From katica at acoma.Stanford.EDU Fri Jan 6 19:50:11 2006 From: katica at acoma.Stanford.EDU (katica at acoma.Stanford.EDU) Date: Fri, 6 Jan 2006 16:50:11 -0800 (PST) Subject: Proposal for the new term in Plant Structure Ont: middle layer Message-ID: Hi All, This is the proposal for introduction of the new term in the Plant Structure Ontology, 'middle layer': New term name: Middle layer Definition: Usually a single cell layer between tapetum and endothecium which almost invariably degenerates early during angiosperm anther development and is eventually absorbed by adjacent cells. Proposed ontology structure: PO:0000002 : anther wall (p) PO:0020002 : endothecium (p) PO:0020004 : exothecium (p) PO:0020005 : placentoid (p) PO:0020101 : stomium (p) PO:0009071 : tapetum (p) new term: middle layer I am planning to introduce this term to the PO a week from today, unless active discussion takes place regarding this term over the next week at po-dev mailing list. I would greatly appreciate your comments and suggestions. Thanks and have a great weekend. Katica Ilic -------------------------------------------------------------------------- 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 Sat Jan 7 13:01:03 2006 From: kellogge at msx.umsl.edu (kellogge) Date: Sat, 7 Jan 2006 12:01:03 -0600 Subject: Proposal for the new term in Plant Structure Ont: middle layer In-Reply-To: References: Message-ID: hi Katica - My only concern is that "middle layer" is such an uninformative term on its own. I"m wondering if this is a case where we need to call it "middle layer of anther wall". (I know - I'm suggesting a complex term where one isn't strictly needed. It just seems that there are a lot of things that could have middle layers.) Toby On Jan 6, 2006, at 6:50 PM, katica at acoma.Stanford.EDU wrote: > Hi All, > > This is the proposal for introduction of the new term in the Plant > Structure Ontology, 'middle layer': > > New term name: Middle layer > Definition: Usually a single cell layer between tapetum and > endothecium which almost invariably degenerates early during > angiosperm anther development and is eventually absorbed by adjacent > cells. > > Proposed ontology structure: > > PO:0000002 : anther wall > (p) PO:0020002 : endothecium > (p) PO:0020004 : exothecium > (p) PO:0020005 : placentoid > (p) PO:0020101 : stomium > (p) PO:0009071 : tapetum > (p) new term: middle layer > > I am planning to introduce this term to the PO a week from today, > unless active discussion takes place regarding this term over the next > week at po-dev mailing list. I would greatly appreciate your comments > and suggestions. > > Thanks and have a great weekend. > > Katica Ilic > > > ----------------------------------------------------------------------- > --- > 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/services/kellogg/ -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 1964 bytes Desc: not available URL: From katica at acoma.Stanford.EDU Sat Jan 7 14:38:16 2006 From: katica at acoma.Stanford.EDU (katica at acoma.Stanford.EDU) Date: Sat, 7 Jan 2006 11:38:16 -0800 (PST) Subject: Proposal for the new term in Plant Structure Ont: middle layer In-Reply-To: References: Message-ID: Hi Toby, I know, I mentioned it yesterday on the conf call. However, its position in the ontology leaves little doubt what the term is. We have other terms that have a bit uninformative term name, for example, 'protective layer', or 'separation layer', of the abscission zone; it becomes obvious only when you see the ontology tree (and definition too). 'Middle layer of the anther wall' as a term name, I guess if we have to (to avoid confussion), it wouldn't be the worst name out there. Google search retrieved mostly middle layer of the anther wall. I did find 'middle layer' in description of the intervascular pit membranes in some woody species (Salix, Acer...). Peter and Quentin could tell us more about how often this term is used in anatomy of woody species. Katica On Sat, 7 Jan 2006, kellogge wrote: > hi Katica - > My only concern is that "middle layer" is such an uninformative term on > its own. I"m wondering if this is a case where we need to call it "middle > layer of anther wall". (I know - I'm suggesting a complex term where one > isn't strictly needed. It just seems that there are a lot of things that > could have middle layers.) > Toby > > On Jan 6, 2006, at 6:50 PM, katica at acoma.Stanford.EDU wrote: > >> Hi All, >> >> This is the proposal for introduction of the new term in the Plant >> Structure Ontology, 'middle layer': >> >> New term name: Middle layer >> Definition: Usually a single cell layer between tapetum and endothecium >> which almost invariably degenerates early during angiosperm anther >> development and is eventually absorbed by adjacent cells. >> >> Proposed ontology structure: >> >> PO:0000002 : anther wall >> (p) PO:0020002 : endothecium >> (p) PO:0020004 : exothecium >> (p) PO:0020005 : placentoid >> (p) PO:0020101 : stomium >> (p) PO:0009071 : tapetum >> (p) new term: middle layer >> >> I am planning to introduce this term to the PO a week from today, unless >> active discussion takes place regarding this term over the next week at >> po-dev mailing list. I would greatly appreciate your comments and >> suggestions. >> >> Thanks and have a great weekend. >> >> Katica Ilic >> >> >> -------------------------------------------------------------------------- >> 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/services/kellogg/ > -- -------------------------------------------------------------------------- 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 Mon Jan 9 18:18:58 2006 From: Leszek at missouri.edu (Vincent, Leszek) Date: Mon, 9 Jan 2006 17:18:58 -0600 Subject: Proposal for the new term in Plant Structure Ont: middle layer Message-ID: I support Toby's view & understand Katica's counter of the placement of the term. My compromise for consideration is provide information in the comment field where the 'middle layer' term's affinity can be explicitly stated. That way, should the PO structure be changed down the line the term's affinity would still be interpretable. Still, my slight preference is for a more explicit term (Toby's choice) so that affinity is clearly recognizable from the term name - straight off. - Leszek -----Original Message----- From: owner-po-dev at plantontology.org [mailto:owner-po-dev at plantontology.org] On Behalf Of katica at acoma.Stanford.EDU Sent: Saturday, January 07, 2006 1:38 PM To: po-dev at plantontology.org; Kellogg, Elizabeth A. Subject: Re: Proposal for the new term in Plant Structure Ont: middle layer Hi Toby, I know, I mentioned it yesterday on the conf call. However, its position in the ontology leaves little doubt what the term is. We have other terms that have a bit uninformative term name, for example, 'protective layer', or 'separation layer', of the abscission zone; it becomes obvious only when you see the ontology tree (and definition too). 