From nm249 at cornell.edu Mon Apr 3 13:04:19 2006 From: nm249 at cornell.edu (Naama Menda) Date: Mon, 03 Apr 2006 13:04:19 -0400 Subject: terms for fruit development stages Message-ID: <44315593.2020308@cornell.edu> I need the following terms for annotating tomato genes expressed during different fruit development stages: -fertilization: The stage of successful pollen germination, penetration, and growth of the pollen tube in the stylar tissue towards the ovule and into the embryo sac for fusion with the egg cell. Dbxref PMID:12271039 -fruit cell division: The initial stage of fruit development triggered in the fruit primordia. Dbxref PMID:12271039 -fruit cell expansion: The stage of increase in cell volume, contributing mostly to fruit growth. Dbxref PMID:12271039 Thanks -Naama Menda From katica at acoma.Stanford.EDU Mon Apr 3 13:35:44 2006 From: katica at acoma.Stanford.EDU (katica at acoma.Stanford.EDU) Date: Mon, 3 Apr 2006 10:35:44 -0700 (PDT) Subject: terms for fruit development stages In-Reply-To: <44315593.2020308@cornell.edu> References: <44315593.2020308@cornell.edu> Message-ID: Hi Naama, Double fertilization is already in GO: "double fertilization (sensu Magnoliophyta)' GO:0009567 Can you use this term? At POC, we agreed to avoid duplication of terms with Gene Ontology. Katica On Mon, 3 Apr 2006, Naama Menda wrote: > I need the following terms for annotating tomato genes expressed during > different fruit development stages: > > -fertilization: The stage of successful pollen germination, penetration, and > growth of the pollen tube in the stylar tissue towards the ovule and into the > embryo sac for fusion with the egg cell. Dbxref PMID:12271039 > > -fruit cell division: The initial stage of fruit development triggered in the > fruit primordia. Dbxref PMID:12271039 > > -fruit cell expansion: The stage of increase in cell volume, contributing > mostly to fruit growth. Dbxref PMID:12271039 > > > Thanks > -Naama Menda > -- -------------------------------------------------------------------------- Katica Ilic katica at acoma.stanford.edu The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253 Carnegie Institution of Washington FAX: (650) 325-6857 Department of Plant Biology URL: http://arabidopsis.org/ 260 Panama St. Stanford, CA 94305 U.S.A. -------------------------------------------------------------------------- From katica at acoma.stanford.edu Mon Apr 3 14:46:28 2006 From: katica at acoma.stanford.edu (katica at acoma.stanford.edu) Date: Mon, 3 Apr 2006 11:46:28 -0700 (PDT) Subject: terms for fruit development stages In-Reply-To: References: Message-ID: Peter and Naama, I see. For the events that precede double fertilization, there are several terms in GO, I pulled out some of them; Naama please take a look in GO process ontology for more: pollen germination GO:0009846 Def: The physiological and developmental changes that occur in a heterosporous plant pollen grain, beginning with hydration and terminating with the emergence of the pollen tube through the aperture. pollen tube guidance GO:0010183 Def: The process by which the growth of pollen tube is directed towards the female gametophyte. pollen tube growth GO:0009860 Growth of pollen via tip extension of the intine wall. Katica On Mon, 3 Apr 2006, Peter Stevens wrote: > Nama is really talking about what goies on before the actual act of double > fertilisation, or at least double fertilisation is at the very end of his > whole process of fertlisation. > > P. > > >> Hi Naama, >> Double fertilization is already in GO: >> >> "double fertilization (sensu Magnoliophyta)' >> GO:0009567 >> >> Can you use this term? At POC, we agreed to avoid duplication of terms >> with Gene Ontology. >> >> Katica >> >> On Mon, 3 Apr 2006, Naama Menda wrote: >> >> > I need the following terms for annotating tomato genes expressed during >>> different fruit development stages: >>> >>> -fertilization: The stage of successful pollen germination, penetration, >>> and >>> growth of the pollen tube in the stylar tissue towards the ovule and into >>> the >>> embryo sac for fusion with the egg cell. Dbxref PMID:12271039 >>> >>> -fruit cell division: The initial stage of fruit development triggered in >>> the >>> fruit primordia. Dbxref PMID:12271039 >>> >>> -fruit cell expansion: The stage of increase in cell volume, contributing >>> mostly to fruit growth. Dbxref PMID:12271039 >>> >>> >>> Thanks >>> -Naama Menda >>> >> >> -- >> -------------------------------------------------------------------------- >> 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. >> -------------------------------------------------------------------------- > -- -------------------------------------------------------------------------- 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 nm249 at cornell.edu Mon Apr 3 14:38:32 2006 From: nm249 at cornell.edu (Naama Menda) Date: Mon, 03 Apr 2006 14:38:32 -0400 Subject: terms for fruit development stages In-Reply-To: References: <44315593.2020308@cornell.edu> Message-ID: <44316BA8.9020800@cornell.edu> Yes, I can use that term. -Naama katica at acoma.Stanford.EDU wrote: > Hi Naama, > Double fertilization is already in GO: > > "double fertilization (sensu Magnoliophyta)' > GO:0009567 > > Can you use this term? At POC, we agreed to avoid duplication of terms > with Gene Ontology. > > Katica > > On Mon, 3 Apr 2006, Naama Menda wrote: > >> I need the following terms for annotating tomato genes expressed >> during different fruit development stages: >> >> -fertilization: The stage of successful pollen germination, >> penetration, and growth of the pollen tube in the stylar tissue >> towards the ovule and into the embryo sac for fusion with the egg >> cell. Dbxref PMID:12271039 >> >> -fruit cell division: The initial stage of fruit development >> triggered in the fruit primordia. Dbxref PMID:12271039 >> >> -fruit cell expansion: The stage of increase in cell volume, >> contributing mostly to fruit growth. Dbxref PMID:12271039 >> >> >> Thanks >> -Naama Menda >> > From peter.stevens at mobot.org Mon Apr 3 13:29:53 2006 From: peter.stevens at mobot.org (Peter Stevens) Date: Mon, 3 Apr 2006 13:29:53 -0400 Subject: terms for fruit development stages In-Reply-To: References: Message-ID: Nama is really talking about what goies on before the actual act of double fertilisation, or at least double fertilisation is at the very end of his whole process of fertlisation. P. >Hi Naama, >Double fertilization is already in GO: > >"double fertilization (sensu Magnoliophyta)' >GO:0009567 > >Can you use this term? At POC, we agreed to avoid duplication of terms >with Gene Ontology. > >Katica > >On Mon, 3 Apr 2006, Naama Menda wrote: > > > I need the following terms for annotating tomato genes expressed during >> different fruit development stages: >> >> -fertilization: The stage of successful pollen germination, penetration, and >> growth of the pollen tube in the stylar tissue towards the ovule >>and into the >> embryo sac for fusion with the egg cell. Dbxref PMID:12271039 >> >> -fruit cell division: The initial stage of fruit development >>triggered in the >> fruit primordia. Dbxref PMID:12271039 >> >> -fruit cell expansion: The stage of increase in cell volume, contributing >> mostly to fruit growth. Dbxref PMID:12271039 >> >> >> Thanks >> -Naama Menda >> > >-- >-------------------------------------------------------------------------- >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. >-------------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From katica at acoma.stanford.edu Mon Apr 3 16:42:56 2006 From: katica at acoma.stanford.edu (katica at acoma.stanford.edu) Date: Mon, 3 Apr 2006 13:42:56 -0700 (PDT) Subject: terms for fruit development stages In-Reply-To: <443186BE.6080008@cornell.edu> References: <443186BE.6080008@cornell.edu> Message-ID: I annotate Arabidopsis mutants to PO terms as well as to GO terms (lately have been using PATO too). Naama's initial request for 'fertilization' sounded like a process term to me, in which case GO would likely have appropriate terms. For this very reason we don't have fertilization as a stage in PO. As for the other two requests, I'll include them as items for the next conf call. Katica On Mon, 3 Apr 2006, Pankaj Jaiswal wrote: > I am not an expert on this, but I presume Naama is trying to annotate her > mutants suggesting the phenotype affects/observed_at this stage. Now the > problem is this stage is also a process term in GO. Which is fine as long as > we call it as a stage. We do have terms like these in plant part > developmental stages like leaf development etc. that overlap with GO > processes. In such cases we appended the term with a X-stage. > > Pankaj > > katica at acoma.stanford.edu wrote: > >> Peter and Naama, >> >> I see. For the events that precede double fertilization, there are several >> terms in GO, I pulled out some of them; Naama please take a look in GO >> process ontology for more: >> >> pollen germination GO:0009846 >> Def: The physiological and developmental changes that occur in a >> heterosporous plant pollen grain, beginning with hydration and terminating >> with the emergence of the pollen tube through the aperture. >> >> pollen tube guidance GO:0010183 >> Def: The process by which the growth of pollen tube is directed towards the >> female gametophyte. >> >> pollen tube growth GO:0009860 >> Growth of pollen via tip extension of the intine wall. >> >> Katica >> >> On Mon, 3 Apr 2006, Peter Stevens wrote: >> >>> Nama is really talking about what goies on before the actual act of double >>> fertilisation, or at least double fertilisation is at the very end of his >>> whole process of fertlisation. >>> >>> P. >>> >>> >>>> Hi Naama, >>>> Double fertilization is already in GO: >>>> >>>> "double fertilization (sensu Magnoliophyta)' >>>> GO:0009567 >>>> >>>> Can you use this term? At POC, we agreed to avoid duplication of terms >>>> with Gene Ontology. >>>> >>>> Katica >>>> >>>> On Mon, 3 Apr 2006, Naama Menda wrote: >>>> >>>> > I need the following terms for annotating tomato genes expressed >>>> during >>>> >>>>> different fruit development stages: >>>>> >>>>> -fertilization: The stage of successful pollen germination, >>>>> penetration, and >>>>> growth of the pollen tube in the stylar tissue towards the ovule and >>>>> into the >>>>> embryo sac for fusion with the egg cell. Dbxref PMID:12271039 >>>>> >>>>> -fruit cell division: The initial stage of fruit development triggered >>>>> in the >>>>> fruit primordia. Dbxref PMID:12271039 >>>>> >>>>> -fruit cell expansion: The stage of increase in cell volume, >>>>> contributing >>>>> mostly to fruit growth. Dbxref PMID:12271039 >>>>> >>>>> >>>>> Thanks >>>>> -Naama Menda >>>>> >>>> >>>> -- >>>> >>>> -------------------------------------------------------------------------- >>>> 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. > > -- -------------------------------------------------------------------------- Katica Ilic katica at acoma.stanford.edu The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253 Carnegie Institution of Washington FAX: (650) 325-6857 Department of Plant Biology URL: http://arabidopsis.org/ 260 Panama St. Stanford, CA 94305 U.S.A. -------------------------------------------------------------------------- From pj37 at cornell.edu Mon Apr 3 16:34:06 2006 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Mon, 03 Apr 2006 16:34:06 -0400 Subject: terms for fruit development stages In-Reply-To: References: Message-ID: <443186BE.6080008@cornell.edu> I am not an expert on this, but I presume Naama is trying to annotate her mutants suggesting the phenotype affects/observed_at this stage. Now the problem is this stage is also a process term in GO. Which is fine as long as we call it as a stage. We do have terms like these in plant part developmental stages like leaf development etc. that overlap with GO processes. In such cases we appended the term with a X-stage. Pankaj katica at acoma.stanford.edu wrote: > Peter and Naama, > > I see. For the events that precede double fertilization, there are > several terms in GO, I pulled out some of them; Naama please take a look > in GO process ontology for more: > > pollen germination GO:0009846 > Def: The physiological and developmental changes that occur in a > heterosporous plant pollen grain, beginning with hydration and > terminating with the emergence of the pollen tube through the aperture. > > pollen tube guidance GO:0010183 > Def: The process by which the growth of pollen tube is directed towards > the female gametophyte. > > pollen tube growth GO:0009860 > Growth of pollen via tip extension of the intine wall. > > Katica > > On Mon, 3 Apr 2006, Peter Stevens wrote: > >> Nama is really talking about what goies on before the actual act of >> double fertilisation, or at least double fertilisation is at the very >> end of his whole process of fertlisation. >> >> P. >> >> >>> Hi Naama, >>> Double fertilization is already in GO: >>> >>> "double fertilization (sensu Magnoliophyta)' >>> GO:0009567 >>> >>> Can you use this term? At POC, we agreed to avoid duplication of terms >>> with Gene Ontology. >>> >>> Katica >>> >>> On Mon, 3 Apr 2006, Naama Menda wrote: >>> >>> > I need the following terms for annotating tomato genes expressed >>> during >>> >>>> different fruit development stages: >>>> >>>> -fertilization: The stage of successful pollen germination, >>>> penetration, and >>>> growth of the pollen tube in the stylar tissue towards the ovule >>>> and into the >>>> embryo sac for fusion with the egg cell. Dbxref PMID:12271039 >>>> >>>> -fruit cell division: The initial stage of fruit development >>>> triggered in the >>>> fruit primordia. Dbxref PMID:12271039 >>>> >>>> -fruit cell expansion: The stage of increase in cell volume, >>>> contributing >>>> mostly to fruit growth. Dbxref PMID:12271039 >>>> >>>> >>>> Thanks >>>> -Naama Menda >>>> >>> >>> -- >>> -------------------------------------------------------------------------- >>> >>> Katica Ilic katica at acoma.stanford.edu >>> The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253 >>> Carnegie Institution of Washington FAX: (650) 325-6857 >>> Department of Plant Biology URL: >>> http://arabidopsis.org/ >>> 260 Panama St. >>> Stanford, CA 94305 >>> U.S.A. From pj37 at cornell.edu Fri Apr 14 10:43:19 2006 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Fri, 14 Apr 2006 10:43:19 -0400 Subject: terms for fruit development stages In-Reply-To: References: Message-ID: <443FB507.6040104@cornell.edu> Can we discuss this in Today's call. Looks like the fertilization is not the correct usage based on the definition. The actual fertilization is mating of gametes. The processes defined in the definition are covered in Pollination as suggested by Sheila McCormick from UC Davis, when we last contacted her while creating the terms in Gene Ontology. Take a look at pollination process as defined in GO http://www.godatabase.org/cgi-bin/amigo/go.cgi?action=plus_node&depth=1&search_constraint=terms&query=GO:0009856&session_id=891b1145025473 Here is something from GO that we can consider for fertilization stage. term: Double fertilization GO:0009567 Definition: Fertilization where one of the two sperm nuclei from the pollen tube fuses with the egg nucleus to form a 2n zygote, and the other fuses with the two polar nuclei to form the 3n primary endosperm nucleus and then develops into the endosperm. The ploidy level of the 2n zygote and 3n primary endosperm nucleus is determined by the ploidy level of the parents involved. Peter Stevens wrote: > Nama is really talking about what goies on before the actual act of > double fertilisation, or at least double fertilisation is at the very > end of his whole process of fertlisation. > > P. > > >> Hi Naama, >> Double fertilization is already in GO: > >> "double fertilization (sensu Magnoliophyta)' >> GO:0009567 > >> Can you use this term? At POC, we agreed to avoid duplication of terms >> with Gene Ontology. > >> Katica > >> On Mon, 3 Apr 2006, Naama Menda wrote: > >> > I need the following terms for annotating tomato genes expressed during >> > different fruit development stages: >> > >> > -fertilization: The stage of successful pollen germination, >> penetration, and >> > growth of the pollen tube in the stylar tissue towards the ovule and >> into the >> > embryo sac for fusion with the egg cell. Dbxref PMID:12271039 >> > >> > -fruit cell division: The initial stage of fruit development >> triggered in the >> > fruit primordia. Dbxref PMID:12271039 >> > >> > -fruit cell expansion: The stage of increase in cell volume, >> contributing >> > mostly to fruit growth. Dbxref PMID:12271039 >> > >> > >> > Thanks >> > -Naama Menda >> > > >> -- >> -------------------------------------------------------------------------- >> 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. >> -------------------------------------------------------------------------- > > -- Pankaj Jaiswal G-15, Bradfield Hall Dept. of Plant Breeding and Genetics Cornell University Ithaca, NY-14853, USA Ph. +1-607-255-3103 / 4199 fax: +1-607-255-6683 From SchaefferM at missouri.edu Mon Apr 24 13:31:25 2006 From: SchaefferM at missouri.edu (Mary (Polacco) Schaeffer) Date: Mon, 24 Apr 2006 12:31:25 -0500 Subject: curation question ATTN Anu, Leszek Message-ID: What is the best way to use PO to describe mature pollen? re developmental and growth stages. Planning on just using 'flowering', but it doesn't seem to capture the pollen stage detail. mary From ap343 at cornell.edu Mon Apr 24 13:41:44 2006 From: ap343 at cornell.edu (Anuradha Pujar) Date: Mon, 24 Apr 2006 13:41:44 -0400 (EDT) Subject: curation question ATTN Anu, Leszek In-Reply-To: References: Message-ID: <4419.71.240.241.188.1145900504.squirrel@webmail.cornell.edu> Hi Mary, > What is the best way to use PO to describe mature pollen? > > re developmental and growth stages. > PO:0001016 : L mature pollen stage Definition: Stage of microgametophyte development during which the pollen reaches mature stage and desiccates. > Planning on just using 'flowering', but it doesn't seem to capture the > pollen stage detail. > anu > > From katica at acoma.stanford.edu Mon Apr 24 14:00:57 2006 From: katica at acoma.stanford.edu (katica at acoma.stanford.edu) Date: Mon, 24 Apr 2006 11:00:57 -0700 (PDT) Subject: curation question ATTN Anu, Leszek In-Reply-To: References: Message-ID: Mary, PO: L mature pollen stage Accession: PO:0001016 Definition: Def: Stage of microgametophyte development during which the pollen reaches mature stage and desiccates. Comment: Mature pollen stages is reached at three-celled pollen in some angiosperms (maize, rice and Arabidopsis), while in others, the mature pollen has two haploid cells (tobacco, snapdragon). Katica On Mon, 24 Apr 2006, Mary (Polacco) Schaeffer wrote: > What is the best way to use PO to describe mature pollen? > > re developmental and growth stages. > > > Planning on just using 'flowering', but it doesn't seem to capture the > pollen stage detail. > > mary > -- -------------------------------------------------------------------------- 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 SchaefferM at missouri.edu Mon Apr 24 16:24:36 2006 From: SchaefferM at missouri.edu (Mary (Polacco) Schaeffer) Date: Mon, 24 Apr 2006 15:24:36 -0500 Subject: Growth&Dev Curation ATTN Anu, Katica, Leszek Message-ID: Anu and I have discussed the vagueness some folks use in describing developmental stages as presenting a major curation challenge. I am asking for some insight into making the calls in matching a precise PO term, with a vague literature or GenBank description, just to be sure I am not out in left field with the intentions of this group. Some example calls are below. In all cases, each gets also a plant anatomy term. Basically I am trying to make a statement that would not be wrong, eg at least 6 leaves (maybe more) should be visible in most 3-4 week maize plants. An immature ear might be considered to be smaller or bigger that 1/4 inflorescence length, etc. So is there a better call for the below? For immature ear PO:0007046 IL.01 1/4 inflorescence length reached For Immature tassel same as for immature ear. For immature seek or kernel PO:0007001 early stage of fruit ripening For 3-4 week leaf primordium PO:0007123 LP.06 six leaves visible For juvenile shoot PO:0006339 juvenile leaf Thanks, mary From msachs at uiuc.edu Mon Apr 24 22:28:16 2006 From: msachs at uiuc.edu (Marty Sachs) Date: Mon, 24 Apr 2006 21:28:16 -0500 Subject: Growth&Dev Curation ATTN Anu, Katica, Leszek In-Reply-To: References: Message-ID: Mary, The problem is trying to relate developmental programs that aren't necessarily related. We've discussed this many times before. The number of leaves a plant has doesn't give an indication of where that plant is in terms of floral development. Gaspe Flint is fully mature and has flowered with only 5 leaves. Tropical varieties won't flower until the plant has more than 20 leaves. The fact that corn-belt hybrids flower with a certain number of leaves only reflects their particular background. Nothing general can be said about this. -Marty At 3:24 PM -0500 4/24/06, Mary (Polacco) Schaeffer wrote: >Anu and I have discussed the vagueness some folks use in describing >developmental stages as presenting a major curation challenge. I am asking >for some insight into making the calls in matching a precise PO term, with a >vague literature or GenBank description, just to be sure I am not out in >left field with the intentions of this group. Some example calls are below. > >In all cases, each gets also a plant anatomy term. Basically I am trying to >make a statement that would not be wrong, eg at least 6 leaves (maybe more) >should be visible in most 3-4 week maize plants. An immature ear might be >considered to be smaller or bigger that 1/4 inflorescence length, etc. > >So is there a better call for the below? > >For immature ear > PO:0007046 IL.01 1/4 inflorescence length reached >For Immature tassel > same as for immature ear. >For immature seek or kernel > PO:0007001 early stage of fruit ripening >For 3-4 week leaf primordium > PO:0007123 LP.06 six leaves visible >For juvenile shoot > PO:0006339 juvenile leaf > > > >Thanks, > mary > > From ap343 at cornell.edu Tue Apr 25 10:13:12 2006 From: ap343 at cornell.edu (Anuradha Pujar) Date: Tue, 25 Apr 2006 10:13:12 -0400 (EDT) Subject: Growth&Dev Curation ATTN Anu, Katica, Leszek In-Reply-To: References: Message-ID: <2163.71.240.241.188.1145974392.squirrel@webmail.cornell.edu> Hi Mary, Marty, Maize mappings provided by Leszek gives considerable flexibility to accomodate different varieties described by Marty. The list below are the maize synonyms (growth stage) that came up for Mary's terms: I would map to the PO term that has the synonym that comes closest to the description in the paper being curated. If not, we could ask for the addition of a more suitable synonym. Which after a round of discussion, has to be added to the maize-mapping file first and then to the ontology file. However, literature describing plant growth stages in weeks or days will remain a problem. And will depend on cuators knowledge about the plant. At gramene-rice curators choose a higher level term such as vegetative growth or reproductive growth. 1. For immature ear > PO:0007046 IL.01 1/4 inflorescence length reached PO:0007123: LP.06 six leaves visible Syn: 3.01-ear initiation in maize, 3.1 ear initiation/mid-whorl stage in maize, ear initiation in maize, early whorl stage in maize PO:0007063 : LP.07 seven leaves visible Syn; 3.01-ear initiation, 3.1 ear initiation/mid-whorl stage in maize, ear initiation in maize PO:0007095: LP.08 eight leaves visible Syn: 3.01-ear initiation in Maize, 3.1 ear initiation/mid-whorl stage in maize, ear initiation in maize 2. For Immature tassel > same as for immature ear. PO:0007115: LP.04 four leaves visible Syn: 2 tassel initiation/early whorl stage in maize, early whorl stage in maize LP.05 five leaves visible Syn: tassel initiation/early whorl stage in maize, early whorl stage in maize PO:0007025: IE.00 inflorescence tip just visible above flag leaf sheath Syn: beginning of tassel emergence in maize PO:0007041: PO:0007041 : inflorescence emergence from flag leaf sheath Syn:tasseling 3. >For immature seek or kernel > PO:0007001 early stage of fruit ripening PO:0007001 early stage of fruit ripening Syn: 7 linear grain-filling in maize, 7.03-early dough in maize, 7.3 early dough stage/embryo 3 in maize, R4 in maize, early dough, kernel content soft, about 45% dry matter 4. >For 3-4 week leaf primordium > PO:0007123 LP.06 six leaves visible I am not sure if this goes to a whole plant growth stage term.. Thanks anu > Mary, > > The problem is trying to relate developmental programs that aren't > necessarily related. We've discussed this many times before. The > number of leaves a plant has doesn't give an indication of where that > plant is in terms of floral development. Gaspe Flint is fully mature > and has flowered with only 5 leaves. Tropical varieties won't flower > until the plant has more than 20 leaves. > > The fact that corn-belt hybrids flower with a certain number of > leaves only reflects their particular background. Nothing general > can be said about this. > > -Marty > > At 3:24 PM -0500 4/24/06, Mary (Polacco) Schaeffer wrote: >>Anu and I have discussed the vagueness some folks use in describing >>developmental stages as presenting a major curation challenge. I am >> asking >>for some insight into making the calls in matching a precise PO term, >> with a >>vague literature or GenBank description, just to be sure I am not out in >>left field with the intentions of this group. Some example calls are >> below. >> >>In all cases, each gets also a plant anatomy term. Basically I am trying >> to >>make a statement that would not be wrong, eg at least 6 leaves (maybe >> more) >>should be visible in most 3-4 week maize plants. An immature ear might be >>considered to be smaller or bigger that 1/4 inflorescence length, etc. >> >>So is there a better call for the below? >> >>For immature ear >> PO:0007046 IL.01 1/4 inflorescence length reached >>For Immature tassel >> same as for immature ear. >>For immature seek or kernel >> PO:0007001 early stage of fruit ripening >>For 3-4 week leaf primordium >> PO:0007123 LP.06 six leaves visible >>For juvenile shoot >> PO:0006339 juvenile leaf >> >> >> >>Thanks, >> mary >> >> > > From msachs at uiuc.edu Tue Apr 25 10:45:51 2006 From: msachs at uiuc.edu (Marty Sachs) Date: Tue, 25 Apr 2006 09:45:51 -0500 Subject: Growth&Dev Curation ATTN Anu, Katica, Leszek In-Reply-To: <2163.71.240.241.188.1145974392.squirrel@webmail.cornell.edu> References: <2163.71.240.241.188.1145974392.squirrel@webmail.cornell.edu> Message-ID: Anu, For the terms LP.06 thru LP.08 a synonym of 'ear initiation in maize' is given. That's fine and shows the flexibility. However, depending on the accession the same synonym can also be given for LP.05 or LP.20. In fact, for Gaspe Flint, ear initiation occurs during embryo development. The same can be said for the synonym 'tassel initiation'. However, for 3-4 week leaf primordium PO:0007123 LP.06 six leaves visible This again is very line dependent. E.g., Gaspe Flint never has 'six leaves visible' and is pretty much done flowering by 4 weeks. -Marty At 10:13 AM -0400 4/25/06, Anuradha Pujar wrote: >Hi Mary, Marty, > >Maize mappings provided by Leszek gives considerable flexibility to >accomodate different varieties described by Marty. > >The list below are the maize synonyms (growth stage) that came up for >Mary's terms: I would map to the PO term that has the synonym that comes >closest to the description in the paper being curated. If not, we could >ask for the addition of a more suitable synonym. Which after a round of >discussion, has to be added to the maize-mapping file first and then to >the ontology file. > >However, literature describing plant growth stages in weeks or days will >remain a problem. And will depend on cuators knowledge about the plant. At >gramene-rice curators choose a higher level term such as vegetative growth >or reproductive growth. > > >1. For immature ear >> PO:0007046 IL.01 1/4 inflorescence length reached > >PO:0007123: LP.06 six leaves visible >Syn: 3.01-ear initiation in maize, 3.1 ear initiation/mid-whorl stage in >maize, ear initiation in maize, early whorl stage in maize > >PO:0007063 : LP.07 seven leaves visible >Syn; 3.01-ear initiation, 3.1 ear initiation/mid-whorl stage in maize, ear >initiation in maize > >PO:0007095: LP.08 eight leaves visible >Syn: 3.01-ear initiation in Maize, 3.1 ear initiation/mid-whorl stage in >maize, ear initiation in maize > >2. For Immature tassel >> same as for immature ear. > >PO:0007115: LP.04 four leaves visible >Syn: 2 tassel initiation/early whorl stage in maize, early whorl stage in >maize > >LP.05 five leaves visible >Syn: tassel initiation/early whorl stage in maize, early whorl stage in maize > >PO:0007025: IE.00 inflorescence tip just visible above flag leaf sheath >Syn: beginning of tassel emergence in maize > >PO:0007041: PO:0007041 : inflorescence emergence from flag leaf sheath >Syn:tasseling > >3. >For immature seek or kernel >> PO:0007001 early stage of fruit ripening > >PO:0007001 early stage of fruit ripening >Syn: 7 linear grain-filling in maize, 7.03-early dough in maize, 7.3 early >dough stage/embryo 3 in maize, R4 in maize, early dough, kernel content >soft, about 45% dry matter > >4. >For 3-4 week leaf primordium >> PO:0007123 LP.06 six leaves visible > I am not sure if this goes to a whole plant growth stage term.. > > >Thanks >anu > > >> Mary, >> >> The problem is trying to relate developmental programs that aren't >> necessarily related. We've discussed this many times before. The >> number of leaves a plant has doesn't give an indication of where that >> plant is in terms of floral development. Gaspe Flint is fully mature >> and has flowered with only 5 leaves. Tropical varieties won't flower >> until the plant has more than 20 leaves. >> >> The fact that corn-belt hybrids flower with a certain number of >> leaves only reflects their particular background. Nothing general >> can be said about this. >> >> -Marty >> >> At 3:24 PM -0500 4/24/06, Mary (Polacco) Schaeffer wrote: >>>Anu and I have discussed the vagueness some folks use in describing >>>developmental stages as presenting a major curation challenge. I am >>> asking >>>for some insight into making the calls in matching a precise PO term, >>> with a >>>vague literature or GenBank description, just to be sure I am not out in >>>left field with the intentions of this group. Some example calls are >>> below. >>> >>>In all cases, each gets also a plant anatomy term. Basically I am trying > >> to >>>make a statement that would not be wrong, eg at least 6 leaves (maybe >>> more) >>>should be visible in most 3-4 week maize plants. An immature ear might be >>>considered to be smaller or bigger that 1/4 inflorescence length, etc. >>> >>>So is there a better call for the below? >>> >>>For immature ear >>> PO:0007046 IL.01 1/4 inflorescence length reached >>>For Immature tassel >>> same as for immature ear. >>>For immature seek or kernel >>> PO:0007001 early stage of fruit ripening >>>For 3-4 week leaf primordium >>> PO:0007123 LP.06 six leaves visible >>>For juvenile shoot >>> PO:0006339 juvenile leaf >>> >>> >>> >>>Thanks, >>> mary >>> >>> >> >> From msachs at uiuc.edu Tue Apr 25 12:39:15 2006 From: msachs at uiuc.edu (Marty Sachs) Date: Tue, 25 Apr 2006 11:39:15 -0500 Subject: Growth&Dev Curation ATTN Anu, Katica, Leszek In-Reply-To: References: Message-ID: Mary, I agree with what you're saying here. In maize, for the most part, the number of leaf nodes is limited by when flowering is initiated (not the other way around as the literature inadvertently seems to indicate). The ultimate number of leaves that a maize plant will have depends on when flowering occurs in a specific cultivar and the rate of producing nodes during growth. You can have late maturing plants a lot of nodes (as seen in many tropical varieties) or relatively few nodes in plants that simply grow