From Leszek at missouri.edu Thu May 3 16:38:21 2007 From: Leszek at missouri.edu (Vincent, Leszek) Date: Thu, 3 May 2007 15:38:21 -0500 Subject: stylar ridge vs stylar ridge (abortive)? In-Reply-To: <40891CFF-21B4-4F75-81C2-87677B130793@cornell.edu> References: <40891CFF-21B4-4F75-81C2-87677B130793@cornell.edu> Message-ID: <2BC371D49E5C86418135172EE7C130370193E865@UM-XMAIL08.um.umsystem.edu> Hi Chih-Wei, Please see my comments below in green. 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 Plant Systematist Associate Curator, Dunn-Palmer Herbarium (UMO); Research Associate, Missouri Botanical Garden (MO), USA; *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* ________________________________ From: Chih-Wei Tung [mailto:cwt6 at cornell.edu] Sent: Wednesday, April 25, 2007 12:35 PM To: Vincent, Leszek Cc: Schaeffer, Mary L. Subject: stylar ridge vs stylar ridge (abortive)? Importance: High Hi Leszek, Mary Schaeffer requested several anatomical terms which are currently missing in PO but presented in MaizeGDB at this time, as seen here: stylar ridge of lower floret of pedicellate spikelet of ear stylar ridge of lower floret of sessile spikelet of ear stylar ridge of upper floret of pedicellate spikelet of ear stylar ridge of upper floret of sessile spikelet of ear Initially, I was thinking to place these four terms as child terms [part of] of followings respectively, # PO:0006424 : gynoecium of lower floret of pedicellate spikelet of ear ( 0 ) # PO:0006423 : gynoecium of lower floret of sessile spikelet of ear ( 0 ) # PO:0006426 : gynoecium of upper floret of pedicellate spikelet of ear ( 0 ) # PO:0006425 : gynoecium of upper floret of sessile spikelet of ear ( 0 ) but now I am little bit confused after seeing the following terms in Zea ontology, term: stylar ridge (abortive) of lower floret of pedicellate spikelet of ear id: ZEA:0015102 definition: The gynoecium development of the lower floret begins with the production of a ridge on the abaxial surface of the apical meristem of the floret, distal to the third stamen (which later degenerates). This is the stylar ridge. While the development of this stylar ridge is very similar to that of the upper florets, the development does not proceed beyond the early ridge stage. term: stylar ridge of upper floret of pedicellate spikelet of ear id: ZEA:0015101 definition: The gynoecium development of the upper floret begins with the production of a ridge on the abaxial surface of the apical meristem of the floret, distal to the third stamen (which later degenerates). This is the stylar ridge. Continued overgrowth of the shoot apex (which becomes the ovule primordium) by the ring of stylar tissue leads to the formation of the stylar canal, which is detected as a slight protruberance on the mature ovary. My question is that the four terms Mary requested are not abortive through ear development, right? are they still present in the mature ovary? XX This structure, when aborted, is not present in the mature ovary. The entire floret/flower aborts leaving just vestiges of its presence in the spikelet. The reason I asked is that we have " PO:0009078 : pistillode: A sterile pistil, often rudimentary", I am wondering if these 4 terms would be placed as child of "pistillode" as well? XX I would not suggest you also using the term pistillode as that structure is typically present on non-aborted gynoecia, implying that much of the rest of the flower structure is present. In the case of Zea this is not the case. - Leszek Sorry for the long email, Thanks, Chih-Wei -------------- next part -------------- An HTML attachment was scrubbed... URL: From cjm at fruitfly.org Fri May 4 21:42:01 2007 From: cjm at fruitfly.org (Chris Mungall) Date: Fri, 4 May 2007 18:42:01 -0700 Subject: EO annotations + plants in space Message-ID: <71C67519-E317-4D48-B52B-571558DA9778@fruitfly.org> Hi all Where can I download EO annotations? They don't seem to be available from the downloads page without resorting to SQL dumps. Have you considered making these available using the GO annotation format (perhaps a generalized form of)? How should I interpret annotations such as this: http://www.gramene.org/db/genes/search_gene?acc=GR:0101182 From the report it doesn't look as if the environments and the traits are explicitly linked. Is this the case? This is one of my favourite OBO terms: http://www.gramene.org/db/ontology/search_term?id=EO:0007315 "The treatment involving use of gravity factor to study various types of responses in the absence of gravity or space like conditions." Unfortunately there are no annotations to it :-( Now I read more closely I see that this term can also be used to annotated space-like conditions on earth. But there are experiments on plants in space aren't there? http://arjournals.annualreviews.org/doi/citedby/10.1146/annurev.pp. 38.060187.001533?cookieSet=1 http://exploration.nasa.gov/programs/station/PESTO_lite.html It's probably not high in your priority queue but I think it would be kind of cool if there was at least one annotation here.. I'll buy a drink for whoever creates the first non-Earthbound OBO annotation! George, are there mouse in space experiments? Not being a plant scientists I can't claim this would help in my research in any way - however, I do have a genuine ontological use case. At the moment, PATO and the Units ontology exhibit a bit of confusion over the weight-mass distinction. As the majority of biology so far discovered happens on earth which has a reasonably constant enough gravity, it may seem overly fussy to insist on a clear distinction. However, I think that there may be practical cases where the confusion could cause problems, such as in interpreting PATO annotations in the context of EO:0007315. Also when mapping TO terms to PATO+PO logical definitions, I had been using PATO:0000128 (weight) for terms like TO:0000181 (seed weight), but I think the actual quality is seed mass is it not? So we should be using PATO:0000125 (mass). If I was really fussy I'd insist on a distinction between apparent weight and weight.. but I'm not. Cheers Chris From pj37 at cornell.edu Sat May 5 07:40:41 2007 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Sat, 05 May 2007 07:40:41 -0400 Subject: EO annotations + plants in space In-Reply-To: <71C67519-E317-4D48-B52B-571558DA9778@fruitfly.org> References: <71C67519-E317-4D48-B52B-571558DA9778@fruitfly.org> Message-ID: <463C6D39.3080608@cornell.edu> download from here. more later http://www.gramene.org/db/ontology/association_report?id=EO:0007359 Chris Mungall wrote: > Hi all > > Where can I download EO annotations? They don't seem to be available > from the downloads page without resorting to SQL dumps. Have you > considered making these available using the GO annotation format > (perhaps a generalized form of)? > > How should I interpret annotations such as this: > http://www.gramene.org/db/genes/search_gene?acc=GR:0101182 > > From the report it doesn't look as if the environments and the traits > are explicitly linked. Is this the case? > > This is one of my favourite OBO terms: > http://www.gramene.org/db/ontology/search_term?id=EO:0007315 > > "The treatment involving use of gravity factor to study various types > of responses in the absence of gravity or space like conditions." > > Unfortunately there are no annotations to it :-( > > Now I read more closely I see that this term can also be used to > annotated space-like conditions on earth. But there are experiments on > plants in space aren't there? > > http://arjournals.annualreviews.org/doi/citedby/10.1146/annurev.pp. > 38.060187.001533?cookieSet=1 > http://exploration.nasa.gov/programs/station/PESTO_lite.html > > It's probably not high in your priority queue but I think it would be > kind of cool if there was at least one annotation here.. I'll buy a > drink for whoever creates the first non-Earthbound OBO annotation! > > George, are there mouse in space experiments? > > Not being a plant scientists I can't claim this would help in my > research in any way - however, I do have a genuine ontological use > case. At the moment, PATO and the Units ontology exhibit a bit of > confusion over the weight-mass distinction. As the majority of biology > so far discovered happens on earth which has a reasonably constant > enough gravity, it may seem overly fussy to insist on a clear > distinction. However, I think that there may be practical cases where > the confusion could cause problems, such as in interpreting PATO > annotations in the context of EO:0007315. > > Also when mapping TO terms to PATO+PO logical definitions, I had been > using PATO:0000128 (weight) for terms like TO:0000181 (seed weight), > but I think the actual quality is seed mass is it not? So we should be > using PATO:0000125 (mass). > > If I was really fussy I'd insist on a distinction between apparent > weight and weight.. but I'm not. > > Cheers > Chris > > From ware at cshl.edu Mon May 7 09:08:54 2007 From: ware at cshl.edu (Ware, Doreen) Date: Mon, 7 May 2007 09:08:54 -0400 Subject: EO annotations + plants in space In-Reply-To: <71C67519-E317-4D48-B52B-571558DA9778@fruitfly.org> References: <71C67519-E317-4D48-B52B-571558DA9778@fruitfly.org> Message-ID: <6F37486D54C31947A3B1414E6267043203402BC6@mailbox04.cshl.edu> Hi Chris, I had a colleague that sent arabidopsis on a shuttle trip, a few years back do you want me to see if they will do some annotations? dor -----Original Message----- From: owner-po-dev at plantontology.org [mailto:owner-po-dev at plantontology.org] On Behalf Of Chris Mungall Sent: Friday, May 04, 2007 9:42 PM To: gramene at gramene.org; Pankaj Jaiswal; po-dev at plantontology.org; Georgios V. Gkoutos (Genetics) Subject: EO annotations + plants in space Hi all Where can I download EO annotations? They don't seem to be available from the downloads page without resorting to SQL dumps. Have you considered making these available using the GO annotation format (perhaps a generalized form of)? How should I interpret annotations such as this: http://www.gramene.org/db/genes/search_gene?acc=GR:0101182 From the report it doesn't look as if the environments and the traits are explicitly linked. Is this the case? This is one of my favourite OBO terms: http://www.gramene.org/db/ontology/search_term?id=EO:0007315 "The treatment involving use of gravity factor to study various types of responses in the absence of gravity or space like conditions." Unfortunately there are no annotations to it :-( Now I read more closely I see that this term can also be used to annotated space-like conditions on earth. But there are experiments on plants in space aren't there? http://arjournals.annualreviews.org/doi/citedby/10.1146/annurev.pp. 38.060187.001533?cookieSet=1 http://exploration.nasa.gov/programs/station/PESTO_lite.html It's probably not high in your priority queue but I think it would be kind of cool if there was at least one annotation here.. I'll buy a drink for whoever creates the first non-Earthbound OBO annotation! George, are there mouse in space experiments? Not being a plant scientists I can't claim this would help in my research in any way - however, I do have a genuine ontological use case. At the moment, PATO and the Units ontology exhibit a bit of confusion over the weight-mass distinction. As the majority of biology so far discovered happens on earth which has a reasonably constant enough gravity, it may seem overly fussy to insist on a clear distinction. However, I think that there may be practical cases where the confusion could cause problems, such as in interpreting PATO annotations in the context of EO:0007315. Also when mapping TO terms to PATO+PO logical definitions, I had been using PATO:0000128 (weight) for terms like TO:0000181 (seed weight), but I think the actual quality is seed mass is it not? So we should be using PATO:0000125 (mass). If I was really fussy I'd insist on a distinction between apparent weight and weight.. but I'm not. Cheers Chris From gg295 at gen.cam.ac.uk Sat May 5 03:52:37 2007 From: gg295 at gen.cam.ac.uk (Georgios V. Gkoutos (Genetics)) Date: Sat, 5 May 2007 08:52:37 +0100 (BST) Subject: EO annotations + plants in space In-Reply-To: <71C67519-E317-4D48-B52B-571558DA9778@fruitfly.org> Message-ID: ------------------------------------------------------ On Fri, 4 May 2007, Chris Mungall wrote: > Hi all > > Where can I download EO annotations? They don't seem to be available > from the downloads page without resorting to SQL dumps. Have you > considered making these available using the GO annotation format > (perhaps a generalized form of)? > > How should I interpret annotations such as this: > http://www.gramene.org/db/genes/search_gene?acc=GR:0101182 > > From the report it doesn't look as if the environments and the > traits are explicitly linked. Is this the case? > > This is one of my favourite OBO terms: > http://www.gramene.org/db/ontology/search_term?id=EO:0007315 > > "The treatment involving use of gravity factor to study various types > of responses in the absence of gravity or space like conditions." > > Unfortunately there are no annotations to it :-( > > Now I read more closely I see that this term can also be used to > annotated space-like conditions on earth. But there are experiments > on plants in space aren't there? > > http://arjournals.annualreviews.org/doi/citedby/10.1146/annurev.pp. > 38.060187.001533?cookieSet=1 > http://exploration.nasa.gov/programs/station/PESTO_lite.html > > It's probably not high in your priority queue but I think it would be > kind of cool if there was at least one annotation here.. I'll buy a > drink for whoever creates the first non-Earthbound OBO annotation! > > George, are there