From kellogge at msx.umsl.edu Wed Feb 1 10:57:25 2006 From: kellogge at msx.umsl.edu (kellogge) Date: Wed, 1 Feb 2006 09:57:25 -0600 Subject: new term request: Hull In-Reply-To: <43E0318F.2040209@cornell.edu> References: <43E0318F.2040209@cornell.edu> Message-ID: <7484069177890f7782d58066e7c93b9e@msx.umsl.edu> Pankaj - I've looked at the paper - I still don't see why it can't be annotated to lemma and palea. Just because the authors use a non-botanical word does not mean that the databases have to use the term. Toby On Jan 31, 2006, at 9:57 PM, Pankaj Jaiswal wrote: > 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&itoo > l=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/ > > 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: 3195 bytes Desc: not available URL: From Leszek at missouri.edu Wed Feb 1 13:33:41 2006 From: Leszek at missouri.edu (Vincent, Leszek) Date: Wed, 1 Feb 2006 12:33:41 -0600 Subject: new term request: Hull Message-ID: I support Toby & Peter's perspective. Furthermore, in a similar situation Lincoln supported the view that the POC can also be something of an educator of users in their understanding & use of internationally recognized botanical terms. "Hull", while widely used as a colloquialism, is rather devoid of good botanical identity & even has varying lose applications (some even nautical!) therefore requiring further defining depending on context of use. I support Toby's most recent comment & suggest an educational comment could be provided in the 'Comments' area regarding the term 'hull' & its compositional affinity with lemma & palea etc. I think the closest "hull" should get to the PO is via a synonym as described by Toby earlier. Let's keep on maintaining our focus on the use of internationally accepted botanical terminology in our PO work - clearly there are researchers out there who need this education. - Leszek *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* P. Leszek D. Vincent Ph.D., FLS Division of Plant Sciences 215 Curtis Hall University of Missouri-Columbia Columbia MO 65211-7020 USA Ph: (573) 884-3716; Skype VoIP: phytosynergy; 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) *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* ________________________________ From: owner-po-dev at plantontology.org [mailto:owner-po-dev at plantontology.org] On Behalf Of kellogge Sent: Wednesday, February 01, 2006 9:57 AM To: Pankaj Jaiswal; po-dev at plantontology.org Subject: Re: new term request: Hull Pankaj - I've looked at the paper - I still don't see why it can't be annotated to lemma and palea. Just because the authors use a non-botanical word does not mean that the databases have to use the term. Toby On Jan 31, 2006, at 9:57 PM, Pankaj Jaiswal wrote: 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&dop t=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/ 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 Wed Feb 1 14:35:53 2006 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Wed, 01 Feb 2006 14:35:53 -0500 Subject: new term request: secondary parietal cell layer Message-ID: <43E10D99.8050207@cornell.edu> I require a new term as follows for curating the rice MSP1 gene expression (http://www.plantcell.org/cgi/content/abstract/15/8/1728) New term: secondary parietal cell layer [part of anther wall] references http://www.plantcell.org/cgi/content/abstract/15/8/1728 http://www.genetics.org/cgi/content/abstract/153/2/933 http://aob.oxfordjournals.org/cgi/content/abstract/90/6/701 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=282801 However if we are looking at the parietal layer, we nee the following as well parietal cell (isa cell and part of parietal cell layer) -- Pankaj Jaiswal G-15, Bradfield Hall Dept. of Plant Breeding and Genetics Cornell University Ithaca, NY-14853, USA Ph. +1-607-255-3103 / 4199 fax: +1-607-255-6683 From pj37 at cornell.edu Wed Feb 1 14:23:32 2006 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Wed, 01 Feb 2006 14:23:32 -0500 Subject: Proposal for the new term in Plant Structure Ont: middle layer In-Reply-To: <9f9feabee4b3cc885911dbdf33225aef@msx.umsl.edu> References: <43C3D003.5060606@cornell.edu> <9f9feabee4b3cc885911dbdf33225aef@msx.umsl.edu> Message-ID: <43E10AB4.8070201@cornell.edu> Can we implement this. I need this term for curation now. -Pankaj kellogge wrote: > Sounds reasonable to me. > Toby > > On Jan 10, 2006, at 9:17 AM, Pankaj Jaiswal wrote: > > 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 > > > > > > > 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/ > -- 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 katica at acoma.stanford.edu Wed Feb 1 15:30:51 2006 From: katica at acoma.stanford.edu (katica at acoma.stanford.edu) Date: Wed, 1 Feb 2006 12:30:51 -0800 (PST) Subject: Proposal for the new term in Plant Structure Ont: middle layer In-Reply-To: <43E10AB4.8070201@cornell.edu> References: <43C3D003.5060606@cornell.edu> <9f9feabee4b3cc885911dbdf33225aef@msx.umsl.edu> <43E10AB4.8070201@cornell.edu> Message-ID: I have this term on the list for the Friday conf call, to briefly disccus the term name. If we agree on the name, the term will be added to the PO on Moday. Katica On Wed, 1 Feb 2006, Pankaj Jaiswal wrote: > Can we implement this. I need this term for curation now. > -Pankaj > > kellogge wrote: > >> Sounds reasonable to me. >> Toby >> >> On Jan 10, 2006, at 9:17 AM, Pankaj Jaiswal wrote: >> >> 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 >> >> >> >> >> >> >> 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 katica at acoma.stanford.edu Wed Feb 1 16:28:52 2006 From: katica at acoma.stanford.edu (katica at acoma.stanford.edu) Date: Wed, 1 Feb 2006 13:28:52 -0800 (PST) Subject: new term request: secondary parietal cell layer In-Reply-To: <43E10D99.8050207@cornell.edu> References: <43E10D99.8050207@cornell.edu> Message-ID: This would be more appropriate term for developmental stages ontology, under 'anther development'. There is a term 'B formation of primary parietal and sporogenous cells', perhaps all we need is to add another term, 'formation of secondary parietal cells'. Neither parietal cells or sporogenous cell form layers, they appear as a few distinct cells within four corners of anther primordia, with cell lineages