gocentral
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19 years ago - assigned_to: nobody --> jenclark
Original comment by: jenclark
Closed gocentral closed 9 years ago
gocentral
commented
19 years ago Original comment by: jenclark
gocentral
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19 years ago Logged In: YES user_id=735846
Hi Pankaj,
Thanks for that request. We already have the two terms below, under which the new terms could be entered as children, but unfortunately these terms are not quite correctly defined.
response to long-day photoperiod ; GO:0030939 def: A change in state or activity of the organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of the perception of a photoperiod, an intermittent cycle of light (day) and dark (night) photoperiod regimes, with the light phase being longer than the dark.
response to short-day photoperiod ; GO:0030940 def: A change in state or activity of the organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of the perception of a photoperiod, an intermittent cycle of light (day) and dark (night) photoperiod regimes, with the dark phase being longer than the light.
Neither of these has any annotations.
These terms include the standard mistake of assuming that the long day plant flowers when the day length is longer than the night length. However, the long day plant actually flowers when the day length is longer than the 'critical daylength' for that species. The equivalent mistake is made with the short day term.
I propose obsoleting these terms and replacing with the following terms:
long-day photoperiodism ; GO:new def: A change in state or activity of the organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of the perception of a daylength that exceeds a particular duration known as the 'critical daylength'. The critical daylength varies between species. Although the term is long-day is used, most species actually respond to the duration of the night, so that the response will occur when a period of darkness falls short of the number of hours defined by 24 hours minus the critical daylength. synonym: short-night photoperiodism synonym: response to short-night synonym: response to long-day
short-day photoperiodism ; GO:new def: A change in state or activity of the organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of the perception of a daylength shorter than a particular duration known as the 'critical daylength'. The critical daylength varies between species. Although the term short-day is used, most species actually respond to the duration of the night, so that the response will occur when a period of darkness exceeds the number of hours defined by 24 hours minus the critical daylength. synonym: long-night photoperiodism synonym: response to long-night synonym: response to short-day
[i]response to light ; GO:0009416 ---[i]photoperiodism ; GO:new ------[i]short-day photoperiodism ; GO:new ------[i]long-day photoperiodism ; GO:new
I'd like to redefine and rename:
response to photoperiod def: A change in state or activity of the organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of the perception of a photoperiod, an intermittent cycle of light (day) and dark (night) photoperiod regimes.
as:
photoperiodism ; GO:new def: A change in state or activity of the organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of the perception of the length of a period of light or dark, measured relative to a particular duration known as the 'critical daylength'. The critical daylength varies between species. synonym: response to daylength synonym: response to nightlength synonym: response to photoperiod
You requested new terms for flowering in response to photoperiod. Would these suit?
photoperiodism; flowering ; GO:new def: A change from vegetative to reproductive phase as a result of the perception of the length of a period of light or dark, measured relative to a particular duration known as the 'critical daylength'. The critical daylength varies between species. synonym: response to daylength; flowering synonym: response to nightlength; flowering synonym: response to photoperiod; flowering synonyms: photoperiodic control of flowering, photoperiodic control of flowering time, photoperiodic control of inflorescence development, photoperiodic control of inflorescence exersion
long-day photoperiodism; flowering ; GO:new def: A change from vegetative to reproductive phase as a result of the perception of a daylength that exceeds a particular duration known as the 'critical daylength'. The critical daylength varies between species. Although the term is long-day is used, most species actually respond to the duration of the night, so that the response will occur when a period of darkness falls short of the number of hours defined by 24 minus the critical daylength. synonym: short-night photoperiodism; flowering synonym: response to short-night; flowering synonym: response to long-day; flowering long-day photoperiodic control of flowering, long-day photoperiodic control of flowering time, long-day photoperiodic control of inflorescence development, long-day photoperiodic control of inflorescence exersion
short-day photoperiodism; flowering ; GO:new def: A change from vegetative to reproductive phase as a result of the perception of a daylength shorter than a particular duration known as the 'critical daylength'. The critical daylength varies between species. Although the term short-day is used, most species actually respond to the duration of the night, so that the response will occur when a period of darkness exceeds the number of hours defined by 24 minus the critical daylength. synonym: long-night photoperiodism; flowering synonym: response to long-night; flowering synonym: response to short-day; flowering short-day photoperiodic control of flowering, short-day photoperiodic control of flowering time, short-day photoperiodic control of inflorescence development, short-day photoperiodic control of inflorescence exersion
[i]response to light ; GO:0009416 ---[i]photoperiodism ; GO:new ------[i]photoperiodism; flowering ; GO:new ---------[i]short-day photoperiodism; flowering ; GO:new ---------[i]long-day photoperiodism; flowering ; GO:new ------[i]short-day photoperiodism ; GO:new ---------[i]short-day photoperiodism; flowering ; GO:new ------[i]long-day photoperiodism ; GO:new ---------[i]long-day photoperiodism; flowering ; GO:new
[i]vegetative to reproductive phase transition ; GO:0010228 ---[p]photoperiodism; flowering ; GO:new ------[i]short-day photoperiodism; flowering ; GO:new ------[i]long-day photoperiodism; flowering ; GO:new
I'd also like to add a few new terms to provide correct parentage for these terms:
[i]post-embryonic development ; GO:0009791 ---[i]reproductive-structure development ; GO:new ------[i]reproductive-structure development (sensu Metazoa); GO:new ------[i]reproductive-structure development (sensu Magnoliophyta); GO:new ---------[i]inflorescence development ; GO:0010229 ---------[i]flower development ; GO:0009908 ---------[i]fruit development ; GO:0010154 ---------[p]photoperiodism; flowering ; GO:new ------------[i]short-day photoperiodism; flowering ; GO:new ------------[i]long-day photoperiodism; flowering ; GO:new
reproductive-structure development ; GO:new def: The process aimed at the progression of the reproductive structures over time, from formation to the mature structures.
reproductive-structure development (sensu Metazoa); GO:new def: The process aimed at the progression of the reproductive structures over time, from formation to the mature structures. As in, but not restricted to, animals (Metazoa, ncbi_taxonomy_id:33208).
reproductive-structure development (sensu Magnoliophyta); GO:new def: The process aimed at the progression of the reproductive structures over time, from formation to the mature structures. As in, but not restricted to, the flowering plants (Magnoliophyta, ncbi_taxonomy_id:3398).
The children for the Metazoa term will need some work before I can put them under the sensu Metazoa parent so I'll do that elsewhere.
Do these terms work for the concept of exersion that you mention? I can't find any mention of this in the online dictionaries or in pubmed and am a bit stumped about how it relates to photoperiodism. If you can give me a bit more information or a paper to look at I'll figure out how to fit it in.
The authorities I've used for the above photoperiodism terms are ISBN:070940886 ISBN:0582015952 ISBN:0697037754
Thanks,
Jen
Original comment by: jenclark
gocentral
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19 years ago Logged In: YES user_id=561361
I think having a semicolon in the following term names could create problems for the Database parsing scripts ---------[p]photoperiodism; flowering ; GO:new ------------[i]short-day photoperiodism; flowering ; GO:new ------------[i]long-day photoperiodism; flowering ; GO:new
I suggest using the names I suggested or something better.
Do you really want to delete the terms GO:0030939 and GO:0030940. Can we update the terms considering that the concepts remained same but the definition was improved significantly.
Here is another request since you are on to revising this section we need to add 4 process terms as
short-day photoperiodism; flowering ; GO:new --[i]--positive regulation of short-day photoperiodism; flowering ; GO:new --[i]--negative regulation of short-day photoperiodism; flowering ; GO:new long-day photoperiodism; flowering ; GO:new --[i]--positive regulation of long-day photoperiodism; flowering ; GO:new --[i]--negative regulation of long-day photoperiodism; flowering ; GO:new
I just found this while curating the rice ortholog of Arabidopsis GIGANTEA. PMID: 12700762
Similarly the protein involved in the above processes (positive and negative regulation of X-day photoperiodism; flowering..) have suppressor / activator activities. I am not sure if they are valid cases of adding function terms. PMID: 12700762 This might be a case of new SF item.
pankaj
Original comment by: jaiswalp
gocentral
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19 years ago Logged In: YES user_id=561361
forgot to say that definitions are fine and so is the structure. pankaj
Original comment by: jaiswalp
gocentral
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19 years ago Logged In: YES user_id=735846
Hi Pankaj,
Would you be happy with the names if they have commas instead of semi- colons? We already have precedent for this in the Drosophila courtship terms e.g. 'male courtship behavior (sensu Insecta), song production', 'male courtship behavior (sensu Insecta), wing vibration', 'male courtship behavior (sensu Insecta), tapping'. Photoperiodism is the term used by biologists for a response to length of day or night so it would be correct and could have any number of synonyms. If you really prefer we could use 'long-day photoperiodic control of flowering', as the term name, though that is quite a mouthful.
I think we do need to obsolete those other terms since the definitions are clearly wrong. There are no annotations so it shouldn't cause any problems for any one.
For the regulation terms, I'd be happy to add those if you need them. From looking at the abstract I'm not sure that you couldn't just annotate those gene products straight to the main terms. Let me know what you prefer.
You only need function ontology repressor/activator terms if you can tell exactly what 'activity' the gene products are repressing or activating. For example if they are repressing or activating the activity of a specific enzyme or repressing/activating translation or something like that. If they are just repressing or activating photoperiodism then process terms will be sufficient.
Are the terms okay to cover 'exersion'?
That's great that you like the structure and the definitions. :-)
Let me know what you think about the rest.
Thanks,
Jen
Original comment by: jenclark
gocentral
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19 years ago Logged In: YES user_id=561361
terms (less informative).
terms, please add " xxx-inflorescence development", " xxx-inflorescence exersion", " xxx-heading".
As I understand often these responses are studied for vegetative meristem being converted to inflorescence meristem under photoperiod response, but the actual term name is associated to the time inflorescence/flowers are visible. You may want to highlight this in comments.
Pankaj
Original comment by: jaiswalp
gocentral
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19 years ago Logged In: YES user_id=735846
I have added these terms:
[Term] id: GO:0048571 name: long-day photoperiodism namespace: biological_process def: "A change in state or activity of the organism (in terms of movement\, secretion\, en zyme production\, gene expression\, etc.) as a result of the perception of a daylength that exceeds a particular duration known as the 'critical daylength'. The critical daylength vari es between species. Although the term long-day is used\, most species actually respond to th e duration of the night\, so that the response will occur when a period of darkness falls sh ort of the number of hours defined by 24 hours minus the critical daylength." [GO:jic, GR:pj , ISBN:070940886, ISBN:0582015952, ISBN:0697037754] exact_synonym: "response to long-day" [] exact_synonym: "response to short-night" [] exact_synonym: "short-night photoperiodism" [] is_a: GO:0009648 ! photoperiodism
[Term] id: GO:0048572 name: short-day photoperiodism namespace: biological_process def: "A change in state or activity of the organism (in terms of movement\, secretion\, en zyme production\, gene expression\, etc.) as a result of the perception of a daylength that falls short of a particular duration known as the 'critical daylength'. The critical dayleng th varies between species. Although the term short-day is used\, most species actually respo nd to the duration of the night\, so that the response will occur when a period of darkness exceeds the number of hours defined by 24 hours minus the critical daylength." [GO:jic, GR:pj, ISBN:0697037754, ISBN:0582015952, ISBN:070940886] exact_synonym: "long-night photoperiodism" [] exact_synonym: "response to long-night" [] exact_synonym: "response to short-day" [] is_a: GO:0009648 ! photoperiodism