'Middle layer of the anther wall' as a term name, I guess if we have to (to avoid confussion), it wouldn't be the worst name out there. Google search retrieved mostly middle layer of the anther wall. I did find 'middle layer' in description of the intervascular pit membranes in some woody species (Salix, Acer...). Peter and Quentin could tell us more about how often this term is used in anatomy of woody species. Katica On Sat, 7 Jan 2006, kellogge wrote: > hi Katica - > My only concern is that "middle layer" is such an uninformative term on > its own. I"m wondering if this is a case where we need to call it "middle > layer of anther wall". (I know - I'm suggesting a complex term where one > isn't strictly needed. It just seems that there are a lot of things that > could have middle layers.) > Toby > > On Jan 6, 2006, at 6:50 PM, katica at acoma.Stanford.EDU wrote: > >> Hi All, >> >> This is the proposal for introduction of the new term in the Plant >> Structure Ontology, 'middle layer': >> >> New term name: Middle layer >> Definition: Usually a single cell layer between tapetum and endothecium >> which almost invariably degenerates early during angiosperm anther >> development and is eventually absorbed by adjacent cells. >> >> Proposed ontology structure: >> >> PO:0000002 : anther wall >> (p) PO:0020002 : endothecium >> (p) PO:0020004 : exothecium >> (p) PO:0020005 : placentoid >> (p) PO:0020101 : stomium >> (p) PO:0009071 : tapetum >> (p) new term: middle layer >> >> I am planning to introduce this term to the PO a week from today, unless >> active discussion takes place regarding this term over the next week at >> po-dev mailing list. I would greatly appreciate your comments and >> suggestions. >> >> Thanks and have a great weekend. >> >> Katica Ilic >> >> >> ------------------------------------------------------------------------ -- >> 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/services/kellogg/ > -- ------------------------------------------------------------------------ -- 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 Tue Jan 10 02:24:14 2006 From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu) Date: Tue, 10 Jan 2006 02:24:14 -0500 Subject: Feedback on POC Message-ID: <200601100724.k0A7OE0B007353@filetta.cshl.org> *** Feedback from Plant Ontology Live Site *** refer_to_url: http://www.plantontology.org/docs/otherdocs/tutorials.html comments: Dear ladies and gentleman, We are writing a chapter in a review book on plant systems biology. The chapter is about ontologies and we are planning to integrate a screen-shot of your ontology browser into our chapter as a figure. It would be very helpful if you granted us permission to do so. Thanks a lot in advance. Best wishes, Ulrich Wagner Ulrich Wagner, PhD Transcriptome Bioinformatics Functional Genomics Center Zurich Uni ETH Z?rich Winterthurerstrasse 190 8057 Z?rich Tel. +41 (0) 44 635 3924 FAX +41 (0) 44 635 3922 ulrich.wagner at fgcz.ethz.ch ulrich.wagner at fgcz.unizh.ch name: Ulrich Wagner email: ulrich.wagner at fgcz.ethz.ch organization: uni eth zurich send_feedback: Send your feedback From pj37 at cornell.edu Tue Jan 10 10:17:23 2006 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 10 Jan 2006 10:17:23 -0500 Subject: Proposal for the new term in Plant Structure Ont: middle layer In-Reply-To: References: Message-ID: <43C3D003.5060606@cornell.edu> Here is my suggestion. As of now this is the only instance of "middle layer' in the ontology. Therefore, we can have the term named 'middle layer' with a clear definition that this is the one found in anthers. Obviously the parent will be anther term. At a later time where there is another instance we can consider revising the name to 'anther wall: middle layer'. Yes having a colon is fine in the term name. -Pankaj Vincent, Leszek wrote: > I support Toby's view & understand Katica's counter of the placement of > the term. My compromise for consideration is provide information in the > comment field where the 'middle layer' term's affinity can be explicitly > stated. That way, should the PO structure be changed down the line the > term's affinity would still be interpretable. Still, my slight > preference is for a more explicit term (Toby's choice) so that affinity > is clearly recognizable from the term name - straight off. > > - Leszek > > > -----Original Message----- > From: owner-po-dev at plantontology.org > [mailto:owner-po-dev at plantontology.org] On Behalf Of > katica at acoma.Stanford.EDU > Sent: Saturday, January 07, 2006 1:38 PM > To: po-dev at plantontology.org; Kellogg, Elizabeth A. > Subject: Re: Proposal for the new term in Plant Structure Ont: middle > layer > > Hi Toby, > > I know, I mentioned it yesterday on the conf call. However, its position > > in the ontology leaves little doubt what the term is. We have other > terms > that have a bit uninformative term name, for example, 'protective > layer', > or 'separation layer', of the abscission zone; it becomes obvious only > when you see the ontology tree (and definition too). > > 'Middle layer of the anther wall' as a term name, I guess if we have to > (to avoid confussion), it wouldn't be the worst name out there. Google > search retrieved mostly middle layer of the anther wall. I did find > 'middle > layer' in description of the intervascular pit membranes in some woody > species (Salix, Acer...). Peter and Quentin could tell us more about how > > often this term is used in anatomy of woody species. > > Katica > > > On Sat, 7 Jan 2006, > kellogge wrote: > > >>hi Katica - >> My only concern is that "middle layer" is such an uninformative term > > on > >>its own. I"m wondering if this is a case where we need to call it > > "middle > >>layer of anther wall". (I know - I'm suggesting a complex term where > > one > >>isn't strictly needed. It just seems that there are a lot of things > > that > >>could have middle layers.) >>Toby >> >>On Jan 6, 2006, at 6:50 PM, katica at acoma.Stanford.EDU wrote: >> >> >>>Hi All, >>> >>>This is the proposal for introduction of the new term in the Plant >>>Structure Ontology, 'middle