that will give rise to particular layers of the anther wall. They are certainly not cell types, and it would be wrong to add them as children under cell type node. Katica On Wed, 1 Feb 2006, Pankaj Jaiswal wrote: > I require a new term as follows for curating the rice MSP1 gene expression > (http://www.plantcell.org/cgi/content/abstract/15/8/1728) > > New term: > secondary parietal cell layer [part of anther wall] > > references > http://www.plantcell.org/cgi/content/abstract/15/8/1728 > http://www.genetics.org/cgi/content/abstract/153/2/933 > http://aob.oxfordjournals.org/cgi/content/abstract/90/6/701 > http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=282801 > > > However if we are looking at the parietal layer, we nee the following as well > > parietal cell (isa cell and part of parietal cell layer) > > > > > > -- -------------------------------------------------------------------------- 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 Feb 1 17:03:18 2006 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Wed, 01 Feb 2006 17:03:18 -0500 Subject: new term request: secondary parietal cell layer In-Reply-To: References: <43E10D99.8050207@cornell.edu> Message-ID: <43E13026.7080709@cornell.edu> I hope this statement helps. -Pankaj cited from: http://www.genetics.org/cgi/content/abstract/153/2/933 Genetics, Vol. 153, 933-941, October 1999, Copyright ? 1999 The mac1 Mutation Alters the Developmental Fate of the Hypodermal Cells and Their Cellular Progeny in the Maize Anther 'In each anther lobe the primary parietal cell and adjacent cells (RAGHAVAN 1988 ) form the primary parietal cell layer and the cells of this layer undergo a periclinal division resulting in the formation of the two secondary parietal layers. The outermost of these two layers differentiates into the endothecium, while the inner layer again divides periclinally to form the middle layer externally and the tapetum internally (KIESSELBACH 1949 ; DAVIS 1966 ). The archesporial cells divide one or more times and their cellular progeny differentiate into the microsporocytes (KIESSELBACH 1949 ). See RAGHAVAN 1988 for a detailed analysis of this developmental sequence in rice.' katica at acoma.stanford.edu wrote: > > This would be more appropriate term for developmental stages ontology, > under 'anther development'. There is a term 'B formation of primary > parietal and sporogenous cells', perhaps all we need is to add another > term, 'formation of secondary parietal cells'. > > Neither parietal cells or sporogenous cell form layers, they appear as a > few distinct cells within four corners of anther primordia, with cell > lineages that will give rise to particular layers of the anther wall. > > They are certainly not cell types, and it would be wrong to add them as > children under cell type node. > > Katica > > On Wed, 1 Feb 2006, Pankaj Jaiswal wrote: > >> I require a new term as follows for curating the rice MSP1 gene >> expression (http://www.plantcell.org/cgi/content/abstract/15/8/1728) >> >> New term: >> secondary parietal cell layer [part of anther wall] >> >> references >> http://www.plantcell.org/cgi/content/abstract/15/8/1728 >> http://www.genetics.org/cgi/content/abstract/153/2/933 >> http://aob.oxfordjournals.org/cgi/content/abstract/90/6/701 >> http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=282801 >> >> >> However if we are looking at the parietal layer, we nee the following >> as well >> >> parietal cell (isa cell and part of parietal cell layer) >> >> >> >> >> >> > -- 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 jclark at ebi.ac.uk Thu Feb 2 08:13:17 2006 From: jclark at ebi.ac.uk (J Clark) Date: Thu, 02 Feb 2006 13:13:17 +0000 Subject: plantlet formation In-Reply-To: References: <43D8CA7E.5090703@ebi.ac.uk> Message-ID: <43E2056D.3010708@ebi.ac.uk> Hi Toby, Thanks for that information. If seed germination on the parent plant is caused by reduction in or insensitivity to abscisic acid levels then perhaps normal 'maintenance of seed dormancy' could be a child of 'response to abscisic acid' and that 'seed germination on parent plant' should not be connected to a hormone term since the hormone is not acting in this case. Does that seem right to you? Thanks, Jen kellogge wrote: > 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/ > From peter.stevens at mobot.org Thu Feb 2 12:03:55 2006 From: peter.stevens at mobot.org (peter.stevens at mobot.org) Date: Thu, 2 Feb 2006 11:03:55 -0600 Subject: new term request: Hull Message-ID: This would seem to be a matter of principle, along the lines of Leszek's recent comments about the educational side of the PO. We cannot take account of misuses of terms, nonce terms, and the like, except by making sure synonymy grows.. After all, many people, inc, botanists of my acquaintance, call a lamina a leaf and do not blush. P. >Pankaj - > >I've looked at the paper - I still don't see why it can't be >annotated to lemma and palea. Just because the authors use a >non-botanical word does not mean that the databases have to use the >term. > >Toby > > >On Jan 31, 2006, at 9:57 PM, Pankaj Jaiswal wrote: > > >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=A bstract&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/ > > > >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 feedback_submission at filetta.cshl.edu Mon Feb 6 20:59:43 2006 From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu) Date: Mon, 6 Feb 2006 20:59:43 -0500 Subject: Feedback on POC Message-ID: <200602070159.k171xhxM005998@filetta.cshl.org> *** Feedback from Plant Ontology Live Site *** refer_to_url: tto6628 at plantontology.org send_feedback: tto6628 at plantontology.org Clear: tto6628 at plantontology.org comments: tto6628 at plantontology.org organization: up Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Subject: they bcc: charleses3229 at aol.com d69739686544e6f298caeef6df9a2c74 . email: tto6628 at plantontology.org name: tto6628 at plantontology.org From feedback_submission at filetta.cshl.edu Mon Feb 6 21:00:29 2006 From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu) Date: Mon, 6 Feb 2006 21:00:29 -0500 Subject: Feedback on POC Message-ID: <200602070200.k1720TCM006032@filetta.cshl.org> *** Feedback from Plant Ontology Live Site *** refer_to_url: with Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Subject: was first posted on ay 13, 2003 dition 10 anguage bcc: charleses3299 at aol.com d3d552e48c8ebac5a2b7ba2936507043 . send_feedback: t7878 at plantontology.org Clear: t7878 at plantontology.org comments: t7878 at plantontology.org organization: t7878 at plantontology.org email: t7878 at plantontology.org name: t7878 at plantontology.org From felipe.zapata at umsl.edu Wed Feb 1 15:34:01 2006 From: felipe.zapata at umsl.edu (Felipe Zapata) Date: Wed, 1 Feb 2006 14:34:01 -0600 Subject: new terms In-Reply-To: <43E10AB4.8070201@cornell.edu> References: <43C3D003.5060606@cornell.edu> <9f9feabee4b3cc885911dbdf33225aef@msx.umsl.edu> <43E10AB4.8070201@cornell.edu> Message-ID: <2E39F0AA-26B0-4F13-8935-CEC4A2214350@umsl.edu> Think I am missing the rationale for requesting/incorporating new terms. Every time a geneticists decides to (mis)use a botanical term we HAVE TO incorporate it in POC?? i would certainly like to know what the rationale (if any) for new terms is. I must accept I may have lost track of something while I was in the field, therefore my question. F From feedback_submission at filetta.cshl.edu Thu Feb 9 11:44:24 2006 From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu) Date: Thu, 9 Feb 2006 11:44:24 -0500 Subject: Feedback on POC Message-ID: <200602091644.k19GiOmw017360@filetta.cshl.org> *** Feedback from Plant Ontology Live Site *** refer_to_url: trivial7754 at plantontology.org send_feedback: trivial7754 at plantontology.org Clear: trivial7754 at plantontology.org comments: trivial7754 at plantontology.org organization: trivial7754 at plantontology.org email: trivial7754 at plantontology.org name: e Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Subject: that it bcc: charleses3299 at aol.com 2fb43ad8a8cc1b8645c7b89a618a03e0 . From feedback_submission at filetta.cshl.edu Thu Feb 9 11:44:25 2006 From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu) Date: Thu, 9 Feb 2006 11:44:25 -0500 Subject: Feedback on POC Message-ID: <200602091644.k19GiPMQ017370@filetta.cshl.org> *** Feedback from Plant Ontology Live Site *** refer_to_url: or2914 at plantontology.org name: or2914 at plantontology.org Clear: or2914 at plantontology.org comments: of Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Subject: take wine. ady ingleton threw a look at her bcc: charieses329 at aol.com a74e101f2e6b5e7903f35c98e72d461f . organization: or2914 at plantontology.org email: or2914 at plantontology.org send_feedback: or2914 at plantontology.org From feedback_submission at filetta.cshl.edu Thu Feb 9 11:44:26 2006 From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu) Date: Thu, 9 Feb 2006 11:44:26 -0500 Subject: Feedback on POC Message-ID: <200602091644.k19GiQJX017380@filetta.cshl.org> *** Feedback from Plant Ontology Live Site *** refer_to_url: had Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Subject: who do, are of a bcc: charleses3229 at aol.com 9b3d7d47939df72b40ff4e825adbef4d . send_feedback: they8295 at plantontology.org Clear: they8295 at plantontology.org comments: they8295 at plantontology.org organization: they8295 at plantontology.org email: they8295 at plantontology.org name: they8295 at plantontology.org From feedback_submission at filetta.cshl.edu Thu Feb 9 11:48:42 2006 From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu) Date: Thu, 9 Feb 2006 11:48:42 -0500 Subject: Feedback on POC Message-ID: <200602091648.k19GmgmQ017524@filetta.cshl.org> *** Feedback from Plant Ontology Live Site *** refer_to_url: there3668 at plantontology.org send_feedback: there3668 at plantontology.org Clear: there3668 at plantontology.org comments: there3668 at plantontology.org organization: come Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Subject: pencils, and occasionally making comical faces for the young ladies bcc: charleses3299 at aol.com d0a13ddd609892d2b0d8b58fa9de8ab4 . email: there3668 at plantontology.org name: there3668 at plantontology.org From feedback_submission at filetta.cshl.edu Fri Feb 10 10:58:52 2006 From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu) Date: Fri, 10 Feb 2006 10:58:52 -0500 Subject: Feedback on POC Message-ID: <200602101558.k1AFwqp9023483@filetta.cshl.org> *** Feedback from Plant Ontology Live Site *** refer_to_url: tis Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Subject: most of those bcc: bob at mdserious.com b9587d8bb37f48770defdf7384984d1c . send_feedback: would4207 at plantontology.org Clear: would4207 at plantontology.org comments: would4207 at plantontology.org organization: would4207 at plantontology.org email: would4207 at plantontology.org name: would4207 at plantontology.org From feedback_submission at filetta.cshl.edu Fri Feb 10 10:59:39 2006 From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu) Date: Fri, 10 Feb 2006 10:59:39 -0500 Subject: Feedback on POC Message-ID: <200602101559.k1AFxdKT023505@filetta.cshl.org> *** Feedback from Plant Ontology Live Site *** refer_to_url: yv765 at plantontology.org name: yv765 at plantontology.org Clear: yv765 at plantontology.org comments: said Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Subject: at this ben trovato, when ady ingleton bustled bcc: bob at mdserious.com d64883ba43d062c739a47a04743767ac . organization: yv765 at plantontology.org email: yv765 at plantontology.org send_feedback: yv765 at plantontology.org From feedback_submission at filetta.cshl.edu Fri Feb 10 11:01:06 2006 From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu) Date: Fri, 10 Feb 2006 11:01:06 -0500 Subject: Feedback on POC Message-ID: <200602101601.k1AG16Kq023537@filetta.cshl.org> *** Feedback from Plant Ontology Live Site *** refer_to_url: governess6511 at plantontology.org send_feedback: governess6511 at plantontology.org Clear: governess6511 at plantontology.org comments: governess6511 at plantontology.org organization: governess6511 at plantontology.org email: governess6511 at plantontology.org name: plate Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Subject: for my happiness bcc: bob at mdserious.com 93f02aecf9277b901b7bb432cec07efb . From feedback_submission at filetta.cshl.edu Fri Feb 10 11:02:14 2006 From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu) Date: Fri, 10 Feb 2006 11:02:14 -0500 Subject: Feedback on POC Message-ID: <200602101602.k1AG2EhD023581@filetta.cshl.org> *** Feedback from Plant Ontology Live Site *** refer_to_url: th1671 at plantontology.org send_feedback: th1671 at plantontology.org Clear: th1671 at plantontology.org comments: th1671 at plantontology.org organization: any Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Subject: of contemplation. he winter was bcc: bob at mdserious.com 8022ebd89ada90357bda0643ad3d955e . email: th1671 at plantontology.org name: th1671 at plantontology.org From pj37 at cornell.edu Tue Feb 14 09:39:31 2006 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 14 Feb 2006 09:39:31 -0500 Subject: new term: carpel anlagen Message-ID: <43F1EBA3.6080504@cornell.edu> I need a new term to describe expression of DL gene in rice. The term is carpel anlagen. definition: A presumptive region (carpel anlagen) on the floral meristem, where carpel primordia would initiate. ref: PMID: 14729915 Here is the cited text from Yamaguchi et al, Plant Cell 16:500-509 (2004) The YABBY Gene DROOPING LEAF Regulates Carpel Specification and Midrib Development in Oryza sativa http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=14729915&dopt=Abstract 'DL expression was detected first in a few cells in the flower meristem at the lemma side (Figure 4E) and then in cells at the flank of the meristem (Figure 4F). These DL expression domains corresponded to the presumptive region (carpel anlagen), where carpel primordia would initiate. Shortly after this expression, carpel primordia began to form. At this stage, DL was expressed specifically and uniformly in carpel primordia (Figures 4G to 4I). No expression was detected in the flower meristem (Figures 4E and 4F) or the ovule primordium (Figures 4G to 4I). By contrast, expression of DL was not observed in dl-sup1 mutants throughout flower development (data not shown). Thus, the expression domains of DL are restricted to the carpel anlagen and the carpel primordia, and these expression patterns of DL are consistent with its specific role in carpel development.' -- 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 katica at acoma.Stanford.EDU Tue Feb 14 10:16:26 2006 From: katica at acoma.Stanford.EDU (katica at acoma.Stanford.EDU) Date: Tue, 14 Feb 2006 07:16:26 -0800 (PST) Subject: new term: carpel anlagen In-Reply-To: <43F1EBA3.6080504@cornell.edu> References: <43F1EBA3.6080504@cornell.edu> Message-ID: Pankaj, I must admit, never heard of 'carpel anlagen', but how is this different from 'carpel primordium'? Isn't 'primordium' what 'analgen' means ? (just looking at Merriam Webster on-line) Katica On Tue, 14 Feb 2006, Pankaj Jaiswal wrote: > > I need a new term to describe expression of DL gene in rice. The term is > carpel anlagen. > > definition: A presumptive region (carpel anlagen) on the floral meristem, > where carpel primordia would initiate. > ref: PMID: 14729915 > > > Here is the cited text from > Yamaguchi et al, Plant Cell 16:500-509 (2004) > The YABBY Gene DROOPING LEAF Regulates Carpel Specification and Midrib > Development in Oryza sativa > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=14729915&dopt=Abstract > > 'DL expression was detected first in a few cells in the flower meristem at > the lemma side (Figure 4E) and then in cells at the flank of the meristem > (Figure 4F). These DL expression domains corresponded to the presumptive > region (carpel anlagen), where carpel primordia would initiate. Shortly after > this expression, carpel primordia began to form. At this stage, DL was > expressed specifically and uniformly in carpel primordia (Figures 4G to 4I). > No expression was detected in the flower meristem (Figures 4E and 4F) or the > ovule primordium (Figures 4G to 4I). By contrast, expression of DL was not > observed in dl-sup1 mutants throughout flower development (data not shown). > Thus, the expression domains of DL are restricted to the carpel anlagen and > the carpel primordia, and these expression patterns of DL are consistent with > its specific role in carpel development.' > > > -- -------------------------------------------------------------------------- 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 Tue Feb 14 10:43:24 2006 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 14 Feb 2006 10:43:24 -0500 Subject: new term: carpel anlagen In-Reply-To: References: <43F1EBA3.6080504@cornell.edu> Message-ID: <43F1FA9C.2060206@cornell.edu> I am not an expert on this. Therefore please read the text from the citation below. Carpel anlagen is a presumptive region. Primordium comes after the anlagen is recognized in terms of development. as far as definition of anlagen is concerned take a look at this Of German origin the term anlagen refers to any group of relatively undifferentiated cells that is destined to become a particular group of differentiated cells at a later time in development. It is used to identify distinct cell groups in fly development and also in vertebrate development for example the "optic anlagen" is the group of cells that will become the eye in many vertebrates. The term is related to fatemaps, defined cell lineages, and differentiation. www.smbs.buffalo.edu/bch/Courses/bch512/definitions2.htm Pankaj katica at acoma.stanford.edu wrote: > > Pankaj, > > I must admit, never heard of 'carpel anlagen', but how is this different > from 'carpel primordium'? > > Isn't 'primordium' what 'analgen' means ? (just looking at Merriam > Webster on-line) > > Katica > > On Tue, 14 Feb 2006, Pankaj Jaiswal wrote: > >> >> I need a new term to describe expression of DL gene in rice. The term >> is carpel anlagen. >> >> definition: A presumptive region (carpel anlagen) on the floral >> meristem, where carpel primordia would initiate. >> ref: PMID: 14729915 >> >> >> Here is the cited text from >> Yamaguchi et al, Plant Cell 16:500-509 (2004) >> The YABBY Gene DROOPING LEAF Regulates Carpel Specification and Midrib >> Development in Oryza sativa >> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=14729915&dopt=Abstract >> >> >> 'DL expression was detected first in a few cells in the flower >> meristem at the lemma side (Figure 4E) and then in cells at the flank >> of the meristem (Figure 4F). These DL expression domains corresponded >> to the presumptive region (carpel anlagen), where carpel primordia >> would initiate. Shortly after this expression, carpel primordia began >> to form. At this stage, DL was expressed specifically and uniformly in >> carpel primordia (Figures 4G to 4I). No expression was detected in the >> flower meristem (Figures 4E and 4F) or the ovule primordium (Figures >> 4G to 4I). By contrast, expression of DL was not observed in dl-sup1 >> mutants throughout flower development (data not shown). Thus, the >> expression domains of DL are restricted to the carpel anlagen and the >> carpel primordia, and these expression patterns of DL are consistent >> with its specific role in carpel development.' >> >> >> > -- 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 felipe.zapata at umsl.edu Tue Feb 14 11:17:23 2006 From: felipe.zapata at umsl.edu (Felipe Zapata) Date: Tue, 14 Feb 2006 10:17:23 -0600 Subject: new term: carpel anlagen In-Reply-To: <43F1FA9C.2060206@cornell.edu> References: <43F1EBA3.6080504@cornell.edu> <43F1FA9C.2060206@cornell.edu> Message-ID: <900F8757-09DE-47F9-846E-704D4BED7979@umsl.edu> Not an expert either, but from the definition Pankaj suggests it is not too clear to me what exactly an anlagen is. Isn't it just a primordium?? also a group of undifferentiated cells that later become differentiated can be anything...(at least to me). The group of cells that will become the eye isn't just the eye primordium?? Pankaj suggests a temporal difference between anlagen and primordium, isn't it just a delusion? F On Feb 14, 2006, at 9:43 AM, Pankaj Jaiswal wrote: > I am not an expert on this. Therefore please read the text from the > citation below. Carpel anlagen is a presumptive region. Primordium > comes after the anlagen is recognized in terms of development. > > > as far as definition of anlagen is concerned take a look at this > > Of German origin the term anlagen refers to any group of relatively > undifferentiated cells that is destined to become a particular > group of differentiated cells at a later time in development. It is > used to identify distinct cell groups in fly development and also > in vertebrate development for example the "optic anlagen" is the > group of cells that will become the eye in many vertebrates. The > term is related to fatemaps, defined cell lineages, and > differentiation. > www.smbs.buffalo.edu/bch/Courses/bch512/definitions2.htm > > Pankaj > > katica at acoma.stanford.edu wrote: > >> Pankaj, >> I must admit, never heard of 'carpel anlagen', but how is this >> different from 'carpel primordium'? >> Isn't 'primordium' what 'analgen' means ? (just looking at Merriam >> Webster on-line) >> Katica >> On Tue, 14 Feb 2006, Pankaj Jaiswal wrote: >>> >>> I need a new term to describe expression of DL gene in rice. The >>> term is carpel anlagen. >>> >>> definition: A presumptive region (carpel anlagen) on the floral >>> meristem, where carpel primordia would initiate. >>> ref: PMID: 14729915 >>> >>> >>> Here is the cited text from >>> Yamaguchi et al, Plant Cell 16:500-509 (2004) >>> The YABBY Gene DROOPING LEAF Regulates Carpel Specification and >>> Midrib Development in Oryza sativa >>> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi? >>> cmd=Retrieve&db=PubMed&list_uids=14729915&dopt=Abstract >>> >>> 'DL expression was detected first in a few cells in the flower >>> meristem at the lemma side (Figure 4E) and then in cells at the >>> flank of the meristem (Figure 4F). These DL expression domains >>> corresponded to the presumptive region (carpel anlagen), where >>> carpel primordia would initiate. Shortly after this expression, >>> carpel primordia began to form. At this stage, DL was expressed >>> specifically and uniformly in carpel primordia (Figures 4G to >>> 4I). No expression was detected in the flower meristem (Figures >>> 4E and 4F) or the ovule primordium (Figures 4G to 4I). By >>> contrast, expression of DL was not observed in dl-sup1 mutants >>> throughout flower development (data not shown). Thus, the >>> expression domains of DL are restricted to the carpel anlagen and >>> the carpel primordia, and these expression patterns of DL are >>> consistent with its specific role in carpel development.' >>> >>> >>> > > > -- > 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 > .............. Felipe Zapata Department of Biology University of Missouri St. Louis One University Boulevard St. Louis, MO 63121 USA p.314.516.7997 f.314.516.7997 -------------- next part -------------- An HTML attachment was scrubbed... URL: From pj37 at cornell.edu Tue Feb 14 11:24:02 2006 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 14 Feb 2006 11:24:02 -0500 Subject: new term: carpel anlagen In-Reply-To: <900F8757-09DE-47F9-846E-704D4BED7979@umsl.edu> References: <43F1EBA3.6080504@cornell.edu> <43F1FA9C.2060206@cornell.edu> <900F8757-09DE-47F9-846E-704D4BED7979@umsl.edu> Message-ID: <43F20422.4090703@cornell.edu> All I request is a term to annotate the DL gene's expression. Definition can be modified based on your expert opinions. I am sure people will be searching for 'carpel anlagen' after reading this paper. So the best would be include these authors in your discussion, since they used it. Pankaj Felipe Zapata wrote: > Not an expert either, but from the definition Pankaj suggests it is not > too clear to me what exactly an anlagen is. Isn't it just a primordium?? > also a group of undifferentiated cells that later become differentiated > can be anything...(at least to me). The group of cells that will become > the eye isn't just the eye primordium?? Pankaj suggests a > temporal difference between anlagen and primordium, isn't it just a > delusion? > > F > > On Feb 14, 2006, at 9:43 AM, Pankaj Jaiswal wrote: > >> I am not an expert on this. Therefore please read the text from the >> citation below. Carpel anlagen is a presumptive region. Primordium >> comes after the anlagen is recognized in terms of development. >> >> >> as far as definition of anlagen is concerned take a look at this >> >> Of German origin the term anlagen refers to any group of relatively >> undifferentiated cells that is destined to become a particular group >> of differentiated cells at a later time in development. It is used to >> identify distinct cell groups in fly development and also in >> vertebrate development for example the "optic anlagen" is the group of >> cells that will become the eye in many vertebrates. The term is >> related to fatemaps, defined cell lineages, and differentiation. >> www.smbs.buffalo.edu/bch/Courses/bch512/definitions2.htm >> >> Pankaj >> >> katica at acoma.stanford.edu wrote: >> >>> Pankaj, >>> I must admit, never heard of 'carpel anlagen', but how is this >>> different from 'carpel primordium'? >>> Isn't 'primordium' what 'analgen' means ? (just looking at Merriam >>> Webster on-line) >>> Katica >>> On Tue, 14 Feb 2006, Pankaj Jaiswal wrote: >>> >>>> >>>> I need a new term to describe expression of DL gene in rice. The >>>> term is carpel anlagen. >>>> >>>> definition: A presumptive region (carpel anlagen) on the floral >>>> meristem, where carpel primordia would initiate. >>>> ref: PMID: 14729915 >>>> >>>> >>>> Here is the cited text from >>>> Yamaguchi et al, Plant Cell 16:500-509 (2004) >>>> The YABBY Gene DROOPING LEAF Regulates Carpel Specification and >>>> Midrib Development in Oryza sativa >>>> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=14729915&dopt=Abstract >>>> >>>> >>>> 'DL expression was detected first in a few cells in the flower >>>> meristem at the lemma side (Figure 4E) and then in cells at the >>>> flank of the meristem (Figure 4F). These DL expression domains >>>> corresponded to the presumptive region (carpel anlagen), where >>>> carpel primordia would initiate. Shortly after this expression, >>>> carpel primordia began to form. At this stage, DL was expressed >>>> specifically and uniformly in carpel primordia (Figures 4G to 4I). >>>> No expression was detected in the flower meristem (Figures 4E and >>>> 4F) or the ovule primordium (Figures 4G to 4I). By contrast, >>>> expression of DL was not observed in dl-sup1 mutants throughout >>>> flower development (data not shown). Thus, the expression domains of >>>> DL are restricted to the carpel anlagen and the carpel primordia, >>>> and these expression patterns of DL are consistent with its specific >>>> role in carpel development.' >>>> >>>> From Felipe.Zapata at umsl.edu Tue Feb 14 11:30:58 2006 From: Felipe.Zapata at umsl.edu (Zapata, Felipe (UMSL-Student)) Date: Tue, 14 Feb 2006 10:30:58 -0600 Subject: new term: carpel anlagen Message-ID: <669A61CC5E816A4FA6A3EA4FAF22C09910E521@stl-mail6.stl.umsl.edu> Can I then ask again what is the rationale for new terms?? are there any rules in POC documentation?? F -----Original Message----- From: owner-po-dev at plantontology.org on behalf of Pankaj Jaiswal Sent: Tue 2/14/2006 10:24 AM Cc: po-dev at plantontology.org Subject: Re: new term: carpel anlagen All I request is a term to annotate the DL gene's expression. Definition can be modified based on your expert opinions. I am sure people will be searching for 'carpel anlagen' after reading this paper. So the best would be include these authors in your discussion, since they used it. Pankaj Felipe Zapata wrote: > Not an expert either, but from the definition Pankaj suggests it is not > too clear to me what exactly an anlagen is. Isn't it just a primordium?? > also a group of undifferentiated cells that later become differentiated > can be anything...(at least to me). The group of cells that will become > the eye isn't just the eye primordium?? Pankaj suggests a > temporal difference between anlagen and primordium, isn't it just a > delusion? > > F > > On Feb 14, 2006, at 9:43 AM, Pankaj Jaiswal wrote: > >> I am not an expert on this. Therefore please read the text from the >> citation below. Carpel anlagen is a presumptive region. Primordium >> comes after the anlagen is recognized in terms of development. >> >> >> as far as definition of anlagen is concerned take a look at this >> >> Of German origin the term anlagen refers to any group of relatively >> undifferentiated cells that is destined to become a particular group >> of differentiated cells at a later time in development. It is used to >> identify distinct cell groups in fly development and also in >> vertebrate development for example the "optic anlagen" is the group of >> cells that will become the eye in many vertebrates. The term is >> related to fatemaps, defined cell lineages, and differentiation. >> www.smbs.buffalo.edu/bch/Courses/bch512/definitions2.htm >> >> Pankaj >> >> katica at acoma.stanford.edu wrote: >> >>> Pankaj, >>> I must admit, never heard of 'carpel anlagen', but how is this >>> different from 'carpel primordium'? >>> Isn't 'primordium' what 'analgen' means ? (just looking at Merriam >>> Webster on-line) >>> Katica >>> On Tue, 14 Feb 2006, Pankaj Jaiswal wrote: >>> >>>> >>>> I need a new term to describe expression of DL gene in rice. The >>>> term is carpel anlagen. >>>> >>>> definition: A presumptive region (carpel anlagen) on the floral >>>> meristem, where carpel primordia would initiate. >>>> ref: PMID: 14729915 >>>> >>>> >>>> Here is the cited text from >>>> Yamaguchi et al, Plant Cell 16:500-509 (2004) >>>> The YABBY Gene DROOPING LEAF Regulates Carpel Specification and >>>> Midrib Development in Oryza sativa >>>> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=14729915&dopt=Abstract >>>> >>>> >>>> 'DL expression was detected first in a few cells in the flower >>>> meristem at the lemma side (Figure 4E) and then in cells at the >>>> flank of the meristem (Figure 4F). These DL expression domains >>>> corresponded to the presumptive region (carpel anlagen), where >>>> carpel primordia would initiate. Shortly after this expression, >>>> carpel primordia began to form. At this stage, DL was expressed >>>> specifically and uniformly in carpel primordia (Figures 4G to 4I). >>>> No expression was detected in the flower meristem (Figures 4E and >>>> 4F) or the ovule primordium (Figures 4G to 4I). By contrast, >>>> expression of DL was not observed in dl-sup1 mutants throughout >>>> flower development (data not shown). Thus, the expression domains of >>>> DL are restricted to the carpel anlagen and the carpel primordia, >>>> and these expression patterns of DL are consistent with its specific >>>> role in carpel development.' >>>> >>>> -------------- next part -------------- A non-text attachment was scrubbed... Name: winmail.dat Type: application/ms-tnef Size: 4457 bytes Desc: not available