From cwt6 at cornell.edu Tue Feb 6 11:18:08 2007 From: cwt6 at cornell.edu (Chih-Wei Tung) Date: Tue, 6 Feb 2007 11:18:08 -0500 Subject: January 2007 release of Plant Ontology database Message-ID: Dear Colleagues, Plant Ontology Consortium (POC, http://www.plantontology.org) is proud to announce the release 0107 (January 2007) of the Plant Ontology Database. Details are as follows. To view these changes please visit the plant ontology browser available at http:// www.plantontology.org/amigo/go.cgi The new ontology files and the database dump is available for download. Please follow the instructions for downloading provided at http://plantontology.org/download/download.html#download -------------------------------------------- Ontology updates: 10 new terms were added PO:0009101 long lateral tassel branch PO:0009102 short tassel branch PO:0009103 short tassel branch meristem PO:0009104 long lateral tassel branch meristem PO:0009105 inflorescence lateral meristem PO:0009106 tassel meristem PO:0009107 tassel lateral meristem PO:0009108 inflorescence apical meristem PO:0009109 ear meristem PO:0009110 ear lateral meristem -------------------------------------------- Associations/annotations: Total number of associations: 13811 (259 are new) Total number of unique objects (genes & germplasms): 6852 (108 are new) -------------------------------------------- Sincerely, The Plant Ontology Consortium web: http:www.plantontology.org e-mail: po-dev at plantontology.org submit requests at: http://sourceforge.net/tracker/?func=browse&group_id=76834&atid=835555 ******************************************************** From pj37 at cornell.edu Tue Feb 13 13:11:12 2007 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 13 Feb 2007 13:11:12 -0500 Subject: Root, stigma, filament veins. In-Reply-To: <45D1125E.7000309@stanford.edu> References: <45D10BC2.1030507@stanford.edu> <45D111C7.5060801@cornell.edu> <45D1125E.7000309@stanford.edu> Message-ID: <45D1FF40.1030501@cornell.edu> Hi Donghui, Can you give us the PMID/citation of the paper that requires these terms. So far my understanding is that vein is nothing but a continuous stretch of vascular system, thus it is just a synonym. However, we would like to go through the paper that refers to these things as vein, before making any more comments. term requests and discussions can be followed at https://sourceforge.net/tracker/?func=detail&atid=835555&aid=1658519&group_id=76834 https://sourceforge.net/tracker/?func=detail&atid=835555&aid=1658517&group_id=76834 https://sourceforge.net/tracker/?func=detail&atid=835555&aid=1658520&group_id=76834 Pankaj From R.BRUSKIEWICH at CGIAR.ORG Wed Feb 14 21:04:04 2007 From: R.BRUSKIEWICH at CGIAR.ORG (Bruskiewich, Richard (IRRI)) Date: Thu, 15 Feb 2007 10:04:04 +0800 Subject: POC Presentation at Plant and Animal genome Meeting, San Diego, January 13-17, 2007 Message-ID: Although I visited the poster, PAG wasn't well attended by CGIAR folks this year. Could the team here get access to a PDF of the poster for review by a wider group in our team? -----Original Message----- From: owner-po-dev at plantontology.org [mailto:owner-po-dev at plantontology.org] On Behalf Of Pankaj Jaiswal Sent: Wednesday, January 10, 2007 3:58 AM To: po-dev at plantontology.org Cc: Chih-Wei Tung; kat23ica at gmail.com; kmayer at gsf.de; yyamazak at lab.nig.ac.jp; rpwise at iastate.edu; Julie Dickerson; Jennifer I Clark; scholl.1 at osu.edu; Dave Matthews; Lukas Mueller; Naama Menda; quentin.cronk at ubc.ca; JAGADISH, MITTUR [AG/8042]; AUGUSTINE, ALICE CLARA [AG/8042]; EDGERTON, MIKE [AG/1000]; PARANJAPE, VIJAY [AG/8042]; david.selinger at pioneer.com; lane.arthur at pioneer.com; sean at arabidopsis.info; curators at arabidopsis.info; Bruskiewich, Richard (IRRI); Tanya Berardini; phz at ethz.ch; kjbradford at ucdavis.edu; Timothy Nelson; Rex Nelson; Carolyn Lawrence; Hiroshi Fujii; Shoshi Kikuchi at nias Subject: POC Presentation at Plant and Animal genome Meeting, San Diego, January 13-17, 2007 Dear All, At the next week's Plant and Animal Genome (PAG) Meeting, to be held at San Diego, January 13-17, 2007 the Plant Ontology project updates will be presented in a poster by Dr. Chih-wei Tung. If you are attending the PAG meeting, we encourage you to meet the project representative (Chih-wei Tung) and visit the poster # P841. The abstract can be found at http://intl-pag.org/15/abstracts/PAG15_P08a_841.html Many thanks Pankaj -- Pankaj Jaiswal G-15, Bradfield Hall Dept. of Plant Breeding and Genetics Cornell University Ithaca, NY-14853, USA Ph. +1-607-255-3103 / 4199 fax: +1-607-255-6683 From pj37 at cornell.edu Thu Feb 15 12:01:55 2007 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Thu, 15 Feb 2007 12:01:55 -0500 Subject: plant structure terms for Banana [feedback needed] Message-ID: <45D49203.5040301@cornell.edu> Hi Everyone, I just received a request from "Rouard, Mathieu (Bioversity-France)" on various plant structure (PSO) terms that they use for evaluating standard phenotypes of a Banana plant. These are based on the document listed at (http://bananas.bioversityinternational.org/files/files/pdf/publications/descriptors_en.pdf). Attached is the edited part that is required for determining PSO terms. Please take a look and let me know what is the best way to proceed on getting these terms in the PO (plant structure) either as stand alone terms or as synonyms. Here is a list I was able to compile based on the attached document. Also listed are the terms that are already present in PSO section of Plant Ontology. 1 Pseudostem 2 sucker = PO:0004544 : root borne shoot 3 leaf III--> a very specific instance 4 cigar leaf --> a very specific instance similar to the 'flag leaf' we have in PSO for cereals. 5 Bunch 6 male bud 7 rachis = PO:0020122 : inflorescence axis 8 peduncle = PO:0009053 : peduncle However I am not sure if this is a correct term based on our definition of peduncle "The stalk of an inflorescence; that part of the inflorescence below the first flower or inflorescence branch and above the last foliage leaf/pair of foliage leaves. Based on what appears for Banana (in attached document) to me looks like the most appropriate terms is PO:0020122 : inflorescence axis Definition: The central supporting structure around which flowers are borne. 9 petiole canal 10 petiole margin 11 wing (petiole wing) 12 Blotch--not necessarily a PO term. Its just colored spots 13 leaf blade = PO:0020039 : leaf lamina 14 midrib = synonym of PO:0020139 : midvein 15 leaf sheath = PO:0020104 : leaf sheath 16 petiole = PO:0020038 : petiole 17 bract (first external bract that still clings to the male bud) 18 bract base 19 bract apex 20 bract scar 21 male flower = generic flower PO:0009046 : flower 22 compound tepal 23 lobes of compound tepal 24 free tepal 25 free tepal apex 26 stigma = PO:0009073 : stigma 27 style = PO:0009074 : style 28 anther = PO:0009066 : anther 29 filament = PO:0009067 : filament 30 ovary = PO:0009072 : ovary -- Pankaj Jaiswal G-15, Bradfield Hall Dept. of Plant Breeding and Genetics Cornell University Ithaca, NY-14853, USA Ph. +1-607-255-3103 / 4199 fax: +1-607-255-6683 -------------- next part -------------- A non-text attachment was scrubbed... Name: banana_descriptors_en.pdf Type: application/pdf Size: 235572 bytes Desc: not available URL: