From SchaefferM at missouri.edu Fri May 5 14:50:59 2006 From: SchaefferM at missouri.edu (Mary (Polacco) Schaeffer) Date: Fri, 05 May 2006 13:50:59 -0500 Subject: root branches - new terms for consideration. Message-ID: Working with Leszek, I have not been able to find terms that describe the branches and the main axes, aka axile, of roots. To adequately annotate root architecture QTL for reported traits to do with branching, it would be helpful to add terms: > primary root branch > lateral root branch > adventitious root branch > If we add those terms we should consider changing the current ones, eg primary root, to a term specifying the main axes, or preferred I would think, have an additional term for the axile: eg primary root primary root axile primary root branch What do you think? mary -------------- next part -------------- An HTML attachment was scrubbed... URL: From kellogge at msx.umsl.edu Fri May 5 15:48:54 2006 From: kellogge at msx.umsl.edu (kellogge) Date: Fri, 5 May 2006 14:48:54 -0500 Subject: root branches - new terms for consideration. In-Reply-To: References: Message-ID: <9faba889361566bbf0f4d4ad5c328ecf@msx.umsl.edu> Hi Mary - Not quite sure what is meant by an axile root, but here's an attempt at a response: The primary root is at one pole of the embryo and is the first root out of the seed. Any root that branches off that is a lateral root. In grasses, the primary root and its lateral roots (i.e. branches) die fairly soon after germination. At the same time, roots form from the scutellar node and nodes higher on the shoot. These have been called adventitious roots in the past, but most morphologists are trying to get away from using the term adventitious (since it implies that they are somehow in the wrong place whereas they are of course quite normal), and instead call these shoot-borne roots. Each of these shoot-borne roots makes lateral roots, and lateral roots can form on the lateral roots. I'd prefer not to introduce the term "branch" for roots. I'm not sure what the phenotype was in the QTL study, but presumably it would be more or less shoot borne roots, more or less lateral roots, etc. Toby On May 5, 2006, at 1:50 PM, Mary (Polacco) Schaeffer wrote: > Working with Leszek, I have not been able to find terms that describe > the branches and the main axes, aka axile, of roots. To adequately > annotate root architecture QTL for ?reported traits to do with > branching, it would be helpful to add terms: > >> primary root branch >> lateral root branch >> adventitious root branch >> > > If we add those terms we should consider changing the current ones, > eg primary root, to a term specifying the main axes, ?or preferred I > would think, have an additional term for the axile: > ??eg ?primary root > ????????????primary root axile > ????????????primary root branch > > What do you think? > > ?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/ This message is for the designated recipient(s) only and may contain privileged or confidential information.? If you received it in error, please notify the sender immediately and delete the original.? Thank you.? -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 2867 bytes Desc: not available URL: From SchaefferM at missouri.edu Mon May 8 12:13:03 2006 From: SchaefferM at missouri.edu (Mary (Polacco) Schaeffer) Date: Mon, 08 May 2006 11:13:03 -0500 Subject: root branches - new terms for consideration. In-Reply-To: <9faba889361566bbf0f4d4ad5c328ecf@msx.umsl.edu> Message-ID: Toby, Thanks for your very considered response. However, while I will gladly, although maybe it's really sadly, admit to not being a root anatomy expert, I still think we need a term(s) for one class of seminal lateral roots. I have checked again (Kiesselbach, the photos in the QTL paper, and then with Ed Coe). They all indicate that there is a class of lateral seminal roots in maize that come off the main 'stem': "at the base of the first internode of the stem, just above the scutellar node" (Kiesselbach p.17). The QTL paper that got me into this, (Hund et al TAG 109:618-629 (2004) has fairly clear photos that show these roots arising from a different part of the embryo "stem" than the radicle, which is at the very bottom of the stem. One is attached to this email. Is there some other information I need to be looking at? The QTL paper references a work by Feix, Hochholdinger and Park for the root nomenclature, a chapter in a book, eds by Waisel, Eshel and Kafkafi 2000: Plant roots: the hidden half. Marcel Dekker, NY 2000. FYI, the QTL paper reports on a correlation of seedling vigor and the length of the seminal lateral root axes (aka axile per Feix et al) and also a bunch of seminal root traits that don't affect seedling vigor but have to do with extent 'branching' and length of the main axes of two seminal roots classes - primary, aka radicle and lateral (as in off the main embryo stem, not the radicle). mary > From: kellogge > Date: Fri, 5 May 2006 14:48:54 -0500 > To: po-dev at plantontology.org, "Mary (Polacco) Schaeffer" > > Subject: Re: root branches - new terms for consideration. > > Hi Mary - > Not quite sure what is meant by an axile root, but here's an attempt > at a response: > > The primary root is at one pole of the embryo and is the first root out > of the seed. Any root that branches off that is a lateral root. In > grasses, the primary root and its lateral roots (i.e. branches) die > fairly soon after germination. >At the same time, roots form from the > scutellar node and nodes higher on the shoot. These have been called > adventitious roots in the past, but most morphologists are trying to > get away from using the term adventitious (since it implies that they > are somehow in the wrong place whereas they are of course quite > normal), and instead call these shoot-borne roots. Each of these > shoot-borne roots makes lateral roots, and lateral roots can form on > the lateral roots. I'd prefer not to introduce the term "branch" for > roots. > > I'm not sure what the phenotype was in the QTL study, but presumably > it would be more or less shoot borne roots, more or less lateral roots, > etc. > > Toby > > > On May 5, 2006, at 1:50 PM, Mary (Polacco) Schaeffer wrote: > >> Working with Leszek, I have not been able to find terms that describe >> the branches and the main axes, aka axile, of roots. To adequately >> annotate root architecture QTL for ?reported traits to do with >> branching, it would be helpful to add terms: >> >>> primary root branch >>> lateral root branch >>> adventitious root branch >>> >> >> If we add those terms we should consider changing the current ones, >> eg primary root, to a term specifying the main axes, ?or preferred I >> would think, have an additional term for the axile: >> ??eg ?primary root >> ????????????primary root axile >> ????????????primary root branch >> >> What do you think? >> >> ?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/ > This message is for the designated recipient(s) only and may contain > privileged or confidential information.? If you received it in error, > please notify the sender immediately and delete the original.? Thank > you.? > -------------- next part -------------- A non-text attachment was scrubbed... Name: maizeSeminalRoots.tiff Type: application/octet-stream Size: 37300 bytes Desc: not available URL: From pj37 at cornell.edu Tue May 9 17:14:23 2006 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 09 May 2006 17:14:23 -0400 Subject: epidermal long cell definition In-Reply-To: <20060504124830.pi36t99shwc000w0@www.mail.yale.edu> References: <20060504124830.pi36t99shwc000w0@www.mail.yale.edu> Message-ID: <4461062F.4080602@cornell.edu> fno.neeru at yale.edu wrote: > Hi Pankaj, > > We had met at the PAG conference last year. I have a question regarding the > correct ontology for the rice epidermal cells called long cells. I am not able > to find it on the website may be you or someone from your group can help me. We > need to add that link to our website of LCM harvested cells. > > Thanks > Neeru > Dear Neeru, Can you provide some images and the literature which our experts can review. Pankaj From katica at acoma.Stanford.EDU Tue May 9 20:59:36 2006 From: katica at acoma.Stanford.EDU (katica at acoma.Stanford.EDU) Date: Tue, 9 May 2006 17:59:36 -0700 (PDT) Subject: epidermal long cell definition In-Reply-To: <4461062F.4080602@cornell.edu> References: <20060504124830.pi36t99shwc000w0@www.mail.yale.edu> <4461062F.4080602@cornell.edu> Message-ID: Pankaj, You can find a short but good description in Silicified Cells of Grasses: A Major Source of Plant Opal in Illinois http://web.aces.uiuc.edu/vista/pdf_pubs/silcell.pdf See the paragraph 'Kinds of epidermal cells'. We briefly discussed different types of epidermal cells in grasses when we introduced 'epidermal cork cell', but at that time, we ended up adding only a type of short cell in epidermis, 'cork cell (sensu Poaceae)'. Later, we changed the name to 'epidermal cork cell' Katica On Tue, 9 May 2006, Pankaj Jaiswal wrote: > fno.neeru at yale.edu wrote: > >> Hi Pankaj, >> >> We had met at the PAG conference last year. I have a question regarding the >> correct ontology for the rice epidermal cells called long cells. I am not >> able >> to find it on the website may be you or someone from your group can help >> me. We >> need to add that link to our website of LCM harvested cells. >> >> Thanks >> Neeru >> > > > Dear Neeru, > > Can you provide some images and the literature which our experts can review. > > Pankaj > -- -------------------------------------------------------------------------- Katica Ilic katica at acoma.stanford.edu The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253 Carnegie Institution of Washington FAX: (650) 325-6857 Department of Plant Biology URL: http://arabidopsis.org/ 260 Panama St. Stanford, CA 94305 U.S.A. -------------------------------------------------------------------------- From kellogge at msx.umsl.edu Wed May 10 11:49:32 2006 From: kellogge at msx.umsl.edu (kellogge) Date: Wed, 10 May 2006 10:49:32 -0500 Subject: epidermal long cell definition In-Reply-To: References: <20060504124830.pi36t99shwc000w0@www.mail.yale.edu> <4461062F.4080602@cornell.edu> Message-ID: <415aa83851b28ea562fffd62868fb6cb@msx.umsl.edu> I think this was one of those "wait-until-we-need-it" terms. Grass epidermes have long cells and short cells in the epidermis, so we should probably introduce both terms. They will be children of "epidermal cell". "long cell" = a more or less rectangular epidermal cell in which the the proximo-distal dimension is several times longer than the transverse dimension "short cell" = an isodiametric epidermal cell "epidermal cork cell" is an instance of "short cell" Comment (for both cell types): In the leaf epidermis of Poaceae and Joinvilleaceae, long cells and short cells often alternate in longitudinal rows. Toby On May 9, 2006, at 7:59 PM, katica at acoma.Stanford.EDU wrote: > Pankaj, > > You can find a short but good description in > > Silicified Cells of Grasses: A Major Source of Plant Opal in Illinois > > http://web.aces.uiuc.edu/vista/pdf_pubs/silcell.pdf > > See the paragraph 'Kinds of epidermal cells'. > > We briefly discussed different types of epidermal cells in grasses > when we introduced 'epidermal cork cell', but at that time, we ended > up adding only a type of short cell in epidermis, 'cork cell (sensu > Poaceae)'. Later, we changed the name to 'epidermal cork cell' > > Katica > > > On Tue, 9 May 2006, Pankaj Jaiswal wrote: > >> fno.neeru at yale.edu wrote: >> >>> Hi Pankaj, >>> We had met at the PAG conference last year. I have a question >>> regarding the >>> correct ontology for the rice epidermal cells called long cells. I >>> am not able >>> to find it on the website may be you or someone from your group can >>> help me. We >>> need to add that link to our website of LCM harvested cells. >>> Thanks >>> Neeru >> >> >> Dear Neeru, >> >> Can you provide some images and the literature which our experts can >> review. >> >> Pankaj >> > > -- > ----------------------------------------------------------------------- > --- > Katica Ilic katica at acoma.stanford.edu > The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253 > Carnegie Institution of Washington FAX: (650) 325-6857 > Department of Plant Biology URL: http://arabidopsis.org/ > 260 Panama St. > Stanford, CA 94305 > U.S.A. > ----------------------------------------------------------------------- > --- > > Elizabeth A. Kellogg E. Desmond Lee and Family Professor of Botanical Studies Department of Biology University of Missouri-St. Louis St. Louis, MO 63121 Tel: 314-516-6217; FAX: 314-516-6233 http://www.umsl.edu/services/kellogg/ This message is for the designated recipient(s) only and may contain privileged or confidential information.? If you received it in error, please notify the sender immediately and delete the original.? Thank you.? From pj37 at cornell.edu Wed May 10 13:26:34 2006 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Wed, 10 May 2006 13:26:34 -0400 Subject: epidermal long cell definition In-Reply-To: <415aa83851b28ea562fffd62868fb6cb@msx.umsl.edu> References: <20060504124830.pi36t99shwc000w0@www.mail.yale.edu> <4461062F.4080602@cornell.edu> <415aa83851b28ea562fffd62868fb6cb@msx.umsl.edu> Message-ID: <4462224A.2030202@cornell.edu> Hi Toby, Many thanks for your inputs. Others, If there are no more comments, I would like to add these terms in the ontology. Pankaj kellogge wrote: > I think this was one of those "wait-until-we-need-it" terms. Grass > epidermes have long cells and short cells in the epidermis, so we > should probably introduce both terms. They will be children of > "epidermal cell". > > "long cell" = a more or less rectangular epidermal cell in which the > the proximo-distal dimension is several times longer than the > transverse dimension > > "short cell" = an isodiametric epidermal cell > > "epidermal cork cell" is an instance of "short cell" > > Comment (for both cell types): In the leaf epidermis of Poaceae and > Joinvilleaceae, long cells and short cells often alternate in > longitudinal rows. > > Toby > > On May 9, 2006, at 7:59 PM, katica at acoma.Stanford.EDU wrote: > >> Pankaj, >> >> You can find a short but good description in >> >> Silicified Cells of Grasses: A Major Source of Plant Opal in Illinois >> >> http://web.aces.uiuc.edu/vista/pdf_pubs/silcell.pdf >> >> See the paragraph 'Kinds of epidermal cells'. >> >> We briefly discussed different types of epidermal cells in grasses >> when we introduced 'epidermal cork cell', but at that time, we ended >> up adding only a type of short cell in epidermis, 'cork cell (sensu >> Poaceae)'. Later, we changed the name to 'epidermal cork cell' >> >> Katica >> >> >> On Tue, 9 May 2006, Pankaj Jaiswal wrote: >> >>> fno.neeru at yale.edu wrote: >>> >>>> Hi Pankaj, >>>> We had met at the PAG conference last year. I have a question >>>> regarding the >>>> correct ontology for the rice epidermal cells called long cells. I >>>> am not able >>>> to find it on the website may be you or someone from your group can >>>> help me. We >>>> need to add that link to our website of LCM harvested cells. >>>> Thanks >>>> Neeru >>> >>> >>> >>> Dear Neeru, >>> >>> Can you provide some images and the literature which our experts can >>> review. >>> >>> Pankaj >>> >> From katica at acoma.stanford.edu Wed May 10 13:39:17 2006 From: katica at acoma.stanford.edu (katica at acoma.stanford.edu) Date: Wed, 10 May 2006 10:39:17 -0700 (PDT) Subject: epidermal long cell definition In-Reply-To: <415aa83851b28ea562fffd62868fb6cb@msx.umsl.edu> References: <20060504124830.pi36t99shwc000w0@www.mail.yale.edu> <4461062F.4080602@cornell.edu> <415aa83851b28ea562fffd62868fb6cb@msx.umsl.edu> Message-ID: Hi Toby, This is all straight forward, just to mentioned that 'silica cell' will be a child of short cell too (is_a). Are there any cases where silica cells are not a part of epidermis? If no, I can go ahead and add two terms, short and long cell under epidermal cell, placing the children the way you described. Katica On Wed, 10 May 2006, kellogge wrote: > I think this was one of those "wait-until-we-need-it" terms. Grass epidermes > have long cells and short cells in the epidermis, so we should probably > introduce both terms. They will be children of "epidermal cell". > > "long cell" = a more or less rectangular epidermal cell in which the the > proximo-distal dimension is several times longer than the transverse > dimension > > "short cell" = an isodiametric epidermal cell > > "epidermal cork cell" is an instance of "short cell" > > Comment (for both cell types): In the leaf epidermis of Poaceae and > Joinvilleaceae, long cells and short cells often alternate in longitudinal > rows. > > Toby > > On May 9, 2006, at 7:59 PM, katica at acoma.Stanford.EDU wrote: > >> Pankaj, >> >> You can find a short but good description in >> >> Silicified Cells of Grasses: A Major Source of Plant Opal in Illinois >> >> http://web.aces.uiuc.edu/vista/pdf_pubs/silcell.pdf >> >> See the paragraph 'Kinds of epidermal cells'. >> >> We briefly discussed different types of epidermal cells in grasses when we >> introduced 'epidermal cork cell', but at that time, we ended up adding only >> a type of short cell in epidermis, 'cork cell (sensu Poaceae)'. Later, we >> changed the name to 'epidermal cork cell' >> >> Katica >> >> >> On Tue, 9 May 2006, Pankaj Jaiswal wrote: >> >>> fno.neeru at yale.edu wrote: >>> >>>> Hi Pankaj, >>>> We had met at the PAG conference last year. I have a question regarding >>>> the >>>> correct ontology for the rice epidermal cells called long cells. I am not >>>> able >>>> to find it on the website may be you or someone from your group can help >>>> me. We >>>> need to add that link to our website of LCM harvested cells. >>>> Thanks >>>> Neeru >>> >>> >>> Dear Neeru, >>> >>> Can you provide some images and the literature which our experts can >>> review. >>> >>> Pankaj >>> >> >> -- ----------------------------------------------------------------------- >> --- >> Katica Ilic katica at acoma.stanford.edu >> The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253 >> Carnegie Institution of Washington FAX: (650) 325-6857 >> Department of Plant Biology URL: http://arabidopsis.org/ >> 260 Panama St. >> Stanford, CA 94305 >> U.S.A. >> -------------------------------------------------------------------------- >> >> > Elizabeth A. Kellogg > E. Desmond Lee and Family Professor of Botanical Studies > Department of Biology > University of Missouri-St. Louis > St. Louis, MO 63121 > Tel: 314-516-6217; FAX: 314-516-6233 > http://www.umsl.edu/services/kellogg/ > This message is for the designated recipient(s) only and may contain > privileged or confidential information.? If you received it in error, please > notify the sender immediately and delete the original.? Thank you.? > > -- -------------------------------------------------------------------------- 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 Thu May 11 20:35:08 2006 From: katica at acoma.Stanford.EDU (katica at acoma.Stanford.EDU) Date: Thu, 11 May 2006 17:35:08 -0700 (PDT) Subject: Plant Structure Ontology update is in the cvs, new revision: 1.21 In-Reply-To: References: Message-ID: New revision of the Plant Structure Ontology is in the POC cvs. I made the following changes: 1. New terms: long cell and short cell (is_a epidermal cell) (i) epidermal cell (i) long cell (PO:0004717) (i) short cell (PO:0004718) (i) epidermal cork cell (i) silica cell Definitions: long cell - a more or less rectangular epidermal cell in which the proximo-distal dimension is several times longer than the transverse dimension. short cell - an isodiametric epidermal cell. To be consistent with existing term 'epidermal cork cell', I modified the definition of silica cell to: "Cells with deposits of silica in them. One of the two types of short cells in the epidermis of grasses and bamboos. It is usually paired with epidermal cork cell." Comment (for both cell types): In the leaf epidermis of Poaceae and Joinvilleaceae, long cells and short cells often alternate in longitudinal rows. 2. New term - hilum groove Def: longitudinal groove in the testa through the prominent hilum of the seed. Synonym: faboid split 3. Stem cell terms Added stem cell as synonym of 'initial cell, and also, added 'columella root cap stem cell' as synonym of 'columella root cap initial' 4. New term - paraclade and paraclade cortex Stem (p) paraclade (PO:0004720) (p) paraclade cortex (PO:0004721) paraclade (PO:0004720) Def: lateral branch which ends in an inflorescence that repeats the main inflorescence (used both refs: APWeb and Weberling, ISBN: 0521251346 Morphology of Flowers and Inflorescences. paraclade cortex (PO:0004721 Def The primary tissue located between the vascular system and the epidermis of the paraclade. 5. Inflorescence stem added as synonym of 'peduncle'. 6. New terms - pedicel cortex and sepal vascular system, pedicel cortex PO:0004722 Def: The primary tissue located between the vascular system and the epidermis of the pedicel. sepal vascular system, PO:0004723 Def: Vascular system of the sepal. 7. New term - hypocotyl-root junction PO:0004724 Def: Junction point of the embryonic root and hypocotyl. Note: the decision was to add this term under 'embryo axis' and also propagate it under shoot. 8. New terms: abaxial and adaxial leaf primorduim abaxial side of leaf primorduim PO:0004725 Def: The abaxial/outer side of the leaf primordium that becomes the abaxial/lower leaf blade adaxial side of leaf primorduim PO:0004726 Def: The adaxial/inner side of the leaf primordium that becomes adaxial/upper leaf blade. Best Regards, Katica -------------------------------------------------------------------------- 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 Mon May 15 07:40:15 2006 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Mon, 15 May 2006 07:40:15 -0400 Subject: [Fwd: Gramene Feedback: http://dev.gramene.org/db/ontology/search_term?id=PO:0009011] Message-ID: <4468689F.2020108@cornell.edu> This is a forwarded message from Barry Smith. Someone from POC project may like to reply. Pankaj -------- Original Message -------- Subject: Gramene Feedback: http://dev.gramene.org/db/ontology/search_term?id=PO:0009011 Date: Sun, 14 May 2006 09:57:14 -0400 From: feedback_submission at acorn.gramene.org Reply-To: gramene-dev at gramene.org To: gramene-dev *** Feedback from the Live Site *** refer_to_url: http://dev.gramene.org/db/ontology/search_term?id=PO:0009011 subject: http://dev.gramene.org/db/ontology/search_term?id=PO:0009011 comments: Can you supply me with your definition of the 'is-a' relation? At the above URL it would seem to follow that cell is-a plant structure What, then, of non-plant cells? name: Barry Smith email: phismith at buffalo.edu organization: http://ncbo.us send_feedback: Send your feedback From pj37 at cornell.edu Mon May 15 15:52:52 2006 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Mon, 15 May 2006 15:52:52 -0400 Subject: [Fwd: Gramene Feedback: http://dev.gramene.org/db/ontology/search_term?id=PO:0009011] In-Reply-To: <4468689F.2020108@cornell.edu> References: <4468689F.2020108@cornell.edu> Message-ID: <4468DC14.8070802@cornell.edu> Dear Barry, The definitions we have for Is a = [i] is: It is used to describe the relationship between a child term that represents a specific type of a more general parent term. For example a guard cell is a type of cell; a root hair is a cell. Since this is a plant structure ontology (dedicated) we did not name the term 'plant cell', as you would have expected had it been a cell type ontology. Also the definition communicates that we are talking about the plant cell. definition: 'Structural and physiological unit of a living organism; it (i.e., plant cell) consists of protoplast and cell wall; in nonliving state, of cell wall only, or cell wall and some nonliving inclusions.' All the children we have for the parent term 'cell (PO:0009002)' are subtypes of plant cells. Thus no question of having non-plant cell types in this ontology or as children. Pankaj > -------- Original Message -------- > Subject: Gramene Feedback: > http://dev.gramene.org/db/ontology/search_term?id=PO:0009011 > Date: Sun, 14 May 2006 09:57:14 -0400 > From: feedback_submission at acorn.gramene.org > Reply-To: gramene-dev at gramene.org > To: gramene-dev > > *** Feedback from the Live Site *** > > refer_to_url: http://dev.gramene.org/db/ontology/search_term?id=PO:0009011 > > subject: http://dev.gramene.org/db/ontology/search_term?id=PO:0009011 > > comments: Can you supply me with your definition of the 'is-a' relation? > At the above URL it would seem to follow that > > cell is-a plant structure > > What, then, of non-plant cells? > > > name: Barry Smith > > email: phismith at buffalo.edu > > organization: http://ncbo.us > > send_feedback: Send your feedback > > > > -- 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 shuly at cshl.edu Tue May 16 01:34:55 2006 From: shuly at cshl.edu (Shuly Avraham) Date: Tue, 16 May 2006 01:34:55 -0400 Subject: Plant Ontology website down on Tuesday 6pm-midnight Message-ID: <796E8995-8A52-4130-8AD2-FDBA400238D3@cshl.edu> Hi, Due to hardware and network maintenance at CSHL, the Plant Ontology web site will be down from 6 pm EDT Tuesday night, May 16, till sometime after midnight. If you have any questions, please email me. Sorry for the inconvenience, Shuly. From pj37 at cornell.edu Tue May 16 11:19:26 2006 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 16 May 2006 