URL: From kellogge at msx.umsl.edu Tue Feb 14 13:59:29 2006 From: kellogge at msx.umsl.edu (kellogge) Date: Tue, 14 Feb 2006 12:59:29 -0600 Subject: new term: carpel anlagen In-Reply-To: <43F20422.4090703@cornell.edu> References: <43F1EBA3.6080504@cornell.edu> <43F1FA9C.2060206@cornell.edu> <900F8757-09DE-47F9-846E-704D4BED7979@umsl.edu> <43F20422.4090703@cornell.edu> Message-ID: <61bc9276ad0ccd2f43d8e394be3d4b6b@msx.umsl.edu> We actually had this discussion when we were working on the growth stages, when we were considering P0 stage. The anlagen are the first few cells that have acquired the identity of a particular structure, so the carpel anlagen will be a handful of cells that ultimately will divide and form a visible primordium. This is completely parallel to PO:0001003, formation of leaf founder cells. I would think that in terms of plant structure, DL should simply be annotated to carpel, and then we may need to define an early developmental stage for carpels in the development ontology. Toby On Feb 14, 2006, at 10:24 AM, Pankaj Jaiswal wrote: > All I request is a term to annotate the DL gene's expression. > Definition can be modified based on your expert opinions. I am sure > people will be searching for 'carpel anlagen' after reading this > paper. So the best would be include these authors in your discussion, > since they used it. > > Pankaj > > Felipe Zapata wrote: > >> Not an expert either, but from the definition Pankaj suggests it is >> not too clear to me what exactly an anlagen is. Isn't it just a >> primordium?? also a group of undifferentiated cells that later become >> differentiated can be anything...(at least to me). The group of >> cells that will become the eye isn't just the eye primordium?? >> Pankaj suggests a temporal difference between anlagen and primordium, >> isn't it just a delusion? >> F On Feb 14, 2006, at 9:43 AM, Pankaj Jaiswal wrote: >>> I am not an expert on this. Therefore please read the text from the >>> citation below. Carpel anlagen is a presumptive region. Primordium >>> comes after the anlagen is recognized in terms of development. >>> >>> >>> as far as definition of anlagen is concerned take a look at this >>> >>> Of German origin the term anlagen refers to any group of relatively >>> undifferentiated cells that is destined to become a particular group >>> of differentiated cells at a later time in development. It is used >>> to identify distinct cell groups in fly development and also in >>> vertebrate development for example the "optic anlagen" is the group >>> of cells that will become the eye in many vertebrates. The term is >>> related to fatemaps, defined cell lineages, and differentiation. >>> www.smbs.buffalo.edu/bch/Courses/bch512/definitions2.htm >>> >>> Pankaj >>> >>> katica at acoma.stanford.edu wrote: >>> >>>> Pankaj, >>>> I must admit, never heard of 'carpel anlagen', but how is this >>>> different from 'carpel primordium'? >>>> Isn't 'primordium' what 'analgen' means ? (just looking at Merriam >>>> Webster on-line) >>>> Katica >>>> On Tue, 14 Feb 2006, Pankaj Jaiswal wrote: >>>> >>>>> >>>>> I need a new term to describe expression of DL gene in rice. The >>>>> term is carpel anlagen. >>>>> >>>>> definition: A presumptive region (carpel anlagen) on the floral >>>>> meristem, where carpel primordia would initiate. >>>>> ref: PMID: 14729915 >>>>> >>>>> >>>>> Here is the cited text from >>>>> Yamaguchi et al, Plant Cell 16:500-509 (2004) >>>>> The YABBY Gene DROOPING LEAF Regulates Carpel Specification and >>>>> Midrib Development in Oryza sativa >>>>> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi? >>>>> cmd=Retrieve&db=PubMed&list_uids=14729915&dopt=Abstract >>>>> >>>> cmd=Retrieve&db=PubMed&list_uids=14729915&dopt=Abstract> >>>>> 'DL expression was detected first in a few cells in the flower >>>>> meristem at the lemma side (Figure 4E) and then in cells at the >>>>> flank of the meristem (Figure 4F). These DL expression domains >>>>> corresponded to the presumptive region (carpel anlagen), where >>>>> carpel primordia would initiate. Shortly after this expression, >>>>> carpel primordia began to form. At this stage, DL was expressed >>>>> specifically and uniformly in carpel primordia (Figures 4G to 4I). >>>>> No expression was detected in the flower meristem (Figures 4E and >>>>> 4F) or the ovule primordium (Figures 4G to 4I). By contrast, >>>>> expression of DL was not observed in dl-sup1 mutants throughout >>>>> flower development (data not shown). Thus, the expression domains >>>>> of DL are restricted to the carpel anlagen and the carpel >>>>> primordia, and these expression patterns of DL are consistent with >>>>> its specific role in carpel 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: 4415 bytes Desc: not available URL: From katica at acoma.Stanford.EDU Tue Feb 14 14:18:24 2006 From: katica at acoma.Stanford.EDU (katica at acoma.Stanford.EDU) Date: Tue, 14 Feb 2006 11:18:24 -0800 (PST) Subject: new term: carpel anlagen In-Reply-To: <61bc9276ad0ccd2f43d8e394be3d4b6b@msx.umsl.edu> References: <43F1EBA3.6080504@cornell.edu> <43F1FA9C.2060206@cornell.edu> <900F8757-09DE-47F9-846E-704D4BED7979@umsl.edu> <43F20422.4090703@cornell.edu> <61bc9276ad0ccd2f43d8e394be3d4b6b@msx.umsl.edu> Message-ID: I agree that this is developmental stage term, and, as far as structure ontology goes, this gene can be annotated to 'carpel primordium'. This term is currently not in PO, but should be added, we recently added several primordium terms, but this one skipped my attention. On one of recent ontology conf calls, we agreed to add remaining 'primordium' terms in the Plant Structure Ontology. Katica On Tue, 14 Feb 2006, kellogge wrote: > We actually had this discussion when we were working on the growth stages, > when we were considering P0 stage. The anlagen are the first few cells that > have acquired the identity of a particular structure, so the carpel anlagen > will be a handful of cells that ultimately will divide and form a visible > primordium. This is completely parallel to PO:0001003, formation of leaf > founder cells. I would think that in terms of plant structure, DL should > simply be annotated to carpel, and then we may need to define an early > developmental stage for carpels in the development ontology. > Toby > > On Feb 14, 2006, at 10:24 AM, Pankaj Jaiswal wrote: > >> All I request is a term to annotate the DL gene's expression. Definition >> can be modified based on your expert opinions. I am sure people will be >> searching for 'carpel anlagen' after reading this paper. So the best would >> be include these authors in your discussion, since they used it. >> >> Pankaj >> >> Felipe Zapata wrote: >> >>> Not an expert either, but from the definition Pankaj suggests it is not >>> too clear to me what exactly an anlagen is. Isn't it just a primordium?? >>> also a group of undifferentiated cells that later become differentiated >>> can be anything...