mouse in space experiments? I bet there are - I haven't come accross such data but ..... > > Not being a plant scientists I can't claim this would help in my > research in any way - however, I do have a genuine ontological use > case. At the moment, PATO and the Units ontology exhibit a bit of > confusion over the weight-mass distinction. As the majority of > biology so far discovered happens on earth which has a reasonably > constant enough gravity, it may seem overly fussy to insist on a > clear distinction. However, I think that there may be practical cases > where the confusion could cause problems, such as in interpreting > PATO annotations in the context of EO:0007315. > > Also when mapping TO terms to PATO+PO logical definitions, I had been > using PATO:0000128 (weight) for terms like TO:0000181 (seed weight), > but I think the actual quality is seed mass is it not? So we should > be using PATO:0000125 (mass). > > If I was really fussy I'd insist on a distinction between apparent > weight and weight.. but I'm not. > > Cheers > Chris > > From cjm at fruitfly.org Wed May 9 23:36:30 2007 From: cjm at fruitfly.org (Chris Mungall) Date: Wed, 9 May 2007 20:36:30 -0700 Subject: EO annotations + plants in space In-Reply-To: <6F37486D54C31947A3B1414E6267043203402BC6@mailbox04.cshl.edu> References: <71C67519-E317-4D48-B52B-571558DA9778@fruitfly.org> <6F37486D54C31947A3B1414E6267043203402BC6@mailbox04.cshl.edu> Message-ID: Hi Doreen - good to see you the other day albeit briefly - I'm back in berkeley now, not staying for the conference like everyone else weed on a space shuttle - sounds like a good experiment seriously - I think it would be kind of cool for OBO to have those annotations On May 7, 2007, at 6:08 AM, Ware, Doreen wrote: > Hi Chris, > > I had a colleague that sent arabidopsis on a shuttle trip, a few years > back do you want me to see if they will do some annotations? > > dor > > -----Original Message----- > From: owner-po-dev at plantontology.org > [mailto:owner-po-dev at plantontology.org] On Behalf Of Chris Mungall > Sent: Friday, May 04, 2007 9:42 PM > To: gramene at gramene.org; Pankaj Jaiswal; po-dev at plantontology.org; > Georgios V. Gkoutos (Genetics) > Subject: EO annotations + plants in space > > Hi all > > Where can I download EO annotations? They don't seem to be available > from the downloads page without resorting to SQL dumps. Have you > considered making these available using the GO annotation format > (perhaps a generalized form of)? > > How should I interpret annotations such as this: > http://www.gramene.org/db/genes/search_gene?acc=GR:0101182 > > From the report it doesn't look as if the environments and the > traits are explicitly linked. Is this the case? > > This is one of my favourite OBO terms: > http://www.gramene.org/db/ontology/search_term?id=EO:0007315 > > "The treatment involving use of gravity factor to study various types > of responses in the absence of gravity or space like conditions." > > Unfortunately there are no annotations to it :-( > > Now I read more closely I see that this term can also be used to > annotated space-like conditions on earth. But there are experiments > on plants in space aren't there? > > http://arjournals.annualreviews.org/doi/citedby/10.1146/annurev.pp. > 38.060187.001533?cookieSet=1 > http://exploration.nasa.gov/programs/station/PESTO_lite.html > > It's probably not high in your priority queue but I think it would be > kind of cool if there was at least one annotation here.. I'll buy a > drink for whoever creates the first non-Earthbound OBO annotation! > > George, are there mouse in space experiments? > > Not being a plant scientists I can't claim this would help in my > research in any way - however, I do have a genuine ontological use > case. At the moment, PATO and the Units ontology exhibit a bit of > confusion over the weight-mass distinction. As the majority of > biology so far discovered happens on earth which has a reasonably > constant enough gravity, it may seem overly fussy to insist on a > clear distinction. However, I think that there may be practical cases > where the confusion could cause problems, such as in interpreting > PATO annotations in the context of EO:0007315. > > Also when mapping TO terms to PATO+PO logical definitions, I had been > using PATO:0000128 (weight) for terms like TO:0000181 (seed weight), > but I think the actual quality is seed mass is it not? So we should > be using PATO:0000125 (mass). > > If I was really fussy I'd insist on a distinction between apparent > weight and weight.. but I'm not. > > Cheers > Chris > > From tberardi at acoma.Stanford.EDU Tue May 29 17:14:05 2007 From: tberardi at acoma.Stanford.EDU (Tanya Berardini) Date: Tue, 29 May 2007 14:14:05 -0700 Subject: Problem with PO files Message-ID: <465C979D.8050408@acoma.stanford.edu> Dear PO folks, We've run into a problem that is causing our term loader to get confused. (1) From the po_temporal file: format-version: 1.0 version: $Revision: 1.31 $ date: 12:04:2007 10:30 saved-by: cwt6 auto-generated-by: DAG-Edit 1.419 rev 3 default-namespace: plant_ontology [Term] id: PO:0009012 name: plant growth and development stages namespace: plant_growth_and_development_stage def: "The succession of changes leading from the zygote to the mature plant. " [Poc:curators ""] synonym: "Arabidopsis growth" [TAIR:0000205] (2) From the po_anatomy file: format-version: 1.0 version: $Revision: 1.43 $ date: 01:05:2007 15:58 saved-by: cwt6 auto-generated-by: DAG-Edit 1.419 rev 3 default-namespace: plant_ontology subsetdef: Rice "Term used for rice" subsetdef: Maize "Term used for maize" subsetdef: Citrus "Term used for citrus" subsetdef: Tomato "Term used for tomato" subsetdef: Arabidopsis "Term used for Arabidopsis" subsetdef: Poaceae "Term used for grasses" subsetdef: reference "reference plant structure term" [Term] id: PO:0009012 name: petiole pulvinus namespace: plant_structure def: "Pulvinus of the petiole" [GR:cwt] is_a: PO:0009000 ! pulvinus relationship: part_of PO:0020038 ! petiole Because the same identifier (PO:0009012) is used for two different terms in two different ontologies, we are running into errors. Thanks very much for your help in resolving this. Tanya ------------------------------------------------------------------------------------------ Tanya Berardini, Ph.D. tberardi at acoma.stanford.edu The Arabidopsis Information Resource FAX: (650) 325-6857 Carnegie Institution of Washington Tel: (650) 325-1521 ext. 325 Department of Plant Biology URL: http://arabidopsis.org/ 260 Panama St. Stanford, CA 94305 ------------------------------------------------------------------------------------------ From pj37 at cornell.edu Wed May 30 10:23:47 2007 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Wed, 30 May 2007 10:23:47 -0400 Subject: Problem with PO files In-Reply-To: <465C979D.8050408@acoma.stanford.edu> References: <465C979D.8050408@acoma.stanford.edu> Message-ID: <465D88F3.8060805@cornell.edu> Sorry for the duplicate use of the ID. It is fixed now in the po_anatomy.obo file new revision: 1.44 Pankaj Tanya Berardini wrote: > Dear PO folks, > > We've run into a problem that is causing our term loader to get confused. > > (1) From the po_temporal file: > > format-version: 1.0 > version: $Revision: 1.31 $ > date: 12:04:2007 10:30 > saved-by: cwt6 > auto-generated-by: DAG-Edit 1.419 rev 3 > default-namespace: plant_ontology > > [Term] > id: PO:0009012 > name: plant growth and development stages > namespace: plant_growth_and_development_stage > def: "The succession of changes leading from the zygote to the mature > plant. " [Poc:curators ""] > synonym: "Arabidopsis growth" [TAIR:0000205] > > > (2) From the po_anatomy file: > > format-version: 1.0 > version: $Revision: 1.43 $ > date: 01:05:2007 15:58 > saved-by: cwt6 > auto-generated-by: DAG-Edit 1.419 rev 3 > default-namespace: plant_ontology > subsetdef: Rice "Term used for rice" > subsetdef: Maize "Term used for maize" > subsetdef: Citrus "Term used for citrus" > subsetdef: Tomato "Term used for tomato" > subsetdef: Arabidopsis "Term used for Arabidopsis" > subsetdef: Poaceae "Term used for grasses" > subsetdef: reference "reference plant structure term" > > [Term] > id: PO:0009012 > name: petiole pulvinus > namespace: plant_structure > def: "Pulvinus of the petiole" [GR:cwt] > is_a: PO:0009000 ! pulvinus > relationship: part_of PO:0020038 ! petiole > > > Because the same identifier (PO:0009012) is used for two different terms > in two different ontologies, we are running into errors. > > > Thanks very much for your help in resolving this. > > > Tanya > > ------------------------------------------------------------------------------------------ > > Tanya Berardini, Ph.D. tberardi at acoma.stanford.edu > The Arabidopsis Information Resource FAX: (650) 325-6857 > Carnegie Institution of Washington Tel: (650) 325-1521 ext. 325 > Department of Plant Biology URL: http://arabidopsis.org/ > 260 Panama St. > Stanford, CA 94305 > ------------------------------------------------------------------------------------------ > > > -- 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