11:19:26 -0400 Subject: renaming request for PO:0009002 : cell Message-ID: <4469ED7E.9010001@cornell.edu> Hi Everyone, I am requesting a renaming of the term PO:0009002 : cell to Plant Cell. Thus making it more intuitive which also avoids usage of the same term name in GO and other ontologies, where they refer it as a generic cell. The suggestion came up while talking to Barry Smith from Univ of Buffalo. He is one of the leading ontology expert. If agreed, I also suggest rewording the definition as well. Current definition: Structural and physiological unit of a living organism; it (i.e., plant cell) consists of protoplast and cell wall; in nonliving state, of cell wall only, or cell wall and some nonliving inclusions. Suggested definition: Structural and physiological unit of a plant, it consists of a protoplasm and cell wall; in non living state, of cell wall only, or cell wall and some non living inclusions. -Pankaj From felipe.zapata at umsl.edu Tue May 16 12:05:15 2006 From: felipe.zapata at umsl.edu (Felipe Zapata) Date: Tue, 16 May 2006 11:05:15 -0500 Subject: renaming request for PO:0009002 : cell In-Reply-To: <4469ED7E.9010001@cornell.edu> References: <4469ED7E.9010001@cornell.edu> Message-ID: <85891449-1AC7-4EF3-91A7-30ED2D610DF2@umsl.edu> On May 16, 2006, at 10:19 AM, Pankaj Jaiswal wrote: > Hi Everyone, > > I am requesting a renaming of the term > PO:0009002 : cell > to > Plant Cell. > > Thus making it more intuitive which also avoids usage of the same > term name in GO and other ontologies, where they refer it as a > generic cell. > How do other ontologies refer to a plant cell?? to me it is mandatory to overlap/communicate with those ontologies so POC should use the term name other ontologies use for a plant cell in order to communicate and do comparative studies across ontologies. If the use plant cell, I would say it's fine to rename cell in POC From pj37 at cornell.edu Tue May 16 15:16:37 2006 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 16 May 2006 15:16:37 -0400 Subject: renaming request for PO:0009002 : cell In-Reply-To: References: Message-ID: <446A2515.7040403@cornell.edu> Hi, I haven't looked at the ontologies from other organisms. Therefore I am posting it to the OBO discussion list to check out from other groups how they manage it. This message id ccied to Barry. Pankaj Mary (Polacco) Schaeffer wrote: > To expand Filipe's question - do other ontologies distinguish cells from > other major groups, eg bacteria or yeast, from animals and plants? > > >>From: Felipe Zapata >>Reply-To: po-dev at plantontology.org, Felipe Zapata >>Date: Tue, 16 May 2006 11:05:15 -0500 >>To: po-dev at plantontology.org, Pankaj Jaiswal >>Subject: Re: renaming request for PO:0009002 : cell >> >> >>On May 16, 2006, at 10:19 AM, Pankaj Jaiswal wrote: >> >> >>>Hi Everyone, >>> >>>I am requesting a renaming of the term >>>PO:0009002 : cell >>>to >>>Plant Cell. >>> >>>Thus making it more intuitive which also avoids usage of the same >>>term name in GO and other ontologies, where they refer it as a >>>generic cell. >>> >> >>How do other ontologies refer to a plant cell?? to me it is mandatory >>to overlap/communicate with those ontologies so POC should use the >>term name other ontologies use for a plant cell in order to >>communicate and do comparative studies across ontologies. If the use >>plant cell, I would say it's fine to rename cell in POC >> >> >> > > > -- 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 SchaefferM at missouri.edu Tue May 16 14:10:12 2006 From: SchaefferM at missouri.edu (Mary (Polacco) Schaeffer) Date: Tue, 16 May 2006 13:10:12 -0500 Subject: renaming request for PO:0009002 : cell In-Reply-To: <85891449-1AC7-4EF3-91A7-30ED2D610DF2@umsl.edu> Message-ID: To expand Filipe's question - do other ontologies distinguish cells from other major groups, eg bacteria or yeast, from animals and plants? > From: Felipe Zapata > Reply-To: po-dev at plantontology.org, Felipe Zapata > Date: Tue, 16 May 2006 11:05:15 -0500 > To: po-dev at plantontology.org, Pankaj Jaiswal > Subject: Re: renaming request for PO:0009002 : cell > > > On May 16, 2006, at 10:19 AM, Pankaj Jaiswal wrote: > >> Hi Everyone, >> >> I am requesting a renaming of the term >> PO:0009002 : cell >> to >> Plant Cell. >> >> Thus