layer': >>> >>>New term name: Middle layer >>>Definition: Usually a single cell layer between tapetum and > > endothecium > >>>which almost invariably degenerates early during angiosperm anther >>>development and is eventually absorbed by adjacent cells. >>> >>>Proposed ontology structure: >>> >>>PO:0000002 : anther wall >>>(p) PO:0020002 : endothecium >>>(p) PO:0020004 : exothecium >>>(p) PO:0020005 : placentoid >>>(p) PO:0020101 : stomium >>>(p) PO:0009071 : tapetum >>>(p) new term: middle layer >>> >>>I am planning to introduce this term to the PO a week from today, > > unless > >>>active discussion takes place regarding this term over the next week > > at > >>>po-dev mailing list. I would greatly appreciate your comments and >>>suggestions. >>> >>>Thanks and have a great weekend. >>> >>>Katica Ilic >>> >>> >>> From jitterbug at plantontology.org Fri Jan 13 18:59:58 2006 From: jitterbug at plantontology.org (Katica Ilic) Date: Fri, 13 Jan 2006 18:59:58 -0500 Subject: Feedback on POC - permission for PO browser screenshot (PR#160) Message-ID: <200601132359.k0DNxwxr010001@brie4.cshl.org> Dear Ulrich, I am happy to hear that you are planning to include screenshot of the PO browser in your book chapter. Of course, you are given permission to use the screenshot; please let us know when the book will be out. I need to mention to you that the same ontology screenshot (top nodes) will appear as a figure in two POC publications, coming out in 2006, so perhaps you would like to include them in the reference list of your chapter. Thanks you for contacting POC. I look forward to reading your book chapter. Sincerely, Katica Ilic, POC Project Coordinator > ---------- Forwarded message ---------- > Date: Tue, 10 Jan 2006 02:24:14 -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/docs/otherdocs/tutorials.html > > comments: Dear ladies and gentleman, > > We are writing a chapter in a review book on plant systems biology. The chapter > is about ontologies and we are planning to integrate a screen-shot of your > ontology browser into our chapter as a figure. It would be very helpful if you > granted us permission to do so. > > Thanks a lot in advance. > > Best wishes, > > Ulrich Wagner > Ulrich Wagner, PhD > Transcriptome Bioinformatics > Functional Genomics Center Zurich > Uni ETH Z?> Winterthurerstrasse 190 > 8057 Z?> Tel. +41 (0) 44 635 3924 > FAX +41 (0) 44 635 3922 > ulrich.wagner at fgcz.ethz.ch > ulrich.wagner at fgcz.unizh.ch > > > > name: Ulrich Wagner > > email: ulrich.wagner at fgcz.ethz.ch > > organization: uni eth zurich > > send_feedback: Send your feedback > --1118555204-2048991237-1137007816=:32051-- > > From alice.clara.augustine at monsanto.com Sun Jan 15 22:12:56 2006 From: alice.clara.augustine at monsanto.com (AUGUSTINE, ALICE CLARA [AG/8042]) Date: Sun, 15 Jan 2006 21:12:56 -0600 Subject: Feedback on POC - permission for PO browser screenshot (PR#160) Message-ID: <3DA5F100F50AEB4D973488B8FBEE850F0DB769@ems8042-01.monsanto.com> Dear Katica, Good luck at the conference PAG! Sorry to bother you about this.....a long time back I had requested to be part of any POC publications (with some inputs from Monsanto of course:):)) Do you see something coming up in the offing, so I can contribute and be part of a publication? Regards, Clare -----Original Message----- From: owner-po-dev at plantontology.org [mailto:owner-po-dev at plantontology.org] On Behalf Of Katica Ilic Sent: Saturday, January 14, 2006 5:30 AM To: ulrich.wagner at fgcz.ethz.ch Cc: po-dev at plantontology.org Subject: Re: Feedback on POC - permission for PO browser screenshot (PR#160) Dear Ulrich, I am happy to hear that you are planning to include screenshot of the PO browser in your book chapter. Of course, you are given permission to use the screenshot; please let us know when the book will be out. I need to mention to you that the same ontology screenshot (top nodes) will appear as a figure in two POC publications, coming out in 2006, so perhaps you would like to include them in the reference list of your chapter. Thanks you for contacting POC. I look forward to reading your book chapter. Sincerely, Katica Ilic, POC Project Coordinator > ---------- Forwarded message ---------- > Date: Tue, 10 Jan 2006 02:24:14 -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/docs/otherdocs/tutorials.html > > comments: Dear ladies and gentleman, > > We are writing a chapter in a review book on plant systems biology. The chapter > is about ontologies and we are planning to integrate a screen-shot of your > ontology browser into our chapter as a figure. It would be very helpful if you > granted us permission to do so. > > Thanks a lot in advance. > > Best wishes, > > Ulrich Wagner > Ulrich Wagner, PhD > Transcriptome Bioinformatics > Functional Genomics Center Zurich > Uni ETH Z?> Winterthurerstrasse 190 > 8057 Z?> Tel. +41 (0) 44 635 3924 > FAX +41 (0) 44 635 3922 > ulrich.wagner at fgcz.ethz.ch > ulrich.wagner at fgcz.unizh.ch > > > > name: Ulrich Wagner > > email: ulrich.wagner at fgcz.ethz.ch > > organization: uni eth zurich > > send_feedback: Send your feedback > --1118555204-2048991237-1137007816=:32051-- > > --------------------------------------------------------------------------------------------------------- This e-mail message may contain privileged and/or confidential information, and is intended to be received only by persons entitled to receive such information. If you have received this e-mail in error, please notify the sender immediately. Please delete it and all attachments from any servers, hard drives or any other media. Other use of this e-mail by you is strictly prohibited. All e-mails and attachments sent and received are subject to monitoring, reading and archival by Monsanto. The recipient of this e-mail is solely responsible for checking for the presence of "Viruses" or other "Malware". Monsanto accepts no liability for any damage caused by any such code transmitted by or accompanying this e-mail or any attachment. --------------------------------------------------------------------------------------------------------- From alice.clara.augustine at monsanto.com Sun Jan 15 22:12:56 2006 From: alice.clara.augustine at monsanto.com (AUGUSTINE, ALICE CLARA [AG/8042]) Date: Sun, 15 Jan 2006 21:12:56 -0600 Subject: Feedback on POC - permission for PO browser screenshot (PR#160) Message-ID: <3DA5F100F50AEB4D973488B8FBEE850F0DB769@ems8042-01.monsanto.com> Dear Katica, Good luck at the conference PAG! Sorry to bother you about this.....a long time back I had requested to be part of any POC publications (with some inputs from Monsanto of course:):)) Do you see something coming up in the offing, so I can contribute and be part of a publication? Regards, Clare -----Original Message----- From: owner-po-dev at plantontology.org [mailto:owner-po-dev at plantontology.org] On Behalf Of Katica Ilic Sent: Saturday, January 14, 2006 5:30 AM To: ulrich.wagner at fgcz.ethz.ch Cc: po-dev at plantontology.org Subject: Re: Feedback on POC - permission for PO browser screenshot (PR#160) Dear Ulrich, I am happy to hear that you are planning to include screenshot of the PO browser in your book chapter. Of course, you are given permission to use the screenshot; please let us know when the book will be out. I need to mention to you that the same ontology screenshot (top nodes) will appear as a figure in two POC publications, coming out in 2006, so perhaps you would like to include them in the reference list of your chapter. Thanks you for contacting POC. I look forward to reading your book chapter. Sincerely, Katica Ilic, POC Project Coordinator > ---------- Forwarded message ---------- > Date: Tue, 10 Jan 2006 02:24:14 -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/docs/otherdocs/tutorials.html > > comments: Dear ladies and gentleman, > > We are writing a chapter in a review book on plant systems biology. The chapter > is about ontologies and we are planning to integrate a screen-shot of your > ontology browser into our chapter as a figure. It would be very helpful if you > granted us permission to do so. > > Thanks a lot in advance. > > Best wishes, > > Ulrich Wagner > Ulrich Wagner, PhD > Transcriptome Bioinformatics > Functional Genomics Center Zurich > Uni ETH Z?> Winterthurerstrasse 190 > 8057 Z?> Tel. +41 (0) 44 635 3924 > FAX +41 (0) 44 635 3922 > ulrich.wagner at fgcz.ethz.ch > ulrich.wagner at fgcz.unizh.ch > > > > name: Ulrich Wagner > > email: ulrich.wagner at fgcz.ethz.ch > > organization: uni eth zurich > > send_feedback: Send your feedback > --1118555204-2048991237-1137007816=:32051-- > > --------------------------------------------------------------------------------------------------------- This e-mail message may contain privileged and/or confidential information, and is intended to be received only by persons entitled to receive such information. If you have received this e-mail in error, please notify the sender immediately. Please delete it and all attachments from any servers, hard drives or any other media. Other use of this e-mail by you is strictly prohibited. All e-mails and attachments sent and received are subject to monitoring, reading and archival by Monsanto. The recipient of this e-mail is solely responsible for checking for the presence of "Viruses" or other "Malware". Monsanto accepts no liability for any damage caused by any such code transmitted by or accompanying this e-mail or any attachment. --------------------------------------------------------------------------------------------------------- From alice.clara.augustine at monsanto.com Sun Jan 15 22:17:33 2006 From: alice.clara.augustine at monsanto.com (AUGUSTINE, ALICE CLARA [AG/8042]) Date: Sun, 15 Jan 2006 21:17:33 -0600 Subject: Recall: Feedback on POC - permission for PO browser screenshot (PR#160) Message-ID: <3DA5F100F50AEB4D973488B8FBEE850F0DB76B@ems8042-01.monsanto.com> The sender would like to recall the message, "Feedback on POC - permission for PO browser screenshot (PR#160)". --------------------------------------------------------------------------------------------------------- This e-mail message may contain privileged and/or confidential information, and is intended to be received only by persons entitled to receive such information. If you have received this e-mail in error, please notify the sender immediately. Please delete it and all attachments from any servers, hard drives or any other media. Other use of this e-mail by you is strictly prohibited. All e-mails and attachments sent and received are subject to monitoring, reading and archival by Monsanto. The recipient of this e-mail is solely responsible for checking for the presence of "Viruses" or other "Malware". Monsanto accepts no liability for any damage caused by any such code transmitted by or accompanying this e-mail or any attachment. --------------------------------------------------------------------------------------------------------- From alice.clara.augustine at monsanto.com Sun Jan 15 22:17:33 2006 From: alice.clara.augustine at monsanto.com (AUGUSTINE, ALICE CLARA [AG/8042]) Date: Sun, 15 Jan 2006 21:17:33 -0600 Subject: Recall: Feedback on POC - permission for PO browser screenshot (PR#160) Message-ID: <3DA5F100F50AEB4D973488B8FBEE850F0DB76B@ems8042-01.monsanto.com> The sender would like to recall the message, "Feedback on POC - permission for PO browser screenshot (PR#160)". --------------------------------------------------------------------------------------------------------- This e-mail message may contain privileged and/or confidential information, and is intended to be received only by persons entitled to receive such information. If you have received this e-mail in error, please notify the sender immediately. Please delete it and all attachments from any servers, hard drives or any other media. Other use of this e-mail by you is strictly prohibited. All e-mails and attachments sent and received are subject to monitoring, reading and archival by Monsanto. The recipient of this e-mail is solely responsible for checking for the presence of "Viruses" or other "Malware". Monsanto accepts no liability for any damage caused by any such code transmitted by or accompanying this e-mail or any attachment. --------------------------------------------------------------------------------------------------------- From alice.clara.augustine at monsanto.com Sun Jan 15 22:18:22 2006 From: alice.clara.augustine at monsanto.com (AUGUSTINE, ALICE CLARA [AG/8042]) Date: Sun, 15 Jan 2006 21:18:22 -0600 Subject: Feedback on POC - permission for PO browser screenshot (PR#160) Message-ID: <3DA5F100F50AEB4D973488B8FBEE850F0DB76C@ems8042-01.monsanto.com> Dear Katica, Good luck at the conference PAG! Sorry to bother you about this.....a long time back I had requested to be part of any POC publications (with some inputs from Monsanto of course:):)) Do you see something coming up in the offing, so I can contribute and be part of a publication? Regards, Clare -----Original Message----- From: owner-po-dev at plantontology.org [mailto:owner-po-dev at plantontology.org] On Behalf Of Katica Ilic Sent: Saturday, January 14, 2006 5:30 AM To: ulrich.wagner at fgcz.ethz.ch Cc: po-dev at plantontology.org Subject: Re: Feedback on POC - permission for PO browser screenshot (PR#160) Dear Ulrich, I am happy to hear that you are planning to include screenshot of the PO browser in your book chapter. Of course, you are given permission to use the screenshot; please let us know when the book will be out. I need to mention to you that the same ontology screenshot (top nodes) will appear as a figure in two POC publications, coming out in 2006, so perhaps you would like to include them in the reference list of your chapter. Thanks you for contacting POC. I look forward to reading your book chapter. Sincerely, Katica Ilic, POC Project Coordinator > ---------- Forwarded message ---------- > Date: Tue, 10 Jan 2006 02:24:14 -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/docs/otherdocs/tutorials.html > > comments: Dear ladies and gentleman, > > We are writing a chapter in a review book on plant systems biology. The chapter > is about ontologies and we are planning to integrate a screen-shot of your > ontology browser into our chapter as a figure. It would be very helpful if you > granted us permission to do so. > > Thanks a lot in advance. > > Best wishes, > > Ulrich Wagner > Ulrich Wagner, PhD > Transcriptome Bioinformatics > Functional Genomics Center Zurich > Uni ETH Z?> Winterthurerstrasse 190 > 8057 Z?> Tel. +41 (0) 44 635 3924 > FAX +41 (0) 44 635 3922 > ulrich.wagner at fgcz.ethz.ch > ulrich.wagner at fgcz.unizh.ch > > > > name: Ulrich Wagner > > email: ulrich.wagner at fgcz.ethz.ch > > organization: uni eth zurich > > send_feedback: Send your feedback > --1118555204-2048991237-1137007816=:32051-- > > --------------------------------------------------------------------------------------------------------- This e-mail message may contain privileged and/or confidential information, and is intended to be received only by persons entitled to receive such information. If you have received this e-mail in error, please notify the sender immediately. Please delete it and all attachments from any servers, hard drives or any other media. Other use of this e-mail by you is strictly prohibited. All e-mails and attachments sent and received are subject to monitoring, reading and archival by Monsanto. The recipient of this e-mail is solely responsible for checking for the presence of "Viruses" or other "Malware". Monsanto accepts no liability for any damage caused by any such code transmitted by or accompanying this e-mail or any attachment. --------------------------------------------------------------------------------------------------------- From alice.clara.augustine at monsanto.com Sun Jan 15 22:19:05 2006 From: alice.clara.augustine at monsanto.com (AUGUSTINE, ALICE CLARA [AG/8042]) Date: Sun, 15 Jan 2006 21:19:05 -0600 Subject: Recall: Feedback on POC - permission for PO browser screenshot (PR#160) Message-ID: <3DA5F100F50AEB4D973488B8FBEE850F0DB76D@ems8042-01.monsanto.com> The sender would like to recall the message, "Feedback on POC - permission for PO browser screenshot (PR#160)". --------------------------------------------------------------------------------------------------------- This e-mail message may contain privileged and/or confidential information, and is intended to be received only by persons entitled to receive such information. If you have received this e-mail in error, please notify the sender immediately. Please delete it and all attachments from any servers, hard drives or any other media. Other use of this e-mail by you is strictly prohibited. All e-mails and attachments sent and received are subject to monitoring, reading and archival by Monsanto. The recipient of this e-mail is solely responsible for checking for the presence of "Viruses" or other "Malware". Monsanto accepts no liability for any damage caused by any such code transmitted by or accompanying this e-mail or any attachment. --------------------------------------------------------------------------------------------------------- From alice.clara.augustine at monsanto.com Sun Jan 15 22:19:05 2006 From: alice.clara.augustine at monsanto.com (AUGUSTINE, ALICE CLARA [AG/8042]) Date: Sun, 15 Jan 2006 21:19:05 -0600 Subject: Recall: Feedback on POC - permission for PO browser screenshot (PR#160) Message-ID: <3DA5F100F50AEB4D973488B8FBEE850F0DB76D@ems8042-01.monsanto.com> The sender would like to recall the message, "Feedback on POC - permission for PO browser screenshot (PR#160)". --------------------------------------------------------------------------------------------------------- This e-mail message may contain privileged and/or confidential information, and is intended to be received only by persons entitled to receive such information. If you have received this e-mail in error, please notify the sender immediately. Please delete it and all attachments from any servers, hard drives or any other media. Other use of this e-mail by you is strictly prohibited. All e-mails and attachments sent and received are subject to monitoring, reading and archival by Monsanto. The recipient of this e-mail is solely responsible for checking for the presence of "Viruses" or other "Malware". Monsanto accepts no liability for any damage caused by any such code transmitted by or accompanying this e-mail or any attachment. --------------------------------------------------------------------------------------------------------- From alice.clara.augustine at monsanto.com Sun Jan 15 22:19:14 2006 From: alice.clara.augustine at monsanto.com (AUGUSTINE, ALICE CLARA [AG/8042]) Date: Sun, 15 Jan 2006 21:19:14 -0600 Subject: Recall: Feedback on POC - permission for PO browser screenshot (PR#160) Message-ID: <3DA5F100F50AEB4D973488B8FBEE850F0DB76E@ems8042-01.monsanto.com> The sender would like to recall the message, "Feedback on POC - permission for PO browser screenshot (PR#160)". --------------------------------------------------------------------------------------------------------- This e-mail message may contain privileged and/or confidential information, and is intended to be received only by persons entitled to receive such information. If you have received this e-mail in error, please notify the sender immediately. Please delete it and all attachments from any servers, hard drives or any other media. Other use of this e-mail by you is strictly prohibited. All e-mails and attachments sent and received are subject to monitoring, reading and archival by Monsanto. The recipient of this e-mail is solely responsible for checking for the presence of "Viruses" or other "Malware". Monsanto accepts no liability for any damage caused by any such code transmitted by or accompanying this e-mail or any attachment. --------------------------------------------------------------------------------------------------------- From alice.clara.augustine at monsanto.com Sun Jan 15 22:19:14 2006 From: alice.clara.augustine at monsanto.com (AUGUSTINE, ALICE CLARA [AG/8042]) Date: Sun, 15 Jan 2006 21:19:14 -0600 Subject: Recall: Feedback on POC - permission for PO browser screenshot (PR#160) Message-ID: <3DA5F100F50AEB4D973488B8FBEE850F0DB76E@ems8042-01.monsanto.com> The sender would like to recall the message, "Feedback on POC - permission for PO browser screenshot (PR#160)". --------------------------------------------------------------------------------------------------------- This e-mail message may contain privileged and/or confidential information, and is intended to be received only by persons entitled to receive such information. If you have received this e-mail in error, please notify the sender immediately. Please delete it and all attachments from any servers, hard drives or any other media. Other use of this e-mail by you is strictly prohibited. All e-mails and attachments sent and received are subject to monitoring, reading and archival by Monsanto. The recipient of this e-mail is solely responsible for checking for the presence of "Viruses" or other "Malware". Monsanto accepts no liability for any damage caused by any such code transmitted by or accompanying this e-mail or any attachment. --------------------------------------------------------------------------------------------------------- From alice.clara.augustine at monsanto.com Sun Jan 15 22:20:05 2006 From: alice.clara.augustine at monsanto.com (AUGUSTINE, ALICE CLARA [AG/8042]) Date: Sun, 15 Jan 2006 21:20:05 -0600 Subject: Recall: Feedback on POC - permission for PO browser screenshot (PR#160) Message-ID: <3DA5F100F50AEB4D973488B8FBEE850F0DB76F@ems8042-01.monsanto.com> The sender would like to recall the message, "Feedback on POC - permission for PO browser screenshot (PR#160)". --------------------------------------------------------------------------------------------------------- This e-mail message may contain privileged and/or confidential information, and is intended to be received only by persons entitled to receive such information. If you have received this e-mail in error, please notify the sender immediately. Please delete it and all attachments from any servers, hard drives or any other media. Other use of this e-mail by you is strictly prohibited. All e-mails and attachments sent and received are subject to monitoring, reading and archival by Monsanto. The recipient of this e-mail is solely responsible for checking for the presence of "Viruses" or other "Malware". Monsanto accepts no liability for any damage caused by any such code transmitted by or accompanying this e-mail or any attachment. --------------------------------------------------------------------------------------------------------- From alice.clara.augustine at monsanto.com Sun Jan 15 22:20:05 2006 From: alice.clara.augustine at monsanto.com (AUGUSTINE, ALICE CLARA [AG/8042]) Date: Sun, 15 Jan 2006 21:20:05 -0600 Subject: Recall: Feedback on POC - permission for PO browser screenshot (PR#160) Message-ID: <3DA5F100F50AEB4D973488B8FBEE850F0DB76F@ems8042-01.monsanto.com> The sender would like to recall the message, "Feedback on POC - permission for PO browser screenshot (PR#160)". --------------------------------------------------------------------------------------------------------- This e-mail message may contain privileged and/or confidential information, and is intended to be received only by persons entitled to receive such information. If you have received this e-mail in error, please notify the sender immediately. Please delete it and all attachments from any servers, hard drives or any other media. Other use of this e-mail by you is strictly prohibited. All e-mails and attachments sent and received are subject to monitoring, reading and archival by Monsanto. The recipient of this e-mail is solely responsible for checking for the presence of "Viruses" or other "Malware". Monsanto accepts no liability for any damage caused by any such code transmitted by or accompanying this e-mail or any attachment. --------------------------------------------------------------------------------------------------------- From feedback_submission at filetta.cshl.edu Tue Jan 24 17:05:20 2006 From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu) Date: Tue, 24 Jan 2006 17:05:20 -0500 Subject: Feedback on POC Message-ID: <200601242205.k0OM5Kck018550@filetta.cshl.org> *** Feedback from Plant Ontology Live Site *** refer_to_url: http://www.plantontology.org/index.html comments: http://plantontology.org shows a naket apache page may want to fix that name: ron shigeta email: ron_shigeta at affymetrix.com organization: send_feedback: Send your feedback From pj37 at cornell.edu Wed Jan 25 16:29:21 2006 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Wed, 25 Jan 2006 16:29:21 -0500 Subject: new term request: Hull Message-ID: <43D7EDB1.3060304@cornell.edu> Hi All, I need a new term to describe 'hull' in cereal plants. I know experts say that it is nothing different than lemma and palea, the two parts found in grass floret. Therefore the options are to put 'hull' as synonyms of both lemma and palea, which I somehow disagree because the term 'hull' is never used in florets/grass flowers. The usage is only in the grass fruits (caryopsis). It also appears that the same term is used in other families as well. So we need a species/organ specific distinction as well. # dry outer covering of a fruit or seed or nut # persistent enlarged calyx at base of e.g. a strawberry or raspberry -Pankaj From jitterbug at plantontology.org Wed Jan 25 17:26:48 2006 From: jitterbug at plantontology.org (Katica Ilic) Date: Wed, 25 Jan 2006 17:26:48 -0500 Subject: Feedback on POC - URL problem (fwd) (PR#232) Message-ID: <200601252226.k0PMQmxr001335@brie4.cshl.org> Dear Ron, Thanks you for bringing this to our attention. We fixed it, the URL:http://plantontology.org is working now. Thank you for contacting POC. Best regards, Katica Ilic, POC Project Coordinator > ---------- Forwarded message ---------- > Date: Tue, 24 Jan 2006 17:05:20 -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: http://plantontology.org > > shows a naket apache page > > may want to fix that > > name: ron shigeta > > email: ron_shigeta at affymetrix.com > > organization: > > send_feedback: Send your feedback > > From jclark at ebi.ac.uk Thu Jan 26 08:11:26 2006 From: jclark at ebi.ac.uk (J Clark) Date: Thu, 26 Jan 2006 13:11:26 +0000 Subject: plantlet formation Message-ID: <43D8CA7E.5090703@ebi.ac.uk> Hi, I am working on some terms in the gene ontology consortium process ontology. They are the two terms pasted below and I am wondering whether they ought to have parentage under 'response to hormone' and if so then which hormone? Is there anybody out there who has expert knowledge of these two processes and who could tell me which hormones cause these two processes to occur? I am having trouble finding a paper with this information. Thanks, Jennifer Clark id: GO:0048623 name: seed germination on parent plant namespace: biological_process def: "The process by which a seed germinates before being shed from the parent plant." [GO :curators] exact_synonym: "non-vegetative vivipary (sensu Magnoliophyta)" [] exact_synonym: "pre-harvest sprouting" [] broad_synonym: "vivipary (sensu Magnoliophyta)" [] is_a: GO:0009845 ! seed germination [Term] id: GO:0048624 name: plantlet formation on parent plant namespace: biological_process def: "The process whereby a new plantlet develops from a meristem on the plant body. As pa rt of this process\, when the plantlet is large enough to live independently\, the physical connection between the new plantlet and the main plant is severed." [GO:curators] exact_synonym: "vegetative vivipary (sensu Magnoliophyta)" [] broad_synonym: "vivipary (sensu Magnoliophyta)" [] is_a: GO:0019954 ! asexual reproduction is_a: GO:0048507 ! meristem development From ap343 at cornell.edu Thu Jan 26 11:31:35 2006 From: ap343 at cornell.edu (Anuradha Pujar) Date: Thu, 26 Jan 2006 11:31:35 -0500 (EST) Subject: Sol growth stage synonyms (ver 1.24) Message-ID: <3736.128.253.184.79.1138293095.squirrel@webmail.cornell.edu> Hi Developers, Temporal ver 1.24 has Solanaceae growth stage synonyms added from the mapping file provided by Naama (SGN). Shuly: can you please load it on amigo so it can be reviewed by all developers. Thanks anu From shuly at cshl.edu Thu Jan 26 12:01:12 2006 From: shuly at cshl.edu (Shuly Avraham) Date: Thu, 26 Jan 2006 12:01:12 -0500 Subject: Sol growth stage synonyms (ver 1.24) In-Reply-To: <3736.128.253.184.79.1138293095.squirrel@webmail.cornell.edu> References: <3736.128.253.184.79.1138293095.squirrel@webmail.cornell.edu> Message-ID: Anu, File was loaded to AmiGO: Please review, http://dev.plantontology.org/amigo/go.cgi Shuly. On Jan 26, 2006, at 11:31 AM, Anuradha Pujar wrote: > Hi Developers, > > Temporal ver 1.24 has Solanaceae growth stage synonyms added from the > mapping file provided by Naama (SGN). > > Shuly: can you please load it on amigo so it can be reviewed by all > developers. > > Thanks > anu > From kellogge at msx.umsl.edu Thu Jan 26 15:46:28 2006 From: kellogge at msx.umsl.edu (kellogge) Date: Thu, 26 Jan 2006 14:46:28 -0600 Subject: plantlet formation In-Reply-To: <43D8CA7E.5090703@ebi.ac.uk> References: <43D8CA7E.5090703@ebi.ac.uk> Message-ID: Seed germination on the parent plant is caused by reduction in or insensitivity to abscisic acid levels. I don't know about the other process, and there may not be information on it; I suspect if there is information it will be in the horticultural literature, rather than the agronomic literature. Toby On Jan 26, 2006, at 7:11 AM, J Clark wrote: > Hi, > > I am working on some terms in the gene ontology consortium process > ontology. They are the two terms pasted below and I am wondering > whether they ought to have parentage under 'response to hormone' and > if so then which hormone? Is there anybody out there who has expert > knowledge of these two processes and who could tell me which hormones > cause these two processes to occur? I am having trouble finding a > paper with this information. > > Thanks, > > Jennifer Clark > > id: GO:0048623 > name: seed germination on parent plant > namespace: biological_process > def: "The process by which a seed germinates > before being shed from the parent plant." [GO > :curators] > exact_synonym: "non-vegetative vivipary (sensu > Magnoliophyta)" [] > exact_synonym: "pre-harvest sprouting" [] > broad_synonym: "vivipary (sensu Magnoliophyta)" [] > is_a: GO:0009845 ! seed germination > > [Term] > id: GO:0048624 > name: plantlet formation on parent plant > namespace: biological_process > def: "The process whereby a new plantlet develops > from a meristem on the plant body. As pa rt of > this process\, when the plantlet is large enough > to live independently\, the physical connection > between the new plantlet and the main plant is > severed." [GO:curators] > exact_synonym: "vegetative vivipary (sensu > Magnoliophyta)" [] > broad_synonym: "vivipary (sensu Magnoliophyta)" [] > is_a: GO:0019954 ! asexual reproduction > is_a: GO:0048507 ! meristem development > > 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/services/kellogg/ -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 2084 bytes Desc: not available URL: From kellogge at msx.umsl.edu Mon Jan 30 18:34:58 2006 From: kellogge at msx.umsl.edu (kellogge) Date: Mon, 30 Jan 2006 17:34:58 -0600 Subject: new term request: Hull In-Reply-To: <43D7EDB1.3060304@cornell.edu> References: <43D7EDB1.3060304@cornell.edu> Message-ID: <92cb9ac9e274b9fa8d62c47235f2e2d7@msx.umsl.edu> Hi Pankaj - I'd still go with synonym of lemma and palea, probably as hull sensu Poaceae. I'd prefer to avoid the first defniition you've listed below, since it doesn't pertain to anything botanical (or maybe pertains to everything). Following the second definition, you could have a synonym of calyx being hull sensu Rosaceae. Toby On Jan 25, 2006, at 3:29 PM, Pankaj Jaiswal wrote: > Hi All, > > I need a new term to describe 'hull' in cereal plants. I know experts > say that it is nothing different than lemma and palea, the two parts > found in grass floret. Therefore the options are to put 'hull' as > synonyms of both lemma and palea, which I somehow disagree because the > term 'hull' is never used in florets/grass flowers. The usage is only > in the grass fruits (caryopsis). It also appears that the same term is > used in other families as well. So we need a species/organ specific > distinction as well. > > # dry outer covering of a fruit or seed or nut > # persistent enlarged calyx at base of e.g. a strawberry or raspberry > > > -Pankaj > > > > 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/services/kellogg/ -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 1324 bytes Desc: not available URL: From peter.stevens at mobot.org Tue Jan 31 13:13:43 2006 From: peter.stevens at mobot.org (peter.stevens at mobot.org) Date: Tue, 31 Jan 2006 12:13:43 -0600 Subject: new term request: Hull Message-ID: I agree with Toby - second would include all sorts of things, and third is difficult - the K of raspberries barely is enlarged at all, and is basically marcescent - marcescent calyces are common, and nobody ever calls then a hull (and I hope never will). P. . >Hi Pankaj - > >I'd still go with synonym of lemma and palea, probably as hull sensu >Poaceae. I'd prefer to avoid the first defniition you've listed >below, since it doesn't pertain to anything botanical (or maybe >pertains to everything). Following the second definition, you could >have a synonym of calyx being hull sensu Rosaceae. > >Toby > > >On Jan 25, 2006, at 3:29 PM, Pankaj Jaiswal wrote: > > >Hi All, > > >I need a new term to describe 'hull' in cereal plants. I know >experts say that it is nothing different than lemma and palea, the >two parts found in grass floret. Therefore the options are to put >'hull' as synonyms of both lemma and palea, which I somehow disagree >because the term 'hull' is never used in florets/grass flowers. The >usage is only in the grass fruits (caryopsis). It also appears that >the same term is used in other families as well. So we need a >species/organ specific distinction as well. > > ># dry outer covering of a fruit or seed or nut > ># persistent enlarged calyx at base of e.g. a strawberry or raspberry > > > >-Pankaj > > > > > >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/services/kellogg/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From pj37 at cornell.edu Tue Jan 31 22:57:03 2006 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 31 Jan 2006 22:57:03 -0500 Subject: new term request: Hull In-Reply-To: References: Message-ID: <43E0318F.2040209@cornell.edu> There is some difficulty on putting hull as synonym. I think there is a precedence on creating a new term even though a part is called by different name in a derive parent structure. e.g. in seed many parts are derived from the ovule, e.g. chalaza, micropyle, testa etc. These are derived structures or rather the same structures but sometimes can be called by different names. Similarly it will be very difficult to annotate phenotypes and gene expression such as in case of http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16443696&query_hl=5&itool=pubmed_docsum to lemma and palea. In this case the actual structure is called as hull. I think we need hull as a new term, and the parentage as follows fruit ---part_of---hull Also floret --part_of--lemma -----develops_from--hull --part_of--palea -----develops_from--hull -Pankaj peter.stevens at mobot.org wrote: > I agree with Toby - second would include all sorts of things, and > third is difficult - the K of raspberries barely is enlarged at all, > and is basically marcescent - marcescent calyces are common, and > nobody ever calls then a hull (and I hope never will). > > P. > > . > >Hi Pankaj - > > > >I'd still go with synonym of lemma and palea, probably as hull sensu > >Poaceae. I'd prefer to avoid the first defniition you've listed > >below, since it doesn't pertain to anything botanical (or maybe > >pertains to everything). Following the second definition, you could > >have a synonym of calyx being hull sensu Rosaceae. > > > >Toby > > > > > >On Jan 25, 2006, at 3:29 PM, Pankaj Jaiswal wrote: > > > > > >Hi All, > > > > > >I need a new term to describe 'hull' in cereal plants. I know > >experts say that it is nothing different than lemma and palea, the > >two parts found in grass floret. Therefore the options are to put > >'hull' as synonyms of both lemma and palea, which I somehow disagree > >because the term 'hull' is never used in florets/grass flowers. The > >usage is only in the grass fruits (caryopsis). It also appears that > >the same term is used in other families as well. So we need a > >species/organ specific distinction as well. > > > > > ># dry outer covering of a fruit or seed or nut > > > ># persistent enlarged calyx at base of e.g. a strawberry or raspberry > > > > > > > >-Pankaj > > > > > > > > > > > >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/services/kellogg/ > From sophiet at agri.gov.il Wed Jan 25 03:44:09 2006 From: sophiet at agri.gov.il (Sophie Tanny) Date: Wed, 25 Jan 2006 10:44:09 +0200 Subject: plant organ question Message-ID: <43D73A59.3020206@agri.gov.il> Hello. I have been trying to connect a list of various cDNA libraries to your plant structure onthology, and I have encountered a few definition problems. For instance: in Apple libraries, some of the libraries were made from vegetative buds. other were made from "bud spurs". Can you help me define these organs so they're compatible with your list? I thank you in advance, Sophie Tanny Hanne Volpin's group ARO, Israel This message was scanned against malicious content by the ARO secure anti-virus and anti-spam system. Volcani Infrastructure & System Department From wendys at aspb.org Thu Jan 26 13:01:08 2006 From: wendys at aspb.org (Wendy Sahli) Date: Thu, 26 Jan 2006 13:01:08 -0500 Subject: Link/Listing Request Message-ID: <70B2F7E296B1AD499A51D0523A482D8C018C5F4F@hawk.monona.aspp.org> Good afternoon, We are writing to request a link to our upcoming meetings for Plant Biology or in general for our ASPB web site. We believe they would be of interest to your users. In return, feel free to submit your site links to our resource links library at http://www.aspb.org/resourcelinks/ Our meetings are listed below. Plant Biology 2006 The Joint Annual Meeting of the American Society of Plant Biologists and the Canadian Society of Plant Physiologists. This meeting features five major symposia, multiple mini symposia, workshops, posters, exhibits, and social events Hynes Convention Center Boston, Massachusetts August 5-9, 2006 http://www.aspb.org/meetings/pb-2006/ The Biology of Transpiration: From Guard Cells to Globe This year's specialty meeting of the American Society of Plant Biologists on the subject of stomata. October 10-14, 2006 Snowbird Mountain Resort Snowbird, Utah http://www.aspb.org/meetings/transpiration06/ __________________________ Wendy Sahli Manager, Marketing & Web Services American Society of Plant Biologists (ASPB) http://www.aspb.org 301-251-0560 x123