From SchaefferM at missouri.edu Thu Apr 5 15:43:21 2007 From: SchaefferM at missouri.edu (Mary (Polacco) Schaeffer) Date: Thu, 05 Apr 2007 14:43:21 -0500 Subject: Pulvinus Message-ID: Dear Chih-Wei --PO-Editor -- right? Looking to link the legacy MaizeGDB anatomy terms not yet used for annotation at MaizeGDB, to an accession in PO I need some help with 'pulvinus'. Is it simply part of the node? Discussion about Dec 2004 indicated this was part of ?node? - do you know if that is considered appropriate for now? If so, should we add pulvinus in the definition or comment part of the term? mary -------------- next part -------------- An HTML attachment was scrubbed... URL: From SchaefferM at missouri.edu Thu Apr 5 16:06:55 2007 From: SchaefferM at missouri.edu (Mary (Polacco) Schaeffer) Date: Thu, 05 Apr 2007 15:06:55 -0500 Subject: Pulvinus In-Reply-To: <27D32279-1DA4-4EE8-B7DF-1D157678352D@cornell.edu> Message-ID: > Thanks much Chih-Wei. > You might wish also to look also at the discussions in our archives which I > found by Google. > m > > Hi Mary, > > I didn't see "pulvinus" in the current PO.? I just set up a request for this > term in?the SourceForge's PO tracker, so we can have opinions from other > experts.? > http://sourceforge.net/tracker/index.php?func=detail&aid=1695236&group_id=7683 > 4&atid=835555 > > Chih-Wei > > > On Apr 5, 2007, at 3:43 PM, Mary (Polacco) Schaeffer wrote: > >> Dear Chih-Wei ?--PO-Editor ?-- right? >> >> Looking to link the legacy MaizeGDB anatomy terms not yet used for >> annotation at MaizeGDB, to an accession in PO I need some help with >> 'pulvinus'. Is it simply part of the node? >> >> Discussion about Dec 2004 indicated this was part of ?node? - do you know if >> that is considered appropriate for now? If so, should we add pulvinus in the >> definition or comment part of the term? >> ?mary > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From kellogge at msx.umsl.edu Mon Apr 9 15:53:12 2007 From: kellogge at msx.umsl.edu (kellogge) Date: Mon, 9 Apr 2007 14:53:12 -0500 Subject: Pulvinus In-Reply-To: References: Message-ID: Hi Mary - Pulvinus is generally a thickened structure of a stem or leaf that is often involved in movement. There probably needs to be a general term (pulvinus - is_a plant structure) with a couple of children - pulvinus of petiole (found in many legumes, among others), and pulvinus of inflorescence branch (found in many grasses). I think it probably should not be part of node, since it's not clear what it's a part of. Bob Schmidt has isolated some inflorescence mutations that lack the pulvinus, and they are just trying to characterize the pulvinus and those mutants in particular. Toby On Apr 5, 2007, at 3:06 PM, Mary (Polacco) Schaeffer wrote: >> Thanks much Chih-Wei. >> You might wish also to look also at the discussions in our archives >> which I found by Google. >> ?m >> >> Hi Mary, >> >> I didn't see "pulvinus" in the current PO.? I just set up a request >> for this term in?the SourceForge's PO tracker, so we can have >> opinions from other experts.? >> http://sourceforge.net/tracker/index.php? >> func=detail&aid=1695236&group_id=76834&atid=835555 >> >> Chih-Wei >> >> >> On Apr 5, 2007, at 3:43 PM, Mary (Polacco) Schaeffer wrote: >> >>> Dear Chih-Wei ?--PO-Editor ?