slowly (e.g., Argentine Pop), but node formation ceases when flowering (especially tassel formation) is initiated. So, the relationship between initiation of flowering and ultimate leaf number a plant will have is cultivar specific (with an environmental component as well; e.g., day-length, light intensity, etc). I agree that this would be the case in many other plants. -Marty At 11:20 AM -0500 4/25/06, Mary (Polacco) Schaeffer wrote: >We might consider introducing some more terms here. If terms based strictly >on numbers of leaves are not truly informative about life stage inter- and >intra-species, the challenge seems to find a better set of terms, at least >in some cases. The stage should be the thing, and not the numbers of leaves >in the species or cultivar. Leaf number might better be a comment or some >species/cultivar-specific synonym rather than the main term. I suspect that >Marty's point about Gaspe Flint life cycle and leaf number may well play out >in other plants than maize. > >Pankaj, thanks for the point about higher term annotation when the stages is >not well-described in literature, eg for a cDNA library. RE leaf numbers vs >stage, If I know the inbred line or cultivar, then I could make an informed >guess at more granular term (right Marty), but in general, it is easier on >to let the user make that leap from comments about the library, etc. > > mary > >> From: Marty Sachs >> Reply-To: po-dev at plantontology.org, Marty Sachs >> Date: Tue, 25 Apr 2006 09:45:51 -0500 >> To: po-dev at plantontology.org >> Subject: Re: Growth&Dev Curation ATTN Anu, Katica, Leszek >> >> Anu, >> >> For the terms LP.06 thru LP.08 a synonym of 'ear initiation in maize' >> is given. That's fine and shows the flexibility. However, depending >> on the accession the same synonym can also be given for LP.05 or >> LP.20. In fact, for Gaspe Flint, ear initiation occurs during embryo >> development. >> >> The same can be said for the synonym 'tassel initiation'. >> >> However, for 3-4 week leaf primordium >> PO:0007123 LP.06 six leaves visible >> >> This again is very line dependent. E.g., Gaspe Flint never has 'six >> leaves visible' and is pretty much done flowering by 4 weeks. >> >> -Marty >> >> At 10:13 AM -0400 4/25/06, Anuradha Pujar wrote: >>> Hi Mary, Marty, >>> >>> Maize mappings provided by Leszek gives considerable flexibility to >>> accomodate different varieties described by Marty. >>> >>> The list below are the maize synonyms (growth stage) that came up for >>> Mary's terms: I would map to the PO term that has the synonym that comes >>> closest to the description in the paper being curated. If not, we could >>> ask for the addition of a more suitable synonym. Which after a round of >>> discussion, has to be added to the maize-mapping file first and then to >>> the ontology file. >>> >>> However, literature describing plant growth stages in weeks or days will >>> remain a problem. And will depend on cuators knowledge about the plant. At >>> gramene-rice curators choose a higher level term such as vegetative growth >>> or reproductive growth. >>> >>> >>> 1. For immature ear >>>> PO:0007046 IL.01 1/4 inflorescence length reached >>> >>> PO:0007123: LP.06 six leaves visible >>> Syn: 3.01-ear initiation in maize, 3.1 ear initiation/mid-whorl stage in >>> maize, ear initiation in maize, early whorl stage in maize > >> >>> PO:0007063 : LP.07 seven leaves visible >>> Syn; 3.01-ear initiation, 3.1 ear initiation/mid-whorl stage in maize, ear >>> initiation in maize >>> >>> PO:0007095: LP.08 eight leaves visible >>> Syn: 3.01-ear initiation in Maize, 3.1 ear initiation/mid-whorl stage in >>> maize, ear initiation in maize >>> >>> 2. For Immature tassel >>>> same as for immature ear. >>> >>> PO:0007115: LP.04 four leaves visible >>> Syn: 2 tassel initiation/early whorl stage in maize, early whorl stage in >>> maize >>> >>> LP.05 five leaves visible >>> Syn: tassel initiation/early whorl stage in maize, early whorl >>>stage in maize >>> >>> PO:0007025: IE.00 inflorescence tip just visible above flag leaf sheath >>> Syn: beginning of tassel emergence in maize >>> >>> PO:0007041: PO:0007041 : inflorescence emergence from flag leaf sheath >>> Syn:tasseling >>> >>> 3. >For immature seek or kernel >>>> PO:0007001 early stage of fruit ripening >>> >>> PO:0007001 early stage of fruit ripening >>> Syn: 7 linear grain-filling in maize, 7.03-early dough in maize, 7.3 early >>> dough stage/embryo 3 in maize, R4 in maize, early dough, kernel content >>> soft, about 45% dry matter >>> >>> 4. >For 3-4 week leaf primordium >>>> PO:0007123 LP.06 six leaves visible >>> I am not sure if this goes to a whole plant growth stage term.. >>> >>> >>> Thanks >>> anu >>> >>> >>>> Mary, >>>> >>>> The problem is trying to relate developmental programs that aren't >>>> necessarily related. We've discussed this many times before. The >>>> number of leaves a plant has doesn't give an indication of where that >>>> plant is in terms of floral development. Gaspe Flint is fully mature >>>> and has flowered with only 5 leaves. Tropical varieties won't flower >>>> until the plant has more than 20 leaves. >>>> >>>> The fact that corn-belt hybrids flower with a certain number of >>>> leaves only reflects their particular background. Nothing general >>>> can be said about this. >>>> >>>> -Marty >>>> >>>> At 3:24 PM -0500 4/24/06, Mary (Polacco) Schaeffer wrote: >>>>> Anu and I have discussed the vagueness some folks use in describing >>>>> developmental stages as presenting a major curation challenge. I am >>>>> asking >>>>> for some insight into making the calls in matching a precise PO term, >>>>> with a >>>>> vague literature or GenBank description, just to be sure I am not out in >>>>> left field with the intentions of this group. Some example calls are >>>>> below. >>>>> >>>>> In all cases, each gets also a plant anatomy term. Basically I am trying >>>>> to >>>>> make a statement that would not be wrong, eg at least 6 leaves (maybe >>>>> more) >>>>> should be visible in most 3-4 week maize plants. An immature ear might be >>>>> considered to be smaller or bigger that 1/4 inflorescence length, etc. >>>>> >>>>> So is there a better call for the below? >>>>> >>>>> For immature ear >>>>> PO:0007046 IL.01 1/4 inflorescence length reached >>>>> For Immature tassel >>>>> same as for immature ear. >>>>> For immature seek or kernel >>>>> PO:0007001 early stage of fruit ripening >>>>> For 3-4 week leaf primordium >>>>> PO:0007123 LP.06 six leaves visible >>>>> For juvenile shoot >>>>> PO:0006339 juvenile leaf >>>>> >>>>> >>>>> >>>>> Thanks, >>>>> mary >>>>> >>>>> >>>> >>>> >> >> From pj37 at cornell.edu Tue Apr 25 11:07:36 2006 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 25 Apr 2006 11:07:36 -0400 Subject: Growth&Dev Curation ATTN Anu, Katica, Leszek In-Reply-To: <2163.71.240.241.188.1145974392.squirrel@webmail.cornell.edu> References: <2163.71.240.241.188.1145974392.squirrel@webmail.cornell.edu> Message-ID: <444E3B38.5070505@cornell.edu> Just to add to this thread. One can assign multiple terms mapped to a single description given by the author. The annotations are not restrictive. Pankaj Anuradha Pujar wrote: > Hi Mary, Marty, > > Maize mappings provided by Leszek gives considerable flexibility to > accomodate different varieties described by Marty. > > The list below are the maize synonyms (growth stage) that came up for > Mary's terms: I would map to the PO term that has the synonym that comes > closest to the description in the paper being curated. If not, we could > ask for the addition of a more suitable synonym. Which after a round of > discussion, has to be added to the maize-mapping file first and then to > the ontology file. > > However, literature describing plant growth stages in weeks or days will > remain a problem. And will depend on cuators knowledge about the plant. At > gramene-rice curators choose a higher level term such as vegetative growth > or reproductive growth. > > > 1. For immature ear > >> PO:0007046 IL.01 1/4 inflorescence length reached > > > PO:0007123: LP.06 six leaves visible > Syn: 3.01-ear initiation in maize, 3.1 ear initiation/mid-whorl stage in > maize, ear initiation in maize, early whorl stage in maize > > PO:0007063 : LP.07 seven leaves visible > Syn; 3.01-ear initiation, 3.1 ear initiation/mid-whorl stage in maize, ear > initiation in maize > > PO:0007095: LP.08 eight leaves visible > Syn: 3.01-ear initiation in Maize, 3.1 ear initiation/mid-whorl stage in > maize, ear initiation in maize > > 2. For Immature tassel > >> same as for immature ear. > > > PO:0007115: LP.04 four leaves visible > Syn: 2 tassel initiation/early whorl stage in maize, early whorl stage in > maize > > LP.05 five leaves visible > Syn: tassel initiation/early whorl stage in maize, early whorl stage in maize > > PO:0007025: IE.00 inflorescence tip just visible above flag leaf sheath > Syn: beginning of tassel emergence in maize > > PO:0007041: PO:0007041 : inflorescence emergence from flag leaf sheath > Syn:tasseling > > 3. >For immature seek or kernel > >> PO:0007001 early stage of fruit ripening > > > PO:0007001 early stage of fruit ripening > Syn: 7 linear grain-filling in maize, 7.03-early dough in maize, 7.3 early > dough stage/embryo 3 in maize, R4 in maize, early dough, kernel content > soft, about 45% dry matter > > > 4. >For 3-4 week leaf primordium > >> PO:0007123 LP.06 six leaves visible > > I am not sure if this goes to a whole plant growth stage term.. > > > Thanks > anu > > > >>Mary, >> >>The problem is trying to relate developmental programs that aren't >>necessarily related. We've discussed this many times before. The >>number of leaves a plant has doesn't give an indication of where that >>plant is in terms of floral development. Gaspe Flint is fully mature >>and has flowered with only 5 leaves. Tropical varieties won't flower >>until the plant has more than 20 leaves. >> >>The fact that corn-belt hybrids flower with a certain number of >>leaves only reflects their particular background. Nothing general >>can be said about this. >> >> -Marty >> >>At 3:24 PM -0500 4/24/06, Mary (Polacco) Schaeffer wrote: >> >>>Anu and I have discussed the vagueness some folks use in describing >>>developmental stages as presenting a major curation challenge. I am >>>asking >>>for some insight into making the calls in matching a precise PO term, >>>with a >>>vague literature or GenBank description, just to be sure I am not out in >>>left field with the intentions of this group. Some example calls are >>>below. >>> >>>In all cases, each gets also a plant anatomy term. Basically I am trying >>>to >>>make a statement that would not be wrong, eg at least 6 leaves (maybe >>>more) >>>should be visible in most 3-4 week maize plants. An immature ear might be >>>considered to be smaller or bigger that 1/4 inflorescence length, etc. >>> >>>So is there a better call for the below? >>> >>>For immature ear >>> PO:0007046 IL.01 1/4 inflorescence length reached >>>For Immature tassel >>> same as for immature ear. >>>For immature seek or kernel >>> PO:0007001 early stage of fruit ripening >>>For 3-4 week leaf primordium >>> PO:0007123 LP.06 six leaves visible >>>For juvenile shoot >>> PO:0006339 juvenile leaf >>> >>> >>> >>>Thanks, >>> mary >>> > From SchaefferM at missouri.edu Tue Apr 25 12:20:46 2006 From: SchaefferM at missouri.edu (Mary (Polacco) Schaeffer) Date: Tue, 25 Apr 2006 11:20:46 -0500 Subject: Growth&Dev Curation ATTN Anu, Katica, Leszek In-Reply-To: Message-ID: We might consider introducing some more terms here. If terms based strictly on numbers of leaves are not truly informative about life stage inter- and intra-species, the challenge seems to find a better set of terms, at least in some cases. The stage should be the thing, and not the numbers of leaves in the species or cultivar. Leaf number might better be a comment or some species/cultivar-specific synonym rather than the main term. I suspect that Marty's point about Gaspe Flint life cycle and leaf number may well play out in other plants than maize. Pankaj, thanks for the point about higher term annotation when the stages is not well-described in literature, eg for a cDNA library. RE leaf numbers vs stage, If I know the inbred line or cultivar, then I could make an informed guess at more granular term (right Marty), but in general, it is easier on to let the user make that leap from comments about the library, etc. mary > From: Marty Sachs > Reply-To: po-dev at plantontology.org, Marty Sachs > Date: Tue, 25 Apr 2006 09:45:51 -0500 > To: po-dev at plantontology.org > Subject: Re: Growth&Dev Curation ATTN Anu, Katica, Leszek > > Anu, > > For the terms LP.06 thru LP.08 a synonym of 'ear initiation in maize' > is given. That's fine and shows the flexibility. However, depending > on the accession the same synonym can also be given for LP.05 or > LP.20. In fact, for Gaspe Flint, ear initiation occurs during embryo > development. > > The same can be said for the synonym 'tassel initiation'. > > However, for 3-4 week leaf primordium > PO:0007123 LP.06 six leaves visible > > This again is very line dependent. E.g., Gaspe Flint never has 'six > leaves visible' and is pretty much done flowering by 4 weeks. > > -Marty > > At 10:13 AM -0400 4/25/06, Anuradha Pujar wrote: >> Hi Mary, Marty, >> >> Maize mappings provided by Leszek gives considerable flexibility to >> accomodate different varieties described by Marty. >> >> The list below are the maize synonyms (growth stage) that came up for >> Mary's terms: I would map to the PO term that has the synonym that comes >> closest to the description in the paper being curated. If not, we could >> ask for the addition of a more suitable synonym. Which after a round of >> discussion, has to be added to the maize-mapping file first and then to >> the ontology file. >> >> However, literature describing plant growth stages in weeks or days will >> remain a problem. And will depend on cuators knowledge about the plant. At >> gramene-rice curators choose a higher level term such as vegetative growth >> or reproductive growth. >> >> >> 1. For immature ear >>> PO:0007046 IL.01 1/4 inflorescence length reached >> >> PO:0007123: LP.06 six leaves visible >> Syn: 3.01-ear initiation in maize, 3.1 ear initiation/mid-whorl stage in >> maize, ear initiation in maize, early whorl stage in maize >> >> PO:0007063 : LP.07 seven leaves visible >> Syn; 3.01-ear initiation, 3.1 ear initiation/mid-whorl stage in maize, ear >> initiation in maize >> >> PO:0007095: LP.08 eight leaves visible >> Syn: 3.01-ear initiation in Maize, 3.1 ear initiation/mid-whorl stage in >> maize, ear initiation in maize >> >> 2. For Immature tassel >>> same as for immature ear. >> >> PO:0007115: LP.04 four leaves visible >> Syn: 2 tassel initiation/early whorl stage in maize, early whorl stage in >> maize >> >> LP.05 five leaves visible >> Syn: tassel initiation/early whorl stage in maize, early whorl stage in maize >> >> PO:0007025: IE.00 inflorescence tip just visible above flag leaf sheath >> Syn: beginning of tassel emergence in maize >> >> PO:0007041: PO:0007041 : inflorescence emergence from flag leaf sheath >> Syn:tasseling >> >> 3. >For immature seek or kernel >>> PO:0007001 early stage of fruit ripening >> >> PO:0007001 early stage of fruit ripening >> Syn: 7 linear grain-filling in maize, 7.03-early dough in maize, 7.3 early >> dough stage/embryo 3 in maize, R4 in maize, early dough, kernel content >> soft, about 45% dry matter >> >> 4. >For 3-4 week leaf primordium >>> PO:0007123 LP.06 six leaves visible >> I am not sure if this goes to a whole plant growth stage term.. >> >> >> Thanks >> anu >> >> >>> Mary, >>> >>> The problem is trying to relate developmental programs that aren't >>> necessarily related. We've discussed this many times before. The >>> number of leaves a plant has doesn't give an indication of where that >>> plant is in terms of floral development. Gaspe Flint is fully mature >>> and has flowered with only 5 leaves. Tropical varieties won't flower >>> until the plant has more than 20 leaves. >>> >>> The fact that corn-belt hybrids flower with a certain number of >>> leaves only reflects their particular background. Nothing general >>> can be said about this. >>> >>> -Marty >>> >>> At 3:24 PM -0500 4/24/06, Mary (Polacco) Schaeffer wrote: >>>> Anu and I have discussed the vagueness some folks use in describing >>>> developmental stages as presenting a major curation challenge. I am >>>> asking >>>> for some insight into making the calls in matching a precise PO term, >>>> with a >>>> vague literature or GenBank description, just to be sure I am not out in >>>> left field with the intentions of this group. Some example calls are >>>> below. >>>> >>>> In all cases, each gets also a plant anatomy term. Basically I am trying >>>> to >>>> make a statement that would not be wrong, eg at least 6 leaves (maybe >>>> more) >>>> should be visible in most 3-4 week maize plants. An immature ear might be >>>> considered to be smaller or bigger that 1/4 inflorescence length, etc. >>>> >>>> So is there a better call for the below? >>>> >>>> For immature ear >>>> PO:0007046 IL.01 1/4 inflorescence length reached >>>> For Immature tassel >>>> same as for immature ear. >>>> For immature seek or kernel >>>> PO:0007001 early stage of fruit ripening >>>> For 3-4 week leaf primordium >>>> PO:0007123 LP.06 six leaves visible >>>> For juvenile shoot >>>> PO:0006339 juvenile leaf >>>> >>>> >>>> >>>> Thanks, >>>> mary >>>> >>>> >>> >>> > > From kjbradford at ucdavis.edu Tue Apr 18 17:32:35 2006 From: kjbradford at ucdavis.edu (KENT BRADFORD) Date: Tue, 18 Apr 2006 14:32:35 -0700 Subject: Compositae vocabulary Message-ID: <70B0CAB623BFDA448F85DA2AFEE8BD4291D855@EXCHANGE.plantsciences.ucdavis.edu> To Whom It May Concern: I am a Co-PI on the Compositae Genome Project that has been developing EST and mapping resources for the Compositae, primarily lettuce and sunflower but now expanding into 15 additional species (http://cgpdb.ucdavis.edu). As part of this project, we have also collected extensive phenotypic data on several hundred accessions in the Compositae. We are in the process of developing a database to compile and store this data and make it accessible via our website. In describing our phenotypic data, we would like to be compatible with your controlled vocabularies in choosing our terms. However, you note on your website that these vocabularies are not yet available for the Compositae, and we have many types of data that I do not see in the current descriptions, (e.g., specific leaf shapes, rosettes, presence of trichomes, inflorescence branching patterns, etc.). I would appreciate your advice on how we should proceed in a way that will remain consistent the goals of the plant ontology project to allow broad and consistent searching on controlled vocabularies. Is anyone working on a list of terms for the Compositae that we could work from? I can send a list of the characteristics that we have recorded if it would help. Sincerely, Kent Bradford Kent J. Bradford Professor Department of Plant Sciences Mail Stop 5 One Shields Ave. University of California Davis, CA 95616-8780 Phone: 1-530-752-6087 Fax: 1-530-754-7222 Email: kjbradford at ucdavis.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: