From ap343 at cornell.edu Wed Jun 1 10:20:27 2005 From: ap343 at cornell.edu (Anuradha Pujar) Date: Wed, 1 Jun 2005 10:20:27 -0400 (EDT) Subject: Rice profiling project - interest in developing cell type terms (PR#64) In-Reply-To: <200506010028.j510SUPx010319@brie4.cshl.org> References: <200506010028.j510SUPx010319@brie4.cshl.org> Message-ID: <1060.128.253.184.79.1117635627.squirrel@128.253.184.79> Hi Katica, >From Neeru's mail i gather she is using gramene ontology for anatomy and growth stages. There is a possibility that she is not aware that PO has a different version of growth stages than the one avaible on gramene. Maybe we could send her a follow-up mail with the link? anu > Dear Neeru, > > Good to hear from you again. I am glad that PO is working for you and that > you > are able to find most of the terms that you need. I'll try addressing your > questions, and also, I may have some specific questions for you too: > > You asked: > "1) the shoot apical meristem definition includes the axillary meristem > and we > were wondering if the two terms could be separated and have an axillary > meristem > and axillary primordium as separate ontological terms." > > No, actually, the second part of the definition of SAM refers to the SAMs > of > the > axillary shoots: > PO:0020148 - shoot apical meristem > Synonyms: apical meristem, primary shoot meristem > Definition: Meristem formed in the apex of the shoot, including meristems > originating as axillary shoot meristems. > > I think what you are you asking about is 'meristem that is part of the > shoot > apex, in the axil of the leaf primordia', right? I think we would need to > change > definitions for some of the existing PO terms, since we already have terms > such > as leaf primordium, SAM, shoot apex and axillary bud meristem. I'll get > back to > you regarding this once our group discusses it. > > These are the terms already in the PO, and I don't think we need to add > new > terms, but rather change definitions of the existing: > > PO:0020148 - shoot apical meristem > Synonyms: apical meristem, primary shoot meristem > Definition: Meristem formed in the apex of the shoot, including meristems > originating as axillary shoot meristems. > > PO:0000037 - shoot apex > Definition: The topmost part of the shoot, situated at the distal > extremity of > the shoot axis, consists of apical meristem the youngest leaf primordia. > > PO:0000232 - axillary bud meristem > Synonyms: axillary meristem > Definition: Meristems formed in the axil of the leaf. > > PO:0000017 - leaf primordium > Definition: An organized group of cells that will differentiate into leaf > that > are emerging as an outgrowth in the shoot apex (flanking the meristem). > > Then, you asked: > "2) under the rice growth stages - rice plant growth stages - the child > term > germination has no further subdivisions and we have been harvesting cell > types > from 0 hr (same as Embryo stage EM10) and 12 and 24 hr post imbibition > time > points from a germinating seed. So it would be great if you could possibly > add > these two ontologies as child terms under germination." > > I am not sure I understand exactly what you are asking, and I don't > remember > what Gramene use to have before, but your '0 hours.' should be equivalent > of > 'dry seed', right? > PO term 'imbibition' covers period up until radicle emergence takes place. > Your > '12 and 24 hours post imbibition' does not indicate if radicle emergence > stage > was reached at 24 hours post imbibition. Having had some experience (and > fun) > growing rice in the lab while I was posdoc, my recollection is that it > takes > little longer for radicle emergence in rice, but it also depends on the > temperature. For this very reason, we insist on morphological landmarks > for > creating and defining terms and not on less relevant and highly variable > parameters, such as days after anthesis, hours post imbibition, or very > disputable 'hours after germination'. Different rice varieties can reach > different stage (placed under different conditions) at '24 hours post > imbibition'. I agree that term 'imbibition' is a bit stretched, but am not > sure > if any new terms would provide adequate granularity that you are asking > for. > > You also asked: > "3. Also the definition of stomatal complex does not include the > subsidiary > cells and from what we have been looking around stomatal complex would be > guard > cell surrounding the stomata with the subsidiary cells." > > The definition doesn't, but 'subsidiary cell' is a child of 'stomatal > complex' > and so is 'guard cell'. Therefore, "guard and subsidiary cells are both a > part > of the stomatal complex", even though the definition of the 'stomatal > complex' > does not specifically say that. The ontology structure and term > relationships > provide such information. That is a benefit of having these terms in the > ontology, a lot of information is provided in the ontology structure > itself. > > I hope this helps, please, let me know if you have additional questions, > and > I'll get back to you regarding definitions of 'meristem' terms. > > Best regards, > > Katica > >> ---------- Forwarded message ---------- >> Date: Thu, 26 May 2005 19:35:44 -0400 >> From: fno.neeru at yale.edu >> To: Katica Ilic >> Subject: Re: Fwd: rice profiling project interest in developing cell >> type >> terms >> >> Hi Katica, >> This is from Neeru at Tim Nelson lab, Yale. We had met at the ontology >> workshop at PAG meeting. Sorry for the long silence. How are you doing. >> Over here we were wondering if you could help us out with some of the >> ontologies. Most of the ontologies that we are using are from the >> gramene website and fit really very well in defining our cell types >> and growth stages. There are few we have questions about... >> 1) the shoot apical meristem definition includes the axillary meristem >> and we were wondering if the two terms could be separated and have an >> axillary meristem and axillary primordium as separate ontological >> terms. >> 2) under the rice growth stages- rice plant growth stages- the child >> term germination has no furhter subdivisions and we have been >> harvesting cell types from 0 hr ( same as Embryo stage EM10) and 12 and >> 24 hr post imbibition time points from a germinating seed. So it would >> be great if you could possibly add these two ontologies as child terms >> under germination. >> 3) Also the definition of stomatal complex does not include the >> subsidiary cells and from what we have been looking around stomatal >> complex would be guard cell surrounding the stomata with the subsidiary >> cells. >> >> Please let us know what you think. Thanks >> Best Regards >> Neeru >> >> Quoting Katica Ilic : >> >>> >>> Dear Tim, >>> >>> Thank you for your message. I am glad to see that you are using >>> Plant >>> Ontologies, and I agree we need to work together to make it better. >>> >>> For the Plant Structure Ontology, this is a very good point you made, >>> we >>> haven't done any instantiation yet, that is, we have not propagated >>> each cell type >>> under every tissue of every organ, for the following reasons: >>> >>> 1. It would be to redundant, and ontology would end up be too large >>> and >>> difficult to search through since each cell type in each tissue of >>> the each organ would be a separate term, resulting in dozens of terms >>> that >>> would refer to for example, parenchyma cell type. This is the major >>> problem of our ontology (in a way, we inherited it from GO, but I >>> can >>> explain this some other time), and we are currently exploring >>> several >>> options. >>> >>> What we want to avoid, is to have several thousand terms in the >>> plant structure ontology, while the sum total of the plant anatomy >>> terms >>> is in fact less that thousand (by my rough estimate). >>> >>> 2. Even if we do end up instantiating terms and propagating plant >>> ontology, there is a fundamental conceptual problem here, that is, >>> this instatiation and term multiplication is against the modular >>> nature >>> that underlines the plant structure, for example, xylem element >>> is xylem element, regardless of its location, >>> therefore having several terms refering to the exact position of the >>> xylem >>> element wouldn't add up much, if there is only a better way to >>> indicate >>> this posiotional information, that is to use several terms in >>> conjuction >>> to describe cell type, it's location and dev stage. This so far is >>> not >>> possible and we are trying to figure out how to tackle this >>> computationaly. >>> >>> Lincoln Stain and toby Kellogg, two PIs on the POC project wrote a >>> document last summer, called 'Multiplicative chrisis" in which they >>> explianed this very problem. If you want to take a look, I can send >>> it to >>> you. >>> >>> For the developmental stages ontology, I understand this problem >>> too, >>> and I'll pass your question to the POC members in charge of this >>> aspect of >>> the ontology. It might be a couple of week before we get back to >>> you, >>> since soon we are all leaving for the PAG meeting in San Diego. >>> >>> I already check the PAG web site out, you are not registered, but if >>> you have >>> anyone from your group who is coming to this meeting, I would like to >>> arrange >>> for a meeting. I fact, I would suggest the Ontology workshop on >>> Monday Jan 17, >>> where all the POC members will be present. >>> >>> We also have our annual POC in-person meeting on Jan 18 and minutes >>> will >>> be posted on the POC web site. The "Multiplicative chrisis" document >>> is on >>> the agenda. >>> >>> Best regards, >>> >>> Katica >>> >>> >>> On Mon, 10 Jan 2005, Timothy Nelson wrote: >>> >>> > Dear Katica, >>> > We are finally at the point of needing to interface with the POC >>> to >>> > assure that our rice cell profiling data is tagged with a >>> > community-standard vocabulary. We have been pleased to see that >>> much >>> > new vocabulary has been added for rice at the Ontology website in >>> > recent weeks. We would like to work with you on several issues: >>> > >>> > 1. We will need to describe our data with greater precision than >>> is >>> > currently available. We find it difficult to distinguish between >>> > "plant" ontological terms and other terms. For example, how does >>> one >>> > tag data that needs info not just as to cell type, but for a >>> > particular cell type, within a particular organ, at a particular >>> zone >>> > within the organ, and all at a particular developmental stage? >>> > >>> > 2. What is the appropriate syntax for adding sub-descriptors? For >>> > example, there currently exist developmental stages described as >>> > "seedling", "1-4 leaf stage", "germination", etc., but our data >>> comes >>> > from much narrower windows than described with those terms. >>> > >>> > We realize it will be an ongoing process to refine the >>> vocabulary, >>> > and we look forward to being part of the process. >>> > >>> > Best regards, >>> > >>> > Tim Nelson >>> > Professor, Dept MCDB, Yale University >>> > >>> > >From: "Ware, Doreen" >>> > >To: "'timothy.nelson at yale.edu'" >>> > >Cc: "'Katica Ilic'" , >>> > > "Pankaj Jaiswal (E-mail)" >>> > > >>> > >Subject: rice profiling project interest in developing cell type >>> terms >>> > >Date: Wed, 29 Sep 2004 09:58:43 -0400 >>> > >X-YaleITSMailFilter: Version 1.1e (attachment(s) not renamed) >>> > >Status: RO >>> > > >>> > >Dear Dr. Nelson, >>> > > >>> > >Thank you for introducing yourself and your project "Virtual >>> center for >>> > >cellular expression profiling of rice" last week. I wanted to >>> follow-up and >>> > >introduce you to Katica Ilic the project coordinator for POC and >>> will be the >>> > >best contact person to discuss working within the POC framework to >>> develop >>> > >the correct terms and relationships for you project. Please feel >>> free to >>> > >email Katica with your specific questions or to use contact link >>> on the POC >>> > >website for po at plantontology.org. >>> > > >>> > >Doreen >>> > > >>> > > >>> > >Doreen Ware USDA ARS >>> > >Research Investigator >>> > >Cold Spring Harbor Laboratory >>> > >1 Bungtown Rd. >>> > >Cold Spring Harbor, NY 11724 >>> > >Phone: 516 367-6979 >>> > >Fax: 516 367-6851 >>> > >E-mail: ware at cshl.edu >>> > >>> >>> --------------------------------------------------------------------- >> ----- >>> 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 ap343 at cornell.edu Wed Jun 1 10:20:27 2005 From: ap343 at cornell.edu (Anuradha Pujar) Date: Wed, 1 Jun 2005 10:20:27 -0400 (EDT) Subject: Rice profiling project - interest in developing cell type terms (PR#64) In-Reply-To: <200506010028.j510SUPx010319@brie4.cshl.org> References: <200506010028.j510SUPx010319@brie4.cshl.org> Message-ID: <1060.128.253.184.79.1117635627.squirrel@128.253.184.79> Hi Katica, >From Neeru's mail i gather she is using gramene ontology for anatomy and growth stages. There is a possibility that she is not aware that PO has a different version of growth stages than the one avaible on gramene. Maybe we could send her a follow-up mail with the link? anu > Dear Neeru, > > Good to hear from you again. I am glad that PO is working for you and that > you > are able to find most of the terms that you need. I'll try addressing your > questions, and also, I may have some specific questions for you too: > > You asked: > "1) the shoot apical meristem definition includes the axillary meristem > and we > were wondering if the two terms could be separated and have an axillary > meristem > and axillary primordium as separate ontological terms." > > No, actually, the second part of the definition of SAM refers to the SAMs > of > the > axillary shoots: > PO:0020148 - shoot apical meristem > Synonyms: apical meristem, primary shoot meristem > Definition: Meristem formed in the apex of the shoot, including meristems > originating as axillary shoot meristems. > > I think what you are you asking about is 'meristem that is part of the > shoot > apex, in the axil of the leaf primordia', right? I think we would need to > change > definitions for some of the existing PO terms, since we already have terms > such > as leaf primordium, SAM, shoot apex and axillary bud meristem. I'll get > back to > you regarding this once our group discusses it. > > These are the terms already in the PO, and I don't think we need to add > new > terms, but rather change definitions of the existing: > > PO:0020148 - shoot apical meristem > Synonyms: apical meristem, primary shoot meristem > Definition: Meristem formed in the apex of the shoot, including meristems > originating as axillary shoot meristems. > > PO:0000037 - shoot apex > Definition: The topmost part of the shoot, situated at the distal > extremity of > the shoot axis, consists of apical meristem the youngest leaf primordia. > > PO:0000232 - axillary bud meristem > Synonyms: axillary meristem > Definition: Meristems formed in the axil of the leaf. > > PO:0000017 - leaf primordium > Definition: An organized group of cells that will differentiate into leaf > that > are emerging as an outgrowth in the shoot apex (flanking the meristem). > > Then, you asked: > "2) under the rice growth stages - rice plant growth stages - the child > term > germination has no further subdivisions and we have been harvesting cell > types > from 0 hr (same as Embryo stage EM10) and 12 and 24 hr post imbibition > time > points from a germinating seed. So it would be great if you could possibly > add > these two ontologies as child terms under germination." > > I am not sure I understand exactly what you are asking, and I don't > remember > what Gramene use to have before, but your '0 hours.' should be equivalent > of > 'dry seed', right? > PO term 'imbibition' covers period up until radicle emergence takes place. > Your > '12 and 24 hours post imbibition' does not indicate if radicle emergence > stage > was reached at 24 hours post imbibition. Having had some experience (and > fun) > growing rice in the lab while I was posdoc, my recollection is that it > takes > little longer for radicle emergence in rice, but it also depends on the > temperature. For this very reason, we insist on morphological landmarks > for > creating and defining terms and not on less relevant and highly variable > parameters, such as days after anthesis, hours post imbibition, or very > disputable 'hours after germination'. Different rice varieties can reach > different stage (placed under different conditions) at '24 hours post > imbibition'. I agree that term 'imbibition' is a bit stretched, but am not > sure > if any new terms would provide adequate granularity that you are asking > for. > > You also asked: > "3. Also the definition of stomatal complex does not include the > subsidiary > cells and from what we have been looking around stomatal complex would be > guard > cell surrounding the stomata with the subsidiary cells." > > The definition doesn't, but 'subsidiary cell' is a child of 'stomatal > complex' > and so is 'guard cell'. Therefore, "guard and subsidiary cells are both a > part > of the stomatal complex", even though the definition of the 'stomatal > complex' > does not specifically say that. The ontology structure and term > relationships > provide such information. That is a benefit of having these terms in the > ontology, a lot of information is provided in the ontology structure > itself. > > I hope this helps, please, let me know if you have additional questions, > and > I'll get back to you regarding definitions of 'meristem' terms. > > Best regards, > > Katica > >> ---------- Forwarded message ---------- >> Date: Thu, 26 May 2005 19:35:44 -0400 >> From: fno.neeru at yale.edu >> To: Katica Ilic >> Subject: Re: Fwd: rice profiling project interest in developing cell >> type >> terms >> >> Hi Katica, >> This is from Neeru at Tim Nelson lab, Yale. We had met at the ontology >> workshop at PAG meeting. Sorry for the long silence. How are you doing. >> Over here we were wondering if you could help us out with some of the >> ontologies. Most of the ontologies that we are using are from the >> gramene website and fit really very well in defining our cell types >> and growth stages. There are few we have questions about... >> 1) the shoot apical meristem definition includes the axillary meristem >> and we were wondering if the two terms could be separated and have an >> axillary meristem and axillary primordium as separate ontological >> terms. >> 2) under the rice growth stages- rice plant growth stages- the child >> term germination has no furhter subdivisions and we have been >> harvesting cell types from 0 hr ( same as Embryo stage EM10) and 12 and >> 24 hr post imbibition time points from a germinating seed. So it would >> be great if you could possibly add these two ontologies as child terms >> under germination. >> 3) Also the definition of stomatal complex does not include the >> subsidiary cells and from what we have been looking around stomatal >> complex would be guard cell surrounding the stomata with the subsidiary >> cells. >> >> Please let us know what you think. Thanks >> Best Regards >> Neeru >> >> Quoting Katica Ilic : >> >>> >>> Dear Tim, >>> >>> Thank you for your message. I am glad to see that you are using >>> Plant >>> Ontologies, and I agree we need to work together to make it better. >>> >>> For the Plant Structure Ontology, this is a very good point you made, >>> we >>> haven't done any instantiation yet, that is, we have not propagated >>> each cell type >>> under every tissue of every organ, for the following reasons: >>> >>> 1. It would be to redundant, and ontology would end up be too large >>> and >>> difficult to search through since each cell type in each tissue of >>> the each organ would be a separate term, resulting in dozens of terms >>> that >>> would refer to for example, parenchyma cell type. This is the major >>> problem of our ontology (in a way, we inherited it from GO, but I >>> can >>> explain this some other time), and we are currently exploring >>> several >>> options. >>> >>> What we want to avoid, is to have several thousand terms in the >>> plant structure ontology, while the sum total of the plant anatomy >>> terms >>> is in fact less that thousand (by my rough estimate). >>> >>> 2. Even if we do end up instantiating terms and propagating plant >>> ontology, there is a fundamental conceptual problem here, that is, >>> this instatiation and term multiplication is against the modular >>> nature >>> that underlines the plant structure, for example, xylem element >>> is xylem element, regardless of its location, >>> therefore having several terms refering to the exact position of the >>> xylem >>> element wouldn't add up much, if there is only a better way to >>> indicate >>> this posiotional information, that is to use several terms in >>> conjuction >>> to describe cell type, it's location and dev stage. This so far is >>> not >>> possible and we are trying to figure out how to tackle this >>> computationaly. >>> >>> Lincoln Stain and toby Kellogg, two PIs on the POC project wrote a >>> document last summer, called 'Multiplicative chrisis" in which they >>> explianed this very problem. If you want to take a look, I can send >>> it to >>> you. >>> >>> For the developmental stages ontology, I understand this problem >>> too, >>> and I'll pass your question to the POC members in charge of this >>> aspect of >>> the ontology. It might be a couple of week before we get back to >>> you, >>> since soon we are all leaving for the PAG meeting in San Diego. >>> >>> I already check the PAG web site out, you are not registered, but if >>> you have >>> anyone from your group who is coming to this meeting, I would like to >>> arrange >>> for a meeting. I fact, I would suggest the Ontology workshop on >>> Monday Jan 17, >>> where all the POC members will be present. >>> >>> We also have our annual POC in-person meeting on Jan 18 and minutes >>> will >>> be posted on the POC web site. The "Multiplicative chrisis" document >>> is on >>> the agenda. >>> >>> Best regards, >>> >>> Katica >>> >>> >>> On Mon, 10 Jan 2005, Timothy Nelson wrote: >>> >>> > Dear Katica, >>> > We are finally at the point of needing to interface with the POC >>> to >>> > assure that our rice cell profiling data is tagged with a >>> > community-standard vocabulary. We have been pleased to see that >>> much >>> > new vocabulary has been added for rice at the Ontology website in >>> > recent weeks. We would like to work with you on several issues: >>> > >>> > 1. We will need to describe our data with greater precision than >>> is >>> > currently available. We find it difficult to distinguish between >>> > "plant" ontological terms and other terms. For example, how does >>> one >>> > tag data that needs info not just as to cell type, but for a >>> > particular cell type, within a particular organ, at a particular >>> zone >>> > within the organ, and all at a particular developmental stage? >>> > >>> > 2. What is the appropriate syntax for adding sub-descriptors? For >>> > example, there currently exist developmental stages described as >>> > "seedling", "1-4 leaf stage", "germination", etc., but our data >>> comes >>> > from much narrower windows than described with those terms. >>> > >>> > We realize it will be an ongoing process to refine the >>> vocabulary, >>> > and we look forward to being part of the process. >>> > >>> > Best regards, >>> > >>> > Tim Nelson >>> > Professor, Dept MCDB, Yale University >>> > >>> > >From: "Ware, Doreen" >>> > >To: "'timothy.nelson at yale.edu'" >>> > >Cc: "'Katica Ilic'" , >>> > > "Pankaj Jaiswal (E-mail)" >>> > > >>> > >Subject: rice profiling project interest in developing cell type >>> terms >>> > >Date: Wed, 29 Sep 2004 09:58:43 -0400 >>> > >X-YaleITSMailFilter: Version 1.1e (attachment(s) not renamed) >>> > >Status: RO >>> > > >>> > >Dear Dr. Nelson, >>> > > >>> > >Thank you for introducing yourself and your project "Virtual >>> center for >>> > >cellular expression profiling of rice" last week. I wanted to >>> follow-up and >>> > >introduce you to Katica Ilic the project coordinator for POC and >>> will be the >>> > >best contact person to discuss working within the POC framework to >>> develop >>> > >the correct terms and relationships for you project. Please feel >>> free to >>> > >email Katica with your specific questions or to use contact link >>> on the POC >>> > >website for po at plantontology.org. >>> > > >>> > >Doreen >>> > > >>> > > >>> > >Doreen Ware USDA ARS >>> > >Research Investigator >>> > >Cold Spring Harbor Laboratory >>> > >1 Bungtown Rd. >>> > >Cold Spring Harbor, NY 11724 >>> > >Phone: 516 367-6979 >>> > >Fax: 516 367-6851 >>> > >E-mail: ware at cshl.edu >>> > >>> >>> --------------------------------------------------------------------- >> ----- >>> 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 fno.neeru at yale.edu Wed Jun 1 13:35:54 2005 From: fno.neeru at yale.edu (fno.neeru at yale.edu) Date: Wed, 1 Jun 2005 13:35:54 -0400 Subject: Rice profiling project - interest in developing cell type terms (PR#64) In-Reply-To: <200506010028.j510SUPx010319@brie4.cshl.org> References: <200506010028.j510SUPx010319@brie4.cshl.org> Message-ID: <1117647354.429df1fa740b9@www.mail.yale.edu> Hi Katica, I agree with you on changing the definition, because when I was looking on the site for axillary meristem I could not find anything but now I do so as you mentioned changing the definition of some of the existing terms. I hope I have answered your questions. Thanks. Regards Neeru Quoting Katica Ilic : > Dear Neeru, > > Good to hear from you again. I am glad that PO is working for you and > that you > are able to find most of the terms that you need. I'll try addressing > your > questions, and also, I may have some specific questions for you > too: > > You asked: > "1) the shoot apical meristem definition includes the axillary > meristem and we > were wondering if the two terms could be separated and have an > axillary > meristem > and axillary primordium as separate ontological terms." > > No, actually, the second part of the definition of SAM refers to the > SAMs of > the > axillary shoots: > PO:0020148 - shoot apical meristem > Synonyms: apical meristem, primary shoot meristem > Definition: Meristem formed in the apex of the shoot, including > meristems > originating as axillary shoot meristems. > > I think what you are you asking about is 'meristem that is part of > the shoot > apex, in the axil of the leaf primordia', right? I think we would > need to > change > definitions for some of the existing PO terms, since we already have > terms such > as leaf primordium, SAM, shoot apex and axillary bud meristem. I'll > get back to > you regarding this once our group discusses it. > > These are the terms already in the PO, and I don't think we need to > add new > terms, but rather change definitions of the existing: > > PO:0020148 - shoot apical meristem > Synonyms: apical meristem, primary shoot meristem > Definition: Meristem formed in the apex of the shoot, including > meristems > originating as axillary shoot meristems. > > PO:0000037 - shoot apex > Definition: The topmost part of the shoot, situated at the distal > extremity of > the shoot axis, consists of apical meristem the youngest leaf > primordia. > > PO:0000232 - axillary bud meristem > Synonyms: axillary meristem > Definition: Meristems formed in the axil of the leaf. > > PO:0000017 - leaf primordium > Definition: An organized group of cells that will differentiate into > leaf that > are emerging as an outgrowth in the shoot apex (flanking the > meristem). > > Then, you asked: > "2) under the rice growth stages - rice plant growth stages - the > child term > germination has no further subdivisions and we have been harvesting > cell types > from 0 hr (same as Embryo stage EM10) and 12 and 24 hr post > imbibition time > points from a germinating seed. So it would be great if you could > possibly add > these two ontologies as child terms under germination." > > I am not sure I understand exactly what you are asking, and I don't > remember > what Gramene use to have before, but your '0 hours.' should be > equivalent of > 'dry seed', right? > PO term 'imbibition' covers period up until radicle emergence takes > place. Your > '12 and 24 hours post imbibition' does not indicate if radicle > emergence stage > was reached at 24 hours post imbibition. Having had some experience > (and fun) > growing rice in the lab while I was posdoc, my recollection is that > it takes > little longer for radicle emergence in rice, but it also depends on > the > temperature. For this very reason, we insist on morphological > landmarks for > creating and defining terms and not on less relevant and highly > variable > parameters, such as days after anthesis, hours post imbibition, or > very > disputable 'hours after germination'. Different rice varieties can > reach > different stage (placed under different conditions) at '24 hours > post > imbibition'. I agree that term 'imbibition' is a bit stretched, but > am not sure > if any new terms would provide adequate granularity that you are > asking for. > > You also asked: > "3. Also the definition of stomatal complex does not include the > subsidiary > cells and from what we have been looking around stomatal complex > would be guard > cell surrounding the stomata with the subsidiary cells." > > The definition doesn't, but 'subsidiary cell' is a child of 'stomatal > complex' > and so is 'guard cell'. Therefore, "guard and subsidiary cells are > both a part > of the stomatal complex", even though the definition of the 'stomatal > complex' > does not specifically say that. The ontology structure and term > relationships > provide such information. That is a benefit of having these terms in > the > ontology, a lot of information is provided in the ontology structure > itself. > > I hope this helps, please, let me know if you have additional > questions, and > I'll get back to you regarding definitions of 'meristem' terms. > > Best regards, > > Katica > > > ---------- Forwarded message ---------- > > Date: Thu, 26 May 2005 19:35:44 -0400 > > From: fno.neeru at yale.edu > > To: Katica Ilic > > Subject: Re: Fwd: rice profiling project interest in developing > cell type > > terms > > > > Hi Katica, > > This is from Neeru at Tim Nelson lab, Yale. We had met at the > ontology > > workshop at PAG meeting. Sorry for the long silence. How are you > doing. > > Over here we were wondering if you could help us out with some of > the > > ontologies. Most of the ontologies that we are using are from the > > gramene website and fit really very well in defining our cell > types > > and growth stages. There are few we have questions about... > > 1) the shoot apical meristem definition includes the axillary > meristem > > and we were wondering if the two terms could be separated and have > an > > axillary meristem and axillary primordium as separate ontological > > terms. > > 2) under the rice growth stages- rice plant growth stages- the > child > > term germination has no furhter subdivisions and we have been > > harvesting cell types from 0 hr ( same as Embryo stage EM10) and 12 > and > > 24 hr post imbibition time points from a germinating seed. So it > would > > be great if you could possibly add these two ontologies as child > terms > > under germination. > > 3) Also the definition of stomatal complex does not include the > > subsidiary cells and from what we have been looking around > stomatal > > complex would be guard cell surrounding the stomata with the > subsidiary > > cells. > > > > Please let us know what you think. Thanks > > Best Regards > > Neeru > > > > Quoting Katica Ilic : > > > >> > >> Dear Tim, > >> > >> Thank you for your message. I am glad to see that you are using > >> Plant > >> Ontologies, and I agree we need to work together to make it > better. > >> > >> For the Plant Structure Ontology, this is a very good point you > made, > >> we > >> haven't done any instantiation yet, that is, we have not > propagated > >> each cell type > >> under every tissue of every organ, for the following reasons: > >> > >> 1. It would be to redundant, and ontology would end up be too > large > >> and > >> difficult to search through since each cell type in each tissue > of > >> the each organ would be a separate term, resulting in dozens of > terms > >> that > >> would refer to for example, parenchyma cell type. This is the > major > >> problem of our ontology (in a way, we inherited it from GO, but > I > >> can > >> explain this some other time), and we are currently exploring > >> several > >> options. > >> > >> What we want to avoid, is to have several thousand terms in the > >> plant structure ontology, while the sum total of the plant > anatomy > >> terms > >> is in fact less that thousand (by my rough estimate). > >> > >> 2. Even if we do end up instantiating terms and propagating > plant > >> ontology, there is a fundamental conceptual problem here, that > is, > >> this instatiation and term multiplication is against the modular > >> nature > >> that underlines the plant structure, for example, xylem element > >> is xylem element, regardless of its location, > >> therefore having several terms refering to the exact position of > the > >> xylem > >> element wouldn't add up much, if there is only a better way to > >> indicate > >> this posiotional information, that is to use several terms in > >> conjuction > >> to describe cell type, it's location and dev stage. This so far > is > >> not > >> possible and we are trying to figure out how to tackle this > >> computationaly. > >> > >> Lincoln Stain and toby Kellogg, two PIs on the POC project wrote > a > >> document last summer, called 'Multiplicative chrisis" in which > they > >> explianed this very problem. If you want to take a look, I can > send > >> it to > >> you. > >> > >> For the developmental stages ontology, I understand this problem > >> too, > >> and I'll pass your question to the POC members in charge of this > >> aspect of > >> the ontology. It might be a couple of week before we get back to > >> you, > >> since soon we are all leaving for the PAG meeting in San Diego. > >> > >> I already check the PAG web site out, you are not registered, but > if > >> you have > >> anyone from your group who is coming to this meeting, I would like > to > >> arrange > >> for a meeting. I fact, I would suggest the Ontology workshop on > >> Monday Jan 17, > >> where all the POC members will be present. > >> > >> We also have our annual POC in-person meeting on Jan 18 and > minutes > >> will > >> be posted on the POC web site. The "Multiplicative chrisis" > document > >> is on > >> the agenda. > >> > >> Best regards, > >> > >> Katica > >> > >> > >> On Mon, 10 Jan 2005, Timothy Nelson wrote: > >> > >> > Dear Katica, > >> > We are finally at the point of needing to interface with the > POC > >> to > >> > assure that our rice cell profiling data is tagged with a > >> > community-standard vocabulary. We have been pleased to see > that > >> much > >> > new vocabulary has been added for rice at the Ontology website > in > >> > recent weeks. We would like to work with you on several > issues: > >> > > >> > 1. We will need to describe our data with greater precision > than > >> is > >> > currently available. We find it difficult to distinguish > between > >> > "plant" ontological terms and other terms. For example, how > does > >> one > >> > tag data that needs info not just as to cell type, but for a > >> > particular cell type, within a particular organ, at a > particular > >> zone > >> > within the organ, and all at a particular developmental stage? > >> > > >> > 2. What is the appropriate syntax for adding sub-descriptors? > For > >> > example, there currently exist developmental stages described > as > >> > "seedling", "1-4 leaf stage", "germination", etc., but our > data > >> comes > >> > from much narrower windows than described with those terms. > >> > > >> > We realize it will be an ongoing process to refine the > >> vocabulary, > >> > and we look forward to being part of the process. > >> > > >> > Best regards, > >> > > >> > Tim Nelson > >> > Professor, Dept MCDB, Yale University > >> > > >> > >From: "Ware, Doreen" > >> > >To: "'timothy.nelson at yale.edu'" > >> > >Cc: "'Katica Ilic'" , > >> > > "Pankaj Jaiswal (E-mail)" > >> > > > >> > >Subject: rice profiling project interest in developing cell > type > >> terms > >> > >Date: Wed, 29 Sep 2004 09:58:43 -0400 > >> > >X-YaleITSMailFilter: Version 1.1e (attachment(s) not renamed) > >> > >Status: RO > >> > > > >> > >Dear Dr. Nelson, > >> > > > >> > >Thank you for introducing yourself and your project "Virtual > >> center for > >> > >cellular expression profiling of rice" last week. I wanted > to > >> follow-up and > >> > >introduce you to Katica Ilic the project coordinator for POC > and > >> will be the > >> > >best contact person to discuss working within the POC framework > to > >> develop > >> > >the correct terms and relationships for you project. Please > feel > >> free to > >> > >email Katica with your specific questions or to use contact > link > >> on the POC > >> > >website for po at plantontology.org. > >> > > > >> > >Doreen > >> > > > >> > > > >> > >Doreen Ware USDA ARS > >> > >Research Investigator > >> > >Cold Spring Harbor Laboratory > >> > >1 Bungtown Rd. > >> > >Cold Spring Harbor, NY 11724 > >> > >Phone: 516 367-6979 > >> > >Fax: 516 367-6851 > >> > >E-mail: ware at cshl.edu > >> > > >> > >> > --------------------------------------------------------------------- > > ----- > >> 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 Wed Jun 1 16:52:36 2005 From: jitterbug at plantontology.org (Katica Ilic) Date: Wed, 1 Jun 2005 16:52:36 -0400 Subject: Rice profiling project - interest in developing cell type terms (PR#64) Message-ID: <200506012052.j51KqaPx025162@brie4.cshl.org> Hi Neeru, Reading back your initial e-mail, it occured to me that you are still using Gramene Growth Stages Ontology. We talked about the release of POC Growth Stages at the meeting in San Diego, and Tim Nelson was invited to participate in the pre-release ontology reviewing process, so I thought that you have seen and used the new POC ontology. However, in case you haven't, I just want to let you know that the Plant Growth Stages Ontology was released about a month ago, you can browse it on the POC web site: www.plantontology.org. I'll let you know soon about the updates of the definitions for the terms in question. Thanks you for contacting POC, I look forward to hearing from you in future. Best regards, Katica > Hi Katica, > I agree with you on changing the definition, because when I was looking > on the site for axillary meristem I could not find anything but now I > do so as you mentioned changing the definition of some of the existing > terms. I hope I have answered your questions. Thanks. > Regards > Neeru > Quoting Katica Ilic : > >> Dear Neeru, >> >> Good to hear from you again. I am glad that PO is working for you and >> that you >> are able to find most of the terms that you need. I'll try addressing >> your >> questions, and also, I may have some specific questions for you >> too: >> >> You asked: >> "1) the shoot apical meristem definition includes the axillary >> meristem and we >> were wondering if the two terms could be separated and have an >> axillary >> meristem >> and axillary primordium as separate ontological terms." >> >> No, actually, the second part of the definition of SAM refers to the >> SAMs of >> the >> axillary shoots: >> PO:0020148 - shoot apical meristem >> Synonyms: apical meristem, primary shoot meristem >> Definition: Meristem formed in the apex of the shoot, including >> meristems >> originating as axillary shoot meristems. >> >> I think what you are you asking about is 'meristem that is part of >> the shoot >> apex, in the axil of the leaf primordia', right? I think we would >> need to >> change >> definitions for some of the existing PO terms, since we already have >> terms such >> as leaf primordium, SAM, shoot apex and axillary bud meristem. I'll >> get back to >> you regarding this once our group discusses it. >> >> These are the terms already in the PO, and I don't think we need to >> add new >> terms, but rather change definitions of the existing: >> >> PO:0020148 - shoot apical meristem >> Synonyms: apical meristem, primary shoot meristem >> Definition: Meristem formed in the apex of the shoot, including >> meristems >> originating as axillary shoot meristems. >> >> PO:0000037 - shoot apex >> Definition: The topmost part of the shoot, situated at the distal >> extremity of >> the shoot axis, consists of apical meristem the youngest leaf >> primordia. >> >> PO:0000232 - axillary bud meristem >> Synonyms: axillary meristem >> Definition: Meristems formed in the axil of the leaf. >> >> PO:0000017 - leaf primordium >> Definition: An organized group of cells that will differentiate into >> leaf that >> are emerging as an outgrowth in the shoot apex (flanking the >> meristem). >> >> Then, you asked: >> "2) under the rice growth stages - rice plant growth stages - the >> child term >> germination has no further subdivisions and we have been harvesting >> cell types >> from 0 hr (same as Embryo stage EM10) and 12 and 24 hr post >> imbibition time >> points from a germinating seed. So it would be great if you could >> possibly add >> these two ontologies as child terms under germination." >> >> I am not sure I understand exactly what you are asking, and I don't >> remember >> what Gramene use to have before, but your '0 hours.' should be >> equivalent of >> 'dry seed', right? >> PO term 'imbibition' covers period up until radicle emergence takes >> place. Your >> '12 and 24 hours post imbibition' does not indicate if radicle >> emergence stage >> was reached at 24 hours post imbibition. Having had some experience >> (and fun) >> growing rice in the lab while I was posdoc, my recollection is that >> it takes >> little longer for radicle emergence in rice, but it also depends on >> the >> temperature. For this very reason, we insist on morphological >> landmarks for >> creating and defining terms and not on less relevant and highly >> variable >> parameters, such as days after anthesis, hours post imbibition, or >> very >> disputable 'hours after germination'. Different rice varieties can >> reach >> different stage (placed under different conditions) at '24 hours >> post >> imbibition'. I agree that term 'imbibition' is a bit stretched, but >> am not sure >> if any new terms would provide adequate granularity that you are >> asking for. >> >> You also asked: >> "3. Also the definition of stomatal complex does not include the >> subsidiary >> cells and from what we have been looking around stomatal complex >> would be guard >> cell surrounding the stomata with the subsidiary cells." >> >> The definition doesn't, but 'subsidiary cell' is a child of 'stomatal >> complex' >> and so is 'guard cell'. Therefore, "guard and subsidiary cells are >> both a part >> of the stomatal complex", even though the definition of the 'stomatal >> complex' >> does not specifically say that. The ontology structure and term >> relationships >> provide such information. That is a benefit of having these terms in >> the >> ontology, a lot of information is provided in the ontology structure >> itself. >> >> I hope this helps, please, let me know if you have additional >> questions, and >> I'll get back to you regarding definitions of 'meristem' terms. >> >> Best regards, >> >> Katica >> >> > ---------- Forwarded message ---------- >> > Date: Thu, 26 May 2005 19:35:44 -0400 >> > From: fno.neeru at yale.edu >> > To: Katica Ilic >> > Subject: Re: Fwd: rice profiling project interest in developing >> cell type >> > terms >> > >> > Hi Katica, >> > This is from Neeru at Tim Nelson lab, Yale. We had met at the >> ontology >> > workshop at PAG meeting. Sorry for the long silence. How are you >> doing. >> > Over here we were wondering if you could help us out with some of >> the >> > ontologies. Most of the ontologies that we are using are from the >> > gramene website and fit really very well in defining our cell >> types >> > and growth stages. There are few we have questions about... >> > 1) the shoot apical meristem definition includes the axillary >> meristem >> > and we were wondering if the two terms could be separated and have >> an >> > axillary meristem and axillary primordium as separate ontological >> > terms. >> > 2) under the rice growth stages- rice plant growth stages- the >> child >> > term germination has no furhter subdivisions and we have been >> > harvesting cell types from 0 hr ( same as Embryo stage EM10) and 12 >> and >> > 24 hr post imbibition time points from a germinating seed. So it >> would >> > be great if you could possibly add these two ontologies as child >> terms >> > under germination. >> > 3) Also the definition of stomatal complex does not include the >> > subsidiary cells and from what we have been looking around >> stomatal >> > complex would be guard cell surrounding the stomata with the >> subsidiary >> > cells. >> > >> > Please let us know what you think. Thanks >> > Best Regards >> > Neeru >> > >> > Quoting Katica Ilic : >> > >> >> >> >> Dear Tim, >> >> >> >> Thank you for your message. I am glad to see that you are using >> >> Plant >> >> Ontologies, and I agree we need to work together to make it >> better. >> >> >> >> For the Plant Structure Ontology, this is a very good point you >> made, >> >> we >> >> haven't done any instantiation yet, that is, we have not >> propagated >> >> each cell type >> >> under every tissue of every organ, for the following reasons: >> >> >> >> 1. It would be to redundant, and ontology would end up be too >> large >> >> and >> >> difficult to search through since each cell type in each tissue >> of >> >> the each organ would be a separate term, resulting in dozens of >> terms >> >> that >> >> would refer to for example, parenchyma cell type. This is the >> major >> >> problem of our ontology (in a way, we inherited it from GO, but >> I >> >> can >> >> explain this some other time), and we are currently exploring >> >> several >> >> options. >> >> >> >> What we want to avoid, is to have several thousand terms in the >> >> plant structure ontology, while the sum total of the plant >> anatomy >> >> terms >> >> is in fact less that thousand (by my rough estimate). >> >> >> >> 2. Even if we do end up instantiating terms and propagating >> plant >> >> ontology, there is a fundamental conceptual problem here, that >> is, >> >> this instatiation and term multiplication is against the modular >> >> nature >> >> that underlines the plant structure, for example, xylem element >> >> is xylem element, regardless of its location, >> >> therefore having several terms refering to the exact position of >> the >> >> xylem >> >> element wouldn't add up much, if there is only a better way to >> >> indicate >> >> this posiotional information, that is to use several terms in >> >> conjuction >> >> to describe cell type, it's location and dev stage. This so far >> is >> >> not >> >> possible and we are trying to figure out how to tackle this >> >> computationaly. >> >> >> >> Lincoln Stain and toby Kellogg, two PIs on the POC project wrote >> a >> >> document last summer, called 'Multiplicative chrisis" in which >> they >> >> explianed this very problem. If you want to take a look, I can >> send >> >> it to >> >> you. >> >> >> >> For the developmental stages ontology, I understand this problem >> >> too, >> >> and I'll pass your question to the POC members in charge of this >> >> aspect of >> >> the ontology. It might be a couple of week before we get back to >> >> you, >> >> since soon we are all leaving for the PAG meeting in San Diego. >> >> >> >> I already check the PAG web site out, you are not registered, but >> if >> >> you have >> >> anyone from your group who is coming to this meeting, I would like >> to >> >> arrange >> >> for a meeting. I fact, I would suggest the Ontology workshop on >> >> Monday Jan 17, >> >> where all the POC members will be present. >> >> >> >> We also have our annual POC in-person meeting on Jan 18 and >> minutes >> >> will >> >> be posted on the POC web site. The "Multiplicative chrisis" >> document >> >> is on >> >> the agenda. >> >> >> >> Best regards, >> >> >> >> Katica >> >> >> >> >> >> On Mon, 10 Jan 2005, Timothy Nelson wrote: >> >> >> >> > Dear Katica, >> >> > We are finally at the point of needing to interface with the >> POC >> >> to >> >> > assure that our rice cell profiling data is tagged with a >> >> > community-standard vocabulary. We have been pleased to see >> that >> >> much >> >> > new vocabulary has been added for rice at the Ontology website >> in >> >> > recent weeks. We would like to work with you on several >> issues: >> >> > >> >> > 1. We will need to describe our data with greater precision >> than >> >> is >> >> > currently available. We find it difficult to distinguish >> between >> >> > "plant" ontological terms and other terms. For example, how >> does >> >> one >> >> > tag data that needs info not just as to cell type, but for a >> >> > particular cell type, within a particular organ, at a >> particular >> >> zone >> >> > within the organ, and all at a particular developmental stage? >> >> > >> >> > 2. What is the appropriate syntax for adding sub-descriptors? >> For >> >> > example, there currently exist developmental stages described >> as >> >> > "seedling", "1-4 leaf stage", "germination", etc., but our >> data >> >> comes >> >> > from much narrower windows than described with those terms. >> >> > >> >> > We realize it will be an ongoing process to refine the >> >> vocabulary, >> >> > and we look forward to being part of the process. >> >> > >> >> > Best regards, >> >> > >> >> > Tim Nelson >> >> > Professor, Dept MCDB, Yale University >> >> > >> >> > >From: "Ware, Doreen" >> >> > >To: "'timothy.nelson at yale.edu'" >> >> > >Cc: "'Katica Ilic'" , >> >> > > "Pankaj Jaiswal (E-mail)" >> >> > > >> >> > >Subject: rice profiling project interest in developing cell >> type >> >> terms >> >> > >Date: Wed, 29 Sep 2004 09:58:43 -0400 >> >> > >X-YaleITSMailFilter: Version 1.1e (attachment(s) not renamed) >> >> > >Status: RO >> >> > > >> >> > >Dear Dr. Nelson, >> >> > > >> >> > >Thank you for introducing yourself and your project "Virtual >> >> center for >> >> > >cellular expression profiling of rice" last week. I wanted >> to >> >> follow-up and >> >> > >introduce you to Katica Ilic the project coordinator for POC >> and >> >> will be the >> >> > >best contact person to discuss working within the POC framework >> to >> >> develop >> >> > >the correct terms and relationships for you project. Please >> feel >> >> free to >> >> > >email Katica with your specific questions or to use contact >> link >> >> on the POC >> >> > >website for po at plantontology.org. >> >> > > >> >> > >Doreen >> >> > > >> >> > > >> >> > >Doreen Ware USDA ARS >> >> > >Research Investigator >> >> > >Cold Spring Harbor Laboratory >> >> > >1 Bungtown Rd. >> >> > >Cold Spring Harbor, NY 11724 >> >> > >Phone: 516 367-6979 >> >> > >Fax: 516 367-6851 >> >> > >E-mail: ware at cshl.edu >> >> > >> >> >> >> >> --------------------------------------------------------------------- >> > ----- >> >> 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 fno.neeru at yale.edu Thu Jun 2 13:45:24 2005 From: fno.neeru at yale.edu (fno.neeru at yale.edu) Date: Thu, 2 Jun 2005 13:45:24 -0400 Subject: Rice profiling project - interest in developing cell type terms (PR#64) In-Reply-To: <200506012052.j51KqaPx025162@brie4.cshl.org> References: <200506012052.j51KqaPx025162@brie4.cshl.org> Message-ID: <1117734324.429f45b41b53b@www.mail.yale.edu> Hi Katica, I thought that Gramene and TAIR were using plant structure and GRO ontologies developed by POC. But anyways I am browsing on the POC site and this site has links to the gramene ontology in itself. So for cereals it has link to the Gramene site and I clicked browse and it shows me the ontologies for rice. Tim could not make it for the meeting and so I attended the ontology workshop on his behalf. I was wondering do you have the email i.d of Anu who was also at the workshop as I have to get a few good references for rice she had mentioned about at the meeting. Thanks for your help. Regards Neeru Quoting Katica Ilic : > Hi Neeru, > > Reading back your initial e-mail, it occured to me that you are still > using > Gramene Growth Stages Ontology. We talked about the release of POC > Growth > Stages at the meeting in San Diego, and Tim Nelson was invited to > participate in > the pre-release ontology reviewing process, so I thought that you > have seen and > used the new POC ontology. However, in case you haven't, I just want > to let you > know that the Plant Growth Stages Ontology was released about a month > ago, you > can browse it on the POC web site: www.plantontology.org. > > I'll let you know soon about the updates of the definitions for the > terms in > question. > > Thanks you for contacting POC, I look forward to hearing from you in > future. > > Best regards, > > Katica > > > Hi Katica, > > I agree with you on changing the definition, because when I was > looking > > on the site for axillary meristem I could not find anything but now > I > > do so as you mentioned changing the definition of some of the > existing > > terms. I hope I have answered your questions. Thanks. > > Regards > > Neeru > > Quoting Katica Ilic : > > > >> Dear Neeru, > >> > >> Good to hear from you again. I am glad that PO is working for you > and > >> that you > >> are able to find most of the terms that you need. I'll try > addressing > >> your > >> questions, and also, I may have some specific questions for you > >> too: > >> > >> You asked: > >> "1) the shoot apical meristem definition includes the axillary > >> meristem and we > >> were wondering if the two terms could be separated and have an > >> axillary > >> meristem > >> and axillary primordium as separate ontological terms." > >> > >> No, actually, the second part of the definition of SAM refers to > the > >> SAMs of > >> the > >> axillary shoots: > >> PO:0020148 - shoot apical meristem > >> Synonyms: apical meristem, primary shoot meristem > >> Definition: Meristem formed in the apex of the shoot, including > >> meristems > >> originating as axillary shoot meristems. > >> > >> I think what you are you asking about is 'meristem that is part > of > >> the shoot > >> apex, in the axil of the leaf primordia', right? I think we > would > >> need to > >> change > >> definitions for some of the existing PO terms, since we already > have > >> terms such > >> as leaf primordium, SAM, shoot apex and axillary bud meristem. > I'll > >> get back to > >> you regarding this once our group discusses it. > >> > >> These are the terms already in the PO, and I don't think we need > to > >> add new > >> terms, but rather change definitions of the existing: > >> > >> PO:0020148 - shoot apical meristem > >> Synonyms: apical meristem, primary shoot meristem > >> Definition: Meristem formed in the apex of the shoot, including > >> meristems > >> originating as axillary shoot meristems. > >> > >> PO:0000037 - shoot apex > >> Definition: The topmost part of the shoot, situated at the > distal > >> extremity of > >> the shoot axis, consists of apical meristem the youngest leaf > >> primordia. > >> > >> PO:0000232 - axillary bud meristem > >> Synonyms: axillary meristem > >> Definition: Meristems formed in the axil of the leaf. > >> > >> PO:0000017 - leaf primordium > >> Definition: An organized group of cells that will differentiate > into > >> leaf that > >> are emerging as an outgrowth in the shoot apex (flanking the > >> meristem). > >> > >> Then, you asked: > >> "2) under the rice growth stages - rice plant growth stages - > the > >> child term > >> germination has no further subdivisions and we have been > harvesting > >> cell types > >> from 0 hr (same as Embryo stage EM10) and 12 and 24 hr post > >> imbibition time > >> points from a germinating seed. So it would be great if you > could > >> possibly add > >> these two ontologies as child terms under germination." > >> > >> I am not sure I understand exactly what you are asking, and I > don't > >> remember > >> what Gramene use to have before, but your '0 hours.' should be > >> equivalent of > >> 'dry seed', right? > >> PO term 'imbibition' covers period up until radicle emergence > takes > >> place. Your > >> '12 and 24 hours post imbibition' does not indicate if radicle > >> emergence stage > >> was reached at 24 hours post imbibition. Having had some > experience > >> (and fun) > >> growing rice in the lab while I was posdoc, my recollection is > that > >> it takes > >> little longer for radicle emergence in rice, but it also depends > on > >> the > >> temperature. For this very reason, we insist on morphological > >> landmarks for > >> creating and defining terms and not on less relevant and highly > >> variable > >> parameters, such as days after anthesis, hours post imbibition, > or > >> very > >> disputable 'hours after germination'. Different rice varieties > can > >> reach > >> different stage (placed under different conditions) at '24 hours > >> post > >> imbibition'. I agree that term 'imbibition' is a bit stretched, > but > >> am not sure > >> if any new terms would provide adequate granularity that you are > >> asking for. > >> > >> You also asked: > >> "3. Also the definition of stomatal complex does not include the > >> subsidiary > >> cells and from what we have been looking around stomatal complex > >> would be guard > >> cell surrounding the stomata with the subsidiary cells." > >> > >> The definition doesn't, but 'subsidiary cell' is a child of > 'stomatal > >> complex' > >> and so is 'guard cell'. Therefore, "guard and subsidiary cells > are > >> both a part > >> of the stomatal complex", even though the definition of the > 'stomatal > >> complex' > >> does not specifically say that. The ontology structure and term > >> relationships > >> provide such information. That is a benefit of having these terms > in > >> the > >> ontology, a lot of information is provided in the ontology > structure > >> itself. > >> > >> I hope this helps, please, let me know if you have additional > >> questions, and > >> I'll get back to you regarding definitions of 'meristem' terms. > >> > >> Best regards, > >> > >> Katica > >> > >> > ---------- Forwarded message ---------- > >> > Date: Thu, 26 May 2005 19:35:44 -0400 > >> > From: fno.neeru at yale.edu > >> > To: Katica Ilic > >> > Subject: Re: Fwd: rice profiling project interest in > developing > >> cell type > >> > terms > >> > > >> > Hi Katica, > >> > This is from Neeru at Tim Nelson lab, Yale. We had met at the > >> ontology > >> > workshop at PAG meeting. Sorry for the long silence. How are > you > >> doing. > >> > Over here we were wondering if you could help us out with some > of > >> the > >> > ontologies. Most of the ontologies that we are using are from > the > >> > gramene website and fit really very well in defining our cell > >> types > >> > and growth stages. There are few we have questions about... > >> > 1) the shoot apical meristem definition includes the axillary > >> meristem > >> > and we were wondering if the two terms could be separated and > have > >> an > >> > axillary meristem and axillary primordium as separate > ontological > >> > terms. > >> > 2) under the rice growth stages- rice plant growth stages- the > >> child > >> > term germination has no furhter subdivisions and we have been > >> > harvesting cell types from 0 hr ( same as Embryo stage EM10) and > 12 > >> and > >> > 24 hr post imbibition time points from a germinating seed. So > it > >> would > >> > be great if you could possibly add these two ontologies as > child > >> terms > >> > under germination. > >> > 3) Also the definition of stomatal complex does not include > the > >> > subsidiary cells and from what we have been looking around > >> stomatal > >> > complex would be guard cell surrounding the stomata with the > >> subsidiary > >> > cells. > >> > > >> > Please let us know what you think. Thanks > >> > Best Regards > >> > Neeru > >> > > >> > Quoting Katica Ilic : > >> > > >> >> > >> >> Dear Tim, > >> >> > >> >> Thank you for your message. I am glad to see that you are > using > >> >> Plant > >> >> Ontologies, and I agree we need to work together to make it > >> better. > >> >> > >> >> For the Plant Structure Ontology, this is a very good point > you > >> made, > >> >> we > >> >> haven't done any instantiation yet, that is, we have not > >> propagated > >> >> each cell type > >> >> under every tissue of every organ, for the following reasons: > >> >> > >> >> 1. It would be to redundant, and ontology would end up be too > >> large > >> >> and > >> >> difficult to search through since each cell type in each > tissue > >> of > >> >> the each organ would be a separate term, resulting in dozens > of > >> terms > >> >> that > >> >> would refer to for example, parenchyma cell type. This is the > >> major > >> >> problem of our ontology (in a way, we inherited it from GO, > but > >> I > >> >> can > >> >> explain this some other time), and we are currently exploring > >> >> several > >> >> options. > >> >> > >> >> What we want to avoid, is to have several thousand terms in > the > >> >> plant structure ontology, while the sum total of the plant > >> anatomy > >> >> terms > >> >> is in fact less that thousand (by my rough estimate). > >> >> > >> >> 2. Even if we do end up instantiating terms and propagating > >> plant > >> >> ontology, there is a fundamental conceptual problem here, > that > >> is, > >> >> this instatiation and term multiplication is against the > modular > >> >> nature > >> >> that underlines the plant structure, for example, xylem > element > >> >> is xylem element, regardless of its location, > >> >> therefore having several terms refering to the exact position > of > >> the > >> >> xylem > >> >> element wouldn't add up much, if there is only a better way > to > >> >> indicate > >> >> this posiotional information, that is to use several terms in > >> >> conjuction > >> >> to describe cell type, it's location and dev stage. This so > far > >> is > >> >> not > >> >> possible and we are trying to figure out how to tackle this > >> >> computationaly. > >> >> > >> >> Lincoln Stain and toby Kellogg, two PIs on the POC project > wrote > >> a > >> >> document last summer, called 'Multiplicative chrisis" in > which > >> they > >> >> explianed this very problem. If you want to take a look, I > can > >> send > >> >> it to > >> >> you. > >> >> > >> >> For the developmental stages ontology, I understand this > problem > >> >> too, > >> >> and I'll pass your question to the POC members in charge of > this > >> >> aspect of > >> >> the ontology. It might be a couple of week before we get back > to > >> >> you, > >> >> since soon we are all leaving for the PAG meeting in San > Diego. > >> >> > >> >> I already check the PAG web site out, you are not registered, > but > >> if > >> >> you have > >> >> anyone from your group who is coming to this meeting, I would > like > >> to > >> >> arrange > >> >> for a meeting. I fact, I would suggest the Ontology workshop > on > >> >> Monday Jan 17, > >> >> where all the POC members will be present. > >> >> > >> >> We also have our annual POC in-person meeting on Jan 18 and > >> minutes > >> >> will > >> >> be posted on the POC web site. The "Multiplicative chrisis" > >> document > >> >> is on > >> >> the agenda. > >> >> > >> >> Best regards, > >> >> > >> >> Katica > >> >> > >> >> > >> >> On Mon, 10 Jan 2005, Timothy Nelson wrote: > >> >> > >> >> > Dear Katica, > >> >> > We are finally at the point of needing to interface with > the > >> POC > >> >> to > >> >> > assure that our rice cell profiling data is tagged with a > >> >> > community-standard vocabulary. We have been pleased to see > >> that > >> >> much > >> >> > new vocabulary has been added for rice at the Ontology > website > >> in > >> >> > recent weeks. We would like to work with you on several > >> issues: > >> >> > > >> >> > 1. We will need to describe our data with greater precision > >> than > >> >> is > >> >> > currently available. We find it difficult to distinguish > >> between > >> >> > "plant" ontological terms and other terms. For example, how > >> does > >> >> one > >> >> > tag data that needs info not just as to cell type, but for > a > >> >> > particular cell type, within a particular organ, at a > >> particular > >> >> zone > >> >> > within the organ, and all at a particular developmental > stage? > >> >> > > >> >> > 2. What is the appropriate syntax for adding > sub-descriptors? > >> For > >> >> > example, there currently exist developmental stages > described > >> as > >> >> > "seedling", "1-4 leaf stage", "germination", etc., but our > >> data > >> >> comes > >> >> > from much narrower windows than described with those terms. > >> >> > > >> >> > We realize it will be an ongoing process to refine the > >> >> vocabulary, > >> >> > and we look forward to being part of the process. > >> >> > > >> >> > Best regards, > >> >> > > >> >> > Tim Nelson > >> >> > Professor, Dept MCDB, Yale University > >> >> > > >> >> > >From: "Ware, Doreen" > >> >> > >To: "'timothy.nelson at yale.edu'" > >> >> > >Cc: "'Katica Ilic'" , > >> >> > > "Pankaj Jaiswal (E-mail)" > >> >> > > > >> >> > >Subject: rice profiling project interest in developing > cell > >> type > >> >> terms > >> >> > >Date: Wed, 29 Sep 2004 09:58:43 -0400 > >> >> > >X-YaleITSMailFilter: Version 1.1e (attachment(s) not > renamed) > >> >> > >Status: RO > >> >> > > > >> >> > >Dear Dr. Nelson, > >> >> > > > >> >> > >Thank you for introducing yourself and your project > "Virtual > >> >> center for > >> >> > >cellular expression profiling of rice" last week. I > wanted > >> to > >> >> follow-up and > >> >> > >introduce you to Katica Ilic the project coordinator for > POC > >> and > >> >> will be the > >> >> > >best contact person to discuss working within the POC > framework > >> to > >> >> develop > >> >> > >the correct terms and relationships for you project. > Please > >> feel > >> >> free to > >> >> > >email Katica with your specific questions or to use > contact > >> link > >> >> on the POC > >> >> > >website for po at plantontology.org. > >> >> > > > >> >> > >Doreen > >> >> > > > >> >> > > > >> >> > >Doreen Ware USDA ARS > >> >> > >Research Investigator > >> >> > >Cold Spring Harbor Laboratory > >> >> > >1 Bungtown Rd. > >> >> > >Cold Spring Harbor, NY 11724 > >> >> > >Phone: 516 367-6979 > >> >> > >Fax: 516 367-6851 > >> >> > >E-mail: ware at cshl.edu > >> >> > > >> >> > >> >> > >> > --------------------------------------------------------------------- > >> > ----- > >> >> 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 Thu Jun 2 16:06:01 2005 From: jitterbug at plantontology.org (Katica Ilic) Date: Thu, 2 Jun 2005 16:06:01 -0400 Subject: Rice profiling project - interest in developing cell type terms (PR#64) Message-ID: <200506022006.j52K61Px004696@brie4.cshl.org> Hi Neeru, I thought that it would confuse people who are using POC and Gramene site interchangeably. The reason is, Gramene (and TAIR) already switched to using Plant Structure Ontology, so if you go to the Gramene site (ontology view) or to TAIR Keword Browser, you would find PO terms from the Plant Structure Ontology, however, you would also come across Gramene and TAIR temporal ontologies, since both databases are still maintaining their species-specific Growth and Development Stages. Therefore, GRO terms in temporal ontology at Gramene site are not the same as the PO Plant Growth Stages terms. Plant Growth Stages can be browsed only at the POC web site, until both databases switch to PO temporal ontology. Here at TAIR, we plan to completely switch to PO by the end of the year, the latest. You will be hearing from Anu soon. Best regards, Katica > Hi Katica, > > I thought that Gramene and TAIR were using plant structure and GRO > ontologies developed by POC. But anyways I am browsing on the POC site > and this site has links to the gramene ontology in itself. So for > cereals it has link to the Gramene site and I clicked browse and it > shows me the ontologies for rice. Tim could not make it for the meeting > and so I attended the ontology workshop on his behalf. > > I was wondering do you have the email i.d of Anu who was also at the > workshop as I have to get a few good references for rice she had > mentioned about at the meeting. > > Thanks for your help. > > Regards > > Neeru > > > > Quoting Katica Ilic : > >> Hi Neeru, >> >> Reading back your initial e-mail, it occured to me that you are still >> using >> Gramene Growth Stages Ontology. We talked about the release of POC >> Growth >> Stages at the meeting in San Diego, and Tim Nelson was invited to >> participate in >> the pre-release ontology reviewing process, so I thought that you >> have seen and >> used the new POC ontology. However, in case you haven't, I just want >> to let you >> know that the Plant Growth Stages Ontology was released about a month >> ago, you >> can browse it on the POC web site: www.plantontology.org. >> >> I'll let you know soon about the updates of the definitions for the >> terms in >> question. >> >> Thanks you for contacting POC, I look forward to hearing from you in >> future. >> >> Best regards, >> >> Katica >> >> > Hi Katica, >> > I agree with you on changing the definition, because when I was >> looking >> > on the site for axillary meristem I could not find anything but now >> I >> > do so as you mentioned changing the definition of some of the >> existing >> > terms. I hope I have answered your questions. Thanks. >> > Regards >> > Neeru >> > Quoting Katica Ilic : >> > >> >> Dear Neeru, >> >> >> >> Good to hear from you again. I am glad that PO is working for you >> and >> >> that you >> >> are able to find most of the terms that you need. I'll try >> addressing >> >> your >> >> questions, and also, I may have some specific questions for you >> >> too: >> >> >> >> You asked: >> >> "1) the shoot apical meristem definition includes the axillary >> >> meristem and we >> >> were wondering if the two terms could be separated and have an >> >> axillary >> >> meristem >> >> and axillary primordium as separate ontological terms." >> >> >> >> No, actually, the second part of the definition of SAM refers to >> the >> >> SAMs of >> >> the >> >> axillary shoots: >> >> PO:0020148 - shoot apical meristem >> >> Synonyms: apical meristem, primary shoot meristem >> >> Definition: Meristem formed in the apex of the shoot, including >> >> meristems >> >> originating as axillary shoot meristems. >> >> >> >> I think what you are you asking about is 'meristem that is part >> of >> >> the shoot >> >> apex, in the axil of the leaf primordia', right? I think we >> would >> >> need to >> >> change >> >> definitions for some of the existing PO terms, since we already >> have >> >> terms such >> >> as leaf primordium, SAM, shoot apex and axillary bud meristem. >> I'll >> >> get back to >> >> you regarding this once our group discusses it. >> >> >> >> These are the terms already in the PO, and I don't think we need >> to >> >> add new >> >> terms, but rather change definitions of the existing: >> >> >> >> PO:0020148 - shoot apical meristem >> >> Synonyms: apical meristem, primary shoot meristem >> >> Definition: Meristem formed in the apex of the shoot, including >> >> meristems >> >> originating as axillary shoot meristems. >> >> >> >> PO:0000037 - shoot apex >> >> Definition: The topmost part of the shoot, situated at the >> distal >> >> extremity of >> >> the shoot axis, consists of apical meristem the youngest leaf >> >> primordia. >> >> >> >> PO:0000232 - axillary bud meristem >> >> Synonyms: axillary meristem >> >> Definition: Meristems formed in the axil of the leaf. >> >> >> >> PO:0000017 - leaf primordium >> >> Definition: An organized group of cells that will differentiate >> into >> >> leaf that >> >> are emerging as an outgrowth in the shoot apex (flanking the >> >> meristem). >> >> >> >> Then, you asked: >> >> "2) under the rice growth stages - rice plant growth stages - >> the >> >> child term >> >> germination has no further subdivisions and we have been >> harvesting >> >> cell types >> >> from 0 hr (same as Embryo stage EM10) and 12 and 24 hr post >> >> imbibition time >> >> points from a germinating seed. So it would be great if you >> could >> >> possibly add >> >> these two ontologies as child terms under germination." >> >> >> >> I am not sure I understand exactly what you are asking, and I >> don't >> >> remember >> >> what Gramene use to have before, but your '0 hours.' should be >> >> equivalent of >> >> 'dry seed', right? >> >> PO term 'imbibition' covers period up until radicle emergence >> takes >> >> place. Your >> >> '12 and 24 hours post imbibition' does not indicate if radicle >> >> emergence stage >> >> was reached at 24 hours post imbibition. Having had some >> experience >> >> (and fun) >> >> growing rice in the lab while I was posdoc, my recollection is >> that >> >> it takes >> >> little longer for radicle emergence in rice, but it also depends >> on >> >> the >> >> temperature. For this very reason, we insist on morphological >> >> landmarks for >> >> creating and defining terms and not on less relevant and highly >> >> variable >> >> parameters, such as days after anthesis, hours post imbibition, >> or >> >> very >> >> disputable 'hours after germination'. Different rice varieties >> can >> >> reach >> >> different stage (placed under different conditions) at '24 hours >> >> post >> >> imbibition'. I agree that term 'imbibition' is a bit stretched, >> but >> >> am not sure >> >> if any new terms would provide adequate granularity that you are >> >> asking for. >> >> >> >> You also asked: >> >> "3. Also the definition of stomatal complex does not include the >> >> subsidiary >> >> cells and from what we have been looking around stomatal complex >> >> would be guard >> >> cell surrounding the stomata with the subsidiary cells." >> >> >> >> The definition doesn't, but 'subsidiary cell' is a child of >> 'stomatal >> >> complex' >> >> and so is 'guard cell'. Therefore, "guard and subsidiary cells >> are >> >> both a part >> >> of the stomatal complex", even though the definition of the >> 'stomatal >> >> complex' >> >> does not specifically say that. The ontology structure and term >> >> relationships >> >> provide such information. That is a benefit of having these terms >> in >> >> the >> >> ontology, a lot of information is provided in the ontology >> structure >> >> itself. >> >> >> >> I hope this helps, please, let me know if you have additional >> >> questions, and >> >> I'll get back to you regarding definitions of 'meristem' terms. >> >> >> >> Best regards, >> >> >> >> Katica >> >> >> >> > ---------- Forwarded message ---------- >> >> > Date: Thu, 26 May 2005 19:35:44 -0400 >> >> > From: fno.neeru at yale.edu >> >> > To: Katica Ilic >> >> > Subject: Re: Fwd: rice profiling project interest in >> developing >> >> cell type >> >> > terms >> >> > >> >> > Hi Katica, >> >> > This is from Neeru at Tim Nelson lab, Yale. We had met at the >> >> ontology >> >> > workshop at PAG meeting. Sorry for the long silence. How are >> you >> >> doing. >> >> > Over here we were wondering if you could help us out with some >> of >> >> the >> >> > ontologies. Most of the ontologies that we are using are from >> the >> >> > gramene website and fit really very well in defining our cell >> >> types >> >> > and growth stages. There are few we have questions about... >> >> > 1) the shoot apical meristem definition includes the axillary >> >> meristem >> >> > and we were wondering if the two terms could be separated and >> have >> >> an >> >> > axillary meristem and axillary primordium as separate >> ontological >> >> > terms. >> >> > 2) under the rice growth stages- rice plant growth stages- the >> >> child >> >> > term germination has no furhter subdivisions and we have been >> >> > harvesting cell types from 0 hr ( same as Embryo stage EM10) and >> 12 >> >> and >> >> > 24 hr post imbibition time points from a germinating seed. So >> it >> >> would >> >> > be great if you could possibly add these two ontologies as >> child >> >> terms >> >> > under germination. >> >> > 3) Also the definition of stomatal complex does not include >> the >> >> > subsidiary cells and from what we have been looking around >> >> stomatal >> >> > complex would be guard cell surrounding the stomata with the >> >> subsidiary >> >> > cells. >> >> > >> >> > Please let us know what you think. Thanks >> >> > Best Regards >> >> > Neeru >> >> > >> >> > Quoting Katica Ilic : >> >> > >> >> >> >> >> >> Dear Tim, >> >> >> >> >> >> Thank you for your message. I am glad to see that you are >> using >> >> >> Plant >> >> >> Ontologies, and I agree we need to work together to make it >> >> better. >> >> >> >> >> >> For the Plant Structure Ontology, this is a very good point >> you >> >> made, >> >> >> we >> >> >> haven't done any instantiation yet, that is, we have not >> >> propagated >> >> >> each cell type >> >> >> under every tissue of every organ, for the following reasons: >> >> >> >> >> >> 1. It would be to redundant, and ontology would end up be too >> >> large >> >> >> and >> >> >> difficult to search through since each cell type in each >> tissue >> >> of >> >> >> the each organ would be a separate term, resulting in dozens >> of >> >> terms >> >> >> that >> >> >> would refer to for example, parenchyma cell type. This is the >> >> major >> >> >> problem of our ontology (in a way, we inherited it from GO, >> but >> >> I >> >> >> can >> >> >> explain this some other time), and we are currently exploring >> >> >> several >> >> >> options. >> >> >> >> >> >> What we want to avoid, is to have several thousand terms in >> the >> >> >> plant structure ontology, while the sum total of the plant >> >> anatomy >> >> >> terms >> >> >> is in fact less that thousand (by my rough estimate). >> >> >> >> >> >> 2. Even if we do end up instantiating terms and propagating >> >> plant >> >> >> ontology, there is a fundamental conceptual problem here, >> that >> >> is, >> >> >> this instatiation and term multiplication is against the >> modular >> >> >> nature >> >> >> that underlines the plant structure, for example, xylem >> element >> >> >> is xylem element, regardless of its location, >> >> >> therefore having several terms refering to the exact position >> of >> >> the >> >> >> xylem >> >> >> element wouldn't add up much, if there is only a better way >> to >> >> >> indicate >> >> >> this posiotional information, that is to use several terms in >> >> >> conjuction >> >> >> to describe cell type, it's location and dev stage. This so >> far >> >> is >> >> >> not >> >> >> possible and we are trying to figure out how to tackle this >> >> >> computationaly. >> >> >> >> >> >> Lincoln Stain and toby Kellogg, two PIs on the POC project >> wrote >> >> a >> >> >> document last summer, called 'Multiplicative chrisis" in >> which >> >> they >> >> >> explianed this very problem. If you want to take a look, I >> can >> >> send >> >> >> it to >> >> >> you. >> >> >> >> >> >> For the developmental stages ontology, I understand this >> problem >> >> >> too, >> >> >> and I'll pass your question to the POC members in charge of >> this >> >> >> aspect of >> >> >> the ontology. It might be a couple of week before we get back >> to >> >> >> you, >> >> >> since soon we are all leaving for the PAG meeting in San >> Diego. >> >> >> >> >> >> I already check the PAG web site out, you are not registered, >> but >> >> if >> >> >> you have >> >> >> anyone from your group who is coming to this meeting, I would >> like >> >> to >> >> >> arrange >> >> >> for a meeting. I fact, I would suggest the Ontology workshop >> on >> >> >> Monday Jan 17, >> >> >> where all the POC members will be present. >> >> >> >> >> >> We also have our annual POC in-person meeting on Jan 18 and >> >> minutes >> >> >> will >> >> >> be posted on the POC web site. The "Multiplicative chrisis" >> >> document >> >> >> is on >> >> >> the agenda. >> >> >> >> >> >> Best regards, >> >> >> >> >> >> Katica >> >> >> >> >> >> >> >> >> On Mon, 10 Jan 2005, Timothy Nelson wrote: >> >> >> >> >> >> > Dear Katica, >> >> >> > We are finally at the point of needing to interface with >> the >> >> POC >> >> >> to >> >> >> > assure that our rice cell profiling data is tagged with a >> >> >> > community-standard vocabulary. We have been pleased to see >> >> that >> >> >> much >> >> >> > new vocabulary has been added for rice at the Ontology >> website >> >> in >> >> >> > recent weeks. We would like to work with you on several >> >> issues: >> >> >> > >> >> >> > 1. We will need to describe our data with greater precision >> >> than >> >> >> is >> >> >> > currently available. We find it difficult to distinguish >> >> between >> >> >> > "plant" ontological terms and other terms. For example, how >> >> does >> >> >> one >> >> >> > tag data that needs info not just as to cell type, but for >> a >> >> >> > particular cell type, within a particular organ, at a >> >> particular >> >> >> zone >> >> >> > within the organ, and all at a particular developmental >> stage? >> >> >> > >> >> >> > 2. What is the appropriate syntax for adding >> sub-descriptors? >> >> For >> >> >> > example, there currently exist developmental stages >> described >> >> as >> >> >> > "seedling", "1-4 leaf stage", "germination", etc., but our >> >> data >> >> >> comes >> >> >> > from much narrower windows than described with those terms. >> >> >> > >> >> >> > We realize it will be an ongoing process to refine the >> >> >> vocabulary, >> >> >> > and we look forward to being part of the process. >> >> >> > >> >> >> > Best regards, >> >> >> > >> >> >> > Tim Nelson >> >> >> > Professor, Dept MCDB, Yale University >> >> >> > >> >> >> > >From: "Ware, Doreen" >> >> >> > >To: "'timothy.nelson at yale.edu'" >> >> >> > >Cc: "'Katica Ilic'" , >> >> >> > > "Pankaj Jaiswal (E-mail)" >> >> >> > > >> >> >> > >Subject: rice profiling project interest in developing >> cell >> >> type >> >> >> terms >> >> >> > >Date: Wed, 29 Sep 2004 09:58:43 -0400 >> >> >> > >X-YaleITSMailFilter: Version 1.1e (attachment(s) not >> renamed) >> >> >> > >Status: RO >> >> >> > > >> >> >> > >Dear Dr. Nelson, >> >> >> > > >> >> >> > >Thank you for introducing yourself and your project >> "Virtual >> >> >> center for >> >> >> > >cellular expression profiling of rice" last week. I >> wanted >> >> to >> >> >> follow-up and >> >> >> > >introduce you to Katica Ilic the project coordinator for >> POC >> >> and >> >> >> will be the >> >> >> > >best contact person to discuss working within the POC >> framework >> >> to >> >> >> develop >> >> >> > >the correct terms and relationships for you project. >> Please >> >> feel >> >> >> free to >> >> >> > >email Katica with your specific questions or to use >> contact >> >> link >> >> >> on the POC >> >> >> > >website for po at plantontology.org. >> >> >> > > >> >> >> > >Doreen >> >> >> > > >> >> >> > > >> >> >> > >Doreen Ware USDA ARS >> >> >> > >Research Investigator >> >> >> > >Cold Spring Harbor Laboratory >> >> >> > >1 Bungtown Rd. >> >> >> > >Cold Spring Harbor, NY 11724 >> >> >> > >Phone: 516 367-6979 >> >> >> > >Fax: 516 367-6851 >> >> >> > >E-mail: ware at cshl.edu >> >> >> > >> >> >> >> >> >> >> >> >> --------------------------------------------------------------------- >> >> > ----- >> >> >> 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 fno.neeru at yale.edu Thu Jun 2 16:21:42 2005 From: fno.neeru at yale.edu (fno.neeru at yale.edu) Date: Thu, 2 Jun 2005 16:21:42 -0400 Subject: Rice profiling project - interest in developing cell type terms (PR#64) In-Reply-To: <200506022006.j52K61Px004696@brie4.cshl.org> References: <200506022006.j52K61Px004696@brie4.cshl.org> Message-ID: <1117743702.429f6a566d252@www.mail.yale.edu> Hi Katica, Thanks, so may be I need to go back and look at the GRO ontologies again. I will keep writing to you as and when I am stuck. Thanks for your all your help. Regards Neeru Quoting Katica Ilic : > Hi Neeru, > > I thought that it would confuse people who are using POC and Gramene > site > interchangeably. The reason is, Gramene (and TAIR) already switched > to using > Plant Structure Ontology, so if you go to the Gramene site (ontology > view) or to > TAIR Keword Browser, you would find PO terms from the Plant Structure > Ontology, > however, you would also come across Gramene and TAIR temporal > ontologies, since > both databases are still maintaining their species-specific Growth > and > Development Stages. Therefore, GRO terms in temporal ontology at > Gramene site > are not the same as the PO Plant Growth Stages terms. > > Plant Growth Stages can be browsed only at the POC web site, until > both > databases switch to PO temporal ontology. Here at TAIR, we plan to > completely > switch to PO by the end of the year, the latest. > > You will be hearing from Anu soon. > > Best regards, > > Katica > > > Hi Katica, > > > > I thought that Gramene and TAIR were using plant structure and GRO > > > ontologies developed by POC. But anyways I am browsing on the POC > site > > and this site has links to the gramene ontology in itself. So for > > > cereals it has link to the Gramene site and I clicked browse and it > > > shows me the ontologies for rice. Tim could not make it for the > meeting > > and so I attended the ontology workshop on his behalf. > > > > I was wondering do you have the email i.d of Anu who was also at > the > > workshop as I have to get a few good references for rice she had > > mentioned about at the meeting. > > > > Thanks for your help. > > > > Regards > > > > Neeru > > > > > > > > Quoting Katica Ilic : > > > >> Hi Neeru, > >> > >> Reading back your initial e-mail, it occured to me that you are > still > >> using > >> Gramene Growth Stages Ontology. We talked about the release of > POC > >> Growth > >> Stages at the meeting in San Diego, and Tim Nelson was invited > to > >> participate in > >> the pre-release ontology reviewing process, so I thought that > you > >> have seen and > >> used the new POC ontology. However, in case you haven't, I just > want > >> to let you > >> know that the Plant Growth Stages Ontology was released about a > month > >> ago, you > >> can browse it on the POC web site: www.plantontology.org. > >> > >> I'll let you know soon about the updates of the definitions for > the > >> terms in > >> question. > >> > >> Thanks you for contacting POC, I look forward to hearing from you > in > >> future. > >> > >> Best regards, > >> > >> Katica > >> > >> > Hi Katica, > >> > I agree with you on changing the definition, because when I > was > >> looking > >> > on the site for axillary meristem I could not find anything but > now > >> I > >> > do so as you mentioned changing the definition of some of the > >> existing > >> > terms. I hope I have answered your questions. Thanks. > >> > Regards > >> > Neeru > >> > Quoting Katica Ilic : > >> > > >> >> Dear Neeru, > >> >> > >> >> Good to hear from you again. I am glad that PO is working for > you > >> and > >> >> that you > >> >> are able to find most of the terms that you need. I'll try > >> addressing > >> >> your > >> >> questions, and also, I may have some specific questions for > you > >> >> too: > >> >> > >> >> You asked: > >> >> "1) the shoot apical meristem definition includes the > axillary > >> >> meristem and we > >> >> were wondering if the two terms could be separated and have > an > >> >> axillary > >> >> meristem > >> >> and axillary primordium as separate ontological terms." > >> >> > >> >> No, actually, the second part of the definition of SAM refers > to > >> the > >> >> SAMs of > >> >> the > >> >> axillary shoots: > >> >> PO:0020148 - shoot apical meristem > >> >> Synonyms: apical meristem, primary shoot meristem > >> >> Definition: Meristem formed in the apex of the shoot, > including > >> >> meristems > >> >> originating as axillary shoot meristems. > >> >> > >> >> I think what you are you asking about is 'meristem that is > part > >> of > >> >> the shoot > >> >> apex, in the axil of the leaf primordia', right? I think we > >> would > >> >> need to > >> >> change > >> >> definitions for some of the existing PO terms, since we > already > >> have > >> >> terms such > >> >> as leaf primordium, SAM, shoot apex and axillary bud > meristem. > >> I'll > >> >> get back to > >> >> you regarding this once our group discusses it. > >> >> > >> >> These are the terms already in the PO, and I don't think we > need > >> to > >> >> add new > >> >> terms, but rather change definitions of the existing: > >> >> > >> >> PO:0020148 - shoot apical meristem > >> >> Synonyms: apical meristem, primary shoot meristem > >> >> Definition: Meristem formed in the apex of the shoot, > including > >> >> meristems > >> >> originating as axillary shoot meristems. > >> >> > >> >> PO:0000037 - shoot apex > >> >> Definition: The topmost part of the shoot, situated at the > >> distal > >> >> extremity of > >> >> the shoot axis, consists of apical meristem the youngest leaf > >> >> primordia. > >> >> > >> >> PO:0000232 - axillary bud meristem > >> >> Synonyms: axillary meristem > >> >> Definition: Meristems formed in the axil of the leaf. > >> >> > >> >> PO:0000017 - leaf primordium > >> >> Definition: An organized group of cells that will > differentiate > >> into > >> >> leaf that > >> >> are emerging as an outgrowth in the shoot apex (flanking the > >> >> meristem). > >> >> > >> >> Then, you asked: > >> >> "2) under the rice growth stages - rice plant growth stages - > >> the > >> >> child term > >> >> germination has no further subdivisions and we have been > >> harvesting > >> >> cell types > >> >> from 0 hr (same as Embryo stage EM10) and 12 and 24 hr post > >> >> imbibition time > >> >> points from a germinating seed. So it would be great if you > >> could > >> >> possibly add > >> >> these two ontologies as child terms under germination." > >> >> > >> >> I am not sure I understand exactly what you are asking, and I > >> don't > >> >> remember > >> >> what Gramene use to have before, but your '0 hours.' should > be > >> >> equivalent of > >> >> 'dry seed', right? > >> >> PO term 'imbibition' covers period up until radicle emergence > >> takes > >> >> place. Your > >> >> '12 and 24 hours post imbibition' does not indicate if > radicle > >> >> emergence stage > >> >> was reached at 24 hours post imbibition. Having had some > >> experience > >> >> (and fun) > >> >> growing rice in the lab while I was posdoc, my recollection > is > >> that > >> >> it takes > >> >> little longer for radicle emergence in rice, but it also > depends > >> on > >> >> the > >> >> temperature. For this very reason, we insist on morphological > >> >> landmarks for > >> >> creating and defining terms and not on less relevant and > highly > >> >> variable > >> >> parameters, such as days after anthesis, hours post > imbibition, > >> or > >> >> very > >> >> disputable 'hours after germination'. Different rice > varieties > >> can > >> >> reach > >> >> different stage (placed under different conditions) at '24 > hours > >> >> post > >> >> imbibition'. I agree that term 'imbibition' is a bit > stretched, > >> but > >> >> am not sure > >> >> if any new terms would provide adequate granularity that you > are > >> >> asking for. > >> >> > >> >> You also asked: > >> >> "3. Also the definition of stomatal complex does not include > the > >> >> subsidiary > >> >> cells and from what we have been looking around stomatal > complex > >> >> would be guard > >> >> cell surrounding the stomata with the subsidiary cells." > >> >> > >> >> The definition doesn't, but 'subsidiary cell' is a child of > >> 'stomatal > >> >> complex' > >> >> and so is 'guard cell'. Therefore, "guard and subsidiary > cells > >> are > >> >> both a part > >> >> of the stomatal complex", even though the definition of the > >> 'stomatal > >> >> complex' > >> >> does not specifically say that. The ontology structure and > term > >> >> relationships > >> >> provide such information. That is a benefit of having these > terms > >> in > >> >> the > >> >> ontology, a lot of information is provided in the ontology > >> structure > >> >> itself. > >> >> > >> >> I hope this helps, please, let me know if you have additional > >> >> questions, and > >> >> I'll get back to you regarding definitions of 'meristem' > terms. > >> >> > >> >> Best regards, > >> >> > >> >> Katica > >> >> > >> >> > ---------- Forwarded message ---------- > >> >> > Date: Thu, 26 May 2005 19:35:44 -0400 > >> >> > From: fno.neeru at yale.edu > >> >> > To: Katica Ilic > >> >> > Subject: Re: Fwd: rice profiling project interest in > >> developing > >> >> cell type > >> >> > terms > >> >> > > >> >> > Hi Katica, > >> >> > This is from Neeru at Tim Nelson lab, Yale. We had met at > the > >> >> ontology > >> >> > workshop at PAG meeting. Sorry for the long silence. How > are > >> you > >> >> doing. > >> >> > Over here we were wondering if you could help us out with > some > >> of > >> >> the > >> >> > ontologies. Most of the ontologies that we are using are > from > >> the > >> >> > gramene website and fit really very well in defining our > cell > >> >> types > >> >> > and growth stages. There are few we have questions about... > >> >> > 1) the shoot apical meristem definition includes the > axillary > >> >> meristem > >> >> > and we were wondering if the two terms could be separated > and > >> have > >> >> an > >> >> > axillary meristem and axillary primordium as separate > >> ontological > >> >> > terms. > >> >> > 2) under the rice growth stages- rice plant growth stages- > the > >> >> child > >> >> > term germination has no furhter subdivisions and we have > been > >> >> > harvesting cell types from 0 hr ( same as Embryo stage EM10) > and > >> 12 > >> >> and > >> >> > 24 hr post imbibition time points from a germinating seed. > So > >> it > >> >> would > >> >> > be great if you could possibly add these two ontologies as > >> child > >> >> terms > >> >> > under germination. > >> >> > 3) Also the definition of stomatal complex does not include > >> the > >> >> > subsidiary cells and from what we have been looking around > >> >> stomatal > >> >> > complex would be guard cell surrounding the stomata with > the > >> >> subsidiary > >> >> > cells. > >> >> > > >> >> > Please let us know what you think. Thanks > >> >> > Best Regards > >> >> > Neeru > >> >> > > >> >> > Quoting Katica Ilic : > >> >> > > >> >> >> > >> >> >> Dear Tim, > >> >> >> > >> >> >> Thank you for your message. I am glad to see that you are > >> using > >> >> >> Plant > >> >> >> Ontologies, and I agree we need to work together to make > it > >> >> better. > >> >> >> > >> >> >> For the Plant Structure Ontology, this is a very good > point > >> you > >> >> made, > >> >> >> we > >> >> >> haven't done any instantiation yet, that is, we have not > >> >> propagated > >> >> >> each cell type > >> >> >> under every tissue of every organ, for the following > reasons: > >> >> >> > >> >> >> 1. It would be to redundant, and ontology would end up be > too > >> >> large > >> >> >> and > >> >> >> difficult to search through since each cell type in each > >> tissue > >> >> of > >> >> >> the each organ would be a separate term, resulting in > dozens > >> of > >> >> terms > >> >> >> that > >> >> >> would refer to for example, parenchyma cell type. This is > the > >> >> major > >> >> >> problem of our ontology (in a way, we inherited it from > GO, > >> but > >> >> I > >> >> >> can > >> >> >> explain this some other time), and we are currently > exploring > >> >> >> several > >> >> >> options. > >> >> >> > >> >> >> What we want to avoid, is to have several thousand terms > in > >> the > >> >> >> plant structure ontology, while the sum total of the plant > >> >> anatomy > >> >> >> terms > >> >> >> is in fact less that thousand (by my rough estimate). > >> >> >> > >> >> >> 2. Even if we do end up instantiating terms and > propagating > >> >> plant > >> >> >> ontology, there is a fundamental conceptual problem here, > >> that > >> >> is, > >> >> >> this instatiation and term multiplication is against the > >> modular > >> >> >> nature > >> >> >> that underlines the plant structure, for example, xylem > >> element > >> >> >> is xylem element, regardless of its location, > >> >> >> therefore having several terms refering to the exact > position > >> of > >> >> the > >> >> >> xylem > >> >> >> element wouldn't add up much, if there is only a better > way > >> to > >> >> >> indicate > >> >> >> this posiotional information, that is to use several terms > in > >> >> >> conjuction > >> >> >> to describe cell type, it's location and dev stage. This > so > >> far > >> >> is > >> >> >> not > >> >> >> possible and we are trying to figure out how to tackle > this > >> >> >> computationaly. > >> >> >> > >> >> >> Lincoln Stain and toby Kellogg, two PIs on the POC project > >> wrote > >> >> a > >> >> >> document last summer, called 'Multiplicative chrisis" in > >> which > >> >> they > >> >> >> explianed this very problem. If you want to take a look, I > >> can > >> >> send > >> >> >> it to > >> >> >> you. > >> >> >> > >> >> >> For the developmental stages ontology, I understand this > >> problem > >> >> >> too, > >> >> >> and I'll pass your question to the POC members in charge > of > >> this > >> >> >> aspect of > >> >> >> the ontology. It might be a couple of week before we get > back > >> to > >> >> >> you, > >> >> >> since soon we are all leaving for the PAG meeting in San > >> Diego. > >> >> >> > >> >> >> I already check the PAG web site out, you are not > registered, > >> but > >> >> if > >> >> >> you have > >> >> >> anyone from your group who is coming to this meeting, I > would > >> like > >> >> to > >> >> >> arrange > >> >> >> for a meeting. I fact, I would suggest the Ontology > workshop > >> on > >> >> >> Monday Jan 17, > >> >> >> where all the POC members will be present. > >> >> >> > >> >> >> We also have our annual POC in-person meeting on Jan 18 > and > >> >> minutes > >> >> >> will > >> >> >> be posted on the POC web site. The "Multiplicative > chrisis" > >> >> document > >> >> >> is on > >> >> >> the agenda. > >> >> >> > >> >> >> Best regards, > >> >> >> > >> >> >> Katica > >> >> >> > >> >> >> > >> >> >> On Mon, 10 Jan 2005, Timothy Nelson wrote: > >> >> >> > >> >> >> > Dear Katica, > >> >> >> > We are finally at the point of needing to interface with > >> the > >> >> POC > >> >> >> to > >> >> >> > assure that our rice cell profiling data is tagged with > a > >> >> >> > community-standard vocabulary. We have been pleased to > see > >> >> that > >> >> >> much > >> >> >> > new vocabulary has been added for rice at the Ontology > >> website > >> >> in > >> >> >> > recent weeks. We would like to work with you on several > >> >> issues: > >> >> >> > > >> >> >> > 1. We will need to describe our data with greater > precision > >> >> than > >> >> >> is > >> >> >> > currently available. We find it difficult to distinguish > >> >> between > >> >> >> > "plant" ontological terms and other terms. For example, > how > >> >> does > >> >> >> one > >> >> >> > tag data that needs info not just as to cell type, but > for > >> a > >> >> >> > particular cell type, within a particular organ, at a > >> >> particular > >> >> >> zone > >> >> >> > within the organ, and all at a particular developmental > >> stage? > >> >> >> > > >> >> >> > 2. What is the appropriate syntax for adding > >> sub-descriptors? > >> >> For > >> >> >> > example, there currently exist developmental stages > >> described > >> >> as > >> >> >> > "seedling", "1-4 leaf stage", "germination", etc., but > our > >> >> data > >> >> >> comes > >> >> >> > from much narrower windows than described with those > terms. > >> >> >> > > >> >> >> > We realize it will be an ongoing process to refine the > >> >> >> vocabulary, > >> >> >> > and we look forward to being part of the process. > >> >> >> > > >> >> >> > Best regards, > >> >> >> > > >> >> >> > Tim Nelson > >> >> >> > Professor, Dept MCDB, Yale University > >> >> >> > > >> >> >> > >From: "Ware, Doreen" > >> >> >> > >To: "'timothy.nelson at yale.edu'" > > >> >> >> > >Cc: "'Katica Ilic'" , > >> >> >> > > "Pankaj Jaiswal (E-mail)" > >> >> >> > > > >> >> >> > >Subject: rice profiling project interest in developing > >> cell > >> >> type > >> >> >> terms > >> >> >> > >Date: Wed, 29 Sep 2004 09:58:43 -0400 > >> >> >> > >X-YaleITSMailFilter: Version 1.1e (attachment(s) not > >> renamed) > >> >> >> > >Status: RO > >> >> >> > > > >> >> >> > >Dear Dr. Nelson, > >> >> >> > > > >> >> >> > >Thank you for introducing yourself and your project > >> "Virtual > >> >> >> center for > >> >> >> > >cellular expression profiling of rice" last week. I > >> wanted > >> >> to > >> >> >> follow-up and > >> >> >> > >introduce you to Katica Ilic the project coordinator > for > >> POC > >> >> and > >> >> >> will be the > >> >> >> > >best contact person to discuss working within the POC > >> framework > >> >> to > >> >> >> develop > >> >> >> > >the correct terms and relationships for you project. > >> Please > >> >> feel > >> >> >> free to > >> >> >> > >email Katica with your specific questions or to use > >> contact > >> >> link > >> >> >> on the POC > >> >> >> > >website for po at plantontology.org. > >> >> >> > > > >> >> >> > >Doreen > >> >> >> > > > >> >> >> > > > >> >> >> > >Doreen Ware USDA ARS > >> >> >> > >Research Investigator > >> >> >> > >Cold Spring Harbor Laboratory > >> >> >> > >1 Bungtown Rd. > >> >> >> > >Cold Spring Harbor, NY 11724 > >> >> >> > >Phone: 516 367-6979 > >> >> >> > >Fax: 516 367-6851 > >> >> >> > >E-mail: ware at cshl.edu > >> >> >> > > >> >> >> > >> >> >> > >> >> > >> > --------------------------------------------------------------------- > >> >> > ----- > >> >> >> 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 shuly at cshl.edu Thu Jun 2 16:49:13 2005 From: shuly at cshl.edu (Shuly) Date: Thu, 02 Jun 2005 16:49:13 -0400 Subject: Mailing lists issues Message-ID: <429F70C9.6000607@cshl.edu> Hi all, We experianced firewall issues which disabled the delivery of a few email messages sent to the list yesterday and today. Problems have been solved, but you may have not gotten those emails. If you are interested with viewing the recently sent emails, please refer to the po-dev mailing list archive: http://www.plantontology.org/mailarch-dev/Jun2005/date.html Sorry for the inconvenience, Shuly. From rugro at psb.ugent.be Fri Jun 10 09:36:58 2005 From: rugro at psb.ugent.be (Ruth De Groodt) Date: Fri, 10 Jun 2005 15:36:58 +0200 Subject: Feedback on POC: granular terms under 'petiole' (PR#56) In-Reply-To: <200505312039.j4VKdIPx005920@brie4.cshl.org> References: <200505312039.j4VKdIPx005920@brie4.cshl.org> Message-ID: <42A9977A.80306@psb.ugent.be> Hi Katica, for the leaves it's fine for me now. Maybe in the future I will submit some proposals for roots, but I still have didn't have a close look at that part. I the future, I will have to do a detailed analysis on that as well. I will let you know. best regards, Ruth Katica Ilic wrote: >Hi Ruth, > >I am glad to hear that proposed structure worked for you. Please let us know if >you would like to see additional, more granular terms in PO. > >Thank you for using Plant Ontologies and for contacting us. Your suggestions and >comments are greatly appreciated. > >Best regards, > >Katica > > > >>Dear Katica, >> >> >>there is indeed no reason why stomatal complexes in the petiole should >>be different from stomatal complexes in leaf lamina seen from the >>anatomical point of view. The new structure that you propose, is fine. >> >>Kind regards, >> >>Ruth >> >> >>Katica Ilic wrote: >> >> >> >>>Dear Ruth, >>> >>>Thank you for your reply. It is essential for us at POC to learn how people >>> >>> >use > > >>>Plant Ontology and what kind of requests and issues they may have once they >>> >>> >get > > >>>familiar with this vocabulary. >>> >>>I have another question for you, regarding gene expressions in petiole and >>> >>> >leaf > > >>>lamina. On your mc slides, have you seen any differential expression of >>> >>> >gene(s) > > >>>in the guard cells of petioles vs. guard cells in leaf blade? If you have, >>> >>> >that > > >>>would be an argument for creating two terms, 'stomatal complex of the leaf >>>lamina' and 'petiole stomatal complex', so that gene x (expressed only in >>> >>> >guard > > >>>cell of the petiole) could be properly associated to term 'petiole stomatal >>>complex'. I couldn't find any evidence of such cases in the published >>>literature, so, our ontology group at POC decided not to distinguish between >>>stomata in the leaf lamina and those in the leaf petiole. Therefore, >>> >>> >>annotation >> >> >>>of the gene expression pattern in guard cells of petiole cannot be >>> >>> >>distinguished >>>from guard cell in the leaf blade. In the example below, you will see that >> >> >the > > >>>same term (stomatal complex) is propagated under both, 'leaf lamina >>> >>> >epidermis' > > >>>and 'petiole epidermis'. If you think this should be corrected, please let me >>>know. >>> >>>This is the illustration: >>>leaf >>> (p) leaf lamina >>> (i) leaf lamina epidermis >>> (p) stomatal complex >>> (i) petiole epidermis >>> (p) stomatal complex >>> >>>The rest of the terms that you requested are now placed under term 'petiole', >>>although we decided not to include all terms, such as interfascicular >>>parenchyma, or pith (neither one is part of vascular system). Please, note >>> >>> >>that, >> >> >>>unlike for the term 'stomatal complex', we included specific subclasses of >>> >>> >>terms >> >> >>>'leaf vascular system' and 'leaf epidermis', that is, 'leaf lamina vascular >>>system' and 'petiole vascular system', and 'leaf lamina epidermis' and >>> >>> >'petiole > > >>>epidermis'. This is dictated by the hierarchical nature of the ontology >>>structure, and by the annotation display requirements. Again, 'stomatal >>> >>> >>complex' >> >> >>>is an exemption of the rule. >>> >>>Here is the new structure (for simplicity, I didn't list all the terms under >>>'leaf': >>> >>> leaf >>> (p) leaf lamina >>> (p) leaf lamina epidermis >>> (p) stomatal complex >>> (p) leaf lamina vascular system >>> (p) leaf apex >>> (p) leaf margin >>> (p) leaf vein >>> >>> (p) petiole >>> (p) petiole cortex >>> (p) petiole vascular system >>> (p) petiole epidermis >>> (p) stomatal complex >>> >>>We are currently experiencing problems with cvs repository, and the new >>> >>> >>ontology >> >> >>>files will not be available to download until the problems are fixed. The >>>updated ontology will be available on our ontology browser after the next >>>scheduled update (end of June). >>> >>>I hope that this new structure with additional children terms under term >>>'petiole' will meet your requirements. Please let me know if this would work >>> >>> >>and >> >> >>>don't hesitate to ask me additional questions you may have about plant >>>ontologies. >>> >>>Best regards, >>> >>>Katica >>> >>> >>> >>> >>> >>>>Dear Katica, >>>> >>>> >>>> I am indeed involved in a functional genomics project. For analysis >>>> of whole mounts and description of patterns we wanted to use a >>>> standardized nomenclature and looking for a solution, we found the >>>> website. As I saw that in leaf lamina and roots, terminology goes >>>> quite in detail, since different cell/ tissue layers are defined, >>>> and as I wanted to describe my results as far as I can see the >>>> pattern of expression with a normal DIC microscope, I saw that with >>>> petioles there were lacking a few terms describing layers that can >>>> be distinguished fairly easy like epidermis, cortex and vascular tissue. >>>> I agree that for the vascular tissue in petioles, it's difficult to >>>> distinguish different layers in whole mounts (on sections you can!), >>>> but to be complete I add them in my suggestion. >>>> >>>> I hope this is an answer to your question. >>>> >>>> kind regards, >>>> >>>> >>>> Ruth >>>> >>>>Katica Ilic wrote: >>>> >>>> >>>> >>>> >>>> >>>>>Dear Ruth, >>>>> >>>>>Thanks for the feedback and suggestion for improving current Plant Ontology >>>>>structure. Term 'petiole' does not have any granular 'children' terms yet, >>>>> >>>>> >>>>> >>>>> >>>>since >>>> >>>> >>>> >>>> >>>>>we deliberately chose not to have very detailed and elaborate ontology, at >>>>> >>>>> >>>>> >>>>> >>>>least >>>> >>>> >>>> >>>> >>>>>not in the initial stage when we were focused on creating a robust and >>>>>extensible structure as a backbone to which granular terms can be added as >>>>>needed. >>>>> >>>>>Our group is now considering your suggestion for adding more granular terms >>>>> >>>>> >>>>> >>>>> >>>for >>> >>> >>> >>> >>>>>'petiole', and I have a couple of questions, to make sure that we can >>>>>accommodate what you would like to see in this segment of the ontology, at >>>>> >>>>> >>>>> >>>>> >>>the >>> >>> >>> >>> >>>>>same time, making sure that we keep the Plant Ontology 'generic', >>>>> >>>>> >>>>> >>>>> >>>encompassing >>> >>> >>> >>> >>>>>both, dicots and monocots. I am assuming that these terms are required for >>>>>functional genomics project that you might be involved and I wonder if a >>>>> >>>>> >>>>> >>>>> >>>>simpler >>>> >>>> >>>> >>>> >>>>>solution that does not have, for instance 'interfascicular parenchyma' >>>>> >>>>> >would > > >>>>>work. I'll get back to you soon with the outline of the structure we are >>>>>currently considering, but in the meantime, it would be useful if you can >>>>> >>>>> >>>>> >>>>> >>>tell >>> >>> >>> >>> >>>>>us few fords about the specific reasons for inquiring the structure you >>>>> >>>>> >>>>> >>>>> >>>>proposed >>>> >>>> >>>> >>>> >>>>>and also how you use the Plant Ontology. >>>>> >>>>>Thank you again for sending us your suggestion. I look forward to hearing >>>>> >>>>> >>>>> >>>>> >>>from >>> >>> >>> >>> >>>>>you. >>>>> >>>>>Best regards, >>>>> >>>>>Katica Ilic, POC Project Coordinator >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>>>---------- Forwarded message ---------- >>>>>>Date: Wed, 20 Apr 2005 04:02:29 -0400 >>>>>>From: feedback_submission at filetta.cshl.edu >>>>>>Reply-To: po-dev at plantontology.org, feedback_submission at filetta.cshl.edu >>>>>>To: po-dev >>>>>>Subject: Feedback on POC >>>>>> >>>>>> *** Feedback from Plant Ontology Live Site *** >>>>>> >>>>>>refer_to_url: http://www.plantontology.org/index.html >>>>>> >>>>>>comments: To whom it may concern: >>>>>> >>>>>>This message proposes a refinement of the anatomical ontology. >>>>>> >>>>>>In dicotelydons, the petiole, like the stem, consists of a dermal, >>>>>> >>>>>> >fundamen= > > >>>>>>tal (ground) and vascular system. Its epidermis consists in one layer of >>>>>> >>>>>> >c= > > >>>>>>ells and contains elongated epidermal cells and stomatal complexes, >>>>>> >>>>>> >althoug= > > >>>>>>h the latter occur less frequently in petioles than in leaf lamina. Under >>>>>> >>>>>> >t= > > >>>>>>he epidermal layer is the ground tissue of which the outer region is the >>>>>> >>>>>> >co= > > >>>>>>rtex and the inner region is the pith. These two regions are >>>>>> >>>>>> >interconnected= > > >>>>>>by the interfascicular parenchyma. In the vascular system (stele), the >>>>>> >>>>>> >vas= > > >>>>>>cular bundles (xylem and phloem) are separated by this interfascicular >>>>>> >>>>>> >pare= > > >>>>>>nchyma. The pith is located in the very centre of the stele. >>>>>> >>>>>>This organisation can be summarized as follows, from the outside in: >>>>>> >>>>>>Petiole >>>>>>=B7=09dermal system >>>>>> - epidermis >>>>>> - stomatal complex >>>>>>=B7=09cortex >>>>>>=B7=09vascular system >>>>>> - phloem >>>>>> - xylem >>>>>> - interfascicular parenchyma >>>>>> - pith >>>>>> >>>>>>As there is presently no subdivision under the term =93petiole=94, would >>>>>> >>>>>> >it= > > >>>>>>be possible to add these categories in the ontology tree? Definitions of >>>>>> >>>>>> >= > > >>>>>>the terminology used above are similar to those listed in the current >>>>>> >>>>>> >ontol= > > >>>>>>ogy but are here applied for petioles. Do not hesitate to contact us back >>>>>> >>>>>> >= > > >>>>>>if you need any additional information regarding this proposal. >>>>>> >>>>>> >>>>>>Ruth De Groodt >>>>>>Bj=F6rn De Meyer >>>>>>Pierre Hilson >>>>>> >>>>>> >>>>>>name: Ruth De Groodt >>>>>> >>>>>>email: ruth.degroodt at psb.ugent.be >>>>>> >>>>>>organization: VIB - Department of Plant Systems Biology >>>>>> >>>>>>send_feedback: Send your feedback >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>-- >>>>================================================================== >>>>Ruth De Groodt TEL:32 (0)9 3313846 >>>>PLANT SYSTEMS BIOLOGY Fax:32 (0)9 2645349 >>>>Department of Functional Genomics >>>>GHENT UNIVERSITY, VIB, Technologie Park 927, B-9052 GENT, Belgium >>>>Vlaams Instituut voor Biotechnologie VIB >>>>mailto:rugro at psb.UGent.be http://www.psb.UGent.be >>>>================================================================== >>>> >>>> >>>> >>>> >>>> >>>> >>-- >>================================================================== >>Ruth De Groodt TEL:32 (0)9 3313846 >>PLANT SYSTEMS BIOLOGY Fax:32 (0)9 2645349 >>Department of Functional Genomics >>GHENT UNIVERSITY, VIB, Technologie Park 927, B-9052 GENT, Belgium >>Vlaams Instituut voor Biotechnologie VIB >>mailto:rugro at psb.UGent.be http://www.psb.UGent.be >>================================================================== >> >> >> >> -- ================================================================== Ruth De Groodt TEL:32 (0)9 3313846 PLANT SYSTEMS BIOLOGY Fax:32 (0)9 2645349 Department of Functional Genomics GHENT UNIVERSITY, VIB, Technologie Park 927, B-9052 GENT, Belgium Vlaams Instituut voor Biotechnologie VIB mailto:rugro at psb.UGent.be http://www.psb.UGent.be ================================================================== From pj37 at cornell.edu Fri Jun 10 16:20:34 2005 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Fri, 10 Jun 2005 16:20:34 -0400 Subject: SAM restructuring suggestion Message-ID: <42A9F612.7050507@cornell.edu> Refer to: http://www.plantontology.org/amigo/go.cgi?view=details&show_associations=terms&search_constraint=terms&depth=0&query=PO:0020148 Looks like we need a specific instance of SAM, ie. "vegetative shoot apical meristem". The current term is too generic for curating vegetative SAM. The reason being, I am curating a lot of flowering time genes and many are involved in regulating the transition of vegetative SAM to reproductive SAM. This event is critical in short-day or long-day light response resulting in early/delayed flowering. Current structure is like follows: # PO:0020148 : shoot apical meristem ( 32 ) * PO:0000224 : central zone * PO:0006362 : embryonic shoot apical meristem * PO:0000229 : floral meristem * PO:0000230 : inflorescence meristem * PO:0009020 : meristem L1 * PO:0009021 : meristem L2 * PO:0009022 : meristem L3 * PO:0000225 : peripheral zone * PO:0005039 : primary thickening meristem * PO:0000226 : rib zone * PO:0006306 : shoot procambium -------------------------------------------------- Proposed # PO:0020148 : shoot apical meristem ( 32 ) i PO:new : vegetative shoot apical meristem p PO:0000224 : central zone i PO:0006362 : embryonic shoot apical meristem p PO:0009020 : meristem L1 p PO:0009021 : meristem L2 p PO:0009022 : meristem L3 p PO:0000225 : peripheral zone p PO:0005039 : primary thickening meristem p PO:0000226 : rib zone p PO:0006306 : shoot procambium i PO:new : reproductive shoot apical meristem i PO:0000229 : floral meristem i PO:0000230 : inflorescence meristem PO:0020148 : shoot apical meristem Def: current Meristem formed in the apex of the shoot, including meristems originating as axillary shoot meristems. Def: proposed Meristem formed in the apex of the shoot or those originating as axillary and reproductive meristems. PO:new : vegetative shoot apical meristem Def: proposed Copy the original SAM definition. PO:new : reproductive shoot apical meristem Def: proposed Meristem formed in the apex of the shoot originating as inflorescence and or flower meristems. -Pankaj From leonore.reiser at gmail.com Fri Jun 10 17:21:43 2005 From: leonore.reiser at gmail.com (Leonore Reiser) Date: Fri, 10 Jun 2005 14:21:43 -0700 Subject: SAM restructuring suggestion In-Reply-To: <42A9F612.7050507@cornell.edu> References: <42A9F612.7050507@cornell.edu> Message-ID: <248c981f0506101421218367ae@mail.gmail.com> So Pankaj your suggestion raises a question about annotations that we were discussing here the other day. Are you proposing to annotate the expression of these genes to these body parts or the phenotype of mutant alleles/germplasms to these body parts? NASC also has a lot of flowering time mutants annotated- in their case, they annotated to the BODY part -flower- possibly because there was/is not term to reflect vegetative-reproductive stage. I find that wildly confusing and its not where I would look to find flowering time mutants. I would annotate something like Constans or FLC as being INVOLVED IN the biological process of flowering (which called flower development in the GO). I would not use an annotation to vegetative or reproductive meristem to describe the phenotype. I think it is a big mistake to try and use the Plant Ontologies to describe every mutant phenotype- its just not possible. Mutants involved in nitrogen assimilation may be chlorotic (pale green or yellow leaves) but the PO cannot effectively describe say sensitivity to a nitrogen analog. So I may be jumping the gun because this could be totally NOT what you are intending to use these terms for. But if so perhaps we could use this as an example and see how other groups would annotate late or early flowering mutant phenotypes? Its a really good exercise. Leonore On 6/10/05, Pankaj Jaiswal wrote: > > > < > http://www.plantontology.org/amigo/go.cgi?action=plus_node&depth=1&search_constraint=terms&query=PO:00201482 > > > > > Refer to: > > http://www.plantontology.org/amigo/go.cgi?view=details&show_associations=terms&search_constraint=terms&depth=0&query=PO:0020148 > > Looks like we need a specific instance of SAM, ie. "vegetative shoot > apical meristem". The current term is too generic for curating > vegetative SAM. > > The reason being, I am curating a lot of flowering time genes and many > are involved in regulating the transition of vegetative SAM to > reproductive SAM. This event is critical in short-day or long-day light > response resulting in early/delayed flowering. > > Current structure is like follows: > > > # PO:0020148 : shoot apical meristem ( 32 ) > > * PO:0000224 : central zone > * PO:0006362 : embryonic shoot apical meristem > * PO:0000229 : floral meristem > * PO:0000230 : inflorescence meristem > * PO:0009020 : meristem L1 > * PO:0009021 : meristem L2 > * PO:0009022 : meristem L3 > * PO:0000225 : peripheral zone > * PO:0005039 : primary thickening meristem > * PO:0000226 : rib zone > * PO:0006306 : shoot procambium > -------------------------------------------------- > > Proposed > > # PO:0020148 : shoot apical meristem ( 32 ) > i PO:new : vegetative shoot apical meristem > p PO:0000224 : central zone > i PO:0006362 : embryonic shoot apical meristem > p PO:0009020 : meristem L1 > p PO:0009021 : meristem L2 > p PO:0009022 : meristem L3 > p PO:0000225 : peripheral zone > p PO:0005039 : primary thickening meristem > p PO:0000226 : rib zone > p PO:0006306 : shoot procambium > i PO:new : reproductive shoot apical meristem > i PO:0000229 : floral meristem > i PO:0000230 : inflorescence meristem > > > PO:0020148 : shoot apical meristem > Def: current > Meristem formed in the apex of the shoot, including meristems > originating as axillary shoot meristems. > Def: proposed > Meristem formed in the apex of the shoot or those originating as > axillary and reproductive meristems. > > PO:new : vegetative shoot apical meristem > Def: proposed > Copy the original SAM definition. > > PO:new : reproductive shoot apical meristem > Def: proposed > Meristem formed in the apex of the shoot originating as > inflorescence and or flower meristems. > > -Pankaj > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From fzqhd at umsl.edu Fri Jun 10 17:39:19 2005 From: fzqhd at umsl.edu (Felipe Zapata) Date: Fri, 10 Jun 2005 16:39:19 -0500 Subject: SAM restructuring suggestion In-Reply-To: <248c981f0506101421218367ae@mail.gmail.com> References: <42A9F612.7050507@cornell.edu> <248c981f0506101421218367ae@mail.gmail.com> Message-ID: <027834AC-D9DE-4C4C-9F48-D028EB88760A@umsl.edu> what a nice way to point out what has been a recurrent point of disagreement on the construction/conceptualization/use of POC: > I think it is a big mistake to try and use the Plant Ontologies to > describe every mutant phenotype- its just not possible. Thanks Leonore, F > > > Leonore > > > > On 6/10/05, Pankaj Jaiswal wrote: > > action=plus_node&depth=1&search_constraint=terms&query=PO:00201482 > > > > Refer to: > http://www.plantontology.org/amigo/go.cgi? > view=details&show_associations=terms&search_constraint=terms&depth=0&q > uery=PO:0020148 > > Looks like we need a specific instance of SAM, ie. "vegetative shoot > apical meristem". The current term is too generic for curating > vegetative SAM. > > The reason being, I am curating a lot of flowering time genes and many > are involved in regulating the transition of vegetative SAM to > reproductive SAM. This event is critical in short-day or long-day > light > response resulting in early/delayed flowering. > > Current structure is like follows: > > > # PO:0020148 : shoot apical meristem ( 32 ) > > * PO:0000224 : central zone > * PO:0006362 : embryonic shoot apical meristem > * PO:0000229 : floral meristem > * PO:0000230 : inflorescence meristem > * PO:0009020 : meristem L1 > * PO:0009021 : meristem L2 > * PO:0009022 : meristem L3 > * PO:0000225 : peripheral zone > * PO:0005039 : primary thickening meristem > * PO:0000226 : rib zone > * PO:0006306 : shoot procambium > -------------------------------------------------- > > Proposed > > # PO:0020148 : shoot apical meristem ( 32 ) > i PO:new : vegetative shoot apical meristem > p PO:0000224 : central zone > i PO:0006362 : embryonic shoot apical meristem > p PO:0009020 : meristem L1 > p PO:0009021 : meristem L2 > p PO:0009022 : meristem L3 > p PO:0000225 : peripheral zone > p PO:0005039 : primary thickening meristem > p PO:0000226 : rib zone > p PO:0006306 : shoot procambium > i PO:new : reproductive shoot apical meristem > i PO:0000229 : floral meristem > i PO:0000230 : inflorescence meristem > > > PO:0020148 : shoot apical meristem > Def: current > Meristem formed in the apex of the shoot, including meristems > originating as axillary shoot meristems. > Def: proposed > Meristem formed in the apex of the shoot or those originating as > axillary and reproductive meristems. > > PO:new : vegetative shoot apical meristem > Def: proposed > Copy the original SAM definition. > > PO:new : reproductive shoot apical meristem > Def: proposed > Meristem formed in the apex of the shoot originating as > inflorescence and or flower meristems. > > -Pankaj > > .............. Felipe Zapata University of Missouri St. Louis Department of Biology 8001 Natural Bridge Rd. St. Louis, MO 63121 USA p.314.516.6200 -------------- next part -------------- An HTML attachment was scrubbed... URL: From leonore.reiser at gmail.com Fri Jun 10 17:43:08 2005 From: leonore.reiser at gmail.com (Leonore Reiser) Date: Fri, 10 Jun 2005 14:43:08 -0700 Subject: SAM restructuring suggestion In-Reply-To: <027834AC-D9DE-4C4C-9F48-D028EB88760A@umsl.edu> References: <42A9F612.7050507@cornell.edu> <248c981f0506101421218367ae@mail.gmail.com> <027834AC-D9DE-4C4C-9F48-D028EB88760A@umsl.edu> Message-ID: <248c981f050610144326b70236@mail.gmail.com> my pleasure- its been bugging me for quite a while- lets hope for some constructive discussion at this point. Leo On 6/10/05, Felipe Zapata wrote: > > what a nice way to point out what has been a recurrent point of > disagreement on the construction/conceptualization/use of POC: > > I think it is a big mistake to try and use the Plant Ontologies to > describe every mutant phenotype- its just not possible. > > > Thanks Leonore, > > F > > > > > Leonore > > > > On 6/10/05, Pankaj Jaiswal wrote: > > > > > > > > > > > > > > Refer to: > > http://www.plantontology.org/amigo/go.cgi?view=details&show_associations=terms&search_constraint=terms&depth=0&query=PO:0020148 > > > > > > Looks like we need a specific instance of SAM, ie. "vegetative shoot > > apical meristem". The current term is too generic for curating > > vegetative SAM. > > > > The reason being, I am curating a lot of flowering time genes and many > > are involved in regulating the transition of vegetative SAM to > > reproductive SAM. This event is critical in short-day or long-day light > > response resulting in early/delayed flowering. > > > > Current structure is like follows: > > > > > > # PO:0020148 : shoot apical meristem ( 32 ) > > > > * PO:0000224 : central zone > > * PO:0006362 : embryonic shoot apical meristem > > * PO:0000229 : floral meristem > > * PO:0000230 : inflorescence meristem > > * PO:0009020 : meristem L1 > > * PO:0009021 : meristem L2 > > * PO:0009022 : meristem L3 > > * PO:0000225 : peripheral zone > > * PO:0005039 : primary thickening meristem > > * PO:0000226 : rib zone > > * PO:0006306 : shoot procambium > > -------------------------------------------------- > > > > Proposed > > > > # PO:0020148 : shoot apical meristem ( 32 ) > > i PO:new : vegetative shoot apical meristem > > p PO:0000224 : central zone > > i PO:0006362 : embryonic shoot apical meristem > > p PO:0009020 : meristem L1 > > p PO:0009021 : meristem L2 > > p PO:0009022 : meristem L3 > > p PO:0000225 : peripheral zone > > p PO:0005039 : primary thickening meristem > > p PO:0000226 : rib zone > > p PO:0006306 : shoot procambium > > i PO:new : reproductive shoot apical meristem > > i PO:0000229 : floral meristem > > i PO:0000230 : inflorescence meristem > > > > > > PO:0020148 : shoot apical meristem > > Def: current > > Meristem formed in the apex of the shoot, including meristems > > originating as axillary shoot meristems. > > Def: proposed > > Meristem formed in the apex of the shoot or those originating as > > axillary and reproductive meristems. > > > > PO:new : vegetative shoot apical meristem > > Def: proposed > > Copy the original SAM definition. > > > > PO:new : reproductive shoot apical meristem > > Def: proposed > > Meristem formed in the apex of the shoot originating as > > inflorescence and or flower meristems. > > > > -Pankaj > > > > > > .............. > > Felipe Zapata > > University of Missouri St. Louis > > Department of Biology > > 8001 Natural Bridge Rd. > > St. Louis, MO 63121 USA > > p.314.516.6200 > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From leonore.reiser at gmail.com Fri Jun 10 18:54:09 2005 From: leonore.reiser at gmail.com (Leonore Reiser) Date: Fri, 10 Jun 2005 15:54:09 -0700 Subject: SAM restructuring suggestion In-Reply-To: <42A9F612.7050507@cornell.edu> References: <42A9F612.7050507@cornell.edu> Message-ID: <248c981f05061015543a2ce2bf@mail.gmail.com> Pankaj Now that there are terms that define stages of plant development- could these mutants be annotated to 'reproductive stage' so in PATOese that might be something like entity:reproductive stage attribute: timing value: early or late? Ill hopefully get a chance to talk to Sean May from NASC at the Arabidopsis meeting and see what he thinks about their annotations as well and maybe compare notes on flowering time mutant annotation. Leonore On 6/10/05, Pankaj Jaiswal wrote: > > > > > > > Refer to: > http://www.plantontology.org/amigo/go.cgi?view=details&show_associations=terms&search_constraint=terms&depth=0&query=PO:0020148 > > > Looks like we need a specific instance of SAM, ie. "vegetative shoot > apical meristem". The current term is too generic for curating > vegetative SAM. > > The reason being, I am curating a lot of flowering time genes and many > are involved in regulating the transition of vegetative SAM to > reproductive SAM. This event is critical in short-day or long-day light > response resulting in early/delayed flowering. > > Current structure is like follows: > > > # PO:0020148 : shoot apical meristem ( 32 ) > > * PO:0000224 : central zone > * PO:0006362 : embryonic shoot apical meristem > * PO:0000229 : floral meristem > * PO:0000230 : inflorescence meristem > * PO:0009020 : meristem L1 > * PO:0009021 : meristem L2 > * PO:0009022 : meristem L3 > * PO:0000225 : peripheral zone > * PO:0005039 : primary thickening meristem > * PO:0000226 : rib zone > * PO:0006306 : shoot procambium > -------------------------------------------------- > > Proposed > > # PO:0020148 : shoot apical meristem ( 32 ) > i PO:new : vegetative shoot apical meristem > p PO:0000224 : central zone > i PO:0006362 : embryonic shoot apical meristem > p PO:0009020 : meristem L1 > p PO:0009021 : meristem L2 > p PO:0009022 : meristem L3 > p PO:0000225 : peripheral zone > p PO:0005039 : primary thickening meristem > p PO:0000226 : rib zone > p PO:0006306 : shoot procambium > i PO:new : reproductive shoot apical meristem > i PO:0000229 : floral meristem > i PO:0000230 : inflorescence meristem > > > PO:0020148 : shoot apical meristem > Def: current > Meristem formed in the apex of the shoot, including meristems > originating as axillary shoot meristems. > Def: proposed > Meristem formed in the apex of the shoot or those originating as > axillary and reproductive meristems. > > PO:new : vegetative shoot apical meristem > Def: proposed > Copy the original SAM definition. > > PO:new : reproductive shoot apical meristem > Def: proposed > Meristem formed in the apex of the shoot originating as > inflorescence and or flower meristems. > > -Pankaj > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From kellogge at msx.umsl.edu Tue Jun 14 12:12:42 2005 From: kellogge at msx.umsl.edu (kellogge) Date: Tue, 14 Jun 2005 11:12:42 -0500 Subject: SAM restructuring suggestion In-Reply-To: <248c981f0506101421218367ae@mail.gmail.com> References: <42A9F612.7050507@cornell.edu> <248c981f0506101421218367ae@mail.gmail.com> Message-ID: <22CC0E72-DCEF-11D9-ADA9-000D93B827BC@msx.umsl.edu> I agree with Leonore on this - I think flowering time mutants are defective in a process, not in a particular organ, so use of the plant structure ontology is not warranted. This exchange also brings up the general situation created by deciding that we'll add terms "as needed." Obviously as our knowledge of plants increases, the ontology will have to change. Also, the ontology is has not been extensively tested for annotation yet, and there may prove to be whole sections that don't work and have to be redone. On the other hand, do we want/need to have a protracted email conversation among 10 or so people every time an annotator sees the need for a new term? It seems as though it might be useful to have some way to accumulate a list of queries/problems that pertain to a particular node, and then once every 6 months or year, sit down and reassess the entire node. Otherwise, I fear that the attempt at unification will get lost pretty quickly. Toby On Jun 10, 2005, at 4:21 PM, Leonore Reiser wrote: > So Pankaj > your suggestion raises a question about annotations that we were > discussing here the other day. Are you proposing to annotate the > expression of these genes to these body parts or the phenotype of > mutant alleles/germplasms to these body parts? > > NASC also has a lot of flowering time mutants annotated- in their > case, they annotated to the BODY part -flower- > possibly because there was/is not term to reflect > vegetative-reproductive stage.? I find that wildly confusing and its > not where I would look to find flowering time mutants. > > ?I would annotate something like Constans or FLC as being INVOLVED IN > the biological process of flowering (which? called flower development > in the GO). I would not use an annotation to vegetative or > reproductive meristem to describe the phenotype. > > I think it is a big mistake to try and use the Plant Ontologies to > describe every mutant phenotype- its just not possible. Mutants > involved in nitrogen assimilation may be chlorotic (pale green or > yellow leaves) but the PO cannot effectively describe say sensitivity > to a nitrogen analog. > So I may be jumping the gun because this could be totally NOT what > you are intending to use these terms for. But if so perhaps we could > use this as an example and see how other groups would annotate late or > early flowering mutant phenotypes? Its a really good exercise. > > > Leonore > > > > On 6/10/05, Pankaj Jaiswal wrote: > > action=plus_node&depth=1&search_constraint=terms&query=PO:00201482 > > > > Refer to: > http://www.plantontology.org/amigo/go.cgi? > view=details&show_associations=terms&search_constraint=terms&depth=0&qu > ery=PO:0020148 > > Looks like we need a specific instance of SAM, ie. "vegetative shoot > apical meristem". The current term is too generic for curating > vegetative SAM. > > The reason being, I am curating a lot of flowering time genes and many > are involved in regulating the transition of vegetative SAM to > reproductive SAM. This event is critical in??short-day or long-day > light > response resulting in early/delayed flowering. > > Current structure is like follows: > > > #??PO:0020148 : shoot apical meristem?? ( 32 ) > > ???? * PO:0000224 : central zone > ???? * PO:0006362 : embryonic shoot apical meristem > ???? * PO:0000229 : floral meristem > ???? * PO:0000230 : inflorescence meristem > ???? * PO:0009020 : meristem L1 > ???? * PO:0009021 : meristem L2 > ???? * PO:0009022 : meristem L3 > ???? * PO:0000225 : peripheral zone > ???? * PO:0005039 : primary thickening meristem > ???? * PO:0000226 : rib zone > ???? * PO:0006306 : shoot procambium > -------------------------------------------------- > > Proposed > > #??PO:0020148 : shoot apical meristem?? ( 32 ) > ?? i PO:new : vegetative shoot apical meristem > ???? p PO:0000224 : central zone > ???? i PO:0006362 : embryonic shoot apical meristem > ???? p PO:0009020 : meristem L1 > ???? p PO:0009021 : meristem L2 > ???? p PO:0009022 : meristem L3 > ???? p PO:0000225 : peripheral zone > ???? p PO:0005039 : primary thickening meristem > ???? p PO:0000226 : rib zone > ???? p PO:0006306 : shoot procambium > ?? i PO:new : reproductive shoot apical meristem > ???? i PO:0000229 : floral meristem > ???? i PO:0000230 : inflorescence meristem > > > PO:0020148 : shoot apical meristem > Def: current > ???? Meristem formed in the apex of the shoot, including meristems > originating as axillary shoot meristems. > Def: proposed > ???? Meristem formed in the apex of the shoot or those originating as > axillary and reproductive meristems. > > PO:new : vegetative shoot apical meristem > Def: proposed > ????????Copy the original SAM definition. > > PO:new : reproductive shoot apical meristem > Def: proposed > ???? Meristem formed in the apex of the shoot originating as > inflorescence and or flower meristems. > > -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/divisions/artscience/biology/Kellogg/Kellogg/ home.html -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 5337 bytes Desc: not available URL: From simon at arabidopsis.info Tue Jun 14 13:37:52 2005 From: simon at arabidopsis.info (Simon Jupp) Date: Tue, 14 Jun 2005 18:37:52 +0100 Subject: SAM restructuring suggestion In-Reply-To: <248c981f05061015543a2ce2bf@mail.gmail.com> References: <42A9F612.7050507@cornell.edu> <248c981f05061015543a2ce2bf@mail.gmail.com> Message-ID: <42AF15F0.9060908@arabidopsis.info> An HTML attachment was scrubbed... URL: From pj37 at cornell.edu Tue Jun 14 15:06:02 2005 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 14 Jun 2005 15:06:02 -0400 Subject: SAM restructuring suggestion In-Reply-To: <42A9F612.7050507@cornell.edu> References: <42A9F612.7050507@cornell.edu> Message-ID: <42AF2A9A.3@cornell.edu> Please take a look at the following text. I proposed the re-organization based on the requirements for gene expression (rice and Arabidopsis). I need these terms for phenotype annotations as well. How we annotate the flowering time phenotypes is a different question and will be dealt in separate mails. Thanks Pankaj FROM THE ARTICLE (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9482818&query_hl=38 ): Before transition to reproductive growth, RFL RNA was detected in epidermal cells at the marginal region in young leaves but not in the vegetative shoot apical meristem or stem tissue (Fig. 2B). .......The RFL RNA expression was observed in the vegetative apical meristem at a very early stage of panicle development (Fig. 2 B and C), then it started to diminish in the corpus of the panicle axis at the middle stage of primary branch differentiation (Fig. 2D). After all the primordia of primary branches had initiated, RFL RNA disappeared entirely from the main axis of the panicle (Fig. 2 E and F) Proc Natl Acad Sci U S A. 1998 Mar 3;95(5):1979-82. Down-regulation of RFL, the FLO/LFY homolog of rice, accompanied with panicle branch initiation. Kyozuka J, Konishi S, Nemoto K, Izawa T, Shimamoto K. FROM THE ARTICLE (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11440721&query_hl=40 ): To investigate possible feedback regulation of WUS by AG, we examined WUS expression in ag mutants. In wild-type, WUS is expressed initially in floral meristems in a pattern similar to that of shoot meristems, but it is not maintained past stage 6, when the floral meristem is consumed in the formation of the central gynoecium (Figure 7A) Cell. 2001 Jun 15;105(6):793-803. A molecular link between stem cell regulation and floral patterning in Arabidopsis. Lohmann JU, Hong RL, Hobe M, Busch MA, Parcy F, Simon R, Weigel D. There are lots of instances where a gene is expressed in SAM(vegetative) and may or may not in the reproductive (inflorescence/flower) meristems. Thus requiring us to make a specific annotation to the two types of meristem. In the existing tree, The annotation for the same gene if expressed in both the vegetative and inflorescence meristems can be annotated to child term:inflorescence meristem and its parent term:SAM. But there is no way we can distinguish that the parent term is only representing vegetative SAM only. By virtue of representing children terms the current term is also saying the it is also a reproductive SAM as well, because by accumulating the annotations from the children terms, the generic term will show up the genes expressed in flower / inflorescence apical meristems. Therefore to make a clear distinction, I suggest re-organizing the SAM section and introduce the concept of vegetative and reproductive SAMs. Thus allowing the curators and users to particularly chose these terms for use and NOT use the current SAM term which is a generic term. This will particularly help in the annotation of various MADs box genes and the transcription factors or other genes that are responsible especially in making a transition from vegetative to reproductive (vegetative-SAM to inflorescence-apical meristem and inflorescence-apical meristem to floral-apical meristem). Both the above citations are such examples. Pankaj Jaiswal wrote: > > > > > > Refer to: > http://www.plantontology.org/amigo/go.cgi?view=details&show_associations=terms&search_constraint=terms&depth=0&query=PO:0020148 > > > Looks like we need a specific instance of SAM, ie. "vegetative shoot > apical meristem". The current term is too generic for curating > vegetative SAM. > > The reason being, I am curating a lot of flowering time genes and many > are involved in regulating the transition of vegetative SAM to > reproductive SAM. This event is critical in short-day or long-day > light response resulting in early/delayed flowering. > > Current structure is like follows: > > > # PO:0020148 : shoot apical meristem ( 32 ) > > * PO:0000224 : central zone > * PO:0006362 : embryonic shoot apical meristem > * PO:0000229 : floral meristem > * PO:0000230 : inflorescence meristem > * PO:0009020 : meristem L1 > * PO:0009021 : meristem L2 > * PO:0009022 : meristem L3 > * PO:0000225 : peripheral zone > * PO:0005039 : primary thickening meristem > * PO:0000226 : rib zone > * PO:0006306 : shoot procambium > -------------------------------------------------- > > Proposed > > # PO:0020148 : shoot apical meristem ( 32 ) > i PO:new : vegetative shoot apical meristem > p PO:0000224 : central zone > i PO:0006362 : embryonic shoot apical meristem > p PO:0009020 : meristem L1 > p PO:0009021 : meristem L2 > p PO:0009022 : meristem L3 > p PO:0000225 : peripheral zone > p PO:0005039 : primary thickening meristem > p PO:0000226 : rib zone > p PO:0006306 : shoot procambium > i PO:new : reproductive shoot apical meristem > i PO:0000229 : floral meristem > i PO:0000230 : inflorescence meristem > > > PO:0020148 : shoot apical meristem > Def: current > Meristem formed in the apex of the shoot, including meristems > originating as axillary shoot meristems. > Def: proposed > Meristem formed in the apex of the shoot or those originating as > axillary and reproductive meristems. > > PO:new : vegetative shoot apical meristem > Def: proposed > Copy the original SAM definition. > > PO:new : reproductive shoot apical meristem > Def: proposed > Meristem formed in the apex of the shoot originating as > inflorescence and or flower meristems. > > -Pankaj > > From pj37 at cornell.edu Tue Jun 14 15:00:21 2005 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 14 Jun 2005 15:00:21 -0400 Subject: SAM restructuring suggestion In-Reply-To: <42AF15F0.9060908@arabidopsis.info> References: <42A9F612.7050507@cornell.edu> <248c981f05061015543a2ce2bf@mail.gmail.com> <42AF15F0.9060908@arabidopsis.info> Message-ID: <42AF2945.6010302@cornell.edu> I will talk about the phenotypes in my other mails. -Pankaj Simon Jupp wrote: > Hi, > > NASC have been using a combination of PO and PATO terms. In the > example you mention we would use a combination to say flower (PO) and > late /early (PATO). If a user is interested in flower mutants, or > comes to our site with the flower PO term they will get a list of > attributes from PATO that have been used with the flower term, they > can then use these to search the germplasm database. By doing PO/PATO > annotations users have the best chance of finding germplasm with > phenotypes they are interested in, it is already proving more powerful > than our basic text search function. > > We have countless examples where PO/PATO annotations for phenotypes > are not true reflections of the phenotypes being explained by the > donor, but we decided we would annotate them the best we could to at > least capture the keywords being observed. Our primary goal is to aid > users in searching our database, so we have often over annotated some > of our lines. As there was (is) no standard for doing these > annotation we decided to carry on regardless with a view publicise the > ontologies to our user base and with a view to refining the > annotations later when standards come in place and PATO matures. > > I have been waiting for interest in phenotype annotations to pick up, > we have over 1500 mutant phenotypes annotated with PO and PATO terms > and would appreciate any feedback from the community on the annotations. > > Simon > NASC > > > > > >> Pankaj >> >> Now that there are terms that define stages of plant development- >> could these mutants be annotated to 'reproductive stage' >> so in PATOese >> that might be something like >> entity:reproductive stage >> attribute: timing >> value: early or late? >> >> Ill hopefully get a chance to talk to Sean May from NASC at the >> Arabidopsis meeting and see what he thinks about their annotations >> as well and maybe compare notes on flowering time mutant annotation. >> >> Leonore >> >> >> On 6/10/05, Pankaj Jaiswal > > wrote: >> >> >> > > >> >> >> Refer to: >> http://www.plantontology.org/amigo/go.cgi?view=details&show_associations=terms&search_constraint=terms&depth=0&query=PO:0020148 >> >> >> Looks like we need a specific instance of SAM, ie. "vegetative shoot >> apical meristem". The current term is too generic for curating >> vegetative SAM. >> >> The reason being, I am curating a lot of flowering time genes and >> many >> are involved in regulating the transition of vegetative SAM to >> reproductive SAM. This event is critical in short-day or >> long-day light >> response resulting in early/delayed flowering. >> >> Current structure is like follows: >> >> >> # PO:0020148 : shoot apical meristem ( 32 ) >> >> * PO:0000224 : central zone >> * PO:0006362 : embryonic shoot apical meristem >> * PO:0000229 : floral meristem >> * PO:0000230 : inflorescence meristem >> * PO:0009020 : meristem L1 >> * PO:0009021 : meristem L2 >> * PO:0009022 : meristem L3 >> * PO:0000225 : peripheral zone >> * PO:0005039 : primary thickening meristem >> * PO:0000226 : rib zone >> * PO:0006306 : shoot procambium >> -------------------------------------------------- >> >> Proposed >> >> # PO:0020148 : shoot apical meristem ( 32 ) >> i PO:new : vegetative shoot apical meristem >> p PO:0000224 : central zone >> i PO:0006362 : embryonic shoot apical meristem >> p PO:0009020 : meristem L1 >> p PO:0009021 : meristem L2 >> p PO:0009022 : meristem L3 >> p PO:0000225 : peripheral zone >> p PO:0005039 : primary thickening meristem >> p PO:0000226 : rib zone >> p PO:0006306 : shoot procambium >> i PO:new : reproductive shoot apical meristem >> i PO:0000229 : floral meristem >> i PO:0000230 : inflorescence meristem >> >> >> PO:0020148 : shoot apical meristem >> Def: current >> Meristem formed in the apex of the shoot, including meristems >> originating as axillary shoot meristems. >> Def: proposed >> Meristem formed in the apex of the shoot or those >> originating as >> axillary and reproductive meristems. >> >> PO:new : vegetative shoot apical meristem >> Def: proposed >> Copy the original SAM definition. >> >> PO:new : reproductive shoot apical meristem >> Def: proposed >> Meristem formed in the apex of the shoot originating as >> inflorescence and or flower meristems. >> >> -Pankaj >> >> > > This message has been checked for viruses but the contents of an > attachment may still contain software viruses, which could damage your > computer system: you are advised to perform your own checks. Email > communications with the University of Nottingham may be monitored as > permitted by UK legislation. > From pj37 at cornell.edu Tue Jun 14 15:25:31 2005 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 14 Jun 2005 15:25:31 -0400 Subject: SAM restructuring suggestion In-Reply-To: <22CC0E72-DCEF-11D9-ADA9-000D93B827BC@msx.umsl.edu> References: <42A9F612.7050507@cornell.edu> <248c981f0506101421218367ae@mail.gmail.com> <22CC0E72-DCEF-11D9-ADA9-000D93B827BC@msx.umsl.edu> Message-ID: <42AF2F2B.5020205@cornell.edu> I disagree with Leonore in some aspects and agree that there are annotation anomalies. Howevere, if there are genes and phenotypes known to be responsible for the biological processes involved in "transition of SAM from vegetative to reproductive meristem", I would not simply annotate them to flower or inflorescence/.shoot/current SAM term, but specifically to the two SAM types. The terms vegetative and reproductive apical meristems are current required for annotation. Here is an example: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12148532&query_hl=42 Plant J. 2002 Mar;29(6):743-50 Overexpression of RCN1 and RCN2, rice TERMINAL FLOWER 1/CENTRORADIALIS homologs, confers delay of phase transition and altered panicle morphology in rice. Nakagawa M, Shimamoto K, Kyozuka J. On historical grounds, many of the Arabidopsis flowering time genes are considered homologs (rather orthologs) of the Heading time/inflorescence exsertion time genes. By saying heading means the flower is not yet ready for flowering (anthesis), whereas in case of Arabidopsis, it is often the flowering (anthesis). This is one classical example where one can see the inflorescence very early in Arabidopsis plant, compared to the much later stage in rice or any other cereal where one looks at the inflorescence for the first time at the heading stage. By heading stage the inflorescence/flower development is almost complete, except for the elongation of the rachis. -Pankaj kellogge wrote: > I agree with Leonore on this - I think flowering time mutants are > defective in a process, not in a particular organ, so use of the plant > structure ontology is not warranted. > > This exchange also brings up the general situation created by deciding > that we'll add terms "as needed." Obviously as our knowledge of plants > increases, the ontology will have to change. Also, the ontology is has > not been extensively tested for annotation yet, and there may prove to > be whole sections that don't work and have to be redone. On the other > hand, do we want/need to have a protracted email conversation among 10 > or so people every time an annotator sees the need for a new term? It > seems as though it might be useful to have some way to accumulate a > list of queries/problems that pertain to a particular node, and then > once every 6 months or year, sit down and reassess the entire node. > Otherwise, I fear that the attempt at unification will get lost pretty > quickly. > > Toby > > On Jun 10, 2005, at 4:21 PM, Leonore Reiser wrote: > > So Pankaj > your suggestion raises a question about annotations that we were > discussing here the other day. Are you proposing to annotate the > expression of these genes to these body parts or the phenotype of > mutant alleles/germplasms to these body parts? > > NASC also has a lot of flowering time mutants annotated- in their > case, they annotated to the BODY part -flower- > possibly because there was/is not term to reflect > vegetative-reproductive stage. I find that wildly confusing and > its not where I would look to find flowering time mutants. > > I would annotate something like Constans or FLC as being INVOLVED > IN the biological process of flowering (which called flower > development in the GO). I would not use an annotation to > vegetative or reproductive meristem to describe the phenotype. > > I think it is a big mistake to try and use the Plant Ontologies to > describe every mutant phenotype- its just not possible. Mutants > involved in nitrogen assimilation may be chlorotic (pale green or > yellow leaves) but the PO cannot effectively describe say > sensitivity to a nitrogen analog. > So I may be jumping the gun because this could be totally NOT what > you are intending to use these terms for. But if so perhaps we > could use this as an example and see how other groups would > annotate late or early flowering mutant phenotypes? Its a really > good exercise. > > > Leonore > > > > On 6/10/05, Pankaj Jaiswal wrote: > > > > > > Refer to: > http://www.plantontology.org/amigo/go.cgi?view=details&show_associations=terms&search_constraint=terms&depth=0&query=PO:0020148 > > > Looks like we need a specific instance of SAM, ie. "vegetative shoot > apical meristem". The current term is too generic for curating > vegetative SAM. > > The reason being, I am curating a lot of flowering time genes and > many > are involved in regulating the transition of vegetative SAM to > reproductive SAM. This event is critical in short-day or long-day > light > response resulting in early/delayed flowering. > > Current structure is like follows: > > > # PO:0020148 : shoot apical meristem ( 32 ) > > * PO:0000224 : central zone > * PO:0006362 : embryonic shoot apical meristem > * PO:0000229 : floral meristem > * PO:0000230 : inflorescence meristem > * PO:0009020 : meristem L1 > * PO:0009021 : meristem L2 > * PO:0009022 : meristem L3 > * PO:0000225 : peripheral zone > * PO:0005039 : primary thickening meristem > * PO:0000226 : rib zone > * PO:0006306 : shoot procambium > -------------------------------------------------- > > Proposed > > # PO:0020148 : shoot apical meristem ( 32 ) > i PO:new : vegetative shoot apical meristem > p PO:0000224 : central zone > i PO:0006362 : embryonic shoot apical meristem > p PO:0009020 : meristem L1 > p PO:0009021 : meristem L2 > p PO:0009022 : meristem L3 > p PO:0000225 : peripheral zone > p PO:0005039 : primary thickening meristem > p PO:0000226 : rib zone > p PO:0006306 : shoot procambium > i PO:new : reproductive shoot apical meristem > i PO:0000229 : floral meristem > i PO:0000230 : inflorescence meristem > > > PO:0020148 : shoot apical meristem > Def: current > Meristem formed in the apex of the shoot, including meristems > originating as axillary shoot meristems. > Def: proposed > Meristem formed in the apex of the shoot or those originating as > axillary and reproductive meristems. > > PO:new : vegetative shoot apical meristem > Def: proposed > Copy the original SAM definition. > > PO:new : reproductive shoot apical meristem > Def: proposed > Meristem formed in the apex of the shoot originating as > inflorescence and or flower meristems. > > -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/divisions/artscience/biology/Kellogg/Kellogg/home.html > > From leonore.reiser at gmail.com Tue Jun 14 15:39:31 2005 From: leonore.reiser at gmail.com (Leonore Reiser) Date: Tue, 14 Jun 2005 12:39:31 -0700 Subject: SAM restructuring suggestion In-Reply-To: <42AF15F0.9060908@arabidopsis.info> References: <42A9F612.7050507@cornell.edu> <248c981f05061015543a2ce2bf@mail.gmail.com> <42AF15F0.9060908@arabidopsis.info> Message-ID: <248c981f0506141239763a6f1@mail.gmail.com> Simon I agree that we need to have some standards defined -thats sorta my main objective.Your comment and Pankaj's both highlight the issue of needing to annotate and not having the 'right term', either because the term didnt exist (like if you wanted to describe a developmental stage using PO terms) or because it requires instantiation of something that might (eventually) be a combinatiorial term. So say for Pankaj's case of needing to annotate to a gene being expressed in the shoot apical meristem during the vegetative stage of growth- I suppose ideally one would want either the combinatorial term or combinatorial annotation,but then how long do you wait for the software to exist. Indeed one of the reasons why i dont think we should wait 6 months to review terms/nodes is precisely for this reason... My main goal is to stimulate discussion and hopefully come to some basic agreements. 'Cause we all probably have had the same questions at some point. I have my point of view- but its just that- succeptible to change based on discussion/good arguments against and the vagueness of my mind. Maybe we can meet at the Arabidopsis meeting and talk about Arabidopsis annotation (I know you wont be there but if Sean and other s are that would be great). Leonore On 6/14/05, Simon Jupp wrote: > > Hi, > > NASC have been using a combination of PO and PATO terms. In the example > you mention we would use a combination to say flower (PO) and late /early > (PATO). If a user is interested in flower mutants, or comes to our site with > the flower PO term they will get a list of attributes from PATO that have > been used with the flower term, they can then use these to search the > germplasm database. By doing PO/PATO annotations users have the best chance > of finding germplasm with phenotypes they are interested in, it is already > proving more powerful than our basic text search function. > > We have countless examples where PO/PATO annotations for phenotypes are > not true reflections of the phenotypes being explained by the donor, but we > decided we would annotate them the best we could to at least capture the > keywords being observed. Our primary goal is to aid users in searching our > database, so we have often over annotated some of our lines. As there was > (is) no standard for doing these annotation we decided to carry on > regardless with a view publicise the ontologies to our user base and with a > view to refining the annotations later when standards come in place and PATO > matures. > > I have been waiting for interest in phenotype annotations to pick up, we > have over 1500 mutant phenotypes annotated with PO and PATO terms and would > appreciate any feedback from the community on the annotations. > > Simon > NASC > > > > > > Pankaj > > Now that there are terms that define stages of plant development- could > these mutants be annotated to 'reproductive stage' > so in PATOese > that might be something like > entity:reproductive stage > attribute: timing > value: early or late? > > Ill hopefully get a chance to talk to Sean May from NASC at the > Arabidopsis meeting and see what he thinks about their annotations as well > and maybe compare notes on flowering time mutant annotation. > > Leonore > > > On 6/10/05, Pankaj Jaiswal wrote: > > > > > > > > > > > > > > Refer to: > > http://www.plantontology.org/amigo/go.cgi?view=details&show_associations=terms&search_constraint=terms&depth=0&query=PO:0020148 > > > > > > Looks like we need a specific instance of SAM, ie. "vegetative shoot > > apical meristem". The current term is too generic for curating > > vegetative SAM. > > > > The reason being, I am curating a lot of flowering time genes and many > > are involved in regulating the transition of vegetative SAM to > > reproductive SAM. This event is critical in short-day or long-day light > > response resulting in early/delayed flowering. > > > > Current structure is like follows: > > > > > > # PO:0020148 : shoot apical meristem ( 32 ) > > > > * PO:0000224 : central zone > > * PO:0006362 : embryonic shoot apical meristem > > * PO:0000229 : floral meristem > > * PO:0000230 : inflorescence meristem > > * PO:0009020 : meristem L1 > > * PO:0009021 : meristem L2 > > * PO:0009022 : meristem L3 > > * PO:0000225 : peripheral zone > > * PO:0005039 : primary thickening meristem > > * PO:0000226 : rib zone > > * PO:0006306 : shoot procambium > > -------------------------------------------------- > > > > Proposed > > > > # PO:0020148 : shoot apical meristem ( 32 ) > > i PO:new : vegetative shoot apical meristem > > p PO:0000224 : central zone > > i PO:0006362 : embryonic shoot apical meristem > > p PO:0009020 : meristem L1 > > p PO:0009021 : meristem L2 > > p PO:0009022 : meristem L3 > > p PO:0000225 : peripheral zone > > p PO:0005039 : primary thickening meristem > > p PO:0000226 : rib zone > > p PO:0006306 : shoot procambium > > i PO:new : reproductive shoot apical meristem > > i PO:0000229 : floral meristem > > i PO:0000230 : inflorescence meristem > > > > > > PO:0020148 : shoot apical meristem > > Def: current > > Meristem formed in the apex of the shoot, including meristems > > originating as axillary shoot meristems. > > Def: proposed > > Meristem formed in the apex of the shoot or those originating as > > axillary and reproductive meristems. > > > > PO:new : vegetative shoot apical meristem > > Def: proposed > > Copy the original SAM definition. > > > > PO:new : reproductive shoot apical meristem > > Def: proposed > > Meristem formed in the apex of the shoot originating as > > inflorescence and or flower meristems. > > > > -Pankaj > > > > > > This message has been checked for viruses but the contents of an > attachment may still contain software viruses, which could damage your > computer system: you are advised to perform your own checks. Email > communications with the University of Nottingham may be monitored as > permitted by UK legislation. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From pj37 at cornell.edu Tue Jun 14 15:40:49 2005 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 14 Jun 2005 15:40:49 -0400 Subject: SAM restructuring suggestion In-Reply-To: <248c981f05061015543a2ce2bf@mail.gmail.com> References: <42A9F612.7050507@cornell.edu> <248c981f05061015543a2ce2bf@mail.gmail.com> Message-ID: <42AF32C1.8090101@cornell.edu> Once again this is a curation anomaly like whether the glass is half empty or half full. A curator can instead say that entity:vegetative stage attribute: phase/length value: extended In this paper http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12148532&query_hl=42 The RCN1/2 overexpression can give a severe phenotype with no-heading. Means the plant never reached the vegetative phase. Then what? entity:reproductive stage attribute: timing value: absent?? Or may require two annotations entity:vegetative stage attribute: phase/length value: extended entity:reproductive stage attribute: timing value: delayed/absent?? In any case Gramene is not doing the EAV type annotations for the moment, though we intend to do it sometime next year. -Pankaj Leonore Reiser wrote: > Pankaj > > Now that there are terms that define stages of plant development- > could these mutants be annotated to 'reproductive stage' > so in PATOese > that might be something like > entity:reproductive stage > attribute: timing > value: early or late? > > Ill hopefully get a chance to talk to Sean May from NASC at the > Arabidopsis meeting and see what he thinks about their annotations as > well and maybe compare notes on flowering time mutant annotation. > > Leonore > > > On 6/10/05, Pankaj Jaiswal > wrote: > > > > > > > Refer to: > http://www.plantontology.org/amigo/go.cgi?view=details&show_associations=terms&search_constraint=terms&depth=0&query=PO:0020148 > > > Looks like we need a specific instance of SAM, ie. "vegetative shoot > apical meristem". The current term is too generic for curating > vegetative SAM. > > The reason being, I am curating a lot of flowering time genes and > many > are involved in regulating the transition of vegetative SAM to > reproductive SAM. This event is critical in short-day or long-day > light > response resulting in early/delayed flowering. > > Current structure is like follows: > > > # PO:0020148 : shoot apical meristem ( 32 ) > > * PO:0000224 : central zone > * PO:0006362 : embryonic shoot apical meristem > * PO:0000229 : floral meristem > * PO:0000230 : inflorescence meristem > * PO:0009020 : meristem L1 > * PO:0009021 : meristem L2 > * PO:0009022 : meristem L3 > * PO:0000225 : peripheral zone > * PO:0005039 : primary thickening meristem > * PO:0000226 : rib zone > * PO:0006306 : shoot procambium > -------------------------------------------------- > > Proposed > > # PO:0020148 : shoot apical meristem ( 32 ) > i PO:new : vegetative shoot apical meristem > p PO:0000224 : central zone > i PO:0006362 : embryonic shoot apical meristem > p PO:0009020 : meristem L1 > p PO:0009021 : meristem L2 > p PO:0009022 : meristem L3 > p PO:0000225 : peripheral zone > p PO:0005039 : primary thickening meristem > p PO:0000226 : rib zone > p PO:0006306 : shoot procambium > i PO:new : reproductive shoot apical meristem > i PO:0000229 : floral meristem > i PO:0000230 : inflorescence meristem > > > PO:0020148 : shoot apical meristem > Def: current > Meristem formed in the apex of the shoot, including meristems > originating as axillary shoot meristems. > Def: proposed > Meristem formed in the apex of the shoot or those originating as > axillary and reproductive meristems. > > PO:new : vegetative shoot apical meristem > Def: proposed > Copy the original SAM definition. > > PO:new : reproductive shoot apical meristem > Def: proposed > Meristem formed in the apex of the shoot originating as > inflorescence and or flower meristems. > > -Pankaj > > From leonore.reiser at gmail.com Tue Jun 14 15:43:25 2005 From: leonore.reiser at gmail.com (Leonore Reiser) Date: Tue, 14 Jun 2005 12:43:25 -0700 Subject: SAM restructuring suggestion In-Reply-To: <42AF32C1.8090101@cornell.edu> References: <42A9F612.7050507@cornell.edu> <248c981f05061015543a2ce2bf@mail.gmail.com> <42AF32C1.8090101@cornell.edu> Message-ID: <248c981f050614124341d895a1@mail.gmail.com> i agree- you dont really know what stage is affected. thats why I think a more accurate term is the process term not a body part or stage. On 6/14/05, Pankaj Jaiswal wrote: > > Once again this is a curation anomaly like whether the glass is half > empty or half full. A curator can instead say that > > entity:vegetative stage > attribute: phase/length > value: extended > > In this paper > > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12148532&query_hl=42 > The RCN1/2 overexpression can give a severe phenotype with no-heading. > Means the plant never reached the vegetative phase. Then what? > > entity:reproductive stage > attribute: timing > value: absent?? > > Or may require two annotations > > entity:vegetative stage > attribute: phase/length > value: extended > > entity:reproductive stage > attribute: timing > value: delayed/absent?? > > In any case Gramene is not doing the EAV type annotations for the > moment, though we intend to do it sometime next year. > > -Pankaj > > > Leonore Reiser wrote: > > > Pankaj > > > > Now that there are terms that define stages of plant development- > > could these mutants be annotated to 'reproductive stage' > > so in PATOese > > that might be something like > > entity:reproductive stage > > attribute: timing > > value: early or late? > > > > Ill hopefully get a chance to talk to Sean May from NASC at the > > Arabidopsis meeting and see what he thinks about their annotations as > > well and maybe compare notes on flowering time mutant annotation. > > > > Leonore > > > > > > On 6/10/05, Pankaj Jaiswal > > wrote: > > > > > > < > http://www.plantontology.org/amigo/go.cgi?action=plus_node&depth=1&search_constraint=terms&query=PO:00201482 > > < > http://www.plantontology.org/amigo/go.cgi?action=plus_node&depth=1&search_constraint=terms&query=PO:00201482 > >> > > > > > > Refer to: > > > http://www.plantontology.org/amigo/go.cgi?view=details&show_associations=terms&search_constraint=terms&depth=0&query=PO:0020148 > > < > http://www.plantontology.org/amigo/go.cgi?view=details&show_associations=terms&search_constraint=terms&depth=0&query=PO:0020148 > > > > > > Looks like we need a specific instance of SAM, ie. "vegetative shoot > > apical meristem". The current term is too generic for curating > > vegetative SAM. > > > > The reason being, I am curating a lot of flowering time genes and > > many > > are involved in regulating the transition of vegetative SAM to > > reproductive SAM. This event is critical in short-day or long-day > > light > > response resulting in early/delayed flowering. > > > > Current structure is like follows: > > > > > > # PO:0020148 : shoot apical meristem ( 32 ) > > > > * PO:0000224 : central zone > > * PO:0006362 : embryonic shoot apical meristem > > * PO:0000229 : floral meristem > > * PO:0000230 : inflorescence meristem > > * PO:0009020 : meristem L1 > > * PO:0009021 : meristem L2 > > * PO:0009022 : meristem L3 > > * PO:0000225 : peripheral zone > > * PO:0005039 : primary thickening meristem > > * PO:0000226 : rib zone > > * PO:0006306 : shoot procambium > > -------------------------------------------------- > > > > Proposed > > > > # PO:0020148 : shoot apical meristem ( 32 ) > > i PO:new : vegetative shoot apical meristem > > p PO:0000224 : central zone > > i PO:0006362 : embryonic shoot apical meristem > > p PO:0009020 : meristem L1 > > p PO:0009021 : meristem L2 > > p PO:0009022 : meristem L3 > > p PO:0000225 : peripheral zone > > p PO:0005039 : primary thickening meristem > > p PO:0000226 : rib zone > > p PO:0006306 : shoot procambium > > i PO:new : reproductive shoot apical meristem > > i PO:0000229 : floral meristem > > i PO:0000230 : inflorescence meristem > > > > > > PO:0020148 : shoot apical meristem > > Def: current > > Meristem formed in the apex of the shoot, including meristems > > originating as axillary shoot meristems. > > Def: proposed > > Meristem formed in the apex of the shoot or those originating as > > axillary and reproductive meristems. > > > > PO:new : vegetative shoot apical meristem > > Def: proposed > > Copy the original SAM definition. > > > > PO:new : reproductive shoot apical meristem > > Def: proposed > > Meristem formed in the apex of the shoot originating as > > inflorescence and or flower meristems. > > > > -Pankaj > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From pj37 at cornell.edu Tue Jun 14 15:44:03 2005 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 14 Jun 2005 15:44:03 -0400 Subject: SAM restructuring suggestion In-Reply-To: <42AF32C1.8090101@cornell.edu> References: <42A9F612.7050507@cornell.edu> <248c981f05061015543a2ce2bf@mail.gmail.com> <42AF32C1.8090101@cornell.edu> Message-ID: <42AF3383.9080604@cornell.edu> Sorry In the RCN1/2 eaxmple The plants with severe phenotype showed no-heading. Means the plant never reached the REPRODUCTIVE phase. -Pankaj Pankaj Jaiswal wrote: > Once again this is a curation anomaly like whether the glass is half > empty or half full. A curator can instead say that > > entity:vegetative stage > attribute: phase/length > value: extended > > In this paper > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12148532&query_hl=42 > > The RCN1/2 overexpression can give a severe phenotype with no-heading. > Means the plant never reached the vegetative phase. Then what? > > entity:reproductive stage > attribute: timing > value: absent?? > > Or may require two annotations > > entity:vegetative stage > attribute: phase/length > value: extended > > entity:reproductive stage > attribute: timing > value: delayed/absent?? > > In any case Gramene is not doing the EAV type annotations for the > moment, though we intend to do it sometime next year. > > -Pankaj > > > Leonore Reiser wrote: > >> Pankaj >> >> Now that there are terms that define stages of plant development- >> could these mutants be annotated to 'reproductive stage' >> so in PATOese >> that might be something like >> entity:reproductive stage >> attribute: timing >> value: early or late? >> >> Ill hopefully get a chance to talk to Sean May from NASC at the >> Arabidopsis meeting and see what he thinks about their annotations >> as well and maybe compare notes on flowering time mutant annotation. >> >> Leonore >> >> >> On 6/10/05, Pankaj Jaiswal > > wrote: >> >> >> >> > >> >> > >> >> >> >> Refer to: >> >> http://www.plantontology.org/amigo/go.cgi?view=details&show_associations=terms&search_constraint=terms&depth=0&query=PO:0020148 >> >> >> >> >> >> Looks like we need a specific instance of SAM, ie. "vegetative shoot >> apical meristem". The current term is too generic for curating >> vegetative SAM. >> >> The reason being, I am curating a lot of flowering time genes and >> many >> are involved in regulating the transition of vegetative SAM to >> reproductive SAM. This event is critical in short-day or long-day >> light >> response resulting in early/delayed flowering. >> >> Current structure is like follows: >> >> >> # PO:0020148 : shoot apical meristem ( 32 ) >> >> * PO:0000224 : central zone >> * PO:0006362 : embryonic shoot apical meristem >> * PO:0000229 : floral meristem >> * PO:0000230 : inflorescence meristem >> * PO:0009020 : meristem L1 >> * PO:0009021 : meristem L2 >> * PO:0009022 : meristem L3 >> * PO:0000225 : peripheral zone >> * PO:0005039 : primary thickening meristem >> * PO:0000226 : rib zone >> * PO:0006306 : shoot procambium >> -------------------------------------------------- >> >> Proposed >> >> # PO:0020148 : shoot apical meristem ( 32 ) >> i PO:new : vegetative shoot apical meristem >> p PO:0000224 : central zone >> i PO:0006362 : embryonic shoot apical meristem >> p PO:0009020 : meristem L1 >> p PO:0009021 : meristem L2 >> p PO:0009022 : meristem L3 >> p PO:0000225 : peripheral zone >> p PO:0005039 : primary thickening meristem >> p PO:0000226 : rib zone >> p PO:0006306 : shoot procambium >> i PO:new : reproductive shoot apical meristem >> i PO:0000229 : floral meristem >> i PO:0000230 : inflorescence meristem >> >> >> PO:0020148 : shoot apical meristem >> Def: current >> Meristem formed in the apex of the shoot, including meristems >> originating as axillary shoot meristems. >> Def: proposed >> Meristem formed in the apex of the shoot or those >> originating as >> axillary and reproductive meristems. >> >> PO:new : vegetative shoot apical meristem >> Def: proposed >> Copy the original SAM definition. >> >> PO:new : reproductive shoot apical meristem >> Def: proposed >> Meristem formed in the apex of the shoot originating as >> inflorescence and or flower meristems. >> >> -Pankaj >> >> > > From pj37 at cornell.edu Tue Jun 14 16:02:16 2005 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 14 Jun 2005 16:02:16 -0400 Subject: SAM restructuring suggestion In-Reply-To: <248c981f050614124341d895a1@mail.gmail.com> References: <42A9F612.7050507@cornell.edu> <248c981f05061015543a2ce2bf@mail.gmail.com> <42AF32C1.8090101@cornell.edu> <248c981f050614124341d895a1@mail.gmail.com> Message-ID: <42AF37C8.7080000@cornell.edu> Rather fortunately, in this example we do know it, based on the experimental designs and phenotypic analyses. The two rice genes are putative orthologs of TFL1. -Pankaj Leonore Reiser wrote: > i agree- you dont really know what stage is affected. > thats why I think a more accurate term is the process term not a body > part or stage. > > On 6/14/05, Pankaj Jaiswal < pj37 at cornell.edu > > wrote: > > Once again this is a curation anomaly like whether the glass is half > empty or half full. A curator can instead say that > > entity:vegetative stage > attribute: phase/length > value: extended > > In this paper > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12148532&query_hl=42 > > The RCN1/2 overexpression can give a severe phenotype with no-heading. > Means the plant never reached the vegetative phase. Then what? > > entity:reproductive stage > attribute: timing > value: absent?? > > Or may require two annotations > > entity:vegetative stage > attribute: phase/length > value: extended > > entity:reproductive stage > attribute: timing > value: delayed/absent?? > > In any case Gramene is not doing the EAV type annotations for the > moment, though we intend to do it sometime next year. > > -Pankaj > > > Leonore Reiser wrote: > > > Pankaj > > > > Now that there are terms that define stages of plant development- > > could these mutants be annotated to 'reproductive stage' > > so in PATOese > > that might be something like > > entity:reproductive stage > > attribute: timing > > value: early or late? > > > > Ill hopefully get a chance to talk to Sean May from NASC at the > > Arabidopsis meeting and see what he thinks about their > annotations as > > well and maybe compare notes on flowering time mutant annotation. > > > > Leonore > > > > > > On 6/10/05, Pankaj Jaiswal > > >> wrote: > > > > > > < > http://www.plantontology.org/amigo/go.cgi?action=plus_node&depth=1&search_constraint=terms&query=PO:00201482 > > > < > http://www.plantontology.org/amigo/go.cgi?action=plus_node&depth=1&search_constraint=terms&query=PO:00201482 > >> > > > > > > Refer to: > > > http://www.plantontology.org/amigo/go.cgi?view=details&show_associations=terms&search_constraint=terms&depth=0&query=PO:0020148 > > > < > http://www.plantontology.org/amigo/go.cgi?view=details&show_associations=terms&search_constraint=terms&depth=0&query=PO:0020148 > > > > > > Looks like we need a specific instance of SAM, ie. > "vegetative shoot > > apical meristem". The current term is too generic for curating > > vegetative SAM. > > > > The reason being, I am curating a lot of flowering time > genes and > > many > > are involved in regulating the transition of vegetative SAM to > > reproductive SAM. This event is critical in short-day or > long-day > > light > > response resulting in early/delayed flowering. > > > > Current structure is like follows: > > > > > > # PO:0020148 : shoot apical meristem ( 32 ) > > > > * PO:0000224 : central zone > > * PO:0006362 : embryonic shoot apical meristem > > * PO:0000229 : floral meristem > > * PO:0000230 : inflorescence meristem > > * PO:0009020 : meristem L1 > > * PO:0009021 : meristem L2 > > * PO:0009022 : meristem L3 > > * PO:0000225 : peripheral zone > > * PO:0005039 : primary thickening meristem > > * PO:0000226 : rib zone > > * PO:0006306 : shoot procambium > > -------------------------------------------------- > > > > Proposed > > > > # PO:0020148 : shoot apical meristem ( 32 ) > > i PO:new : vegetative shoot apical meristem > > p PO:0000224 : central zone > > i PO:0006362 : embryonic shoot apical meristem > > p PO:0009020 : meristem L1 > > p PO:0009021 : meristem L2 > > p PO:0009022 : meristem L3 > > p PO:0000225 : peripheral zone > > p PO:0005039 : primary thickening meristem > > p PO:0000226 : rib zone > > p PO:0006306 : shoot procambium > > i PO:new : reproductive shoot apical meristem > > i PO:0000229 : floral meristem > > i PO:0000230 : inflorescence meristem > > > > > > PO:0020148 : shoot apical meristem > > Def: current > > Meristem formed in the apex of the shoot, including > meristems > > originating as axillary shoot meristems. > > Def: proposed > > Meristem formed in the apex of the shoot or those > originating as > > axillary and reproductive meristems. > > > > PO:new : vegetative shoot apical meristem > > Def: proposed > > Copy the original SAM definition. > > > > PO:new : reproductive shoot apical meristem > > Def: proposed > > Meristem formed in the apex of the shoot originating as > > inflorescence and or flower meristems. > > > > -Pankaj > > > > > > From feedback_submission at filetta.cshl.edu Tue Jun 14 16:27:11 2005 From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu) Date: Tue, 14 Jun 2005 16:27:11 -0400 Subject: Feedback on POC Message-ID: <200506142027.j5EKRBt4013591@filetta.cshl.org> *** Feedback from Plant Ontology Live Site *** refer_to_url: http://www.plantontology.org/index.html comments: Ref: http://www.plantontology.org/amigo/go.cgi?view=details&show_associations=terms&search_constraint=terms&depth=0&query=PO:0000025 Looks like going by the definition, the terms PO:0020123 : root cap PO:0006085 : root meristem should become part_of PO:0000025 : root tip Also the do you think that "root tip" be renamed to "root apex" to be consistent with the term "shoot apex" or atleast have the synonym. name: Pankaj email: pj37 at cornell.edu organization: CU send_feedback: Send your feedback From pj37 at cornell.edu Tue Jun 28 09:57:44 2005 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 28 Jun 2005 09:57:44 -0400 Subject: [Fwd: [ geneontology-Curator requests-929957 ] vivipary] Message-ID: <42C15758.8030205@cornell.edu> Hi Everyone, I though that some people from the plant community may be interested in the discussion on adding a new term VIVIPARY (and its instances ??) in the Gene Ontology. Please follow the link below on the discussion https://sourceforge.net/tracker/?func=detail&atid=440764&aid=929957&group_id=36855 A couple of questions are: #1 whether we need the two instances of a generic term VIVIPARY vegetative vivipary (sensu Magnoliophyta) non-vegetative vivipary (sensu Magnoliophyta) #2 Is there anything called as vegetative vivipary. BY definition, in cereal plants or elsewhere, vivipary is defined as "A process promoting the germination of embryos while still attached to the mother plant. " -Pankaj From jclark at ebi.ac.uk Tue Jun 28 09:52:00 2005 From: jclark at ebi.ac.uk (Jennifer I Clark) Date: Tue, 28 Jun 2005 14:52:00 +0100 Subject: [Fwd: [ geneontology-Curator requests-929957 ] vivipary] In-Reply-To: <42C15758.8030205@cornell.edu> References: <42C15758.8030205@cornell.edu> Message-ID: <42C15600.4000005@ebi.ac.uk> Hi Pankaj, Thanks for passing that on. If people would like to comment without registering on sourceforge then they can write directly to me and I will add their comments to the sourceforge item. I myself have never heard the term 'vegetative vivipary'. However, I need to be able to define the term 'vivipary' so that it includes the situation where a seed germinates while still attached to a plant, alongside the situation where a small plant forms vegetatively on the leaf margins, as in Bryophyllum. Then I need a way to relate this term 'vivipary' to 'seed germination'. This is the difficulty. If anybody can see a good way out of this I'd be interested to hear it. Thanks, Jen Pankaj Jaiswal wrote: > Hi Everyone, > > I though that some people from the plant community may be interested > in the discussion on adding a new term VIVIPARY (and its instances ??) > in the Gene Ontology. > > Please follow the link below on the discussion > https://sourceforge.net/tracker/?func=detail&atid=440764&aid=929957&group_id=36855 > > > A couple of questions are: > > #1 whether we need the two instances of a generic term VIVIPARY > > vegetative vivipary (sensu Magnoliophyta) > non-vegetative vivipary (sensu Magnoliophyta) > > > #2 Is there anything called as vegetative vivipary. > > > BY definition, in cereal plants or elsewhere, vivipary is defined as > > "A process promoting the germination of embryos while still attached > to the mother plant. " > > -Pankaj > > > From fzqhd at umsl.edu Tue Jun 28 10:26:50 2005 From: fzqhd at umsl.edu (Felipe Zapata) Date: Tue, 28 Jun 2005 09:26:50 -0500 Subject: [Fwd: [ geneontology-Curator requests-929957 ] vivipary] In-Reply-To: <42C15758.8030205@cornell.edu> References: <42C15758.8030205@cornell.edu> Message-ID: From APWeb's Glossary: Viviparous: of seeds, germinating before being shed from the parent plant, often also including plants that produce plantlets in the inflorescence. Vivparous seeds are common in Mangroves (Rhizophoraceae). What do you mean by non-vegetative vivipary? and would be the instances of this term? F On Jun 28, 2005, at 8:57 AM, Pankaj Jaiswal wrote: > Hi Everyone, > > I though that some people from the plant community may be > interested in the discussion on adding a new term VIVIPARY (and its > instances ??) in the Gene Ontology. > > Please follow the link below on the discussion > https://sourceforge.net/tracker/? > func=detail&atid=440764&aid=929957&group_id=36855 > > A couple of questions are: > > #1 whether we need the two instances of a generic term VIVIPARY > > vegetative vivipary (sensu Magnoliophyta) > non-vegetative vivipary (sensu Magnoliophyta) > > > #2 Is there anything called as vegetative vivipary. > > > BY definition, in cereal plants or elsewhere, vivipary is defined as > > "A process promoting the germination of embryos while still > attached to the mother plant. " > > -Pankaj > > > > .............. Felipe Zapata University of Missouri St. Louis Department of Biology 8001 Natural Bridge Rd. St. Louis, MO 63121 USA p.314.516.6200 -------------- next part -------------- An HTML attachment was scrubbed... URL: From PolaccoM at missouri.edu Tue Jun 28 12:04:18 2005 From: PolaccoM at missouri.edu (Mary Polacco) Date: Tue, 28 Jun 2005 11:04:18 -0500 Subject: [Fwd: [ geneontology-Curator requests-929957 ] vivipary] In-Reply-To: <42C15758.8030205@cornell.edu> Message-ID: Is there going to be consideration of the related process, dormancy? > From: Pankaj Jaiswal > Reply-To: po-dev at plantontology.org, Pankaj Jaiswal > Date: Tue, 28 Jun 2005 09:57:44 -0400 > To: POC-dev > Cc: Jennifer I Clark , rice-e-net at chanko.lab.nig.ac.jp, > grains at greengenes.cit.cornell.edu > Subject: [Fwd: [ geneontology-Curator requests-929957 ] vivipary] > > Hi Everyone, > > I though that some people from the plant community may be interested in > the discussion on adding a new term VIVIPARY (and its instances ??) in > the Gene Ontology. > > Please follow the link below on the discussion > https://sourceforge.net/tracker/?func=detail&atid=440764&aid=929957&group_id=3 > 6855 > > A couple of questions are: > > #1 whether we need the two instances of a generic term VIVIPARY > > vegetative vivipary (sensu Magnoliophyta) > non-vegetative vivipary (sensu Magnoliophyta) > > > #2 Is there anything called as vegetative vivipary. > > > BY definition, in cereal plants or elsewhere, vivipary is defined as > > "A process promoting the germination of embryos while still attached to > the mother plant. " > > -Pankaj > > > > From Blake at Montana.edu Tue Jun 28 13:26:33 2005 From: Blake at Montana.edu (Tom Blake) Date: Tue, 28 Jun 2005 12:26:33 -0500 Subject: [Fwd: [ geneontology-Curator requests-929957 ] vivipary] In-Reply-To: Message-ID: <200506281726.j5SHQdv11395873@castor.msu.montana.edu> Hi folks, In the small grains, this is called preharvest sprouting. It's well-understood, and as Mary suggests is the result of lack of seed dormancy and a wet harvest environment. Calling it vivipary won't improve understanding of the process. In both barley and wheat the genetics of dormancy and of preharvest sprouting is pretty well-understood. Cheers, Tom Blake, barley breeder, Montana State University -----Original Message----- From: grains-request at greengenes.cit.cornell.edu [mailto:grains-request at greengenes.cit.cornell.edu] On Behalf Of Mary Polacco Sent: Tuesday, June 28, 2005 11:04 AM To: po-dev at plantontology.org, Pankaj Jaiswal; POC-dev Cc: Jennifer I Clark; rice-e-net at chanko.lab.nig.ac.jp; grains at greengenes.cit.cornell.edu Subject: Re: [Fwd: [ geneontology-Curator requests-929957 ] vivipary] Is there going to be consideration of the related process, dormancy? > From: Pankaj Jaiswal > Reply-To: po-dev at plantontology.org, Pankaj Jaiswal > Date: Tue, 28 Jun 2005 09:57:44 -0400 > To: POC-dev > Cc: Jennifer I Clark , rice-e-net at chanko.lab.nig.ac.jp, > grains at greengenes.cit.cornell.edu > Subject: [Fwd: [ geneontology-Curator requests-929957 ] vivipary] > > Hi Everyone, > > I though that some people from the plant community may be interested in > the discussion on adding a new term VIVIPARY (and its instances ??) in > the Gene Ontology. > > Please follow the link below on the discussion > https://sourceforge.net/tracker/?func=detail&atid=440764&aid=929957&group_id =3 > 6855 > > A couple of questions are: > > #1 whether we need the two instances of a generic term VIVIPARY > > vegetative vivipary (sensu Magnoliophyta) > non-vegetative vivipary (sensu Magnoliophyta) > > > #2 Is there anything called as vegetative vivipary. > > > BY definition, in cereal plants or elsewhere, vivipary is defined as > > "A process promoting the germination of embryos while still attached to > the mother plant. " > > -Pankaj > > > > From TINKERNA at AGR.GC.CA Tue Jun 28 14:05:01 2005 From: TINKERNA at AGR.GC.CA (Tinker, Nicholas) Date: Tue, 28 Jun 2005 14:05:01 -0400 Subject: [Fwd: [ geneontology-Curator requests-929957 ] vivipary] Message-ID: But, If an ontology defines "vivipary" as a "type of" preharvest sprouting (or vice-versa) then won't it help the corn people do comparative genomics with the barley people? > > Hi folks, > In the small grains, this is called preharvest sprouting. It's > well-understood, and as Mary suggests is the result of lack of seed > dormancy > and a wet harvest environment. Calling it vivipary won't improve > understanding of the process. In both barley and wheat the genetics of > dormancy and of preharvest sprouting is pretty well-understood. > Cheers, > Tom Blake, barley breeder, Montana State University > > -----Original Message----- > From: grains-request at greengenes.cit.cornell.edu > [mailto:grains-request at greengenes.cit.cornell.edu] On Behalf Of Mary > Polacco > Sent: Tuesday, June 28, 2005 11:04 AM > To: po-dev at plantontology.org, Pankaj Jaiswal; POC-dev > Cc: Jennifer I Clark; rice-e-net at chanko.lab.nig.ac.jp; > grains at greengenes.cit.cornell.edu > Subject: Re: [Fwd: [ geneontology-Curator requests-929957 ] vivipary] > > Is there going to be consideration of the related process, dormancy? > > > From: Pankaj Jaiswal > > Reply-To: po-dev at plantontology.org, Pankaj Jaiswal > > Date: Tue, 28 Jun 2005 09:57:44 -0400 > > To: POC-dev > > Cc: Jennifer I Clark , > rice-e-net at chanko.lab.nig.ac.jp, > > grains at greengenes.cit.cornell.edu > > Subject: [Fwd: [ geneontology-Curator requests-929957 ] vivipary] > > > > Hi Everyone, > > > > I though that some people from the plant community may be interested in > > the discussion on adding a new term VIVIPARY (and its instances ??) in > > the Gene Ontology. > > > > Please follow the link below on the discussion > > > https://sourceforge.net/tracker/?func=detail&atid=440764&aid=929957&grou p_ > id > =3 > > 6855 > > > > A couple of questions are: > > > > #1 whether we need the two instances of a generic term VIVIPARY > > > > vegetative vivipary (sensu Magnoliophyta) > > non-vegetative vivipary (sensu Magnoliophyta) > > > > > > #2 Is there anything called as vegetative vivipary. > > > > > > BY definition, in cereal plants or elsewhere, vivipary is defined as > > > > "A process promoting the germination of embryos while still attached to > > the mother plant. " > > > > -Pankaj > > > > > > > > From kellogge at msx.umsl.edu Wed Jun 29 13:10:34 2005 From: kellogge at msx.umsl.edu (kellogge) Date: Wed, 29 Jun 2005 12:10:34 -0500 Subject: [Fwd: [ geneontology-Curator requests-929957 ] vivipary] In-Reply-To: References: Message-ID: What about putting it under germination - "on the parent plant" vs. "independent of the parent", or something more or less equivalent? The word "vivipary sensu plants" would then be a synonym, so if a corn person searched on vivipary, the term would appear. The same thing happens in mangroves; the seed never goes through the dessication process - no increase in ABA, no accumulation of lea proteins, etc. Development perfectly normal, but is continuous. And as Tom points out, the process is reasonably well understood. In vivipary as occurs in Bryophyllum and other piggy-back plants, a new meristem is organized on the margin of the leaf, and a little plantlet forms. It's mechanistically different from mangrove and cereal vivipary so probably needs a different term. Toby On Jun 28, 2005, at 1:05 PM, Tinker, Nicholas wrote: > But, > If an ontology defines "vivipary" as a "type of" preharvest sprouting > (or vice-versa) then won't it help the corn people do comparative > genomics with the barley people? > >> >> Hi folks, >> In the small grains, this is called preharvest sprouting. It's >> well-understood, and as Mary suggests is the result of lack of seed >> dormancy >> and a wet harvest environment. Calling it vivipary won't improve >> understanding of the process. In both barley and wheat the genetics > of >> dormancy and of preharvest sprouting is pretty well-understood. >> Cheers, >> Tom Blake, barley breeder, Montana State University >> >> -----Original Message----- >> From: grains-request at greengenes.cit.cornell.edu >> [mailto:grains-request at greengenes.cit.cornell.edu] On Behalf Of Mary >> Polacco >> Sent: Tuesday, June 28, 2005 11:04 AM >> To: po-dev at plantontology.org, Pankaj Jaiswal; POC-dev >> Cc: Jennifer I Clark; rice-e-net at chanko.lab.nig.ac.jp; >> grains at greengenes.cit.cornell.edu >> Subject: Re: [Fwd: [ geneontology-Curator requests-929957 ] vivipary] >> >> Is there going to be consideration of the related process, dormancy? >> >>> From: Pankaj Jaiswal >>> Reply-To: po-dev at plantontology.org, Pankaj Jaiswal > >>> Date: Tue, 28 Jun 2005 09:57:44 -0400 >>> To: POC-dev >>> Cc: Jennifer I Clark , >> rice-e-net at chanko.lab.nig.ac.jp, >>> grains at greengenes.cit.cornell.edu >>> Subject: [Fwd: [ geneontology-Curator requests-929957 ] vivipary] >>> >>> Hi Everyone, >>> >>> I though that some people from the plant community may be interested > in >>> the discussion on adding a new term VIVIPARY (and its instances ??) > in >>> the Gene Ontology. >>> >>> Please follow the link below on the discussion >>> >> > https://sourceforge.net/tracker/? > func=detail&atid=440764&aid=929957&grou > p_ >> id >> =3 >>> 6855 >>> >>> A couple of questions are: >>> >>> #1 whether we need the two instances of a generic term VIVIPARY >>> >>> vegetative vivipary (sensu Magnoliophyta) >>> non-vegetative vivipary (sensu Magnoliophyta) >>> >>> >>> #2 Is there anything called as vegetative vivipary. >>> >>> >>> BY definition, in cereal plants or elsewhere, vivipary is defined as >>> >>> "A process promoting the germination of embryos while still attached > to >>> the mother plant. " >>> >>> -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/divisions/artscience/biology/Kellogg/Kellogg/ home.html -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 3652 bytes Desc: not available URL: From David.Marshall at scri.ac.uk Wed Jun 29 02:41:07 2005 From: David.Marshall at scri.ac.uk (David Marshall) Date: Wed, 29 Jun 2005 07:41:07 +0100 Subject: [Fwd: [ geneontology-Curator requests-929957 ] vivipary] Message-ID: preharvest sprouting is of particular interest. There are a number of advances at the molecular level. It is interesting to place preharvest sprouting in the context of related processes i.e. grain development, "normal germination", dormance and in the case of barley- malting. David Marshall -----Original Message----- From: owner-po-dev at plantontology.org on behalf of Tinker, Nicholas Sent: Tue 28/06/2005 19:05 To: Tom Blake; Mary Polacco; po-dev at plantontology.org, Pankaj Jaiswal; POC-dev Cc: Subject: RE: [Fwd: [ geneontology-Curator requests-929957 ] vivipary] But, If an ontology defines "vivipary" as a "type of" preharvest sprouting (or vice-versa) then won't it help the corn people do comparative genomics with the barley people? > > Hi folks, > In the small grains, this is called preharvest sprouting. It's > well-understood, and as Mary suggests is the result of lack of seed > dormancy > and a wet harvest environment. Calling it vivipary won't improve > understanding of the process. In both barley and wheat the genetics of > dormancy and of preharvest sprouting is pretty well-understood. > Cheers, > Tom Blake, barley breeder, Montana State University > > -----Original Message----- > From: grains-request at greengenes.cit.cornell.edu > [mailto:grains-request at greengenes.cit.cornell.edu] On Behalf Of Mary > Polacco > Sent: Tuesday, June 28, 2005 11:04 AM > To: po-dev at plantontology.org, Pankaj Jaiswal; POC-dev > Cc: Jennifer I Clark; rice-e-net at chanko.lab.nig.ac.jp; > grains at greengenes.cit.cornell.edu > Subject: Re: [Fwd: [ geneontology-Curator requests-929957 ] vivipary] > > Is there going to be consideration of the related process, dormancy? > > > From: Pankaj Jaiswal > > Reply-To: po-dev at plantontology.org, Pankaj Jaiswal > > Date: Tue, 28 Jun 2005 09:57:44 -0400 > > To: POC-dev > > Cc: Jennifer I Clark , > rice-e-net at chanko.lab.nig.ac.jp, > > grains at greengenes.cit.cornell.edu > > Subject: [Fwd: [ geneontology-Curator requests-929957 ] vivipary] > > > > Hi Everyone, > > > > I though that some people from the plant community may be interested in > > the discussion on adding a new term VIVIPARY (and its instances ??) in > > the Gene Ontology. > > > > Please follow the link below on the discussion > > > https://sourceforge.net/tracker/?func=detail&atid=440764&aid=929957&grou p_ > id > =3 > > 6855 > > > > A couple of questions are: > > > > #1 whether we need the two instances of a generic term VIVIPARY > > > > vegetative vivipary (sensu Magnoliophyta) > > non-vegetative vivipary (sensu Magnoliophyta) > > > > > > #2 Is there anything called as vegetative vivipary. > > > > > > BY definition, in cereal plants or elsewhere, vivipary is defined as > > > > "A process promoting the germination of embryos while still attached to > > the mother plant. " > > > > -Pankaj > > > > > > > > _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ DISCLAIMER: This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries. This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed. It may not be disclosed or used by any other than that addressee. If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify postmaster at scri.sari.ac.uk quoting the name of the sender and delete the email from your system. 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