(at least to me). The group of cells that will become >>> the eye isn't just the eye primordium?? Pankaj suggests a temporal >>> difference between anlagen and primordium, isn't it just a delusion? >>> F On Feb 14, 2006, at 9:43 AM, Pankaj Jaiswal wrote: >>>> I am not an expert on this. Therefore please read the text from the >>>> citation below. Carpel anlagen is a presumptive region. Primordium comes >>>> after the anlagen is recognized in terms of development. >>>> >>>> >>>> as far as definition of anlagen is concerned take a look at this >>>> >>>> Of German origin the term anlagen refers to any group of relatively >>>> undifferentiated cells that is destined to become a particular group of >>>> differentiated cells at a later time in development. It is used to >>>> identify distinct cell groups in fly development and also in vertebrate >>>> development for example the "optic anlagen" is the group of cells that >>>> will become the eye in many vertebrates. The term is related to fatemaps, >>>> defined cell lineages, and differentiation. >>>> www.smbs.buffalo.edu/bch/Courses/bch512/definitions2.htm >>>> >>>> Pankaj >>>> >>>> katica at acoma.stanford.edu wrote: >>>> >>>>> Pankaj, >>>>> I must admit, never heard of 'carpel anlagen', but how is this different >>>>> from 'carpel primordium'? >>>>> Isn't 'primordium' what 'analgen' means ? (just looking at Merriam >>>>> Webster on-line) >>>>> Katica >>>>> On Tue, 14 Feb 2006, Pankaj Jaiswal wrote: >>>>> >>>>>> >>>>>> I need a new term to describe expression of DL gene in rice. The term >>>>>> is carpel anlagen. >>>>>> >>>>>> definition: A presumptive region (carpel anlagen) on the floral >>>>>> meristem, where carpel primordia would initiate. >>>>>> ref: PMID: 14729915 >>>>>> >>>>>> >>>>>> Here is the cited text from >>>>>> Yamaguchi et al, Plant Cell 16:500-509 (2004) >>>>>> The YABBY Gene DROOPING LEAF Regulates Carpel Specification and Midrib >>>>>> Development in Oryza sativa >>>>>> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi? >>>>>> cmd=Retrieve&db=PubMed&list_uids=14729915&dopt=Abstract >>>>>> >>>>> cmd=Retrieve&db=PubMed&list_uids=14729915&dopt=Abstract> >>>>>> 'DL expression was detected first in a few cells in the flower meristem >>>>>> at the lemma side (Figure 4E) and then in cells at the flank of the >>>>>> meristem (Figure 4F). These DL expression domains corresponded to the >>>>>> presumptive region (carpel anlagen), where carpel primordia would >>>>>> initiate. Shortly after this expression, carpel primordia began to >>>>>> form. At this stage, DL was expressed specifically and uniformly in >>>>>> carpel primordia (Figures 4G to 4I). No expression was detected in the >>>>>> flower meristem (Figures 4E and 4F) or the ovule primordium (Figures 4G >>>>>> to 4I). By contrast, expression of DL was not observed in dl-sup1 >>>>>> mutants throughout flower development (data not shown). Thus, the >>>>>> expression domains of DL are restricted to the carpel anlagen and the >>>>>> carpel primordia, and these expression patterns of DL are consistent >>>>>> with its specific role in carpel 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/ > -- -------------------------------------------------------------------------- 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 Sat Feb 18 00:20:54 2006 From: jitterbug at plantontology.org (Katica Ilic) Date: Sat, 18 Feb 2006 00:20:54 -0500 Subject: plant organ question (fwd) (PR#314) Message-ID: <200602180521.k1I5KsCm004977@brie4.cshl.org> Dear Sophie, I apologize for delayed reply. Following your request, we added two new terms in the PO, 'short shoot' and 'long shoot' under the 'shoot' node. Please note that 'bud spur is synonym of 'short shoot'. These new terms appear in the following lineage: PO:0009006 shoot (i) PO:0004545 shoot borne shoot (i) PO:0006343 axillary shoot (i) PO:0004702 long shoot (i) PO:0004701 short shoot short shoot (PO:0004701) Def: Shoot in which the internodes elongate little or at all, bearing reproductive structures and/or leaves. Synonyms: brachyblast, bud spur long shoot (PO:0004702) Def: Shoot in which all or most of the internodes elongate. As for your request for term 'vegetative bud', we don't have such term in the PO, and such term could be either plant structure term or a growth stage term. The ontology group will discuss it on the next meeting and I will get beck to you moth more details. Please note that POC monthly ontology release is coming up next week, and you could see these new terms in the AmiGO browser after this release. I hope this helps. Please feel free to contact me with any additional questions you may have. Sincerely, Katica Ilic, POC Project Coordinator > ---------- Forwarded message ---------- > Date: Wed, 25 Jan 2006 10:44:09 +0200 > From: Sophie Tanny > Reply-To: po-dev at plantontology.org, Sophie Tanny > To: po at plantontology.org > Subject: plant organ question > > 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 feedback_submission at filetta.cshl.edu Mon Feb 6 21:01:12 2006 From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu) Date: Mon, 6 Feb 2006 21:01:12 -0500 Subject: Feedback on POC Message-ID: <200602070201.k1721Cmh006057@filetta.cshl.org> *** Feedback from Plant Ontology Live Site *** refer_to_url: an5868 at plantontology.org name: an5868 at plantontology.org Clear: an5868 at plantontology.org comments: a Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Subject: here. here was in bcc: charleses3229 at aol.com 94a022604efc1f5f5a7d756ff422d5d9 . organization: an5868 at plantontology.org email: an5868 at plantontology.org send_feedback: an5868 at plantontology.org