From pj37 at cornell.edu Mon May 2 12:36:44 2005 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Mon, 02 May 2005 12:36:44 -0400 Subject: ontology In-Reply-To: <5.2.1.1.2.20050429173712.021942f0@wiscmail.wisc.edu> References: <5.2.1.1.2.20050429173712.021942f0@wiscmail.wisc.edu> Message-ID: <4276571C.7060500@cornell.edu> Dear Ron, The plant Ontologies we have in Gramene are developed by the Plant Ontology consortium. Therefore, I am forwarding your message to the Plant Ontology project list. Someone will contact you from the project within a day or two about your request. For the search problem, it was so because the actual term name has a singular form "cell" and not "cells". Search for "cork cell" in Gramene yields 3 results http://www.gramene.org/db/ontology/search?query=cork+cell&btn=Search&ontology_type=PO Thanks Pankaj Ron Skadsen wrote: > Dear Ontologists, > > I tried your site to find some information on cork cells. These are > small cells commonly paired with silica cells in grasses. We have a > gene promoter that causes expression of a reporter gene in cork cells. > Your listing has only the common cork cell, as derived from the > cambium. Is there a way to tease out an entry for the different cork > cells? Also, a search of "cork cells" on your site yield zero matches. > > Cheers, > > Ron Skadsen > > USDA/ARS > Cereal Crops Research Unit > 506 Walnut St. > Madison, WI 53726 > ph (608)262-3672 > FAX (608)264-5528 > -- ************************ Pankaj Jaiswal, PhD G15-Bradfield Hall Dept. of Plant Breeding Cornell University Ithaca, NY-14853, USA Tel: +1-607-255-3103 +1-607-255-4199 Fax: +1-607-255-6683 http://www.gramene.org ************************ From kellogge at msx.umsl.edu Tue May 3 12:01:50 2005 From: kellogge at msx.umsl.edu (kellogge) Date: Tue, 3 May 2005 11:01:50 -0500 Subject: Nodal root innstances (crown and seminal roots) In-Reply-To: <426FCE73.8010902@cornell.edu> References: <426FCE73.8010902@cornell.edu> Message-ID: Seems reasonable to me to bring these back. How about: crown root (definition): adventitious root initiating from one of the earliest-formed nodes on the plant. (Comment: these roots are normally formed at or just above ground level.) seminal root (definition): adventitious root initiating from the scutellar node in a grass. Toby On Apr 27, 2005, at 12:40 PM, Pankaj Jaiswal wrote: > > view=details&show_associations=terms&search_constraint=terms&depth=0&qu > ery=PO:0003005> > > Can we bring back the two instances of the nodal root, > > nodal root ; PO:0003005 > ---%crown root ; PO:0003008 > ---seminal root ; PO:0003009 > > These terms were merged to nodal root (PO:0003005) as synonyms. They > were introduced to the anatomy.ontology in version 1.11 > > Their development is genetically controlled > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi? > cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14980975 > > Also I need these terms for annotating the genes expressed in them > > > #1 > cDNA-AFLP analysis of inducible gene expression in rice > seminal root tips under a water deficit > doi:10.1016/S0378-1119(03)00713-3 > http://www.paper.edu.cn/scholar/download.jsp?file=wuping-5 > > > #2 > The Crown rootless1 Gene in Rice Is Essential for Crown Root > Formation and Is a Target of an AUXIN RESPONSE FACTOR in Auxin > Signaling. > Plant Cell. 2005 Apr 13 > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi? > cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15829602 > > > -- > ************************ > Pankaj Jaiswal, PhD > G15-Bradfield Hall > Dept. of Plant Breeding > Cornell University > Ithaca, NY-14853, USA > > Tel: +1-607-255-3103 > +1-607-255-4109 > Fax: +1-607-255-6683 > http://www.gramene.org > ************************ > > Elizabeth A. Kellogg E. Desmond Lee and Family Professor of Botanical Studies Department of Biology University of Missouri-St. Louis St. Louis, MO 63121 Tel: 314-516-6217 FAX: 314-516-6233 http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ home.html -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 2055 bytes Desc: not available URL: From pj37 at cornell.edu Tue May 3 12:10:15 2005 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 03 May 2005 12:10:15 -0400 Subject: Nodal root innstances (crown and seminal roots) In-Reply-To: References: <426FCE73.8010902@cornell.edu> Message-ID: <4277A267.7000706@cornell.edu> Sounds good to me. If everyone agrees, I will add the terms on Friday. -Pankaj kellogge wrote: > Seems reasonable to me to bring these back. > How about: > crown root (definition): adventitious root initiating from one of the > earliest-formed nodes on the plant. (Comment: these roots are normally > formed at or just above ground level.) > seminal root (definition): adventitious root initiating from the > scutellar node in a grass. > Toby > > On Apr 27, 2005, at 12:40 PM, Pankaj Jaiswal wrote: > > > > > > Can we bring back the two instances of the nodal root, > > nodal root ; PO:0003005 > ---%crown root ; PO:0003008 > ---seminal root ; PO:0003009 > > These terms were merged to nodal root (PO:0003005) as synonyms. They > were introduced to the anatomy.ontology in version 1.11 > > Their development is genetically controlled > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14980975 > > > Also I need these terms for annotating the genes expressed in them > > > #1 > cDNA-AFLP analysis of inducible gene expression in rice > seminal root tips under a water deficit > doi:10.1016/S0378-1119(03)00713-3 > http://www.paper.edu.cn/scholar/download.jsp?file=wuping-5 > > > #2 > The Crown rootless1 Gene in Rice Is Essential for Crown Root > Formation and Is a Target of an AUXIN RESPONSE FACTOR in Auxin > Signaling. > Plant Cell. 2005 Apr 13 > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15829602 > > > > -- > ************************ > Pankaj Jaiswal, PhD > G15-Bradfield Hall > Dept. of Plant Breeding > Cornell University > Ithaca, NY-14853, USA > > Tel: +1-607-255-3103 > +1-607-255-4109 > Fax: +1-607-255-6683 > http://www.gramene.org > ************************ > > > Elizabeth A. Kellogg > E. Desmond Lee and Family Professor of Botanical Studies > Department of Biology > University of Missouri-St. Louis > St. Louis, MO 63121 > Tel: 314-516-6217 > FAX: 314-516-6233 > http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/home.html > -- ************************ Pankaj Jaiswal, PhD G15-Bradfield Hall Dept. of Plant Breeding Cornell University Ithaca, NY-14853, USA Tel: +1-607-255-3103 +1-607-255-4109 Fax: +1-607-255-6683 http://www.gramene.org ************************ From Leszek at missouri.edu Tue May 3 12:58:13 2005 From: Leszek at missouri.edu (Vincent, Leszek) Date: Tue, 3 May 2005 11:58:13 -0500 Subject: Nodal root innstances (crown and seminal roots) Message-ID: Hi Toby, Pankaj (& others), It would seem essential that these terms be brought back. I provide the detailed definitions for these terms from the Zea mays ontology. If you'd like me to offer tweaked definitions for the definitions offered by Toby, based on my Zea definitions, I could attempt those. Crown roots - The crown roots are the predominant component of the adventitious root system. They are termed crown roots because they originate from the basal portion of the growing stem known as the crown. The crown roots are subterranean in origin. The first crown roots (4-5), arranged in a whorl, appear at the base of the second internode about as soon as the tip of the coleoptile reaches the soil surface. A few of the subsequent higher internodes may have a similar number of crown roots (in whorls), after which the successive internodes have more and larger crown roots. The crown roots are usually extensively branched, via the production of numerous lateral adventitious roots. Note that the adventitious roots which arise from 2-3 internodes immediately above the soil surface (aerial in origin) are a separate component of the adventitious root system, called 'prop' or 'brace roots'. (Feldman in Freeling & Walbot (eds), 1994. The Maize Handbook, ID#60920; Kiesselbach, ID#59445; Poethig in Sheridan, WF (ed), 1982. Maize for Biological Research, ID#25744; Vincent, ID#165572, 2002) Seminal root system - The seminal root system consists of the adventitious lateral roots which are present in the ungerminated caryopsis (kernel, seed) - they are formed during embryogenesis. The adventitious seminal lateral roots arise from 3 to 7 seminal root primordia. These primordia originate 30-40 days post-anthesis, and emerge between the scutellum and the first internode. The adventitious seminal lateral root system, the primary root and its associated adventitious lateral roots, forms a small part of the total root system of the plant. These roots are of greatest importance during the early growth of the seedling before the adventitious crown roots of higher internodes become well established. (Feldman in Freeling & Walbot (eds), 1994. The Maize Handbook, ID#60920; Kiesselbach, ID#59445; Poethig in Sheridan, WF (ed), 1982. Maize for Biological Research, ID#25744; Vincent ID#165572, 2002) - Leszek ________________________________ From: owner-po-dev at brie4.cshl.org [mailto:owner-po-dev at brie4.cshl.org] On Behalf Of kellogge Sent: Tuesday, May 03, 2005 11:02 AM To: Pankaj Jaiswal; po-dev at plantontology.org Subject: Re: Nodal root innstances (crown and seminal roots) Seems reasonable to me to bring these back. How about: crown root (definition): adventitious root initiating from one of the earliest-formed nodes on the plant. (Comment: these roots are normally formed at or just above ground level.) seminal root (definition): adventitious root initiating from the scutellar node in a grass. Toby On Apr 27, 2005, at 12:40 PM, Pankaj Jaiswal wrote: Can we bring back the two instances of the nodal root, nodal root ; PO:0003005 ---%crown root ; PO:0003008 ---seminal root ; PO:0003009 These terms were merged to nodal root (PO:0003005) as synonyms. They were introduced to the anatomy.ontology in version 1.11 Their development is genetically controlled http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dop t=Abstract&list_uids=14980975 Also I need these terms for annotating the genes expressed in them #1 cDNA-AFLP analysis of inducible gene expression in rice seminal root tips under a water deficit doi:10.1016/S0378-1119(03)00713-3 http://www.paper.edu.cn/scholar/download.jsp?file=wuping-5 #2 The Crown rootless1 Gene in Rice Is Essential for Crown Root Formation and Is a Target of an AUXIN RESPONSE FACTOR in Auxin Signaling. Plant Cell. 2005 Apr 13 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dop t=Abstract&list_uids=15829602 -- ************************ Pankaj Jaiswal, PhD G15-Bradfield Hall Dept. of Plant Breeding Cornell University Ithaca, NY-14853, USA Tel: +1-607-255-3103 +1-607-255-4109 Fax: +1-607-255-6683 http://www.gramene.org ************************ Elizabeth A. Kellogg E. Desmond Lee and Family Professor of Botanical Studies Department of Biology University of Missouri-St. Louis St. Louis, MO 63121 Tel: 314-516-6217 FAX: 314-516-6233 http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/home.ht ml -------------- next part -------------- An HTML attachment was scrubbed... URL: From pj37 at cornell.edu Tue May 3 14:35:04 2005 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 03 May 2005 14:35:04 -0400 Subject: Nodal root innstances (crown and seminal roots) In-Reply-To: References: Message-ID: <4277C458.7080305@cornell.edu> Vincent, Leszek wrote: > Hi Toby, Pankaj (& others), > > > > It would seem essential that these terms be brought back. I provide the > detailed definitions for these terms from the Zea mays ontology. If > you?d like me to offer tweaked definitions for the definitions offered > by Toby, based on my Zea definitions, I could attempt those. > > > > Crown roots - The crown roots are the predominant component of the > adventitious root system. They are termed crown roots because they > originate from the basal portion of the growing stem known as the crown. > The crown roots are subterranean in origin. The first crown roots (4-5), > arranged in a whorl, appear at the base of the second internode about as > soon as the tip of the coleoptile reaches the soil surface. A few of the > subsequent higher internodes may have a similar number of crown roots > (in whorls), after which the successive internodes have more and larger > crown roots. The crown roots are usually extensively branched, via the > production of numerous lateral adventitious roots. Note that the > adventitious roots which arise from 2-3 internodes immediately above the > soil surface (aerial in origin) are a separate component of the > adventitious root system, called 'prop' or 'brace roots'. (Feldman in > Freeling & Walbot (eds), 1994. The Maize Handbook, ID#60920; > Kiesselbach, ID#59445; Poethig in Sheridan, WF (ed), 1982. Maize for > Biological Research, ID#25744; Vincent, ID#165572, 2002) > Most part of this definition can actually go to the comments section. However, this raises a question about # adding new term "brace roots, synonym: prop roots". These are different from "crown roots", if I go with Leszek's definition. # What is "crown" or "seedling crown" [not the crown of tree]? We need to define it somewhere in ontology or add it as synonym to multiple terms suggesting that X-plant_part is grouped to form seedling crown. Or create a new term "seedling crown" which we all know is not a biologically correct term, but can be treated as a bin/grouping term. It's children with part of relationships will more precisely tell what region is called as "crown". -Pankaj From katica at acoma.Stanford.EDU Tue May 3 17:31:17 2005 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Tue, 3 May 2005 14:31:17 -0700 (PDT) Subject: Nodal root innstances (crown and seminal roots) In-Reply-To: <4277A267.7000706@cornell.edu> Message-ID: Hi all, I apologize for not responding to this thread on time, the e-mail was sent on the day of the ontology release and I simply didn't have time to respond. In fact, I would greatly appreciate if internal ontology requests are not sent off on the day of the ontology release, unless they are urgent. Now that Pankaj is suggesting to bring back terms crown and seminal root, the question is: do we then need term 'nodal root'; it is now just a grouping term? Could we make crown and seminal root instances of adventitious root (obsoleting nodal root), with definitions that Toby provided? And perhaps adding 'brace root' too if needed. adventitious root % crown root ; PO:0003008 % seminal root ; PO:0003009 % brace root (new) Regarding Leszek's definitions, I don't think we should be providing references as part of definitions, and definitions should be short and concise, if possible (considering the AmiGO display of definitions). Katica P.S. Pankaj, once we agree on this, if you don't mind, I can do these changes in the file, together with a few other corrections and typos (on Friday). On Tue, 3 May 2005, Pankaj Jaiswal wrote: > Sounds good to me. If everyone agrees, I will add the terms on Friday. > -Pankaj > > > > kellogge wrote: > > > Seems reasonable to me to bring these back. > > How about: > > crown root (definition): adventitious root initiating from one of the > > earliest-formed nodes on the plant. (Comment: these roots are normally > > formed at or just above ground level.) > > seminal root (definition): adventitious root initiating from the > > scutellar node in a grass. > > Toby > > > > On Apr 27, 2005, at 12:40 PM, Pankaj Jaiswal wrote: > > > > > > > > > > > > Can we bring back the two instances of the nodal root, > > > > nodal root ; PO:0003005 > > ---%crown root ; PO:0003008 > > ---seminal root ; PO:0003009 > > > > These terms were merged to nodal root (PO:0003005) as synonyms. They > > were introduced to the anatomy.ontology in version 1.11 > > > > Their development is genetically controlled > > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14980975 > > > > > > Also I need these terms for annotating the genes expressed in them > > > > > > #1 > > cDNA-AFLP analysis of inducible gene expression in rice > > seminal root tips under a water deficit > > doi:10.1016/S0378-1119(03)00713-3 > > http://www.paper.edu.cn/scholar/download.jsp?file=wuping-5 > > > > > > #2 > > The Crown rootless1 Gene in Rice Is Essential for Crown Root > > Formation and Is a Target of an AUXIN RESPONSE FACTOR in Auxin > > Signaling. > > Plant Cell. 2005 Apr 13 > > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15829602 > > > > > > > > -- > > ************************ > > Pankaj Jaiswal, PhD > > G15-Bradfield Hall > > Dept. of Plant Breeding > > Cornell University > > Ithaca, NY-14853, USA > > > > Tel: +1-607-255-3103 > > +1-607-255-4109 > > Fax: +1-607-255-6683 > > http://www.gramene.org > > ************************ > > > > > > Elizabeth A. Kellogg > > E. Desmond Lee and Family Professor of Botanical Studies > > Department of Biology > > University of Missouri-St. Louis > > St. Louis, MO 63121 > > Tel: 314-516-6217 > > FAX: 314-516-6233 > > http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/home.html > > > > -- > ************************ > Pankaj Jaiswal, PhD > G15-Bradfield Hall > Dept. of Plant Breeding > Cornell University > Ithaca, NY-14853, USA > > Tel: +1-607-255-3103 > +1-607-255-4109 > Fax: +1-607-255-6683 > http://www.gramene.org > ************************ > -------------------------------------------------------------------------- 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 Tue May 3 20:09:34 2005 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Tue, 3 May 2005 17:09:34 -0700 (PDT) Subject: Plant ontology updates In-Reply-To: Message-ID: Hi all, The following changes to the Plant Structure Ontology are to be made this week: I. Bringing back from the obsolete node terms 'crown root' and 'seminal root', and obsoleting 'nodal root' Ontology structure: adventitious root % crown root ; PO:0003008 % seminal root ; PO:0003009 Please, let me know if term 'brace root' is needed at present time. II. From St Louis meeting, the following terms are to be added (which we already agreed on): New term: 1. stem vascular system Def: Total of the vascular tissues in their specific arrangements in the stem. 2. root vascular bundle (new term, requested by Pankaj) Def: A strandlike part of vascular system of root, composed of phloem, xylem and associated transfusion tissue 3. add 'leaf vascular bundle' as a synonym of 'leaf vein' NOTE: we now have three highly redundant terms: root vascular system, root stele and root vascular bundle. For a curator, it is going to be a very arbitrary decision to make on which one to use for annotation. 4. Renaming the term 'nodule' to 'root nodule' and adding a new structure for the term 'nodule: New term: adventitious root nodule (syn. stem nodule) Def: Enlargement or swelling on adventitious aerial roots in some legumes (e.g., Sesbania rostrata), inhabited by nitrogen-fixing bacteria. Unlike the root nodules, these contain functioning chloroplasts in the nodule cortex and are therefore capable of carbon fixation. (TAIR:ki) Ontology structure: root (p) root nodule (i) adventitious root (p) adventitious root nodule (synonym: stem nodule) IV. Corrections of typos and minor errors in the ontology file : 1. Term: stem cortex Definition: The primary tissue located between the vascular system and the epidermis of the root. (It should be 'of the stem"). 2. Sillica cell to silica cell 3. Cotyledon vascular system (to correct the definition) 4. Also, several minor typos in the text of the following: Terms: stolon, valve, phloem, chlorenchyma, and shoot procambium. Thanks, Katica -------------------------------------------------------------------------- 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 Leszek at missouri.edu Wed May 4 10:32:01 2005 From: Leszek at missouri.edu (Vincent, Leszek) Date: Wed, 4 May 2005 09:32:01 -0500 Subject: Nodal root innstances (crown and seminal roots) Message-ID: Katica (& colleagues), Just for clarification - The references in the definitions associated with the two terms (crown roots & seminal roots) came from my Zea ontology 'sand box' - an excel spreadsheet. They're not included in the Zea ontology file. - Leszek *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* P. Leszek D. Vincent Ph.D., FLS Division of Plant Sciences Res. Prof. Dept. of Horticulture 215 Curtis Hall University of Missouri-Columbia Columbia MO 65211-7020 USA Ph: (573) 884-3716; Fax:(573) 884-7850; Email: Leszek at missouri.edu Associate Curator, Dunn-Palmer Herbarium (UMO); Research Associate, Missouri Botanical Garden (MO), USA; Plant Systematist on The Plant Ontology Consortium - NSF award 0321666 (www.plantontology.org) *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* -----Original Message----- From: owner-po-dev at brie4.cshl.org [mailto:owner-po-dev at brie4.cshl.org] On Behalf Of Katica Ilic Sent: Tuesday, May 03, 2005 4:31 PM To: po-dev at plantontology.org; Pankaj Jaiswal Cc: Kellogg, Elizabeth A. Subject: Re: Nodal root innstances (crown and seminal roots) Hi all, I apologize for not responding to this thread on time, the e-mail was sent on the day of the ontology release and I simply didn't have time to respond. In fact, I would greatly appreciate if internal ontology requests are not sent off on the day of the ontology release, unless they are urgent. Now that Pankaj is suggesting to bring back terms crown and seminal root, the question is: do we then need term 'nodal root'; it is now just a grouping term? Could we make crown and seminal root instances of adventitious root (obsoleting nodal root), with definitions that Toby provided? And perhaps adding 'brace root' too if needed. adventitious root % crown root ; PO:0003008 % seminal root ; PO:0003009 % brace root (new) Regarding Leszek's definitions, I don't think we should be providing references as part of definitions, and definitions should be short and concise, if possible (considering the AmiGO display of definitions). Katica P.S. Pankaj, once we agree on this, if you don't mind, I can do these changes in the file, together with a few other corrections and typos (on Friday). On Tue, 3 May 2005, Pankaj Jaiswal wrote: > Sounds good to me. If everyone agrees, I will add the terms on Friday. > -Pankaj > > > > kellogge wrote: > > > Seems reasonable to me to bring these back. > > How about: > > crown root (definition): adventitious root initiating from one of the > > earliest-formed nodes on the plant. (Comment: these roots are normally > > formed at or just above ground level.) > > seminal root (definition): adventitious root initiating from the > > scutellar node in a grass. > > Toby > > > > On Apr 27, 2005, at 12:40 PM, Pankaj Jaiswal wrote: > > > > > > > > > > > > Can we bring back the two instances of the nodal root, > > > > nodal root ; PO:0003005 > > ---%crown root ; PO:0003008 > > ---seminal root ; PO:0003009 > > > > These terms were merged to nodal root (PO:0003005) as synonyms. They > > were introduced to the anatomy.ontology in version 1.11 > > > > Their development is genetically controlled > > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dop t=Abstract&list_uids=14980975 > > > > > > Also I need these terms for annotating the genes expressed in them > > > > > > #1 > > cDNA-AFLP analysis of inducible gene expression in rice > > seminal root tips under a water deficit > > doi:10.1016/S0378-1119(03)00713-3 > > http://www.paper.edu.cn/scholar/download.jsp?file=wuping-5 > > > > > > #2 > > The Crown rootless1 Gene in Rice Is Essential for Crown Root > > Formation and Is a Target of an AUXIN RESPONSE FACTOR in Auxin > > Signaling. > > Plant Cell. 2005 Apr 13 > > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dop t=Abstract&list_uids=15829602 > > > > > > > > -- > > ************************ > > Pankaj Jaiswal, PhD > > G15-Bradfield Hall > > Dept. of Plant Breeding > > Cornell University > > Ithaca, NY-14853, USA > > > > Tel: +1-607-255-3103 > > +1-607-255-4109 > > Fax: +1-607-255-6683 > > http://www.gramene.org > > ************************ > > > > > > Elizabeth A. Kellogg > > E. Desmond Lee and Family Professor of Botanical Studies > > Department of Biology > > University of Missouri-St. Louis > > St. Louis, MO 63121 > > Tel: 314-516-6217 > > FAX: 314-516-6233 > > http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/home.ht ml > > > > -- > ************************ > Pankaj Jaiswal, PhD > G15-Bradfield Hall > Dept. of Plant Breeding > Cornell University > Ithaca, NY-14853, USA > > Tel: +1-607-255-3103 > +1-607-255-4109 > Fax: +1-607-255-6683 > http://www.gramene.org > ************************ > ------------------------------------------------------------------------ -- 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 kellogge at msx.umsl.edu Wed May 4 11:07:35 2005 From: kellogge at msx.umsl.edu (kellogge) Date: Wed, 4 May 2005 10:07:35 -0500 Subject: Plant ontology updates In-Reply-To: References: Message-ID: <3F3D950A-BCAE-11D9-AD5B-000D93B827BC@msx.umsl.edu> The difficulty with the root terms is created by the differences in root anatomy. In monocots plus a few of the early-diverging angiosperms (e.g. Piperaceae), the vascular system of the root is made up of vascular bundles scattered all over the place as seen in cross section, and not organized into a central cylinder. In eudicots, the term root vascular bundle doesn't have much meaning, since the stele is a cylindrical unit without separate bundles. Thus for monocots and Piperaceae, you'd need the terms root vascular bundle and root vascular system (all the bundles as a group), whereas in eudicots and other of the early diverging lineages you'd need stele (which would include the endodermis) and root vascular system, which would be the vascular tissue encompassed by the stele. So the accurate definition of the terms - to avoid confusing the annotators - would have to include some sort of comment on where the terms are to be applied. Toby On May 3, 2005, at 7:09 PM, Katica Ilic wrote: > Hi all, > > The following changes to the Plant Structure Ontology are to be made > this > week: > > I. Bringing back from the obsolete node terms 'crown root' and 'seminal > root', and obsoleting 'nodal root' > > Ontology structure: > > adventitious root > % crown root ; PO:0003008 > % seminal root ; PO:0003009 > > Please, let me know if term 'brace root' is needed at present time. > > II. From St Louis meeting, the following terms are to be added (which > we > already agreed on): > > New term: > 1. stem vascular system > Def: Total of the vascular tissues in their specific arrangements in > the > stem. > > 2. root vascular bundle (new term, requested by Pankaj) > Def: A strandlike part of vascular system of root, composed of phloem, > xylem and associated transfusion tissue > > 3. add 'leaf vascular bundle' as a synonym of 'leaf vein' > > NOTE: we now have three highly redundant terms: root vascular system, > root > stele and root vascular bundle. For a curator, it is going to be a very > arbitrary decision to make on which one to use for annotation. > > 4. Renaming the term 'nodule' to 'root nodule' and adding a new > structure > for the term 'nodule: > > New term: adventitious root nodule (syn. stem nodule) > Def: Enlargement or swelling on adventitious aerial roots in some > legumes > (e.g., Sesbania rostrata), inhabited by nitrogen-fixing bacteria. > Unlike > the root nodules, these contain functioning chloroplasts in the nodule > cortex and are therefore capable of carbon fixation. (TAIR:ki) > > Ontology structure: > > root > (p) root nodule > (i) adventitious root > (p) adventitious root nodule (synonym: stem nodule) > > > IV. Corrections of typos and minor errors in the ontology file : > 1. Term: stem cortex > Definition: The primary tissue located between the vascular system and > the > epidermis of the root. > (It should be 'of the stem"). > > 2. Sillica cell to silica cell > > 3. Cotyledon vascular system (to correct the definition) > > 4. Also, several minor typos in the text of the following: > Terms: stolon, valve, phloem, chlorenchyma, and shoot procambium. > > Thanks, > > Katica > > > ----------------------------------------------------------------------- > --- > 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. > ----------------------------------------------------------------------- > --- > > > Elizabeth A. Kellogg E. Desmond Lee and Family Professor of Botanical Studies Department of Biology University of Missouri-St. Louis St. Louis, MO 63121 Tel: 314-516-6217 FAX: 314-516-6233 http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ home.html -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 3820 bytes Desc: not available URL: From pj37 at cornell.edu Wed May 4 12:18:34 2005 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Wed, 04 May 2005 12:18:34 -0400 Subject: Plant ontology updates In-Reply-To: References: Message-ID: <4278F5DA.2050100@cornell.edu> I suggest leaving the vascular system and bundle terms until I come up with a proposal. Still working on those. Toby has some issues as well. Rest is fine, you can go ahead and add the terms I proposed to bring back. -Pankaj Katica Ilic wrote: > Hi all, > > The following changes to the Plant Structure Ontology are to be made this > week: > > I. Bringing back from the obsolete node terms 'crown root' and 'seminal > root', and obsoleting 'nodal root' > > Ontology structure: > > adventitious root > % crown root ; PO:0003008 > % seminal root ; PO:0003009 > > Please, let me know if term 'brace root' is needed at present time. > > II. From St Louis meeting, the following terms are to be added (which we > already agreed on): > > New term: > 1. stem vascular system > Def: Total of the vascular tissues in their specific arrangements in the > stem. > > 2. root vascular bundle (new term, requested by Pankaj) > Def: A strandlike part of vascular system of root, composed of phloem, > xylem and associated transfusion tissue > > 3. add 'leaf vascular bundle' as a synonym of 'leaf vein' > > NOTE: we now have three highly redundant terms: root vascular system, root > stele and root vascular bundle. For a curator, it is going to be a very > arbitrary decision to make on which one to use for annotation. > > 4. Renaming the term 'nodule' to 'root nodule' and adding a new structure > for the term 'nodule: > > New term: adventitious root nodule (syn. stem nodule) > Def: Enlargement or swelling on adventitious aerial roots in some legumes > (e.g., Sesbania rostrata), inhabited by nitrogen-fixing bacteria. Unlike > the root nodules, these contain functioning chloroplasts in the nodule > cortex and are therefore capable of carbon fixation. (TAIR:ki) > > Ontology structure: > > root > (p) root nodule > (i) adventitious root > (p) adventitious root nodule (synonym: stem nodule) > > > IV. Corrections of typos and minor errors in the ontology file : > 1. Term: stem cortex > Definition: The primary tissue located between the vascular system and the > epidermis of the root. > (It should be 'of the stem"). > > 2. Sillica cell to silica cell > > 3. Cotyledon vascular system (to correct the definition) > > 4. Also, several minor typos in the text of the following: > Terms: stolon, valve, phloem, chlorenchyma, and shoot procambium. > > Thanks, > > Katica > > > -------------------------------------------------------------------------- > 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, PhD G15-Bradfield Hall Dept. of Plant Breeding Cornell University Ithaca, NY-14853, USA Tel: +1-607-255-3103 +1-607-255-4109 Fax: +1-607-255-6683 http://www.gramene.org ************************ From peter.stevens at mobot.org Wed May 4 12:35:57 2005 From: peter.stevens at mobot.org (Peter Stevens) Date: Wed, 4 May 2005 12:35:57 -0400 Subject: Plant ontology updates In-Reply-To: <3F3D950A-BCAE-11D9-AD5B-000D93B827BC@msx.umsl.edu> References: <3F3D950A-BCAE-11D9-AD5B-000D93B827BC@msx.umsl.edu> Message-ID: >Ummm, I think Homer nodded. As far as I can work out, differences >between young roots in monocots and BLAs, certainly in eudicots, has >to do more with the number of protoxylem poles than anything else; >BLAs are 1-few, monocots tend to be many (and to have a pith, too, >although this is certainly at least sporadic in BLAs). Furthermore, >roots don't really have vascular bundles at all, so the term should >not be used here; the aylem and phloem poles alternate regularly >around the circumference of the stele. So the vascular system of >the root consists of the vascular tissue, initially alternating >xylem and phloem, which may take up the whole of the central part of >the root - or not. The stele can be clearly recognised, unlike in >many stems (strictly speaking, 'stele' and 'vascular system' are not >synonyms, although they have been treated as such). Incidentally, >the direction of development of the xylem in the root and stem >differs; the root is exarch, the stem endarch; this is true of all >seed plants. What goes on in the stem is roughly what Toby described; most monocots and things like Piperaceae tend to have scattered vbs; Ranunculaceae Cucurbitaceae Asteraceae (e.g.) have initially a ring of separate bundles, whether or not later joined by vascular cambium, while other BLAs have a ring of vascular tissue from the beginning - but I am not sure of the distribution of this latter feature. P. >The difficulty with the root terms is created by the differences in root >anatomy. In monocots plus a few of the early-diverging angiosperms >(e.g. Piperaceae), the vascular system of the root is made up of >vascular bundles scattered all over the place as seen in cross section, >and not organized into a central cylinder. In eudicots, the term root >vascular bundle doesn't have much meaning, since the stele is a >cylindrical unit without separate bundles. Thus for monocots and >Piperaceae, you'd need the terms root vascular bundle and root vascular >system (all the bundles as a group), whereas in eudicots and other of >the early diverging lineages you'd need stele (which would include the >endodermis) and root vascular system, which would be the vascular tissue >encompassed by the stele. So the accurate definition of the terms - to >avoid confusing the annotators - would have to include some sort of >comment on where the terms are to be applied. >Toby > >On May 3, 2005, at 7:09 PM, Katica Ilic wrote: > > >> Hi all, >> >> The following changes to the Plant Structure Ontology are to be made >> this >> week: >> >> I. Bringing back from the obsolete node terms 'crown root' and >> 'seminal >> root', and obsoleting 'nodal root' >> >> Ontology structure: >> >> adventitious root >> % crown root ; PO:0003008 >> % seminal root ; PO:0003009 >> >> Please, let me know if term 'brace root' is needed at present time. >> >> II. From St Louis meeting, the following terms are to be added (which >> we >> already agreed on): >> >> New term: >> 1. stem vascular system >> Def: Total of the vascular tissues in their specific arrangements in >> the >> stem. >> >> 2. root vascular bundle (new term, requested by Pankaj) >> Def: A strandlike part of vascular system of root, composed of phloem, >> >> xylem and associated transfusion tissue >> >> 3. add 'leaf vascular bundle' as a synonym of 'leaf vein' >> >> NOTE: we now have three highly redundant terms: root vascular system, >> root >> stele and root vascular bundle. For a curator, it is going to be a >> very >> arbitrary decision to make on which one to use for annotation. >> >> 4. Renaming the term 'nodule' to 'root nodule' and adding a new >> structure >> for the term 'nodule: >> >> New term: adventitious root nodule (syn. stem nodule) >> Def: Enlargement or swelling on adventitious aerial roots in some >> legumes >> (e.g., Sesbania rostrata), inhabited by nitrogen-fixing bacteria. >> Unlike >> the root nodules, these contain functioning chloroplasts in the nodule >> >> cortex and are therefore capable of carbon fixation. (TAIR:ki) > > >> Ontology structure: >> >> root >> (p) root nodule >> (i) adventitious root >> (p) adventitious root nodule (synonym: stem nodule) >> >> >> IV. Corrections of typos and minor errors in the ontology file : >> 1. Term: stem cortex >> Definition: The primary tissue located between the vascular system and >> the >> epidermis of the root. >> (It should be 'of the stem"). >> >> 2. Sillica cell to silica cell >> >> 3. Cotyledon vascular system (to correct the definition) >> >> 4. Also, several minor typos in the text of the following: >> Terms: stolon, valve, phloem, chlorenchyma, and shoot procambium. >> >> Thanks, >> >> Katica >> >> >> ---------------------------------------------------------------------- >> ---- >> 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. >> ---------------------------------------------------------------------- >> ---- >> >> >> >> >Elizabeth A. Kellogg >E. Desmond Lee and Family Professor of Botanical Studies >Department of Biology >University of Missouri-St. Louis >St. Louis, MO 63121 >Tel: 314-516-6217 >FAX: 314-516-6233 >http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/home.ht >ml From katica at acoma.Stanford.EDU Wed May 4 14:42:55 2005 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Wed, 4 May 2005 11:42:55 -0700 (PDT) Subject: Plant ontology updates In-Reply-To: <4278F5DA.2050100@cornell.edu> Message-ID: Pankaj, I don't mind leaving vascular bundle out for now, but for the 'stem vascular system' I see no major reason of not including it, I have a few annotations sitting and waiting for this ter. we already have the following terms in PO (in no particular order): cotyledon vascular system leaf vascular system root vascular system vascular system and stem vascular system is clearly missing. Whatever we decide on 'vascular bundle', the existance of this new term is justified as a need for the grouping term which is required for annotation (since we don't have term 'stele' in the PO, only 'root stele'). So, I would vote to introduce 'stem vascular system' in this round. Let me know what you think. Katica On Wed, 4 May 2005, Pankaj Jaiswal wrote: > I suggest leaving the vascular system and bundle terms until I come up > with a proposal. Still working on those. Toby has some issues as well. > Rest is fine, you can go ahead and add the terms I proposed to bring back. > > -Pankaj > > Katica Ilic wrote: > > > Hi all, > > > > The following changes to the Plant Structure Ontology are to be made this > > week: > > > > I. Bringing back from the obsolete node terms 'crown root' and 'seminal > > root', and obsoleting 'nodal root' > > > > Ontology structure: > > > > adventitious root > > % crown root ; PO:0003008 > > % seminal root ; PO:0003009 > > > > Please, let me know if term 'brace root' is needed at present time. > > > > II. From St Louis meeting, the following terms are to be added (which we > > already agreed on): > > > > New term: > > 1. stem vascular system > > Def: Total of the vascular tissues in their specific arrangements in the > > stem. > > > > 2. root vascular bundle (new term, requested by Pankaj) > > Def: A strandlike part of vascular system of root, composed of phloem, > > xylem and associated transfusion tissue > > > > 3. add 'leaf vascular bundle' as a synonym of 'leaf vein' > > > > NOTE: we now have three highly redundant terms: root vascular system, root > > stele and root vascular bundle. For a curator, it is going to be a very > > arbitrary decision to make on which one to use for annotation. > > > > 4. Renaming the term 'nodule' to 'root nodule' and adding a new structure > > for the term 'nodule: > > > > New term: adventitious root nodule (syn. stem nodule) > > Def: Enlargement or swelling on adventitious aerial roots in some legumes > > (e.g., Sesbania rostrata), inhabited by nitrogen-fixing bacteria. Unlike > > the root nodules, these contain functioning chloroplasts in the nodule > > cortex and are therefore capable of carbon fixation. (TAIR:ki) > > > > Ontology structure: > > > > root > > (p) root nodule > > (i) adventitious root > > (p) adventitious root nodule (synonym: stem nodule) > > > > > > IV. Corrections of typos and minor errors in the ontology file : > > 1. Term: stem cortex > > Definition: The primary tissue located between the vascular system and the > > epidermis of the root. > > (It should be 'of the stem"). > > > > 2. Sillica cell to silica cell > > > > 3. Cotyledon vascular system (to correct the definition) > > > > 4. Also, several minor typos in the text of the following: > > Terms: stolon, valve, phloem, chlorenchyma, and shoot procambium. > > > > Thanks, > > > > Katica > > > > > > -------------------------------------------------------------------------- > > 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, PhD > G15-Bradfield Hall > Dept. of Plant Breeding > Cornell University > Ithaca, NY-14853, USA > > Tel: +1-607-255-3103 > +1-607-255-4109 > Fax: +1-607-255-6683 > http://www.gramene.org > ************************ > -------------------------------------------------------------------------- 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 Wed May 4 14:47:11 2005 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Wed, 4 May 2005 11:47:11 -0700 (PDT) Subject: Plant ontology updates In-Reply-To: <3F3D950A-BCAE-11D9-AD5B-000D93B827BC@msx.umsl.edu> Message-ID: Toby, This certainly clarifies it for me. We need to think of the best way to include this in the definition/comment section. Katica On Wed, 4 May 2005, kellogge wrote: > The difficulty with the root terms is created by the differences in > root anatomy. In monocots plus a few of the early-diverging > angiosperms (e.g. Piperaceae), the vascular system of the root is made > up of vascular bundles scattered all over the place as seen in cross > section, and not organized into a central cylinder. In eudicots, the > term root vascular bundle doesn't have much meaning, since the stele is > a cylindrical unit without separate bundles. Thus for monocots and > Piperaceae, you'd need the terms root vascular bundle and root vascular > system (all the bundles as a group), whereas in eudicots and other of > the early diverging lineages you'd need stele (which would include the > endodermis) and root vascular system, which would be the vascular > tissue encompassed by the stele. So the accurate definition of the > terms - to avoid confusing the annotators - would have to include some > sort of comment on where the terms are to be applied. > Toby > > On May 3, 2005, at 7:09 PM, Katica Ilic wrote: > > > Hi all, > > > > The following changes to the Plant Structure Ontology are to be made > > this > > week: > > > > I. Bringing back from the obsolete node terms 'crown root' and 'seminal > > root', and obsoleting 'nodal root' > > > > Ontology structure: > > > > adventitious root > > % crown root ; PO:0003008 > > % seminal root ; PO:0003009 > > > > Please, let me know if term 'brace root' is needed at present time. > > > > II. From St Louis meeting, the following terms are to be added (which > > we > > already agreed on): > > > > New term: > > 1. stem vascular system > > Def: Total of the vascular tissues in their specific arrangements in > > the > > stem. > > > > 2. root vascular bundle (new term, requested by Pankaj) > > Def: A strandlike part of vascular system of root, composed of phloem, > > xylem and associated transfusion tissue > > > > 3. add 'leaf vascular bundle' as a synonym of 'leaf vein' > > > > NOTE: we now have three highly redundant terms: root vascular system, > > root > > stele and root vascular bundle. For a curator, it is going to be a very > > arbitrary decision to make on which one to use for annotation. > > > > 4. Renaming the term 'nodule' to 'root nodule' and adding a new > > structure > > for the term 'nodule: > > > > New term: adventitious root nodule (syn. stem nodule) > > Def: Enlargement or swelling on adventitious aerial roots in some > > legumes > > (e.g., Sesbania rostrata), inhabited by nitrogen-fixing bacteria. > > Unlike > > the root nodules, these contain functioning chloroplasts in the nodule > > cortex and are therefore capable of carbon fixation. (TAIR:ki) > > > > Ontology structure: > > > > root > > (p) root nodule > > (i) adventitious root > > (p) adventitious root nodule (synonym: stem nodule) > > > > > > IV. Corrections of typos and minor errors in the ontology file : > > 1. Term: stem cortex > > Definition: The primary tissue located between the vascular system and > > the > > epidermis of the root. > > (It should be 'of the stem"). > > > > 2. Sillica cell to silica cell > > > > 3. Cotyledon vascular system (to correct the definition) > > > > 4. Also, several minor typos in the text of the following: > > Terms: stolon, valve, phloem, chlorenchyma, and shoot procambium. > > > > Thanks, > > > > Katica > > > > > > ----------------------------------------------------------------------- > > --- > > 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. > > ----------------------------------------------------------------------- > > --- > > > > > > > Elizabeth A. Kellogg > E. Desmond Lee and Family Professor of Botanical Studies > Department of Biology > University of Missouri-St. Louis > St. Louis, MO 63121 > Tel: 314-516-6217 > FAX: 314-516-6233 > http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ > home.html > -------------------------------------------------------------------------- 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 pj37 at cornell.edu Wed May 4 16:01:08 2005 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Wed, 04 May 2005 16:01:08 -0400 Subject: Plant ontology updates In-Reply-To: References: Message-ID: <42792A04.40402@cornell.edu> Fine. -Pankaj Katica Ilic wrote: > Pankaj, > > I don't mind leaving vascular bundle out for now, but for the 'stem > vascular system' I see no major reason of not including it, I have a few > annotations sitting and waiting for this ter. > we already have the following terms in PO (in no particular order): > > cotyledon vascular system > leaf vascular system > root vascular system > vascular system > > and stem vascular system is clearly missing. > > Whatever we decide on 'vascular bundle', the existance of this new term is > justified as a need for the grouping term which is required for annotation > (since we don't have term 'stele' in the PO, only 'root stele'). > > So, I would vote to introduce 'stem vascular system' in this round. > > Let me know what you think. > > Katica > > On Wed, 4 May 2005, Pankaj Jaiswal wrote: > > >>I suggest leaving the vascular system and bundle terms until I come up >>with a proposal. Still working on those. Toby has some issues as well. >>Rest is fine, you can go ahead and add the terms I proposed to bring back. >> >>-Pankaj >> >>Katica Ilic wrote: >> >> >>>Hi all, >>> >>>The following changes to the Plant Structure Ontology are to be made this >>>week: >>> >>>I. Bringing back from the obsolete node terms 'crown root' and 'seminal >>>root', and obsoleting 'nodal root' >>> >>>Ontology structure: >>> >>>adventitious root >>> % crown root ; PO:0003008 >>> % seminal root ; PO:0003009 >>> >>>Please, let me know if term 'brace root' is needed at present time. >>> >>>II. From St Louis meeting, the following terms are to be added (which we >>>already agreed on): >>> >>>New term: >>>1. stem vascular system >>>Def: Total of the vascular tissues in their specific arrangements in the >>>stem. >>> >>>2. root vascular bundle (new term, requested by Pankaj) >>>Def: A strandlike part of vascular system of root, composed of phloem, >>>xylem and associated transfusion tissue >>> >>>3. add 'leaf vascular bundle' as a synonym of 'leaf vein' >>> >>>NOTE: we now have three highly redundant terms: root vascular system, root >>>stele and root vascular bundle. For a curator, it is going to be a very >>>arbitrary decision to make on which one to use for annotation. >>> >>>4. Renaming the term 'nodule' to 'root nodule' and adding a new structure >>>for the term 'nodule: >>> >>>New term: adventitious root nodule (syn. stem nodule) >>>Def: Enlargement or swelling on adventitious aerial roots in some legumes >>>(e.g., Sesbania rostrata), inhabited by nitrogen-fixing bacteria. Unlike >>>the root nodules, these contain functioning chloroplasts in the nodule >>>cortex and are therefore capable of carbon fixation. (TAIR:ki) >>> >>>Ontology structure: >>> >>>root >>> (p) root nodule >>> (i) adventitious root >>> (p) adventitious root nodule (synonym: stem nodule) >>> >>> >>>IV. Corrections of typos and minor errors in the ontology file : >>>1. Term: stem cortex >>>Definition: The primary tissue located between the vascular system and the >>>epidermis of the root. >>>(It should be 'of the stem"). >>> >>>2. Sillica cell to silica cell >>> >>>3. Cotyledon vascular system (to correct the definition) >>> >>>4. Also, several minor typos in the text of the following: >>>Terms: stolon, valve, phloem, chlorenchyma, and shoot procambium. >>> >>>Thanks, >>> >>>Katica >>> >>> >>>-------------------------------------------------------------------------- >>>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, PhD >>G15-Bradfield Hall >>Dept. of Plant Breeding >>Cornell University >>Ithaca, NY-14853, USA >> >>Tel: +1-607-255-3103 >> +1-607-255-4109 >>Fax: +1-607-255-6683 >>http://www.gramene.org >>************************ >> > > > -------------------------------------------------------------------------- > 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, PhD G15-Bradfield Hall Dept. of Plant Breeding Cornell University Ithaca, NY-14853, USA Tel: +1-607-255-3103 +1-607-255-4109 Fax: +1-607-255-6683 http://www.gramene.org ************************ From katica at acoma.Stanford.EDU Wed May 4 17:39:45 2005 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Wed, 4 May 2005 14:39:45 -0700 (PDT) Subject: Plant ontology updates In-Reply-To: Message-ID: Hi all, I have no problem leaving 'root vascular bundle' out for now, and I like the idea of clarifying the usage of the 'vascular' terms, once we decide on the root vascular bundle. Right now, there is 'root vascular system' and 'root stele', and it is not too confusing to decide which one of the two to use in particular cases (at least for Arabidopsis annotations). We can include in Comment section Toby's clarification once the vascular terms are revisited. After the comments I got today, here is the new version of this week ontology update: I. To bring back terms crown root seminal root, and obsoleting nodal rot adventitious root % crown root ; PO:0003008 % seminal root ; PO:0003009 II. From St Louis meeting, add the following terms (which we already agreed on): New term: 1. stem vascular system NEW def: Vascular tissues in their specific arrangements in the stem. 2. Renaming the term 'nodule' to 'root nodule' and adding a new structure for the term 'nodule: 3. New term: adventitious root nodule (syn. stem nodule) NEW def: Enlargement or swelling on adventitious aerial roots, inhabited by nitrogen-fixing bacteria. Comment: Unlike the root nodules, these contain functioning chloroplasts in the nodule cortex and are therefore capable of carbon fixation. Ontology structure: root (p) root nodule (i) adventitious root (p) adventitious root nodule (synonym: stem nodule) 4. Corrections of typos in the ontology file (as described earlier). I appreciate your comments and your prompt responses to this thread. Katica On Wed, 4 May 2005, Peter Stevens wrote: > >Ummm, I think Homer nodded. As far as I can work out, differences > >between young roots in monocots and BLAs, certainly in eudicots, has > >to do more with the number of protoxylem poles than anything else; > >BLAs are 1-few, monocots tend to be many (and to have a pith, too, > >although this is certainly at least sporadic in BLAs). Furthermore, > >roots don't really have vascular bundles at all, so the term should > >not be used here; the aylem and phloem poles alternate regularly > >around the circumference of the stele. So the vascular system of > >the root consists of the vascular tissue, initially alternating > >xylem and phloem, which may take up the whole of the central part of > >the root - or not. The stele can be clearly recognised, unlike in > >many stems (strictly speaking, 'stele' and 'vascular system' are not > >synonyms, although they have been treated as such). Incidentally, > >the direction of development of the xylem in the root and stem > >differs; the root is exarch, the stem endarch; this is true of all > >seed plants. > > > What goes on in the stem is roughly what Toby described; most > monocots and things like Piperaceae tend to have scattered vbs; > Ranunculaceae Cucurbitaceae Asteraceae (e.g.) have initially a ring > of separate bundles, whether or not later joined by vascular cambium, > while other BLAs have a ring of vascular tissue from the beginning - > but I am not sure of the distribution of this latter feature. > > P. > > > > > > >The difficulty with the root terms is created by the differences in root > >anatomy. In monocots plus a few of the early-diverging angiosperms > >(e.g. Piperaceae), the vascular system of the root is made up of > >vascular bundles scattered all over the place as seen in cross section, > >and not organized into a central cylinder. In eudicots, the term root > >vascular bundle doesn't have much meaning, since the stele is a > >cylindrical unit without separate bundles. Thus for monocots and > >Piperaceae, you'd need the terms root vascular bundle and root vascular > >system (all the bundles as a group), whereas in eudicots and other of > >the early diverging lineages you'd need stele (which would include the > >endodermis) and root vascular system, which would be the vascular tissue > >encompassed by the stele. So the accurate definition of the terms - to > >avoid confusing the annotators - would have to include some sort of > >comment on where the terms are to be applied. > >Toby > > > >On May 3, 2005, at 7:09 PM, Katica Ilic wrote: > > > > > >> Hi all, > >> > >> The following changes to the Plant Structure Ontology are to be made > >> this > >> week: > >> > >> I. Bringing back from the obsolete node terms 'crown root' and > >> 'seminal > >> root', and obsoleting 'nodal root' > >> > >> Ontology structure: > >> > >> adventitious root > >> % crown root ; PO:0003008 > >> % seminal root ; PO:0003009 > >> > >> Please, let me know if term 'brace root' is needed at present time. > >> > >> II. From St Louis meeting, the following terms are to be added (which > >> we > >> already agreed on): > >> > >> New term: > >> 1. stem vascular system > >> Def: Total of the vascular tissues in their specific arrangements in > >> the > >> stem. > >> > >> 2. root vascular bundle (new term, requested by Pankaj) > >> Def: A strandlike part of vascular system of root, composed of phloem, > >> > >> xylem and associated transfusion tissue > >> > >> 3. add 'leaf vascular bundle' as a synonym of 'leaf vein' > >> > >> NOTE: we now have three highly redundant terms: root vascular system, > >> root > >> stele and root vascular bundle. For a curator, it is going to be a > >> very > >> arbitrary decision to make on which one to use for annotation. > >> > >> 4. Renaming the term 'nodule' to 'root nodule' and adding a new > >> structure > >> for the term 'nodule: > >> > >> New term: adventitious root nodule (syn. stem nodule) > >> Def: Enlargement or swelling on adventitious aerial roots in some > >> legumes > >> (e.g., Sesbania rostrata), inhabited by nitrogen-fixing bacteria. > >> Unlike > >> the root nodules, these contain functioning chloroplasts in the nodule > >> > >> cortex and are therefore capable of carbon fixation. (TAIR:ki) > > > > >> Ontology structure: > >> > >> root > >> (p) root nodule > >> (i) adventitious root > >> (p) adventitious root nodule (synonym: stem nodule) > >> > >> > >> IV. Corrections of typos and minor errors in the ontology file : > >> 1. Term: stem cortex > >> Definition: The primary tissue located between the vascular system and > >> the > >> epidermis of the root. > >> (It should be 'of the stem"). > >> > >> 2. Sillica cell to silica cell > >> > >> 3. Cotyledon vascular system (to correct the definition) > >> > >> 4. Also, several minor typos in the text of the following: > >> Terms: stolon, valve, phloem, chlorenchyma, and shoot procambium. > >> > >> Thanks, > >> > >> Katica > >> > >> > >> ---------------------------------------------------------------------- > >> ---- > >> 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. > >> ---------------------------------------------------------------------- > >> ---- > >> > >> > >> > >> > >Elizabeth A. Kellogg > >E. Desmond Lee and Family Professor of Botanical Studies > >Department of Biology > >University of Missouri-St. Louis > >St. Louis, MO 63121 > >Tel: 314-516-6217 > >FAX: 314-516-6233 > >http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/home.ht > >ml > -------------------------------------------------------------------------- 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 jitterbug at plantontology.org Wed May 4 19:12:57 2005 From: jitterbug at plantontology.org (Katica Ilic) Date: Wed, 4 May 2005 19:12:57 -0400 Subject: Question about cork cells in grasses (fwd) (PR#58) Message-ID: <200505042312.j44NCvfg015404@brie4.cshl.org> Dear Ron, Thank you for the request for a new term in Plant Ontology. Cork cells in the epidermis of grasses and bamboos are certainly different from the 'bark' cork cells (phellem, derived from the cork cambium), common in dicots and many monocots. Following your request, we are going to introduce a new term to PO, 'cork cell (sensu Poaceae)', which will be placed under tissue node, under term 'epidermis' (and also in the cell type node, as an instance of epidermal cell). The proposed structure will appear as following: PO:0009002 : cell (i) PO:0004013 : epidermal cell (i) PO:0004009 : silica cell (i) cork cell (sensu Poaceae) and PO:0009007 : tissue (i) PO:0009014 : dermal tissue (i) PO:0005679 : epidermis (p) PO:0004013 : epidermal cell (i) cork cell (sensu Poaceae) (i) PO:0004009 : silica cell In both nodes, silica cell and cork cell are at the same level (instances of epidermal cell). Although silica cell and cork cell usually appear in pairs in the epidermis of grasses, and both are types of short cells, I did not include term 'short cell' in this proposal, to avoid proliferation of sensu terms. Now, I need to explain why the new term 'cork cell (sensu Poaceae)' has 'sensu' designation and silica cell doesn't (nor the other cork cell term), and why 'sensu' is used in the term name. The reason to create terms with 'sensu' designation in PO is to distinguish different concepts that are named with the same word or phrase. There are cases where a term has different meaning depending on to which taxa the term is applied. Such terms are distinguished from one another by their definitions and by the sensu designation (sensu means 'in the sense of') in the term name. Therefore, cork cell (sensu Poaceae) means 'cork cell as in grasses'; not to be confused with the existing PO term 'cork cell' (PO:0004003), since there is no relationship in the ontology between these two terms. Silica cell doesn't have sensu designation since this cell is common for many dicots too, it is not specific for Poaceae. Similarly, 'cork cell' (phellem) is common throughout angiosperms and gymnosperms, and this term doesn't have specific sensu designation either. I hope this would meet your requirement. Please let us know if you need additional terms in Plant Ontology. The updated version of the PO can be viewed at the end of the month (after next scheduled update) using ontology browser. However, you can download the new ontology OBO file with the new term (and assigned PO ID) early next week from our cvs on the POC web site. Pankaj has already addressed your question about a failed query when using term names in plural. Best regards, Katica Ilic, POC Project Coordinator > Ron Skadsen wrote: > >> Dear Ontologists, >> >> I tried your site to find some information on cork cells. These are >> small cells commonly paired with silica cells in grasses. We have a >> gene promoter that causes expression of a reporter gene in cork cells. >> Your listing has only the common cork cell, as derived from the >> cambium. Is there a way to tease out an entry for the different cork >> cells? Also, a search of "cork cells" on your site yield zero matches. >> >> Cheers, >> >> Ron Skadsen >> >> USDA/ARS >> Cereal Crops Research Unit >> 506 Walnut St. >> Madison, WI 53726 >> ph (608)262-3672 >> FAX (608)264-5528 From msachs at uiuc.edu Wed May 4 23:21:14 2005 From: msachs at uiuc.edu (Marty Sachs) Date: Wed, 4 May 2005 22:21:14 -0500 Subject: Nodal root innstances (crown and seminal roots) In-Reply-To: <4277C458.7080305@cornell.edu> References: <4277C458.7080305@cornell.edu> Message-ID: At 2:35 PM -0400 5/3/05, Pankaj Jaiswal wrote: >Vincent, Leszek wrote: > >>Hi Toby, Pankaj (& others), >> >> >>It would seem essential that these terms be brought back. I provide >>the detailed definitions for these terms from the Zea mays >>ontology. If you'd like me to offer tweaked definitions for the >>definitions offered by Toby, based on my Zea definitions, I could >>attempt those. >> >> >>Crown roots - The crown roots are the predominant component of the >>adventitious root system. They are termed crown roots because they >>originate from the basal portion of the growing stem known as the >>crown. The crown roots are subterranean in origin. The first crown >>roots (4-5), arranged in a whorl, appear at the base of the second >>internode about as soon as the tip of the coleoptile reaches the >>soil surface. A few of the subsequent higher internodes may have a >>similar number of crown roots (in whorls), after which the >>successive internodes have more and larger crown roots. The crown >>roots are usually extensively branched, via the production of >>numerous lateral adventitious roots. Note that the adventitious >>roots which arise from 2-3 internodes immediately above the soil >>surface (aerial in origin) are a separate component of the >>adventitious root system, called 'prop' or 'brace roots'. (Feldman >>in Freeling & Walbot (eds), 1994. The Maize Handbook, ID#60920; >>Kiesselbach, ID#59445; Poethig in Sheridan, WF (ed), 1982. Maize >>for Biological Research, ID#25744; Vincent, ID#165572, 2002) >> > >Most part of this definition can actually go to the comments >section. However, this raises a question about > ># adding new term "brace roots, synonym: prop roots". These are >different from "crown roots", if I go with Leszek's definition. > ># What is "crown" or "seedling crown" [not the crown of tree]? We >need to define it somewhere in ontology or add it as synonym to >multiple terms suggesting that X-plant_part is grouped to form >seedling crown. Or create a new term "seedling crown" which we all >know is not a biologically correct term, but can be treated as a >bin/grouping term. It's children with part of relationships will >more precisely tell what region is called as "crown". > >-Pankaj What is being called the crown seems (at least to me) to be really different in the triticeae (e.g., wheat, barley) vs. maize (and apparently oats and rice). In maize the mesocotyl elongates during germination (especially when the kernel is deeply sown). In maize, there is a separation between the seminal roots (formed below the germinating kernel) and adventitious roots (forming at the base of the coleoptile near the soil surface). In wheat and barely, unlike oats and maize, the internode between the scutellum and coleoptile (the mesocotyl) does not elongate. In the case of very deeply sown seeds (more than 100 mm), the internode between leaves 1 and 2 and sometimes between leaves 2 and 3 may also elongate. See: http://www.fao.org/documents/show_cdr.asp?url_file=/DOCREP/006/Y4011E/y4011e05.htm http://www.ikisan.com/links/ap_ricemorp.shtml Also the corn development sections of: http://web.extension.uiuc.edu/RockfordCenter/newsletters/morrisonj/Issue3Vol4.htm http://web.extension.uiuc.edu/RockfordCenter/newsletters/morrisonj/Issue4Vol4.htm I'm not sure what the origin of the term 'crown roots' is, but I'm guessing it comes from the triticeae where the structure looks somewhat like a 'crown' and the name is apparently used by some (e.g., in the links given above) in maize and other cereals as a synonym of adventitious roots (unless I'm missing something). It's not completely clear to me that maize has a true 'crown' as in the sense one sees it in the triticeae. I would suggest that we find out exactly what the origin of the term 'crown' is in this regard, before including it as a term in the database. -Marty From pj37 at cornell.edu Thu May 5 11:53:32 2005 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Thu, 05 May 2005 11:53:32 -0400 Subject: GO and Cell ontologies In-Reply-To: References: Message-ID: <427A417C.7050100@cornell.edu> Sorry for the late reply, I agree with Sue, but there is another problem. If we remove the cell types from PO or for that reason in any anatomy ontology, then there is no mechanism (at least in the present day) we can connect to say X-cell is a part_of Y-Tissue/organ from plant/fly/any_organism. As an alternative, I still strongly believe, that all the cell types be maintained in individual organism/clade specific anatomy ontologies and whenever required, a complete but flat vocabulary of cell type (aka cell ontology) be created. This will also help to maintain the sensu aspects. However we may lose the comparative aspects, the moment we go down the sensu path. -Pankaj Sue Rhee wrote: > I can think of two pragmatic issues at hand with respect to the > possibility of obsoleting cell type terms in PO. One is whether the scope > of the cell type node within PO is comparable to that of the plant cell > type node within CL. The other is how quickly the databases using PO can > switch to using CL for the cell types. Before these two issues are > addressed, we cannot obsolete the cell type node within PO. > > Regarding the first issue, PO's current goal is to accomodate plants > within the angiosperm taxa only. This means that we may not cover cell > types in lower plants that might be useful to have in a more generic cell > type onology. On the other hand, even within this subdomain of plant > taxanomy, we could have some quite granular terms (e.g. that are > applicable to only a few species) that might be too specific for the scope > of CL. I'm amenable to changing the scope of either or both of the > ontologies to allow the mutual exclusivity of the two ontologies in terms > of primary terms, but this is something that needs to be agreed upon all > pertinent developers of both of the ontologies. > > Regarding the second issue, it took TAIR 8 months to switch from TAIR > anatomy to PO structure ontology, with plenty of time to plan for it. So > this is probably something we need to plan quite a bit in advance.. > > Sue > > > On Mon, 25 Apr 2005, Pankaj Jaiswal wrote: > > >> >>Chris Mungall wrote: >> >> >> >>>Regarding PO and CL - at the plant ontology meeting I suggested simply >>>removing all cell terms from PO - is there any need to duplicate them? >>> >> >> >>I agree on maintaining the cell types in cell.ontology, but the BIG >>questions are: >> #1 How many different ontologies are we expecting a database to use in >>their annotations? >> #2 What is the border line for each ontology, so that we do not overlap? >> #3 Is it good for the users or is it confusing? Users being both the >>actual wetlab scientists and the curators. >> # Is there a better way of semantically using an integrated version of >>all the required ontologies, despite being maintained independently? >> >>-Pankaj >> From Leszek at missouri.edu Thu May 5 15:23:48 2005 From: Leszek at missouri.edu (Vincent, Leszek) Date: Thu, 5 May 2005 14:23:48 -0500 Subject: Nodal root instances (crown and seminal roots) Message-ID: Hi Marty (& colleagues), Comments on your last paragraph first (copy just below): Kiesselbach (1949) in "The Structure and Reproduction of Corn" provides something of a 'definition' of "crown" in the following: "The term adventitious roots has come to apply to all of those roots that arise in the basal intercalary meristem of the lower internodes of the stem. Through common usage this is synonymous with crown roots, so designated because of origin in the basal portion of the growing stem known as the crown. Following the seedling stage, they constitute the principal part of the root system. Any aerial brace roots are included in this category." (p. 21). Elsewhere in this section one can further glean the following: The first whorl of crown roots (nodal/adventitious roots) appears from the base of the 2nd internode which is just above the mesocotyl. The underground internodes, immediately above the mesocotyl, don't elongate. This region with several nodes & very short internodes is the region from which the nodal roots (crown/adventitious roots) emerge - from the base of most of these very short internodes. This short, multiple node region is considered the crown. The crown region is considered to extend to above the soil surface, where further nodal roots are produced (brace/prop roots) So the "crown" is the region which produces adventitious roots (syn.: crown/nodal roots) at and near the base of the maize culm (stem). Feldman (1993) in 'The Maize Handbook', provides the following: "Permanent, adventitious roots originate from the nodes on the belowground portion of the stem. Usually many whorls of roots arise from these nodes. Because underground internodes fail to elongate, and hence are very short, close inspection is often necessary to ascertain the node of origin of each root. Collectively, the whorls comprise the root crown." (p. 31) In wheat nodal roots (syn.: adventitious or crown roots) emerge from the lower 3-7 nodes (presumably those just above the non-elongating mesocotyl. Nodal roots from at least the 7th node are typically above the soil surface. Comparing maize with wheat - while it appears that the crown in maize is a more contracted region than in wheat, the term "crown" seems to be used similarly (?). The terminology of crown roots & nodal roots is used rather differently in rice. Crown roots (mat roots) emerge from nodes below the soil surface. Nodal roots emerge from nodes above the soil surface. However, the 'crown roots' (mat roots) do emerge from a fairly compact region at the base of the culm - seemingly similar to the occurrence in maize (I haven't checked this carefully - others are welcome to correct me). While one might be tempted to use the terms 'crown roots' & 'nodal roots' as synonyms of 'adventitious roots' it should be noted that 'adventitious' is used atypically in maize & wheat with respect to the internationally recognized definition for the term. The typical definition of 'adventitious' is "structures or organs developing in an unusual position, as roots originating on the stem." Notwithstanding this, my inclination is to use 'crown roots' & 'nodal roots' as synonyms of 'adventitious roots' (well, that's what I 'root' for ;-) ). >From Marty: " I'm not sure what the origin of the term 'crown roots' is, but I'm guessing it comes from the triticeae where the structure looks somewhat like a 'crown' and the name is apparently used by some (e.g., in the links given above) in maize and other cereals as a synonym of adventitious roots (unless I'm missing something). It's not completely clear to me that maize has a true 'crown' as in the sense one sees it in the triticeae. I would suggest that we find out exactly what the origin of the term 'crown' is in this regard, before including it as a term in the database." Comments? - Leszek *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* P. Leszek D. Vincent Ph.D., FLS Division of Plant Sciences Res. Prof. Dept. of Horticulture 215 Curtis Hall University of Missouri-Columbia Columbia MO 65211-7020 USA Ph: (573) 884-3716; Fax:(573) 884-7850; Email: Leszek at missouri.edu Associate Curator, Dunn-Palmer Herbarium (UMO); Research Associate, Missouri Botanical Garden (MO), USA; Plant Systematist on The Plant Ontology Consortium - NSF award 0321666 (www.plantontology.org) *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* -----Original Message----- From: owner-po-dev at brie4.cshl.org [mailto:owner-po-dev at brie4.cshl.org] On Behalf Of Marty Sachs Sent: Wednesday, May 04, 2005 10:21 PM To: po-dev at plantontology.org; Pankaj Jaiswal Subject: Re: Nodal root innstances (crown and seminal roots) At 2:35 PM -0400 5/3/05, Pankaj Jaiswal wrote: >Vincent, Leszek wrote: > >>Hi Toby, Pankaj (& others), >> >> >>It would seem essential that these terms be brought back. I provide >>the detailed definitions for these terms from the Zea mays >>ontology. If you'd like me to offer tweaked definitions for the >>definitions offered by Toby, based on my Zea definitions, I could >>attempt those. >> >> >>Crown roots - The crown roots are the predominant component of the >>adventitious root system. They are termed crown roots because they >>originate from the basal portion of the growing stem known as the >>crown. The crown roots are subterranean in origin. The first crown >>roots (4-5), arranged in a whorl, appear at the base of the second >>internode about as soon as the tip of the coleoptile reaches the >>soil surface. A few of the subsequent higher internodes may have a >>similar number of crown roots (in whorls), after which the >>successive internodes have more and larger crown roots. The crown >>roots are usually extensively branched, via the production of >>numerous lateral adventitious roots. Note that the adventitious >>roots which arise from 2-3 internodes immediately above the soil >>surface (aerial in origin) are a separate component of the >>adventitious root system, called 'prop' or 'brace roots'. (Feldman >>in Freeling & Walbot (eds), 1994. The Maize Handbook, ID#60920; >>Kiesselbach, ID#59445; Poethig in Sheridan, WF (ed), 1982. Maize >>for Biological Research, ID#25744; Vincent, ID#165572, 2002) >> > >Most part of this definition can actually go to the comments >section. However, this raises a question about > ># adding new term "brace roots, synonym: prop roots". These are >different from "crown roots", if I go with Leszek's definition. > ># What is "crown" or "seedling crown" [not the crown of tree]? We >need to define it somewhere in ontology or add it as synonym to >multiple terms suggesting that X-plant_part is grouped to form >seedling crown. Or create a new term "seedling crown" which we all >know is not a biologically correct term, but can be treated as a >bin/grouping term. It's children with part of relationships will >more precisely tell what region is called as "crown". > >-Pankaj What is being called the crown seems (at least to me) to be really different in the triticeae (e.g., wheat, barley) vs. maize (and apparently oats and rice). In maize the mesocotyl elongates during germination (especially when the kernel is deeply sown). In maize, there is a separation between the seminal roots (formed below the germinating kernel) and adventitious roots (forming at the base of the coleoptile near the soil surface). In wheat and barely, unlike oats and maize, the internode between the scutellum and coleoptile (the mesocotyl) does not elongate. In the case of very deeply sown seeds (more than 100 mm), the internode between leaves 1 and 2 and sometimes between leaves 2 and 3 may also elongate. See: http://www.fao.org/documents/show_cdr.asp?url_file=/DOCREP/006/Y4011E/y4 011e05.htm http://www.ikisan.com/links/ap_ricemorp.shtml Also the corn development sections of: http://web.extension.uiuc.edu/RockfordCenter/newsletters/morrisonj/Issue 3Vol4.htm http://web.extension.uiuc.edu/RockfordCenter/newsletters/morrisonj/Issue 4Vol4.htm I'm not sure what the origin of the term 'crown roots' is, but I'm guessing it comes from the triticeae where the structure looks somewhat like a 'crown' and the name is apparently used by some (e.g., in the links given above) in maize and other cereals as a synonym of adventitious roots (unless I'm missing something). It's not completely clear to me that maize has a true 'crown' as in the sense one sees it in the triticeae. I would suggest that we find out exactly what the origin of the term 'crown' is in this regard, before including it as a term in the database. -Marty From msachs at uiuc.edu Thu May 5 18:04:05 2005 From: msachs at uiuc.edu (Marty Sachs) Date: Thu, 5 May 2005 17:04:05 -0500 Subject: Nodal root instances (crown and seminal roots) In-Reply-To: References: Message-ID: Leszek, In maize is there any difference between the roots that form between the coleoptile and mesocotyl and those that form in above ground nodes (a.k.a. prop roots)? It seems to me that these root types are the same in the triticeae where roots will form in any nodes that are below soil surface (the deeper the seed is planted, the more nodes that have roots). In maize, the mesocotyl elogates so that the roots forming below the coleoptile are just below soil surface. Prop roots form in nodes above soil surface. My question about the origin of the term 'crown' is still open. Is this term used by some in maize, simply to give a similar name to the place in maize where adventicious roots form, to the structure in the triticeae that looks like a 'crown'? Concerning your question on the use of 'adventitious' to describe these roots. They are indeed structures or organs developing in an unusual position; they are indeed roots originating on the stem. I agree that crown roots' & 'nodal roots' should be used as synonyms of 'adventitious roots'. -Marty At 2:23 PM -0500 5/5/05, Vincent, Leszek wrote: >Hi Marty (& colleagues), > >Comments on your last paragraph first (copy just below): Kiesselbach >(1949) in "The Structure and Reproduction of Corn" provides something of >a 'definition' of "crown" in the following: > >"The term adventitious roots has come to apply to all of those roots >that arise in the basal intercalary meristem of the lower internodes of >the stem. Through common usage this is synonymous with crown roots, so >designated because of origin in the basal portion of the growing stem >known as the crown. Following the seedling stage, they constitute the >principal part of the root system. Any aerial brace roots are included >in this category." (p. 21). > >Elsewhere in this section one can further glean the following: The first >whorl of crown roots (nodal/adventitious roots) appears from the base of >the 2nd internode which is just above the mesocotyl. The underground >internodes, immediately above the mesocotyl, don't elongate. This region >with several nodes & very short internodes is the region from which the >nodal roots (crown/adventitious roots) emerge - from the base of most of >these very short internodes. This short, multiple node region is >considered the crown. The crown region is considered to extend to above >the soil surface, where further nodal roots are produced (brace/prop >roots) > >So the "crown" is the region which produces adventitious roots (syn.: >crown/nodal roots) at and near the base of the maize culm (stem). > >Feldman (1993) in 'The Maize Handbook', provides the following: >"Permanent, adventitious roots originate from the nodes on the >belowground portion of the stem. Usually many whorls of roots arise from >these nodes. Because underground internodes fail to elongate, and hence >are very short, close inspection is often necessary to ascertain the >node of origin of each root. Collectively, the whorls comprise the root >crown." (p. 31) > >In wheat nodal roots (syn.: adventitious or crown roots) emerge from the >lower 3-7 nodes (presumably those just above the non-elongating >mesocotyl. Nodal roots from at least the 7th node are typically above >the soil surface. > >Comparing maize with wheat - while it appears that the crown in maize is >a more contracted region than in wheat, the term "crown" seems to be >used similarly (?). > >The terminology of crown roots & nodal roots is used rather differently >in rice. Crown roots (mat roots) emerge from nodes below the soil >surface. Nodal roots emerge from nodes above the soil surface. However, >the 'crown roots' (mat roots) do emerge from a fairly compact region at >the base of the culm - seemingly similar to the occurrence in maize (I >haven't checked this carefully - others are welcome to correct me). > >While one might be tempted to use the terms 'crown roots' & 'nodal >roots' as synonyms of 'adventitious roots' it should be noted that >'adventitious' is used atypically in maize & wheat with respect to the >internationally recognized definition for the term. The typical >definition of 'adventitious' is "structures or organs developing in an >unusual position, as roots originating on the stem." Notwithstanding >this, my inclination is to use 'crown roots' & 'nodal roots' as synonyms >of 'adventitious roots' (well, that's what I 'root' for ;-) ). > >>From Marty: " I'm not sure what the origin of the term 'crown roots' is, >but I'm >guessing it comes from the triticeae where the structure looks >somewhat like a 'crown' and the name is apparently used by some >(e.g., in the links given above) in maize and other cereals as a >synonym of adventitious roots (unless I'm missing something). It's >not completely clear to me that maize has a true 'crown' as in the >sense one sees it in the triticeae. I would suggest that we find out >exactly what the origin of the term 'crown' is in this regard, before >including it as a term in the database." > >Comments? > >- Leszek >*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* >P. Leszek D. Vincent Ph.D., FLS >Division of Plant Sciences >Res. Prof. Dept. of Horticulture >215 Curtis Hall >University of Missouri-Columbia >Columbia >MO 65211-7020 >USA >Ph: (573) 884-3716; Fax:(573) 884-7850; >Email: Leszek at missouri.edu >Associate Curator, Dunn-Palmer Herbarium (UMO); >Research Associate, Missouri Botanical Garden (MO), USA; >Plant Systematist on The Plant Ontology Consortium - NSF award 0321666 >(www.plantontology.org) >*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* > > >-----Original Message----- >From: owner-po-dev at brie4.cshl.org [mailto:owner-po-dev at brie4.cshl.org] >On Behalf Of Marty Sachs >Sent: Wednesday, May 04, 2005 10:21 PM >To: po-dev at plantontology.org; Pankaj Jaiswal >Subject: Re: Nodal root innstances (crown and seminal roots) > >At 2:35 PM -0400 5/3/05, Pankaj Jaiswal wrote: >>Vincent, Leszek wrote: >> >>>Hi Toby, Pankaj (& others), >>> >>> >>>It would seem essential that these terms be brought back. I provide >>>the detailed definitions for these terms from the Zea mays >>>ontology. If you'd like me to offer tweaked definitions for the >>>definitions offered by Toby, based on my Zea definitions, I could >>>attempt those. >>> >>> >>>Crown roots - The crown roots are the predominant component of the >>>adventitious root system. They are termed crown roots because they >>>originate from the basal portion of the growing stem known as the >>>crown. The crown roots are subterranean in origin. The first crown >>>roots (4-5), arranged in a whorl, appear at the base of the second >>>internode about as soon as the tip of the coleoptile reaches the >>>soil surface. A few of the subsequent higher internodes may have a >>>similar number of crown roots (in whorls), after which the >>>successive internodes have more and larger crown roots. The crown >>>roots are usually extensively branched, via the production of >>>numerous lateral adventitious roots. Note that the adventitious >>>roots which arise from 2-3 internodes immediately above the soil >>>surface (aerial in origin) are a separate component of the >>>adventitious root system, called 'prop' or 'brace roots'. (Feldman >>>in Freeling & Walbot (eds), 1994. The Maize Handbook, ID#60920; >>>Kiesselbach, ID#59445; Poethig in Sheridan, WF (ed), 1982. Maize >>>for Biological Research, ID#25744; Vincent, ID#165572, 2002) >>> >> >>Most part of this definition can actually go to the comments >>section. However, this raises a question about >> >># adding new term "brace roots, synonym: prop roots". These are >>different from "crown roots", if I go with Leszek's definition. >> >># What is "crown" or "seedling crown" [not the crown of tree]? We >>need to define it somewhere in ontology or add it as synonym to >>multiple terms suggesting that X-plant_part is grouped to form >>seedling crown. Or create a new term "seedling crown" which we all >>know is not a biologically correct term, but can be treated as a >>bin/grouping term. It's children with part of relationships will >>more precisely tell what region is called as "crown". >> >>-Pankaj > >What is being called the crown seems (at least to me) to be really >different in the triticeae (e.g., wheat, barley) vs. maize (and >apparently oats and rice). In maize the mesocotyl elongates during >germination (especially when the kernel is deeply sown). In maize, >there is a separation between the seminal roots (formed below the >germinating kernel) and adventitious roots (forming at the base of >the coleoptile near the soil surface). > >In wheat and barely, unlike oats and maize, the internode between the >scutellum and coleoptile (the mesocotyl) does not elongate. In the >case of very deeply sown seeds (more than 100 mm), the internode >between leaves 1 and 2 and sometimes between leaves 2 and 3 may also >elongate. > >See: > >http://www.fao.org/documents/show_cdr.asp?url_file=/DOCREP/006/Y4011E/y4 >011e05.htm > >http://www.ikisan.com/links/ap_ricemorp.shtml > > >Also the corn development sections of: > >http://web.extension.uiuc.edu/RockfordCenter/newsletters/morrisonj/Issue >3Vol4.htm > >http://web.extension.uiuc.edu/RockfordCenter/newsletters/morrisonj/Issue >4Vol4.htm > >I'm not sure what the origin of the term 'crown roots' is, but I'm >guessing it comes from the triticeae where the structure looks >somewhat like a 'crown' and the name is apparently used by some >(e.g., in the links given above) in maize and other cereals as a >synonym of adventitious roots (unless I'm missing something). It's >not completely clear to me that maize has a true 'crown' as in the >sense one sees it in the triticeae. I would suggest that we find out >exactly what the origin of the term 'crown' is in this regard, before >including it as a term in the database. > > -Marty From katica at acoma.Stanford.EDU Fri May 6 21:49:01 2005 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Fri, 6 May 2005 18:49:01 -0700 (PDT) Subject: new ontology files in the cvs (rev 1.34 and 1.38) In-Reply-To: Message-ID: Hi all, The new ontology files are in the cvs. I updated GO flat file anatomy.ontology and ontology.definition and committed them back to cvs as GO flat files (till we solve problem with obo2 flat conversion script). The following changes to the Plant Structure Ontology are made: I. new terms: 1. stem vascular system PO:0000039 Def: Vascular tissues in their specific arrangements in the stem. 2. primary endosperm cell PO:0000038 Def: Cell produced by the fusion of sperm cell nucleus and two polar nuclei of the central cell (or diploid secondary endosperm nucleus, in cases where two polar nuclei fuse together before double fertilization). The first cell of the endosperm, often triploid. 3. Renaming the term 'nodule' to 'root nodule' and adding a new structure for the term 'nodule: New term: adventitious root nodule (syn. stem nodule) PO:0000040 Def: Enlargement or swelling at position of dormant adventitious root primordium (on the stem), inhabited by nitrogen-fixing bacteria. Comment: Unlike the root nodules, these contain functioning chloroplasts in the nodule cortex and are therefore capable of carbon fixation. Note: stem nodule is commonly used term for this structure, although the nodules are formed at positions of dormant adventitious root primordia. Ontology structure: root (p) root nodule (i) adventitious root (p) adventitious root nodule (synonym: stem nodule) Changed definition of PO:0006221 : articulated laticifer New def: Latex-containing cells in which the walls between contiguous cells may partly or completely disappear. Added new term: cork cell (sensu Poaceae) (i) PO:0004013 : epidermal cell (i) PO:0004009 : silica cell (i) cork cell (sensu Poaceae) and PO:0009007 : tissue (i) PO:0009014 : dermal tissue (i) PO:0005679 : epidermis (p) PO:0004013 : epidermal cell (i) cork cell (sensu Poaceae) (i) silica cell Cork cell (sensu Poaceae) PO:0000041 Def: One of the two types of short cells in the epidermis of grasses and bamboos. It is usually paired with silica cell. Comment: Developmentally different from periderm cork cell (i.e., phellem), produced by cork cambium. Corrected error in the definition of term: stem cortex Definition: The primary tissue located between the vascular system and the epidermis of the stem. Also, I corrected typos in the text of several terms. Thanks and have a nice weekend. Katica -------------------------------------------------------------------------- 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 feedback_submission at filetta.cshl.edu Mon May 9 11:15:01 2005 From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu) Date: Mon, 9 May 2005 11:15:01 -0400 Subject: Feedback on POC Message-ID: <200505091515.j49FF1Cl031827@filetta.cshl.org> *** Feedback from Plant Ontology Live Site *** refer_to_url: http://www.plantontology.org/docs/otherdocs/poc_file.html comments: this site wasnt very helpfull!!!!!!!!!!!!!!!!!1 name: F.O.D. email: tajh_stanford at hotmail.com organization: S.A.B. send_feedback: Send your feedback From jitterbug at plantontology.org Tue May 10 11:20:56 2005 From: jitterbug at plantontology.org (Katica Ilic) Date: Tue, 10 May 2005 11:20:56 -0400 Subject: User's feedback - POC web site (fwd) (PR#60) Message-ID: <200505101520.j4AFKufg031457@brie4.cshl.org> Dear Sir/Madam, Thank you for your feedback. I assume you are referring t a particular page, the one that describes flat file formats, (tracing back the feedback details, that is,"refer_to_url: http://www.plantontology.org/docs/otherdocs/poc_file.html"). I can understand your frustration and would like to assure you that this page will be updated very soon. The page still describes only GO flat file format, although we recently switched to OBO format, and the POC cvs repository (see Downloads) has both, GO flat files and OBO flat files of the Plant Ontologies. Since the conversion to the OBO format took place recently, we are still working on some important technical issues, such as implementation of the script for GO2OBO flat file conversion. Once everything is in place, we will update the page you visited, adding information about OBO flat file format. In the meantime, I would like to direct you to the GO documentation page, which has description of the OBO flat files, that is, File Format Guide: URL: http://www.geneontology.org/GO.format.shtml I hope this is helpful. Please let us know if there is any other page on the POC web site that has not met your expectations. Best regards, Katica Ilic, POC project Coordinator > ---------- Forwarded message ---------- > Date: Mon, 9 May 2005 11:15:01 -0400 > From: feedback_submission at filetta.cshl.edu > Reply-To: po-dev at plantontology.org, feedback_submission at filetta.cshl.edu > To: po-dev > Subject: Feedback on POC > > *** Feedback from Plant Ontology Live Site *** > > refer_to_url: http://www.plantontology.org/docs/otherdocs/poc_file.html > > comments: this site wasnt very helpfull!!!!!!!!!!!!!!!!!1 > > name: F.O.D. > > email: tajh_stanford at hotmail.com > > organization: S.A.B. > > send_feedback: Send your feedback > > From rugro at psb.ugent.be Thu May 19 03:57:39 2005 From: rugro at psb.ugent.be (Ruth De Groodt) Date: Thu, 19 May 2005 09:57:39 +0200 Subject: Feedback on POC: granular terms under 'petiole' (PR#56) In-Reply-To: <200504222210.j3MMAnAe015388@brie4.cshl.org> References: <200504222210.j3MMAnAe015388@brie4.cshl.org> Message-ID: <428C46F3.2040409@psb.ugent.be> Dear Katica, I am indeed involved in a functional genomics project. For analysis of whole mounts and description of patterns we wanted to use a standardized nomenclature and looking for a solution, we found the website. As I saw that in leaf lamina and roots, terminology goes quite in detail, since different cell/ tissue layers are defined, and as I wanted to describe my results as far as I can see the pattern of expression with a normal DIC microscope, I saw that with petioles there were lacking a few terms describing layers that can be distinguished fairly easy like epidermis, cortex and vascular tissue. I agree that for the vascular tissue in petioles, it's difficult to distinguish different layers in whole mounts (on sections you can!), but to be complete I add them in my suggestion. I hope this is an answer to your question. kind regards, Ruth Katica Ilic wrote: >Dear Ruth, > >Thanks for the feedback and suggestion for improving current Plant Ontology >structure. Term 'petiole' does not have any granular 'children' terms yet, since >we deliberately chose not to have very detailed and elaborate ontology, at least >not in the initial stage when we were focused on creating a robust and >extensible structure as a backbone to which granular terms can be added as >needed. > >Our group is now considering your suggestion for adding more granular terms for >'petiole', and I have a couple of questions, to make sure that we can >accommodate what you would like to see in this segment of the ontology, at the >same time, making sure that we keep the Plant Ontology 'generic', encompassing >both, dicots and monocots. I am assuming that these terms are required for >functional genomics project that you might be involved and I wonder if a simpler >solution that does not have, for instance 'interfascicular parenchyma' would >work. I'll get back to you soon with the outline of the structure we are >currently considering, but in the meantime, it would be useful if you can tell >us few fords about the specific reasons for inquiring the structure you proposed >and also how you use the Plant Ontology. > >Thank you again for sending us your suggestion. I look forward to hearing from >you. > >Best regards, > >Katica Ilic, POC Project Coordinator > > > > >>---------- Forwarded message ---------- >>Date: Wed, 20 Apr 2005 04:02:29 -0400 >>From: feedback_submission at filetta.cshl.edu >>Reply-To: po-dev at plantontology.org, feedback_submission at filetta.cshl.edu >>To: po-dev >>Subject: Feedback on POC >> >> *** Feedback from Plant Ontology Live Site *** >> >>refer_to_url: http://www.plantontology.org/index.html >> >>comments: To whom it may concern: >> >>This message proposes a refinement of the anatomical ontology. >> >>In dicotelydons, the petiole, like the stem, consists of a dermal, fundamen= >>tal (ground) and vascular system. Its epidermis consists in one layer of c= >>ells and contains elongated epidermal cells and stomatal complexes, althoug= >>h the latter occur less frequently in petioles than in leaf lamina. Under t= >>he epidermal layer is the ground tissue of which the outer region is the co= >>rtex and the inner region is the pith. These two regions are interconnected= >> by the interfascicular parenchyma. In the vascular system (stele), the vas= >>cular bundles (xylem and phloem) are separated by this interfascicular pare= >>nchyma. The pith is located in the very centre of the stele. >> >>This organisation can be summarized as follows, from the outside in: >> >>Petiole >>=B7=09dermal system >> - epidermis >> - stomatal complex >>=B7=09cortex >>=B7=09vascular system >> - phloem >> - xylem >> - interfascicular parenchyma >> - pith >> >>As there is presently no subdivision under the term =93petiole=94, would it= >> be possible to add these categories in the ontology tree? Definitions of = >>the terminology used above are similar to those listed in the current ontol= >>ogy but are here applied for petioles. Do not hesitate to contact us back = >>if you need any additional information regarding this proposal. >> >> >>Ruth De Groodt >>Bj=F6rn De Meyer >>Pierre Hilson >> >> >>name: Ruth De Groodt >> >>email: ruth.degroodt at psb.ugent.be >> >>organization: VIB - Department of Plant Systems Biology >> >>send_feedback: Send your feedback >> >> >> >> >> -- ================================================================== Ruth De Groodt TEL:32 (0)9 3313846 PLANT SYSTEMS BIOLOGY Fax:32 (0)9 2645349 Department of Functional Genomics GHENT UNIVERSITY, VIB, Technologie Park 927, B-9052 GENT, Belgium Vlaams Instituut voor Biotechnologie VIB mailto:rugro at psb.UGent.be http://www.psb.UGent.be ================================================================== From katica at acoma.Stanford.EDU Thu May 19 21:16:38 2005 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Thu, 19 May 2005 18:16:38 -0700 (PDT) Subject: New ontology update is in cvs (anatomy.ontology, rev 1.35 and definition, rev 1.39) In-Reply-To: Message-ID: Hi All, I've just committted new anatomy ontology files to the cvs. New revisions Anatomy.ontology 1.35 Anatomy.definition 1.39 Note: These are both GO flat files. The OBO file will be generated manually and committed to cvs tomorrow. The following changes were made: New structure for the root node, with new terms (shoot borne root, crown root, prop root, embryonic root, seminal root), and merged terms (adventitious root merged to shoot borne root, and tap root merged to primary root) New ontology structure : root (i) shoot borne roots (synonym: adventitious) (i) nodal root (i) crown root (i) prop root (syn. brace root) (i) embryonic root (i) primary root (i) radicle (i) seminal root (i) lateral DEFINITIONS: New term: shoot borne root (synonym: adventitious root, stilt root) PO:0000042 New definition: Post-embryonic root developed from stem. Note: (PO:0020129) adventitious root is merged to this term, and became its synonym. Term: nodal root (PO:0003005) New definition: Adventitious root that forms at a shoot node. New term: crown root PO:0000043 Definition: Adventitious root formed at the base of the growing stem (known as a crown). New term: prop root (syn. brace root) PO:0000044 New Def: Adventitious root formed at stem nodes above the ground and growing directly into the soil. Comment: This term is perhaps best defined functionally: these roots serve to prop the plant up. New term: embryonic root PO:0000045 Definition: Root that is initiated in developing embryo. New term: seminal root PO:0000046 Definition: Root formed at the scutelar node of the embryo in some monocotyledonous plants. Best Regards, Katica -------------------------------------------------------------------------- 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 PolaccoM at missouri.edu Tue May 24 15:41:27 2005 From: PolaccoM at missouri.edu (Mary Polacco) Date: Tue, 24 May 2005 14:41:27 -0500 Subject: 2 PO citing articles Message-ID: http://bioinformatics.oupjournals.org/cgi/content/full/21/3/399 BarleyExpress: a web-based submission tool for enriched microarray database annotations Xiaoyun Tang 1, Lishuang Shen 2 and Julie A. Dickerson 1,* Bioinformatics 2005 21(3):399-401 http://www.plantphysiol.org/cgi/content/full/135/2/602 Positioning Arabidopsis in Plant Biology. A Key Step Toward Unification of Plant Research1 Michael Bevan* and Sean Walsh Plant Physiology, June 2004, Vol. 135, pp. 602-606 From jitterbug at plantontology.org Wed May 25 20:57:05 2005 From: jitterbug at plantontology.org (Katica Ilic) Date: Wed, 25 May 2005 20:57:05 -0400 Subject: Feedback on POC: granular terms under 'petiole' (PR#56) Message-ID: <200505260057.j4Q0v5Px004280@brie4.cshl.org> Dear Ruth, Thank you for your reply. It is essential for us at POC to learn how people use Plant Ontology and what kind of requests and issues they may have once they get familiar with this vocabulary. I have another question for you, regarding gene expressions in petiole and leaf lamina. On your mc slides, have you seen any differential expression of gene(s) in the guard cells of petioles vs. guard cells in leaf blade? If you have, that would be an argument for creating two terms, 'stomatal complex of the leaf lamina' and 'petiole stomatal complex', so that gene x (expressed only in guard cell of the petiole) could be properly associated to term 'petiole stomatal complex'. I couldn't find any evidence of such cases in the published literature, so, our ontology group at POC decided not to distinguish between stomata in the leaf lamina and those in the leaf petiole. Therefore, annotation of the gene expression pattern in guard cells of petiole cannot be distinguished from guard cell in the leaf blade. In the example below, you will see that the same term (stomatal complex) is propagated under both, 'leaf lamina epidermis' and 'petiole epidermis'. If you think this should be corrected, please let me know. This is the illustration: leaf (p) leaf lamina (i) leaf lamina epidermis (p) stomatal complex (i) petiole epidermis (p) stomatal complex The rest of the terms that you requested are now placed under term 'petiole', although we decided not to include all terms, such as interfascicular parenchyma, or pith (neither one is part of vascular system). Please, note that, unlike for the term 'stomatal complex', we included specific subclasses of terms 'leaf vascular system' and 'leaf epidermis', that is, 'leaf lamina vascular system' and 'petiole vascular system', and 'leaf lamina epidermis' and 'petiole epidermis'. This is dictated by the hierarchical nature of the ontology structure, and by the annotation display requirements. Again, 'stomatal complex' is an exemption of the rule. Here is the new structure (for simplicity, I didn't list all the terms under 'leaf': leaf (p) leaf lamina (p) leaf lamina epidermis (p) stomatal complex (p) leaf lamina vascular system (p) leaf apex (p) leaf margin (p) leaf vein (p) petiole (p) petiole cortex (p) petiole vascular system (p) petiole epidermis (p) stomatal complex We are currently experiencing problems with cvs repository, and the new ontology files will not be available to download until the problems are fixed. The updated ontology will be available on our ontology browser after the next scheduled update (end of June). I hope that this new structure with additional children terms under term 'petiole' will meet your requirements. Please let me know if this would work and don't hesitate to ask me additional questions you may have about plant ontologies. Best regards, Katica > Dear Katica, > > > I am indeed involved in a functional genomics project. For analysis > of whole mounts and description of patterns we wanted to use a > standardized nomenclature and looking for a solution, we found the > website. As I saw that in leaf lamina and roots, terminology goes > quite in detail, since different cell/ tissue layers are defined, > and as I wanted to describe my results as far as I can see the > pattern of expression with a normal DIC microscope, I saw that with > petioles there were lacking a few terms describing layers that can > be distinguished fairly easy like epidermis, cortex and vascular tissue. > I agree that for the vascular tissue in petioles, it's difficult to > distinguish different layers in whole mounts (on sections you can!), > but to be complete I add them in my suggestion. > > I hope this is an answer to your question. > > kind regards, > > > Ruth > > Katica Ilic wrote: > >>Dear Ruth, >> >>Thanks for the feedback and suggestion for improving current Plant Ontology >>structure. Term 'petiole' does not have any granular 'children' terms yet, > since >>we deliberately chose not to have very detailed and elaborate ontology, at > least >>not in the initial stage when we were focused on creating a robust and >>extensible structure as a backbone to which granular terms can be added as >>needed. >> >>Our group is now considering your suggestion for adding more granular terms for >>'petiole', and I have a couple of questions, to make sure that we can >>accommodate what you would like to see in this segment of the ontology, at the >>same time, making sure that we keep the Plant Ontology 'generic', encompassing >>both, dicots and monocots. I am assuming that these terms are required for >>functional genomics project that you might be involved and I wonder if a > simpler >>solution that does not have, for instance 'interfascicular parenchyma' would >>work. I'll get back to you soon with the outline of the structure we are >>currently considering, but in the meantime, it would be useful if you can tell >>us few fords about the specific reasons for inquiring the structure you > proposed >>and also how you use the Plant Ontology. >> >>Thank you again for sending us your suggestion. I look forward to hearing from >>you. >> >>Best regards, >> >>Katica Ilic, POC Project Coordinator >> >> >> >> >>>---------- Forwarded message ---------- >>>Date: Wed, 20 Apr 2005 04:02:29 -0400 >>>From: feedback_submission at filetta.cshl.edu >>>Reply-To: po-dev at plantontology.org, feedback_submission at filetta.cshl.edu >>>To: po-dev >>>Subject: Feedback on POC >>> >>> *** Feedback from Plant Ontology Live Site *** >>> >>>refer_to_url: http://www.plantontology.org/index.html >>> >>>comments: To whom it may concern: >>> >>>This message proposes a refinement of the anatomical ontology. >>> >>>In dicotelydons, the petiole, like the stem, consists of a dermal, fundamen= >>>tal (ground) and vascular system. Its epidermis consists in one layer of c= >>>ells and contains elongated epidermal cells and stomatal complexes, althoug= >>>h the latter occur less frequently in petioles than in leaf lamina. Under t= >>>he epidermal layer is the ground tissue of which the outer region is the co= >>>rtex and the inner region is the pith. These two regions are interconnected= >>> by the interfascicular parenchyma. In the vascular system (stele), the vas= >>>cular bundles (xylem and phloem) are separated by this interfascicular pare= >>>nchyma. The pith is located in the very centre of the stele. >>> >>>This organisation can be summarized as follows, from the outside in: >>> >>>Petiole >>>=B7=09dermal system >>> - epidermis >>> - stomatal complex >>>=B7=09cortex >>>=B7=09vascular system >>> - phloem >>> - xylem >>> - interfascicular parenchyma >>> - pith >>> >>>As there is presently no subdivision under the term =93petiole=94, would it= >>> be possible to add these categories in the ontology tree? Definitions of = >>>the terminology used above are similar to those listed in the current ontol= >>>ogy but are here applied for petioles. Do not hesitate to contact us back = >>>if you need any additional information regarding this proposal. >>> >>> >>>Ruth De Groodt >>>Bj=F6rn De Meyer >>>Pierre Hilson >>> >>> >>>name: Ruth De Groodt >>> >>>email: ruth.degroodt at psb.ugent.be >>> >>>organization: VIB - Department of Plant Systems Biology >>> >>>send_feedback: Send your feedback >>> >>> >>> >>> >>> > > > -- > ================================================================== > Ruth De Groodt TEL:32 (0)9 3313846 > PLANT SYSTEMS BIOLOGY Fax:32 (0)9 2645349 > Department of Functional Genomics > GHENT UNIVERSITY, VIB, Technologie Park 927, B-9052 GENT, Belgium > Vlaams Instituut voor Biotechnologie VIB > mailto:rugro at psb.UGent.be http://www.psb.UGent.be > ================================================================== > > From rugro at psb.ugent.be Tue May 31 03:21:05 2005 From: rugro at psb.ugent.be (Ruth De Groodt) Date: Tue, 31 May 2005 09:21:05 +0200 Subject: Feedback on POC: granular terms under 'petiole' (PR#56) In-Reply-To: <200505260057.j4Q0v5Px004280@brie4.cshl.org> References: <200505260057.j4Q0v5Px004280@brie4.cshl.org> Message-ID: <429C1061.5030406@psb.ugent.be> Dear Katica, there is indeed no reason why stomatal complexes in the petiole should be different from stomatal complexes in leaf lamina seen from the anatomical point of view. The new structure that you propose, is fine. Kind regards, Ruth Katica Ilic wrote: >Dear Ruth, > >Thank you for your reply. It is essential for us at POC to learn how people use >Plant Ontology and what kind of requests and issues they may have once they get >familiar with this vocabulary. > >I have another question for you, regarding gene expressions in petiole and leaf >lamina. On your mc slides, have you seen any differential expression of gene(s) >in the guard cells of petioles vs. guard cells in leaf blade? If you have, that >would be an argument for creating two terms, 'stomatal complex of the leaf >lamina' and 'petiole stomatal complex', so that gene x (expressed only in guard >cell of the petiole) could be properly associated to term 'petiole stomatal >complex'. I couldn't find any evidence of such cases in the published >literature, so, our ontology group at POC decided not to distinguish between >stomata in the leaf lamina and those in the leaf petiole. Therefore, annotation >of the gene expression pattern in guard cells of petiole cannot be distinguished >from guard cell in the leaf blade. In the example below, you will see that the >same term (stomatal complex) is propagated under both, 'leaf lamina epidermis' >and 'petiole epidermis'. If you think this should be corrected, please let me >know. > >This is the illustration: >leaf > (p) leaf lamina > (i) leaf lamina epidermis > (p) stomatal complex > (i) petiole epidermis > (p) stomatal complex > >The rest of the terms that you requested are now placed under term 'petiole', >although we decided not to include all terms, such as interfascicular >parenchyma, or pith (neither one is part of vascular system). Please, note that, >unlike for the term 'stomatal complex', we included specific subclasses of terms >'leaf vascular system' and 'leaf epidermis', that is, 'leaf lamina vascular >system' and 'petiole vascular system', and 'leaf lamina epidermis' and 'petiole >epidermis'. This is dictated by the hierarchical nature of the ontology >structure, and by the annotation display requirements. Again, 'stomatal complex' >is an exemption of the rule. > >Here is the new structure (for simplicity, I didn't list all the terms under >'leaf': > > leaf > (p) leaf lamina > (p) leaf lamina epidermis > (p) stomatal complex > (p) leaf lamina vascular system > (p) leaf apex > (p) leaf margin > (p) leaf vein > > (p) petiole > (p) petiole cortex > (p) petiole vascular system > (p) petiole epidermis > (p) stomatal complex > >We are currently experiencing problems with cvs repository, and the new ontology >files will not be available to download until the problems are fixed. The >updated ontology will be available on our ontology browser after the next >scheduled update (end of June). > >I hope that this new structure with additional children terms under term >'petiole' will meet your requirements. Please let me know if this would work and >don't hesitate to ask me additional questions you may have about plant >ontologies. > >Best regards, > >Katica > > > >>Dear Katica, >> >> >> I am indeed involved in a functional genomics project. For analysis >> of whole mounts and description of patterns we wanted to use a >> standardized nomenclature and looking for a solution, we found the >> website. As I saw that in leaf lamina and roots, terminology goes >> quite in detail, since different cell/ tissue layers are defined, >> and as I wanted to describe my results as far as I can see the >> pattern of expression with a normal DIC microscope, I saw that with >> petioles there were lacking a few terms describing layers that can >> be distinguished fairly easy like epidermis, cortex and vascular tissue. >> I agree that for the vascular tissue in petioles, it's difficult to >> distinguish different layers in whole mounts (on sections you can!), >> but to be complete I add them in my suggestion. >> >> I hope this is an answer to your question. >> >> kind regards, >> >> >> Ruth >> >>Katica Ilic wrote: >> >> >> >>>Dear Ruth, >>> >>>Thanks for the feedback and suggestion for improving current Plant Ontology >>>structure. Term 'petiole' does not have any granular 'children' terms yet, >>> >>> >>since >> >> >>>we deliberately chose not to have very detailed and elaborate ontology, at >>> >>> >>least >> >> >>>not in the initial stage when we were focused on creating a robust and >>>extensible structure as a backbone to which granular terms can be added as >>>needed. >>> >>>Our group is now considering your suggestion for adding more granular terms >>> >>> >for > > >>>'petiole', and I have a couple of questions, to make sure that we can >>>accommodate what you would like to see in this segment of the ontology, at >>> >>> >the > > >>>same time, making sure that we keep the Plant Ontology 'generic', >>> >>> >encompassing > > >>>both, dicots and monocots. I am assuming that these terms are required for >>>functional genomics project that you might be involved and I wonder if a >>> >>> >>simpler >> >> >>>solution that does not have, for instance 'interfascicular parenchyma' would >>>work. I'll get back to you soon with the outline of the structure we are >>>currently considering, but in the meantime, it would be useful if you can >>> >>> >tell > > >>>us few fords about the specific reasons for inquiring the structure you >>> >>> >>proposed >> >> >>>and also how you use the Plant Ontology. >>> >>>Thank you again for sending us your suggestion. I look forward to hearing >>> >>> >from > > >>>you. >>> >>>Best regards, >>> >>>Katica Ilic, POC Project Coordinator >>> >>> >>> >>> >>> >>> >>>>---------- Forwarded message ---------- >>>>Date: Wed, 20 Apr 2005 04:02:29 -0400 >>>>From: feedback_submission at filetta.cshl.edu >>>>Reply-To: po-dev at plantontology.org, feedback_submission at filetta.cshl.edu >>>>To: po-dev >>>>Subject: Feedback on POC >>>> >>>> *** Feedback from Plant Ontology Live Site *** >>>> >>>>refer_to_url: http://www.plantontology.org/index.html >>>> >>>>comments: To whom it may concern: >>>> >>>>This message proposes a refinement of the anatomical ontology. >>>> >>>>In dicotelydons, the petiole, like the stem, consists of a dermal, fundamen= >>>>tal (ground) and vascular system. Its epidermis consists in one layer of c= >>>>ells and contains elongated epidermal cells and stomatal complexes, althoug= >>>>h the latter occur less frequently in petioles than in leaf lamina. Under t= >>>>he epidermal layer is the ground tissue of which the outer region is the co= >>>>rtex and the inner region is the pith. These two regions are interconnected= >>>>by the interfascicular parenchyma. In the vascular system (stele), the vas= >>>>cular bundles (xylem and phloem) are separated by this interfascicular pare= >>>>nchyma. The pith is located in the very centre of the stele. >>>> >>>>This organisation can be summarized as follows, from the outside in: >>>> >>>>Petiole >>>>=B7=09dermal system >>>> - epidermis >>>> - stomatal complex >>>>=B7=09cortex >>>>=B7=09vascular system >>>> - phloem >>>> - xylem >>>> - interfascicular parenchyma >>>> - pith >>>> >>>>As there is presently no subdivision under the term =93petiole=94, would it= >>>>be possible to add these categories in the ontology tree? Definitions of = >>>>the terminology used above are similar to those listed in the current ontol= >>>>ogy but are here applied for petioles. Do not hesitate to contact us back = >>>>if you need any additional information regarding this proposal. >>>> >>>> >>>>Ruth De Groodt >>>>Bj=F6rn De Meyer >>>>Pierre Hilson >>>> >>>> >>>>name: Ruth De Groodt >>>> >>>>email: ruth.degroodt at psb.ugent.be >>>> >>>>organization: VIB - Department of Plant Systems Biology >>>> >>>>send_feedback: Send your feedback >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>-- >>================================================================== >>Ruth De Groodt TEL:32 (0)9 3313846 >>PLANT SYSTEMS BIOLOGY Fax:32 (0)9 2645349 >>Department of Functional Genomics >>GHENT UNIVERSITY, VIB, Technologie Park 927, B-9052 GENT, Belgium >>Vlaams Instituut voor Biotechnologie VIB >>mailto:rugro at psb.UGent.be http://www.psb.UGent.be >>================================================================== >> >> >> >> -- ================================================================== Ruth De Groodt TEL:32 (0)9 3313846 PLANT SYSTEMS BIOLOGY Fax:32 (0)9 2645349 Department of Functional Genomics GHENT UNIVERSITY, VIB, Technologie Park 927, B-9052 GENT, Belgium Vlaams Instituut voor Biotechnologie VIB mailto:rugro at psb.UGent.be http://www.psb.UGent.be ================================================================== From jitterbug at plantontology.org Tue May 31 16:39:18 2005 From: jitterbug at plantontology.org (Katica Ilic) Date: Tue, 31 May 2005 16:39:18 -0400 Subject: Feedback on POC: granular terms under 'petiole' (PR#56) Message-ID: <200505312039.j4VKdIPx005920@brie4.cshl.org> Hi Ruth, I am glad to hear that proposed structure worked for you. Please let us know if you would like to see additional, more granular terms in PO. Thank you for using Plant Ontologies and for contacting us. Your suggestions and comments are greatly appreciated. Best regards, Katica > Dear Katica, > > > there is indeed no reason why stomatal complexes in the petiole should > be different from stomatal complexes in leaf lamina seen from the > anatomical point of view. The new structure that you propose, is fine. > > Kind regards, > > Ruth > > > Katica Ilic wrote: > >>Dear Ruth, >> >>Thank you for your reply. It is essential for us at POC to learn how people use >>Plant Ontology and what kind of requests and issues they may have once they get >>familiar with this vocabulary. >> >>I have another question for you, regarding gene expressions in petiole and leaf >>lamina. On your mc slides, have you seen any differential expression of gene(s) >>in the guard cells of petioles vs. guard cells in leaf blade? If you have, that >>would be an argument for creating two terms, 'stomatal complex of the leaf >>lamina' and 'petiole stomatal complex', so that gene x (expressed only in guard >>cell of the petiole) could be properly associated to term 'petiole stomatal >>complex'. I couldn't find any evidence of such cases in the published >>literature, so, our ontology group at POC decided not to distinguish between >>stomata in the leaf lamina and those in the leaf petiole. Therefore, > annotation >>of the gene expression pattern in guard cells of petiole cannot be > distinguished >>from guard cell in the leaf blade. In the example below, you will see that the >>same term (stomatal complex) is propagated under both, 'leaf lamina epidermis' >>and 'petiole epidermis'. If you think this should be corrected, please let me >>know. >> >>This is the illustration: >>leaf >> (p) leaf lamina >> (i) leaf lamina epidermis >> (p) stomatal complex >> (i) petiole epidermis >> (p) stomatal complex >> >>The rest of the terms that you requested are now placed under term 'petiole', >>although we decided not to include all terms, such as interfascicular >>parenchyma, or pith (neither one is part of vascular system). Please, note > that, >>unlike for the term 'stomatal complex', we included specific subclasses of > terms >>'leaf vascular system' and 'leaf epidermis', that is, 'leaf lamina vascular >>system' and 'petiole vascular system', and 'leaf lamina epidermis' and 'petiole >>epidermis'. This is dictated by the hierarchical nature of the ontology >>structure, and by the annotation display requirements. Again, 'stomatal > complex' >>is an exemption of the rule. >> >>Here is the new structure (for simplicity, I didn't list all the terms under >>'leaf': >> >> leaf >> (p) leaf lamina >> (p) leaf lamina epidermis >> (p) stomatal complex >> (p) leaf lamina vascular system >> (p) leaf apex >> (p) leaf margin >> (p) leaf vein >> >> (p) petiole >> (p) petiole cortex >> (p) petiole vascular system >> (p) petiole epidermis >> (p) stomatal complex >> >>We are currently experiencing problems with cvs repository, and the new > ontology >>files will not be available to download until the problems are fixed. The >>updated ontology will be available on our ontology browser after the next >>scheduled update (end of June). >> >>I hope that this new structure with additional children terms under term >>'petiole' will meet your requirements. Please let me know if this would work > and >>don't hesitate to ask me additional questions you may have about plant >>ontologies. >> >>Best regards, >> >>Katica >> >> >> >>>Dear Katica, >>> >>> >>> I am indeed involved in a functional genomics project. For analysis >>> of whole mounts and description of patterns we wanted to use a >>> standardized nomenclature and looking for a solution, we found the >>> website. As I saw that in leaf lamina and roots, terminology goes >>> quite in detail, since different cell/ tissue layers are defined, >>> and as I wanted to describe my results as far as I can see the >>> pattern of expression with a normal DIC microscope, I saw that with >>> petioles there were lacking a few terms describing layers that can >>> be distinguished fairly easy like epidermis, cortex and vascular tissue. >>> I agree that for the vascular tissue in petioles, it's difficult to >>> distinguish different layers in whole mounts (on sections you can!), >>> but to be complete I add them in my suggestion. >>> >>> I hope this is an answer to your question. >>> >>> kind regards, >>> >>> >>> Ruth >>> >>>Katica Ilic wrote: >>> >>> >>> >>>>Dear Ruth, >>>> >>>>Thanks for the feedback and suggestion for improving current Plant Ontology >>>>structure. Term 'petiole' does not have any granular 'children' terms yet, >>>> >>>> >>>since >>> >>> >>>>we deliberately chose not to have very detailed and elaborate ontology, at >>>> >>>> >>>least >>> >>> >>>>not in the initial stage when we were focused on creating a robust and >>>>extensible structure as a backbone to which granular terms can be added as >>>>needed. >>>> >>>>Our group is now considering your suggestion for adding more granular terms >>>> >>>> >>for >> >> >>>>'petiole', and I have a couple of questions, to make sure that we can >>>>accommodate what you would like to see in this segment of the ontology, at >>>> >>>> >>the >> >> >>>>same time, making sure that we keep the Plant Ontology 'generic', >>>> >>>> >>encompassing >> >> >>>>both, dicots and monocots. I am assuming that these terms are required for >>>>functional genomics project that you might be involved and I wonder if a >>>> >>>> >>>simpler >>> >>> >>>>solution that does not have, for instance 'interfascicular parenchyma' would >>>>work. I'll get back to you soon with the outline of the structure we are >>>>currently considering, but in the meantime, it would be useful if you can >>>> >>>> >>tell >> >> >>>>us few fords about the specific reasons for inquiring the structure you >>>> >>>> >>>proposed >>> >>> >>>>and also how you use the Plant Ontology. >>>> >>>>Thank you again for sending us your suggestion. I look forward to hearing >>>> >>>> >>from >> >> >>>>you. >>>> >>>>Best regards, >>>> >>>>Katica Ilic, POC Project Coordinator >>>> >>>> >>>> >>>> >>>> >>>> >>>>>---------- Forwarded message ---------- >>>>>Date: Wed, 20 Apr 2005 04:02:29 -0400 >>>>>From: feedback_submission at filetta.cshl.edu >>>>>Reply-To: po-dev at plantontology.org, feedback_submission at filetta.cshl.edu >>>>>To: po-dev >>>>>Subject: Feedback on POC >>>>> >>>>> *** Feedback from Plant Ontology Live Site *** >>>>> >>>>>refer_to_url: http://www.plantontology.org/index.html >>>>> >>>>>comments: To whom it may concern: >>>>> >>>>>This message proposes a refinement of the anatomical ontology. >>>>> >>>>>In dicotelydons, the petiole, like the stem, consists of a dermal, fundamen= >>>>>tal (ground) and vascular system. Its epidermis consists in one layer of c= >>>>>ells and contains elongated epidermal cells and stomatal complexes, althoug= >>>>>h the latter occur less frequently in petioles than in leaf lamina. Under t= >>>>>he epidermal layer is the ground tissue of which the outer region is the co= >>>>>rtex and the inner region is the pith. These two regions are interconnected= >>>>>by the interfascicular parenchyma. In the vascular system (stele), the vas= >>>>>cular bundles (xylem and phloem) are separated by this interfascicular pare= >>>>>nchyma. The pith is located in the very centre of the stele. >>>>> >>>>>This organisation can be summarized as follows, from the outside in: >>>>> >>>>>Petiole >>>>>=B7=09dermal system >>>>> - epidermis >>>>> - stomatal complex >>>>>=B7=09cortex >>>>>=B7=09vascular system >>>>> - phloem >>>>> - xylem >>>>> - interfascicular parenchyma >>>>> - pith >>>>> >>>>>As there is presently no subdivision under the term =93petiole=94, would it= >>>>>be possible to add these categories in the ontology tree? Definitions of = >>>>>the terminology used above are similar to those listed in the current ontol= >>>>>ogy but are here applied for petioles. Do not hesitate to contact us back = >>>>>if you need any additional information regarding this proposal. >>>>> >>>>> >>>>>Ruth De Groodt >>>>>Bj=F6rn De Meyer >>>>>Pierre Hilson >>>>> >>>>> >>>>>name: Ruth De Groodt >>>>> >>>>>email: ruth.degroodt at psb.ugent.be >>>>> >>>>>organization: VIB - Department of Plant Systems Biology >>>>> >>>>>send_feedback: Send your feedback >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>-- >>>================================================================== >>>Ruth De Groodt TEL:32 (0)9 3313846 >>>PLANT SYSTEMS BIOLOGY Fax:32 (0)9 2645349 >>>Department of Functional Genomics >>>GHENT UNIVERSITY, VIB, Technologie Park 927, B-9052 GENT, Belgium >>>Vlaams Instituut voor Biotechnologie VIB >>>mailto:rugro at psb.UGent.be http://www.psb.UGent.be >>>================================================================== >>> >>> >>> >>> > > > -- > ================================================================== > Ruth De Groodt TEL:32 (0)9 3313846 > PLANT SYSTEMS BIOLOGY Fax:32 (0)9 2645349 > Department of Functional Genomics > GHENT UNIVERSITY, VIB, Technologie Park 927, B-9052 GENT, Belgium > Vlaams Instituut voor Biotechnologie VIB > mailto:rugro at psb.UGent.be http://www.psb.UGent.be > ================================================================== > > From jitterbug at plantontology.org Tue May 31 20:28:30 2005 From: jitterbug at plantontology.org (Katica Ilic) Date: Tue, 31 May 2005 20:28:30 -0400 Subject: Rice profiling project - interest in developing cell type terms (PR#64) Message-ID: <200506010028.j510SUPx010319@brie4.cshl.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 > 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 : > >> >> 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" >> > >To: "'timothy.nelson at yale.edu'" >> > >Cc: "'Katica Ilic'" , >> > > "Pankaj Jaiswal (E-mail)" >> > > >> > >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. >> --------------------------------------------------------------------- > ----- >> >> > > >