[Term] id: GO:0048573 name: photoperiodism, flowering namespace: biological_process def: "A change from the vegetative to the reproductive phase as a result of the perception of a period of light or dark of a given length. The length of the period of light or dark r equired to initiate the change is set relative to a particular duration known as the 'critic al daylength'. The critical daylength varies between species. " [GR:pj, GO:jic, ISBN:0709408 86, ISBN:0582015952, ISBN:0697037754] exact_synonym: "response to daylength\, flowering" [] exact_synonym: "response to nightlength\, flowering" [] exact_synonym: "response to photoperiod\, flowering" [] is_a: GO:0009648 ! photoperiodism relationship: part_of GO:0010228 ! vegetative to reproductive phase transition
[Term] id: GO:0048574 name: long-day photoperiodism, flowering namespace: biological_process def: "A change from the vegetative to the reproductive phase as a result of the perception of a period of light that exceeds the critical daylength. The critical daylength varies bet ween species. Although the term is long-day is used\, most species actually respond to the d uration of the night\, so that the response will occur when a period of darkness falls short of the number of hours defined by 24 minus the critical daylength." [GO:jic, GR:pj, ISBN:06 97037754, ISBN:0582015952, ISBN:070940886] exact_synonym: "response to long-day\, flowering" [] exact_synonym: "response to short-night\, flowering" [] exact_synonym: "short-night photoperiodism\, flowering" [] is_a: GO:0048571 ! long-day photoperiodism is_a: GO:0048573 ! photoperiodism, flowering
[Term] id: GO:0048575 name: short-day photoperiodism, flowering namespace: biological_process def: "A change from vegetative to reproductive phase as a result of the perception of a pe riod of light that falls short of the critical daylength. The critical daylength varies betw een species. Although the term is short-day is used\, most species actually respond to the d uration of the night\, so that the response will occur when a period of darkness exceeds the number of hours defined by 24 minus the critical daylength." [GO:jic, GR:pj, ISBN:070940886 , ISBN:0582015952, ISBN:0697037754] exact_synonym: "long-night photoperiodism\, flowering" [] exact_synonym: "response to long-night\, flowering" [] exact_synonym: "response to short-day\, flowering" [] is_a: GO:0048572 ! short-day photoperiodism is_a: GO:0048573 ! photoperiodism, flowering
I'll do the rest tomorrow or Wednesday.
Jen
Original comment by: jenclark
gocentral
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19 years ago Logged In: YES user_id=735846
The item [ 1224241 ] reproductive developmental process
https://sourceforge.net/tracker/index.php?func=detail&aid=1224241&group\_id=36855&atid=440764 also relates to this item.
Thanks,
Jen
Original comment by: jenclark
gocentral
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19 years ago Logged In: YES user_id=735846
New terms added:
[Term] id: GO:0048576 name: positive regulation of short-day photoperiodism, flowering namespace: biological_process def: "Any process that activates\, maintains or increases short-day photoperiodism\, where the response associated with the photoperiodism is flowering. Flowering is defined by the s witch from the vegetative to the reproductive phase." [GO:jic, ISBN:0582015952 "", ISBN:0697 037754 "", ISBN:070940886 "", GR:pj] is_a: GO:0048582 ! positive regulation of post-embryonic development is_a: GO:0048584 ! positive regulation of response to stimulus is_a: GO:0048587 ! regulation of short-day photoperiodism, flowering
[Term] id: GO:0048577 name: negative regulation of short-day photoperiodism, flowering namespace: biological_process def: "Any process that stops\, prevents or reduces short-day photoperiodism\, where the re sponse associated with the photoperiodism is flowering. Flowering is defined by the switch f rom the vegetative to the reproductive phase." [GO:jic, ISBN:0582015952 "", ISBN:0697037754 "", ISBN:070940886 "", GR:pj] is_a: GO:0048581 ! negative regulation of post-embryonic development is_a: GO:0048585 ! negative regulation of response to stimulus is_a: GO:0048587 ! regulation of short-day photoperiodism, flowering
[Term] id: GO:0048578 name: positive regulation of long-day photoperiodism, flowering namespace: biological_process def: "Any process that activates\, maintains or increases long-day photoperiodism\, where the response associated with the photoperiodism is flowering. Flowering is defined by the sw itch from the vegetative to the reproductive phase." [GO:jic, ISBN:0582015952 "", ISBN:06970 37754 "", ISBN:070940886 "", GR:pj] is_a: GO:0048582 ! positive regulation of post-embryonic development is_a: GO:0048584 ! positive regulation of response to stimulus is_a: GO:0048586 ! regulation of long-day photoperiodism, flowering
[Term] id: GO:0048579 name: negative regulation of long-day photoperiodism, flowering namespace: biological_process def: "Any process that stops\, prevents or reduces long-day photoperiodism\, where the res ponse associated with the photoperiodism is flowering. Flowering is defined by the switch fr om the vegetative to the reproductive phase." [GO:jic, ISBN:0582015952 "", ISBN:0697037754 " ", ISBN:070940886 "", GR:pj] is_a: GO:0048581 ! negative regulation of post-embryonic development is_a: GO:0048585 ! negative regulation of response to stimulus is_a: GO:0048586 ! regulation of long-day photoperiodism, flowering
[Term] id: GO:0048580 name: regulation of post-embryonic development namespace: biological_process def: "Any process that modulates the frequency\, rate or extent of post-embryonic developm ent. Post-embryonic development is defined as the process aimed at the progression of the or ganism over time\, from the completion of embryonic development to the mature structure." [G O:jic] is_a: GO:0050793 ! regulation of development
[Term] id: GO:0048581 name: negative regulation of post-embryonic development namespace: biological_process def: "Any process that stops\, prevents or reduces the rate of post-embryonic development. Post-embryonic development is defined as the process aimed at the progression of the organi sm over time\, from the completion of embryonic development to the mature structure." [GO:ji c] is_a: GO:0048519 ! negative regulation of biological process is_a: GO:0048580 ! regulation of post-embryonic development
[Term] id: GO:0048582 name: positive regulation of post-embryonic development namespace: biological_process def: "Any process that activates or increases the rate of post-embryonic development. Post -embryonic development is defined as the process aimed at the progression of the organism ov er time\, from the completion of embryonic development to the mature structure." [GO:jic] is_a: GO:0048518 ! positive regulation of biological process is_a: GO:0048580 ! regulation of post-embryonic development
[Term] id: GO:0048583 name: regulation of response to stimulus namespace: biological_process def: "Any process that modulates the frequency\, rate or extent of response to stimulus. R esponse to stimulus is a change in state or activity of a cell or organism (in terms of move ment\, secretion\, enzyme production\, gene expression\, etc.) as a result of the perception of a stimulus." [GO:jic] is_a: GO:0050791 ! regulation of physiological process
[Term] id: GO:0048584 name: positive regulation of response to stimulus namespace: biological_process def: "Any process that activates\, maintains or increases the rate of response to stimulus . Response to stimulus is a change in state or activity of a cell or organism (in terms of m ovement\, secretion\, enzyme production\, gene expression\, etc.) as a result of the percept ion of a stimulus." [GO:jic] is_a: GO:0048518 ! positive regulation of biological process is_a: GO:0048583 ! regulation of response to stimulus
[Term] id: GO:0048585 name: negative regulation of response to stimulus namespace: biological_process def: "Any process that stops\, prevents or reduces the rate of response to stimulus. Respo nse to stimulus is a change in state or activity of a cell or organism (in terms of movement \, secretion\, enzyme production\, gene expression\, etc.) as a result of the perception of a stimulus." [GO:jic] is_a: GO:0048519 ! negative regulation of biological process is_a: GO:0048583 ! regulation of response to stimulus
[Term] id: GO:0048586 name: regulation of long-day photoperiodism, flowering namespace: biological_process def: "Any process that modulates the frequency\, rate or extent of long-day photoperiodism \, where the response associated with the photoperiodism is flowering. Flowering is defined by the switch from the vegetative to the reproductive phase." [GO:jic "", GR:pj "", ISBN:058 2015952 "", ISBN:0697037754 "", ISBN:070940886 ""] is_a: GO:0048580 ! regulation of post-embryonic development is_a: GO:0048583 ! regulation of response to stimulus relationship: part_of GO:0048574 ! long-day photoperiodism, flowering
[Term] id: GO:0048587 name: regulation of short-day photoperiodism, flowering namespace: biological_process def: "Any process that modulates the frequency\, rate or extent of short-day photoperiodis m\, where the response associated with the photoperiodism is flowering. Flowering is defined by the switch from the vegetative to the reproductive phase." [GO:jic "", GR:pj "", ISBN:05 82015952 "", ISBN:0697037754 "", ISBN:070940886 ""] is_a: GO:0048580 ! regulation of post-embryonic development is_a: GO:0048583 ! regulation of response to stimulus relationship: part_of GO:0048575 ! short-day photoperiodism, flowering
new synonyms added:
exact_synonym: "photoperiodic control of flowering time" exact_synonym: "photoperiodic control of inflorescence development" exact_synonym: "long-day photoperiodic control of flowering" exact_synonym: "long-day photoperiodic control of flowering time" exact_synonym: "long-day photoperiodic control of inflorescence development" exact_synonym: "short-day photoperiodic control of flowering" exact_synonym: "short-day photoperiodic control of flowering time" exact_synonym: "short-day photoperiodic control of inflorescence development"
(Added to terms as proposed below.)
Jen
Original comment by: jenclark
gocentral
commented
19 years ago Logged In: YES user_id=735846
Everything is done here now except the reproductive structure development parentage which is awaiting developments in another sourceforge item, and the exersion related synonyms.
Can you clarify exactly which synonyms you want for which terms? You wrote:
terms, please add " xxx-inflorescence development", " xxx-inflorescence exersion", " xxx-heading".
but I'm not completely clear on which terms you want them on and what the XXX stands for. If you let me know exactly I'll add them. Thanks ever so much.
Jen
Original comment by: jenclark
gocentral
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19 years ago Logged In: YES user_id=735846
Sent a reminder to Pankaj.
Jen
Original comment by: jenclark
gocentral
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19 years ago Logged In: YES user_id=561361
Hi Jen,
So far most of the synonyms I wanted were added by you. Will let you know later, if I need some more.
Thanks a lot -Pankaj
Original comment by: jaiswalp
gocentral
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19 years ago Logged In: YES user_id=735846
Great, thanks. :-)
Jen
Original comment by: jenclark
gocentral
commented
19 years ago Original comment by: jenclark
id: new-1 Term: photoperiod control of flowering Definition: "The process(s) that control either the development and/or growth of the inflorescence until the time of flowering (anthesis) as a result of the response to the short/long day photoperiod treatment." [GR:pj] is_a: GO:0009648 synonyms: photoperiodic control of flowering, photoperiodic control of flowering time, photoperiodic control of inflorescence development, photoperiodic control of inflorescence exersion **
id: new-2 Term: short-day photoperiod control of flowering Definition: "The process(s) that control either the development and/or growth of the inflorescence until the time of flowering (anthesis) as a result of the response to the short-day photoperiod treatment." [GR:pj] is_a: new-1 ynonyms: short-day photoperiodic control of flowering, short-day photoperiodic control of flowering time, short-day photoperiodic control of inflorescence development, short-day photoperiodic control of inflorescence exersion **
id: new-3 Term: long-day photoperiod control of flowering Definition: "The process(s) that control either the development and/or growth of the inflorescence until the time of flowering (anthesis) as a result of the response to the long-day photoperiod treatment." [GR:pj] is_a: new-1 synonyms: long-day photoperiodic control of flowering, long-day photoperiodic control of flowering time, long-day photoperiodic control of inflorescence development, long-day photoperiodic control of inflorescence exersion **
** this synonym is very species specific e.g. in grasses, associated to when the majority of the inflorescence has emerged from the top most leaf (flag leaf).
Note : the word "control" can be replaced with "regulation"
-Pankaj
Reported by: jaiswalp
Original Ticket: "geneontology/ontology-requests/2547":https://sourceforge.net/p/geneontology/ontology-requests/2547