette name: Juliette Colinas email: jhc16 at duke.edu organization: Duke University/ Benfey lab send_feedback: Send your feedback From feedback_submission at filetta.cshl.edu Fri Jul 28 19:16:53 2006 From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu) Date: Fri, 28 Jul 2006 19:16:53 -0400 Subject: Feedback on POC Message-ID: <200607282316.k6SNGrLn001255@filetta.cshl.org> *** Feedback from Plant Ontology Live Site *** refer_to_url: http://www.plantontology.org/index.html comments: Hello, We look at roots in terms of days post-germination. I cannot find terms to best describe this in the growth ontology. Do you have a suggestion, or else will you make some terms? 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I was away for five weeks. I have received all your messages that you sent through the Plant Ontology Feedback system, and am planning to respond to each of your question very soon. Thank you very much for your patience. Best regards, Katica Ilic, POC project coordinator On Mon, 26 Jun 2006 feedback_submission at filetta.cshl.edu wrote: > *** Feedback from Plant Ontology Live Site *** > > refer_to_url: http://www.plantontology.org/index.html > > comments: Hello, > > I am searching for a term for the initial of the cortex/endodermis in the root tip, but cannot find one, has it been forgotten or is it another term that I should use? > > name: Juliette Colinas > > email: jhc16 at duke.edu > > organization: Duke University/ Benfey lab > > send_feedback: Send your feedback > -- -------------------------------------------------------------------------- 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. -------------------------------------------------------------------------- From katica at acoma.Stanford.EDU Mon Jul 31 14:00:17 2006 From: katica at acoma.Stanford.EDU (katica at acoma.Stanford.EDU) Date: Mon, 31 Jul 2006 11:00:17 -0700 (PDT) Subject: Feedback on POC In-Reply-To: <200607271753.k6RHrX87001565@filetta.cshl.org> References: <200607271753.k6RHrX87001565@filetta.cshl.org> Message-ID: Juliette, Do you still have problems loading the ontology file to OBO-editor? If so, please let me know exactly what file and what version did you download, and I'll try to reproduce the error and see what is causing the problem. Katica On Thu, 27 Jul 2006 feedback_submission at filetta.cshl.edu wrote: > *** Feedback from Plant Ontology Live Site *** > > refer_to_url: http://www.plantontology.org/index.html > > comments: Hello, > > when I load the ontology in OBO-Edit, I do not get the full ontology loaded anymore, it used to work in the past, maybe it is a new version of the ontology file that has some problem? > > name: Juliette Colinas > > email: jhc16 at duke.edu > > organization: Duke University/ Benfey lab > > send_feedback: Send your feedback > -- -------------------------------------------------------------------------- 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. -------------------------------------------------------------------------- From katica at acoma.Stanford.EDU Mon Jul 31 14:05:28 2006 From: katica at acoma.Stanford.EDU (katica at acoma.Stanford.EDU) Date: Mon, 31 Jul 2006 11:05:28 -0700 (PDT) Subject: Feedback on POC In-Reply-To: <200607271817.k6RIHBSV001790@filetta.cshl.org> References: <200607271817.k6RIHBSV001790@filetta.cshl.org> Message-ID: Juliette, Terms for the initial cells in the root apex are on my list to introduce to Plant Structure Ontology, they should be discussed on our ontology group meeting in mid August. I'll let you know when the ontology file will be updated. Best regards, Katica On Thu, 27 Jul 2006 feedback_submission at filetta.cshl.edu wrote: > *** Feedback from Plant Ontology Live Site *** > > refer_to_url: http://www.plantontology.org/index.html > > comments: Hello, > > I asked this question earlier but I might have mistaken your answer for spam. I am looking for terms describing the endodermis/cortex initial and its daughter cells, are there any, if not will you make some? > > Thank you, > > Juliette > > name: Juliette Colinas > > email: jhc16 at duke.edu > > organization: Duke University/ Benfey lab > > send_feedback: Send your feedback > -- -------------------------------------------------------------------------- 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. -------------------------------------------------------------------------- From katica at acoma.Stanford.EDU Mon Jul 31 14:23:04 2006 From: katica at acoma.Stanford.EDU (katica at acoma.Stanford.EDU) Date: Mon, 31 Jul 2006 11:23:04 -0700 (PDT) Subject: Feedback on POC In-Reply-To: <200607282316.k6SNGrLn001255@filetta.cshl.org> References: <200607282316.k6SNGrLn001255@filetta.cshl.org> Message-ID: Dear Juliette, Plant Structure Developmental Stages aspect of the PO has "root development stages" node, in which the stages are described based on succession of morphological/anatomical landmarks that are observable during root development. I hope you would agree with me that 'x days post-germination' is not a stage of root development, as it is not a stage of seedling development either. The best you can do is to 'convert' your staging system based on days after germination to the existing PO terms, based on the progression of root development at a particular day after germination that you picked as 'stage'. Hope this helps, Katica On Fri, 28 Jul 2006 feedback_submission at filetta.cshl.edu wrote: > *** Feedback from Plant Ontology Live Site *** > > refer_to_url: http://www.plantontology.org/index.html > > comments: Hello, > > We look at roots in terms of days post-germination. I cannot find terms to best describe this in the growth ontology. 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