making it more intuitive which also avoids usage of the same >> term name in GO and other ontologies, where they refer it as a >> generic cell. >> > > How do other ontologies refer to a plant cell?? to me it is mandatory > to overlap/communicate with those ontologies so POC should use the > term name other ontologies use for a plant cell in order to > communicate and do comparative studies across ontologies. If the use > plant cell, I would say it's fine to rename cell in POC > > > From pj37 at cornell.edu Wed May 17 12:31:37 2006 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Wed, 17 May 2006 12:31:37 -0400 Subject: renaming request for PO:0009002 : cell In-Reply-To: References: Message-ID: <446B4FE9.10905@cornell.edu> I just checked various anatomy, cell type and GO. Except GO and cell type ontology there is no instance of use of 'cell' as a generic one. All the anatomy ontologies have cell types but no grouping term such as 'cell'. SO looks like we should be okay to rename it and put a DBXref to cell type ontology term 'plant cell'. Pankaj Mary (Polacco) Schaeffer wrote: > To expand Filipe's question - do other ontologies distinguish cells from > other major groups, eg bacteria or yeast, from animals and plants? > > >>From: Felipe Zapata >>Reply-To: po-dev at plantontology.org, Felipe Zapata >>Date: Tue, 16 May 2006 11:05:15 -0500 >>To: po-dev at plantontology.org, Pankaj Jaiswal >>Subject: Re: renaming request for PO:0009002 : cell >> >> >>On May 16, 2006, at 10:19 AM, Pankaj Jaiswal wrote: >> >> >>>Hi Everyone, >>> >>>I am requesting a renaming of the term >>>PO:0009002 : cell >>>to >>>Plant Cell. >>> >>>Thus making it more intuitive which also avoids usage of the same >>>term name in GO and other ontologies, where they refer it as a >>>generic cell. >>> >> >>How do other ontologies refer to a plant cell?? to me it is mandatory >>to overlap/communicate with those ontologies so POC should use the >>term name other ontologies use for a plant cell in order to >>communicate and do comparative studies across ontologies. If the use >>plant cell, I would say it's fine to rename cell in POC >> >> >> > > > -- 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 kjbradford at ucdavis.edu Mon May 1 17:13:12 2006 From: kjbradford at ucdavis.edu (KENT BRADFORD) Date: Mon, 1 May 2006 14:13:12 -0700 Subject: Compositae vocabulary Message-ID: <70B0CAB623BFDA448F85DA2AFEE8BD429974C6@EXCHANGE.plantsciences.ucdavis.edu> I did not get any response to the message below. Is this address listed on the Plant Ontology website viable? Kent Bradford _____________________________________________ From: KENT BRADFORD Sent: Tuesday, April 18, 2006 2:33 PM To: 'po at plantontology.org' Subject: Compositae vocabulary To Whom It May Concern: I am a Co-PI on the Compositae Genome Project that has been developing EST and mapping resources for the Compositae, primarily lettuce and sunflower but now expanding into 15 additional species (http://cgpdb.ucdavis.edu). As part of this project, we have also collected extensive phenotypic data on several hundred accessions in the Compositae. We are in the process of developing a database to compile and store this data and make it accessible via our website. In describing our phenotypic data, we would like to be compatible with your controlled vocabularies in choosing our terms. However, you note on your website that these vocabularies are not yet available for the Compositae, and we have many types of data that I do not see in the current descriptions, (e.g., specific leaf shapes, rosettes, presence of trichomes, inflorescence branching patterns, etc.). I would appreciate your advice on how we should proceed in a way that will remain consistent the goals of the plant ontology project to allow broad and consistent searching on controlled vocabularies. Is anyone working on a list of terms for the Compositae that we could work from? I can send a list of the characteristics that we have recorded if it would help. Sincerely, Kent Bradford Kent J. Bradford Professor Department of Plant Sciences Mail Stop 5 One Shields Ave. University of California Davis, CA 95616-8780 Phone: 1-530-752-6087 Fax: 1-530-754-7222 Email: kjbradford at ucdavis.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: