From katica at acoma.Stanford.EDU Tue Feb 1 00:48:13 2005 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Mon, 31 Jan 2005 21:48:13 -0800 (PST) Subject: New revision of Plant Ontology is in cvs In-Reply-To: Message-ID: Hi All, I've commited the new revision of Plant Ontology to cvs: anatomy.ontology rev 1.31 ontology.definition rev 1.33 temporal.ontology rev 1.3 I added 12 new terms to Plant Structure Ontology (see the thread from Jan 27): Term: cuticle Term: casparian strip Term: filiform apparatus Term: root tip Term: primary root tip Term: lateral root tip Term: pollen tube tip Term: root hair tip Term: septum Term: lenticel Term: tetrad of microspores Term: valve Changes incorporated on Jan 31 2005. Term: cuticle Def: A layer of fatty material, cutin, rather impervious to water, located on the outer walls of epidermal cells. Cell (i) epidermal cell (p) cuticle Term: casparian strip Def: A band-like wall formation within primary walls that contains suberin and lignin; typical of endodermal cells in roots, in which it occurs in radial and transverse anticlinal walls. root (p) root cortex (p) root endodermis (p) casparian strip Term: filiform apparatus Def: A complex of cell wall invaginations in a synergid cell similar to those in transfer cells. Synergid cell (p) filiform apparatus Term: root tip Def: Top portion of the root including meristem and root cap Term: primary root tip Def: The portion of the primary root including the meristem and root cap. Term: lateral root tip Def: The portion of the lateral root including the meristem and root cap. root (p) root tip (i) lateral root (p) lateral root tip (i) primary root (p) primary root tip (i) lateral root tip (i) primary root tip Term: pollen tube tip Def: Tip portion of the pollen tube that is rapidly growing. male gametophyte (p) pollen tube (p) pollen tube tip Term: root hair tip Def: Tip portion of an outgrowth of a root epidermal cell. epidermis (p) epidermal cell (i) root hair (p) root hair tip Term: septum Def: A thin partition or membrane that divides a cavity or a mass of tissue, e.g., in anther, ovary or fruit. carpel (p) septum and anther (p) septum and fruit (p) septum Term: lenticel Def: Loosely-packed mass of cork cells occurring especially in the young stem, bark or even leaf of a plant, visible on the surface as a raised, often powdery-appearing spot, through which gaseous exchange occurs. stem (p) lenticel Term: tetrad of microspores A group of four haploid cells that remained joined together shortly after meiosis. Each cell will give rise to the male gametophyte. androecium (p) stamen (p) anther (p) microsporangium (p) microsporocyte (d) tetrads of microspore (d) microspore In this case, we have 'tetrad of microspores' with only develops_from relationship. Term: valve Def: valve: a portion of an organ that is fragmented; in capsule, theportions into which the pericarp splits at maturity. fruit (p) fruit abscission zone (p) pericarp (p) seed (p) valve 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 katica at acoma.Stanford.EDU Tue Feb 1 19:12:50 2005 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Tue, 1 Feb 2005 16:12:50 -0800 (PST) Subject: Embryo (fwd) Message-ID: Hi All, The message below is the e-mail from Teresa Tykarska (published a series of papers on Brassica embryogenesis, 1979-1987) who I contacted last summer asking about the embryo proper, definition and developmental connotation of this term. I got her reply just before aspb meeting in Florida and didn't forward it to po-dev. Peter may recall this, last June in St Louis, we were not sure about definition, and also whether to use an instance_of or part_of relationship to the parent term 'embryo'. Katica ---------- Forwarded message ---------- Date: Thu, 15 Jul 2004 23:52:48 +0200 (CEST) From: Leonard Tykarski To: katica at acoma.Stanford.EDU Subject: Embryo Dear Dr Ilic, As I wrote you before, I.m sending you my comments, that you ask me for. Till now on there is no unified terminology regarding embryo and such work would be very useful. My opinion is mainly based on the best source, i.e. the work of Hanstein (1870): 1. Embryo development is divided into the period of proembryo and the period of embryo proper (globular, heart-shaped, torpedo,........., maturing and mature stages). 2. Transition of the proembryo to the embryo proper occurs at the moment of initiation of the basic parts of axis of the future plant, i.e.: plerome mother cells (axial cylinder) and periblem mother cells (primary cortex). 3. Hypophysis is the highest cell of the suspensor. It joins the body of embryo during its first division, closing the embryo sphere (globe) from the bottom. Hainstein named .embryo sphere. also as .the embryobody., which I used in my work. Some researchers when referring to the .embryo proper. think of the embryo body. I.m not sure if these explanations are sufficient to you. I will be out of Warsaw for a week. If you would have any questions, please use the address, which I use at home (it.s my husband.s address): tykarski at if.pw.edu.pl Best regards, Teresa Tykarska From feedback_submission at filetta.cshl.edu Mon Feb 14 15:23:07 2005 From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu) Date: Mon, 14 Feb 2005 15:23:07 -0500 Subject: Feedback on POC Message-ID: <200502142023.j1EKN7Z2004801@filetta.cshl.org> *** Feedback from Plant Ontology Live Site *** refer_to_url: http://www.plantontology.org/index.html comments: PO amigo link on front page does not work name: Roger Wise email: rpwise at iastate.edu organization: ISU send_feedback: Send your feedback From shuly at cshl.edu Mon Feb 14 15:28:02 2005 From: shuly at cshl.edu (Shuly Avraham) Date: Mon, 14 Feb 2005 15:28:02 -0500 Subject: Feedback on POC In-Reply-To: <200502142023.j1EKN6Gj004796@filetta.cshl.org> References: <200502142023.j1EKN6Gj004796@filetta.cshl.org> Message-ID: <421109D2.1080803@cshl.edu> Hi Rojer, My name is Shuly, I am maintaining the web site. May you please try again and tell me what you get ? I am connecting to it from home, and I do see it. Thanks, Shuly. feedback_submission at filetta.cshl.edu wrote: > *** Feedback from Plant Ontology Live Site *** > >refer_to_url: http://www.plantontology.org/index.html > >comments: PO amigo link on front page does not work > >name: Roger Wise > >email: rpwise at iastate.edu > >organization: ISU > >send_feedback: Send your feedback > > > From shuly at cshl.edu Mon Feb 14 15:41:30 2005 From: shuly at cshl.edu (Shuly Avraham) Date: Mon, 14 Feb 2005 15:41:30 -0500 Subject: Feedback on POC In-Reply-To: <200502142023.j1EKN7Z2004801@filetta.cshl.org> References: <200502142023.j1EKN7Z2004801@filetta.cshl.org> Message-ID: <42110CFA.5000306@cshl.edu> Hi Roger, Thanks for the notification. I initially thought you refered to the link on the top navigaton bar "Ontology Browser". Now I understand you referned to the link on the News section - they link to the same place: AmiGO - Plant Ontology Browser. It is now fixed! Thank you, Shuly. feedback_submission at filetta.cshl.edu wrote: > *** Feedback from Plant Ontology Live Site *** > >refer_to_url: http://www.plantontology.org/index.html > >comments: PO amigo link on front page does not work > >name: Roger Wise > >email: rpwise at iastate.edu > >organization: ISU > >send_feedback: Send your feedback > > > From jitterbug at plantontology.org Mon Feb 14 15:45:39 2005 From: jitterbug at plantontology.org (Katica Ilic) Date: Mon, 14 Feb 2005 15:45:39 -0500 Subject: Feedback on POC (fwd) (PR#54) Message-ID: <200502142045.j1EKjdVV019157@brie4.cshl.org> Dear Dr. Wise, Thank you for bringing this to our attention. You are probably referring to the AmiGO link in the "What's New" section (news from Dec 16, 2004). It's been fixed now, you could try again, and you can also use our main link to the PO AmiGo from the navigation bar on the top of the POC home page (Next to the Home link, there is Ontology Browser link, this is the link to PO AmiGO). Please let me know if you still have problems accessing the PO browser. Best Regards, Katica Ilic, POC Project Coordinator > ---------- Forwarded message ---------- > Date: Mon, 14 Feb 2005 15:23:07 -0500 > 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: PO amigo link on front page does not work > > name: Roger Wise > > email: rpwise at iastate.edu > > organization: ISU > > send_feedback: Send your feedback > > From rpwise at iastate.edu Mon Feb 14 16:10:03 2005 From: rpwise at iastate.edu (Roger Wise) Date: Mon, 14 Feb 2005 15:10:03 -0600 Subject: Feedback on POC In-Reply-To: <421109D2.1080803@cshl.edu> References: <200502142023.j1EKN6Gj004796@filetta.cshl.org> <421109D2.1080803@cshl.edu> Message-ID: It works now - I was in another building on campus where I noticed the broken link Thanks, Roger >Hi Rojer, > >My name is Shuly, I am maintaining the web site. >May you please try again and tell me what you get ? >I am connecting to it from home, and I do see it. > >Thanks, >Shuly. > >feedback_submission at filetta.cshl.edu wrote: > >> *** Feedback from Plant Ontology Live Site *** >> >>refer_to_url: http://www.plantontology.org/index.html >> >>comments: PO amigo link on front page does not work >> >>name: Roger Wise >> >>email: rpwise at iastate.edu >> >>organization: ISU >> >>send_feedback: Send your feedback >> >> -- _____________________________ Roger Wise, USDA-ARS Department of Plant Pathology 411 Bessey Hall Iowa State University, Ames, IA 50011-1020 USA Phone: 515-294-9756 Fax: 515-294-9420 E-mail: rpwise at iastate.edu _____________________________ http://wiselab.org/ http://barleybase.org/ http://www.plantstress.iastate.edu/ From pj37 at cornell.edu Tue Feb 15 15:04:50 2005 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 15 Feb 2005 15:04:50 -0500 Subject: new version(1.36) of anatomy.definition file in cvs Message-ID: <421255E2.3070801@cornell.edu> Dear all, We identified a mistake in the last version (1.35) of the /definition/anatomy.definition file. The following term was committed accidentally. term: plant growth and development goid: PO:0009012 definition: Any growth and developmental stage of a plant. definition_reference: Poc:curators This problem has been rectified and the changes were committed to the cvs. Please update your cvs copies of the file. Thanks Pankaj -- ************************ 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 pj37 at cornell.edu Mon Feb 28 19:20:44 2005 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Mon, 28 Feb 2005 19:20:44 -0500 Subject: Fruit AOE Bud Stage Reference Message-ID: <4223B55C.8030000@cornell.edu> An interesting website with information on few commercially important fruit crops. http://www.msue.msu.edu/fruit/indexbud.htm -Pankaj