-- right? >>> ? >>> ?Looking to link the legacy MaizeGDB anatomy terms not yet used for >>> annotation at MaizeGDB, to an accession in PO I need some help with >>> 'pulvinus'. Is it simply part of the node? >>> ? >>> ?Discussion about Dec 2004 indicated this was part of ?node? - do >>> you know if that is considered appropriate for now? If so, should we >>> add pulvinus in the definition or comment part of the term? >>> ??mary ? >> >> > > 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: 2873 bytes Desc: not available URL: From shuly at cshl.edu Tue Apr 10 13:51:24 2007 From: shuly at cshl.edu (Shuly Avraham) Date: Tue, 10 Apr 2007 13:51:24 -0400 Subject: System upgrade Message-ID: <5A3ADDDE-D67E-4D97-9E08-33A728885C89@cshl.edu> Hi All, We will be performing system upgrade on Plant Ontology development and live servers. The development server (dev.plantontology.org) will be inaccessible Tuesday through Wednesday (April 10-11, 2007) and the live server (www.plantontology.org) will be inaccessible Wednesday through Thursday (April 11-12, 2007). Shuly From SchaefferM at missouri.edu Wed Apr 11 17:30:20 2007 From: SchaefferM at missouri.edu (Mary (Polacco) Schaeffer) Date: Wed, 11 Apr 2007 16:30:20 -0500 Subject: Definition nit Message-ID: Hi - there seems to be a small problem with the definition for the growth and development stage: PO:0001072 lodicule primordia visible "Stage of palea development that begins when the palea primordia arise." [POC:fz] comment: Two lodicules form on the side of the lemma in rice spikelet. is_a: PO:0001049 ! lodicule developmental stages Looks like someone did a paste of the definition for palea primordia visible: "Stage of palea development that begins when the palea primordia arise." Take care, mary From cwt6 at cornell.edu Thu Apr 12 10:33:58 2007 From: cwt6 at cornell.edu (Chih-Wei Tung) Date: Thu, 12 Apr 2007 10:33:58 -0400 Subject: Definition nit In-Reply-To: References: Message-ID: <0C5E9A35-4249-4770-B4D8-52E733B588DF@cornell.edu> Hi Mary, Thank you for pointing this out. I fixed it. You should be able to see the correct one in http://brebiou.cshl.edu/viewcvs/Poc/ontology/ OBO_format/po_temporal.obo in few hours. Chih-Wei On Apr 11, 2007, at 5:30 PM, Mary (Polacco) Schaeffer wrote: > Hi - there seems to be a small problem with the definition for the > growth > and development stage: PO:0001072 lodicule primordia visible > "Stage of palea development that begins when the palea primordia > arise." > [POC:fz] comment: Two lodicules form on the side of the lemma in rice > spikelet. is_a: PO:0001049 ! lodicule developmental stages > > > Looks like someone did a paste of the definition for palea primordia > visible: > > "Stage of palea development that begins when the palea primordia > arise." > > Take care, > mary > > From cwt6 at cornell.edu Tue Apr 24 12:06:06 2007 From: cwt6 at cornell.edu (Chih-Wei Tung) Date: Tue, 24 Apr 2007 12:06:06 -0400 Subject: Pulvinus In-Reply-To: References: Message-ID: <2601896E-BA94-4CF5-9D88-1301BEAD3D80@cornell.edu> Hi Toby and Mary, Would you take a look at following lineage for "Pulvinus", and let me know if it works. Thank you. Plant Structure [i] Organ [i] Pulvinus [i] petiole pulvinus [i] inflorescence branch pulvinus Inflorescence branch [p] inflorescence branch pulvinus Petiole [p] petiole pulvinus Chih-Wei On Apr 9, 2007, at 3:53 PM, kellogge wrote: > Hi Mary - > Pulvinus is generally a thickened structure of a stem or leaf that > is often involved in movement. There probably needs to be a > general term (pulvinus - is_a plant structure) with a couple of > children - pulvinus of petiole (found in many legumes, among > others), and pulvinus of inflorescence branch (found in many > grasses). I think it probably should not be part of node, since > it's not clear what it's a part of. Bob Schmidt has isolated some > inflorescence mutations that lack the pulvinus, and they are just > trying to characterize the pulvinus and those mutants in particular. > Toby > > On Apr 5, 2007, at 3:06 PM, Mary (Polacco) Schaeffer wrote: > >>> Thanks much Chih-Wei. >>> You might wish also to look also at the discussions in our >>> archives which I found by Google. >>> m >>> >>> Hi Mary, >>> >>> I didn't see "pulvinus" in the current PO. I just set up a >>> request for this term in the SourceForge's PO tracker, so we can >>> have opinions from other experts. >>> http://sourceforge.net/tracker/index.php? >>> func=detail&aid=1695236&group_id=76834&atid=835555 >>> >>> Chih-Wei >>> >>> >>> On Apr 5, 2007, at 3:43 PM, Mary (Polacco) Schaeffer wrote: >>> >>>> Dear Chih-Wei --PO-Editor -- right? >>>> >>>> Looking to link the legacy MaizeGDB anatomy terms not yet used >>>> for annotation at MaizeGDB, to an accession in PO I need some >>>> help with 'pulvinus'. Is it simply part of the node? >>>> >>>> Discussion about Dec 2004 indicated this was part of ?node? - >>>> do you know if that is considered appropriate for now? If so, >>>> should we add pulvinus in the definition or comment part of the >>>> term? >>>> mary >>> >>> >> >> > 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 SchaefferM at missouri.edu Tue Apr 24 13:09:40 2007 From: SchaefferM at missouri.edu (Mary (Polacco) Schaeffer) Date: Tue, 24 Apr 2007 12:09:40 -0500 Subject: Pulvinus In-Reply-To: <2601896E-BA94-4CF5-9D88-1301BEAD3D80@cornell.edu> Message-ID: > Chih-Wei, > This seems fine to me. Thanks much! > mary > > > Hi Toby and Mary, > > Would you take a look at following lineage for "Pulvinus", and let me know if > it works. Thank you. > > Plant Structure > [i] Organ > [i] Pulvinus > [i] petiole pulvinus > [i] inflorescence branch pulvinus > > > Inflorescence branch > [p] inflorescence branch pulvinus > > > Petiole > [p] petiole pulvinus > > > > Chih-Wei > > > > > On Apr 9, 2007, at 3:53 PM, kellogge wrote: > >> Hi Mary -? >> Pulvinus is generally a thickened structure of a stem or leaf that is often >> involved in movement.? There probably needs to be a general term (pulvinus - >> is_a plant structure) with a couple of children - pulvinus of petiole (found >> in many legumes, among others), and pulvinus of inflorescence branch (found >> in many grasses).? I think it probably should not be part of node, since it's >> not clear what it's a part of.? Bob Schmidt has isolated some inflorescence >> mutations that lack the pulvinus, and they are just trying to characterize >> the pulvinus and those mutants in particular. >> Toby >> >> On Apr 5, 2007, at 3:06 PM, Mary (Polacco) Schaeffer wrote: >> >> >>>> Thanks much Chih-Wei. >>>> ?You might wish also to look also at the discussions in our archives which >>>> I found by Google. >>>> ??m >>>> >>>> ?Hi Mary, >>>> >>>> ?I didn't see "pulvinus" in the current PO.? I just set up a request for >>>> this term in?the SourceForge's PO tracker, so we can have opinions from >>>> other experts.? >>>> http://sourceforge.net/tracker/index.php?func=detail&aid=1695236&group_id=7 >>>> 6834&atid=835555 >>>> >>>> ?Chih-Wei >>>> >>>> >>>> ?On Apr 5, 2007, at 3:43 PM, Mary (Polacco) Schaeffer wrote: >>>> >>>> >>>>> ?Dear Chih-Wei ?--PO-Editor ?-- right? >>>>> ?? >>>>> >>>>> ??Looking to link the legacy MaizeGDB anatomy terms not yet used for >>>>> annotation at MaizeGDB, to an accession in PO I need some help with >>>>> 'pulvinus'. Is it simply part of the node? >>>>> ?? >>>>> >>>>> ??Discussion about Dec 2004 indicated this was part of ?node? - do you >>>>> know if that is considered appropriate for now? If so, should we add >>>>> pulvinus in the definition or comment part of the term? >>>>> ???mary ? >>>>> >>>> >>>> >>>> >>> >>> >>> ? >>> >> 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: