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19 years ago Original comment by: smundodi
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gocentral
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19 years ago Original comment by: smundodi
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Process terms-July, 2005
response to organic nitrogen ISA response to endogenous stimulus GO:0009719 Def: Responses to nitrogen contained as amines in organic compounds such as amino acids and proteins. Ref:PMID: 9869419
response to low fluence blue light ISA response to blue light GO:0009637 Def: Responses to low fluence (threshold = 10(-1) micromol m-2) of blue light. Excitation of the Blue Low Fluence (BLF)-System induces the transcription of a number of nuclear and plastid coded genes. Ref: PMID:10398709
anthocyanin accumulation ISA ? photomorphogenesis GO: 0009640 or response to light GO:0009416 or response to photoperiod GO:0009648? (since antho accumulation is photoregulated and in response to light) Def: The process(es) which control or direct the tissue specific accumulation of the pigment anthocyanin. Ref:TAIR:lr
root hair elongation ISA root morphogenesis GO:0010015 Def: Elongation of root hair cell of higher plants. Ref: TAIR:syr
radial microtubular system formation ISA male meiosis cytokinesis GO:0007112 and microtubule cytoskeleton organization and biogenesis GO:0000226 Def: Formation of radial microtubular systems during male meiotic cytokinesis in plants. Ref:TAIR:syr
rhamnogalacturonan I biosynthesis ISA pectin biosynthesis GO:0045489 Def: Biosynthesis of the rhamonogalacturonan I component of pectin, a rhamnose-rich pectic polysaccharide. Ref:TAIR:pz
phosphate ion sensing ISA detection of chemical substance GO:0009593 Def: The series of events by which a phosphate stimulus is received and converted into a molecular signal. Ref: TAIR:sm
differentiation of tapetal layer PART OF stamen development GO:0048443 (actually it should be anther development but the term doesnt exist in GO. Is there any plan to add anther development term Jen?) Def: The process by which a cell layer in the anther wall acquires the cellular and morphological characteristics of a tapetum. Ref: TAIR:lr
establishment and/or maintenance of transmembrane electrochemical gradient ISA transport GO: GO:0006810 Def: The specification, formation and maintenance of electrochemical gradient across the membrane. Ref:TAIR:sm and PMID: 1311852
(ps: should this also be a parent of hydrogen transport?)
initiation of organ primordial PART OF organogenesis GO:0009887 Def: Initiation of an organized group of cells to differentiate into an organ. Ref:TAIR:sm
organ senescence ISA senescence (sensu Magnoliophyta) GO:0010149 and parent for leaf senescence GO:0010150 Def: The process that occurs in a plant organ near the end of its active life that is associated with the dismantling of cell components and membranes, loss of functional chloroplasts, and an overall decline in metabolism. Ref:TAIR:sm
trichome patterning ISA pattern specification GO:0007389 Def: The spacial arrangement of differentiated cells in trichome, a single-celled hair. Ref: PMID:10368181
somatic embryogenesis ISA embryonic development (sensu Magnoliophyta) GO:0009793 Def: Initiation of embryos from previously differentiated somatic cells. Ref: http://www.uwrf.edu/~dc01/somatlab.html
auxin conjugate metabolism part of auxin metabolism GO:0009850 Def: The chemical reaction involving auxin conjugate, a bound form of free auxin. Ref: TAIR:sm
S-methylmethionine metabolism Def: Synthesis of S-methyl-Methionine (SMM) from Methionine and S-adenosyl-Methionine (Ado-Met) catalyzed by Methionine (Met) S-methyltransferase (MMT). SMM can be reconverted to Met by donating a methyl group to homocysteine (homo-Cys), and concurrent operation of this reaction and that mediated by MMT sets up the SMM cycle. Ref: PMID:12692340
photosystem I assembly PART OF photosynthesis, light reaction GO:0019684 Def: Formation and assembly of photosystem I complex on thylakoid membrane. Ref: TAIR:sm
root hair initiation ISA trichoblast differentiation GO:0010054 Def: Initiation of root hair from root epidermal cell or trichoblast cell. Ref:TAIR:sm
auxin homeostasis ISA auxin metabolism GO:0009850 Def: Maintenance of endogenous concentration of primary auxin equilibrium, or constant level of auxin in a biological system by a number of biochemical processes including transport, biosynthesis, catabolism and conjugation. Ref: http://diss-epsilon.slu.se/archive/00000215/
UDP-rhamnose biosynthesis ISA rhamnose biosynthesis GO:0019300 Def: The formation from simpler components of UDP-L-rhamnose, a substance composed of rhamnose in glycosidic linkage with uridine diphosphate. Ref: PMID:15134748
nectary development PART OF flower development GO:0009908 Def: The process aimed at the progression of the floral nectaries over time, from its formation to the mature structure. Ref: TAIR:lr
glucose mediated signaling ISA hexose mediated signaling GO:0009757 Def: The process by which a change in the level of mono- and disaccharide glucose trigger the expression of genes controlling metabolic and developmental processes. Ref: TAIR:sm
(Ps. The term glucose is included in the definition for sugar mediated signaling. So, should this term also then be a child of sugar mediated signaling? Glucose is a hexose and hence I put this as a child of hexose mediated signaling.)
endomembrane organization ISA membrane organization and biogenesis GO:0016044 Def: The assembly and arrangement of endomembrane. Ref: TAIR:sm
NADH dehydrogenase complex (plastoquinone) assembly PART OF NADH dehydrogenase complex assembly (new) ISA protein complex assembly GO:0006461 Def: The formation of NADH:plastoquinone dehydrogenase complex, which is involved in the non-photochemical reduction of plastoquinones, as well as the cyclic electron transport around photosystem I. Ref: PMID 15608332
Original comment by: mah11
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general comments: The 'response to' terms (1 & 2) should use the standard definition (bottom of the page at http://www.geneontology.org/GO.process.guidelines.shtml). There are also a couple other ones (6 & 15) that should use standard definitions.
There are also a few definitions that need minor corrections (typos, missing words, etc.).
specific comments 'n' questions:
> 1. response to organic nitrogen ISA response to endogenous > stimulus GO:0009719
are we sure that the N-containing amines are always endogenous?
> > 10. initiation of organ primordial PART OF organogenesis > GO:0009887
should be 'organ primordium'
> 12. trichome patterning ISA pattern specification > GO:0007389 > Def: The spacial arrangement of differentiated cells in > trichome, a single-celled hair. > Ref: PMID:10368181
should there also be a trichome parent. e.g. GO:0010026?
> > 21. glucose mediated signaling ISA hexose mediated > signaling GO:0009757 > Def: The process by which a change in the level of mono- > and disaccharide glucose trigger the expression of genes > controlling metabolic and developmental processes. > Ref: TAIR:sm > > (Ps. The term glucose is included in the definition for > sugar mediated signaling. So, should this term also then be > a child of sugar mediated signaling? Glucose is a hexose > and hence I put this as a child of hexose mediated > signaling.)
The parentage looks fine. The def of sugar mediated signaling needed its punctuation fixed (which I've now done).
Original comment by: mah11
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Couple of things:
Can you make sure anthocyanin accumulation has an 'organismal process' parent somewhere.
Also need standard defs for metabolism and biosynthesis terms - btw I think S-methylmethionine metabolism might have the wrong term name - def describes biosynthesis.
organ senescence should be made specific to plants somehow - either plant organ senescence or a sensu designation (I'm sure other groups have organ senescence too). And also needs 'organismal xxx' parentage somewhere.
Original comment by: jl242
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... and a couple more from me:
> 2. response to low fluence blue light ISA response to blue > light GO:0009637 > Def: Responses to low fluence (threshold = 10(-1) micromol > m-2) of blue light. Excitation of the Blue Low Fluence > (BLF)-System induces the transcription of a number of > nuclear and plastid coded genes. > Ref: PMID:10398709
We already have 'response to low fluence' (GO:0010202) and 'response to very low fluence' (GO:0010203), which are defined specifically with respect to red light:
GO:0010202 A change in state or activity of an organism or cell (in terms of movement, secretion, enzyme production, gene expression etc.) as a result of exposure to red light pulses followed by darkness, which occurs at red light levels of 0.001-0.1 mmol/m2/sec and is red/far-red reversible." [TAIR:sm]
GO:0010203 same except def ends '... light levels of less than 0.001 mmol/m2/sec red light and is not far-red reversible'.
Should these existing terms be renamed?
> 4. root hair elongation ISA root morphogenesis GO:0010015 > Def: Elongation of root hair cell of higher plants. > Ref: TAIR:syr
Also see SF 1012287.
Original comment by: mah11
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I took a look at the terms and added some comments shown below. My comments start with a *.
Some of these would need to be on separate sourceforge items so we can discuss them. Do you want to open those or shall I?
Jen
Process terms-July, 2005
* Just these two I reckon:
or response to light GO:0009416 or response to photoperiod GO:0009648?
photomorphogenesis GO:0009640 is the control of the generation of form (shape) in response to light and anthocyanin is just a pigment. It doesn't affect form.
* This section needs some work. We should probably make this a new sourceforge item on trichomes.
* Yes I can fit that in somehow. Can this be a separate sourceforge item?
* Maybe like this?
[i]development ---[i]organ development ------[p]organ primordium development ---------[p]initiation of an organ primordium
This needs to be a new sourceforge item too so we can discuss it.
* also part_of 'organ development' ; GO:0048513
* This can go in the new trichome sourceforge item.
* Term seems good. This may also need to be connected to the new vivpary terms being discussed in [ 929957 ] vivipary https://sourceforge.net/tracker/index.php? func=detail&aid=929957&group_id=36855&atid=440764
* This can go in the new trichome item too.
* Seems good.
Original comment by: jenclark
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I've copied the root hair/trichoblast requests over to: [ 1012287 ] root hair related terms
I'll deal with them there.
Jen
Original comment by: jenclark
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Hi,
Thanx for all the comments. I have included separate headings for Midori, jane and Jen answering some of your specific questions.
Below, I have also included the terms with the new/updated definitions.
For Jane:
I am not able to find any parent term for anthocyanin accumulation under organismal parent unless we add it directly as a child of organismal physiological process. Do you have any suggestions? Anthocyanins are flavonoid substances-if you are looking for extra clues. Same for organ senescence. Should we add a organismal senescence term?
Organ senescence- What other organisms have senescence happening as they age? I cant think of one but then I dont know about all the organisms. Do you know of any? Should we ask this question to the whole group?
Changed the term SMM metabolism to SMM biosynthesis.
Midori:
I think we can change the term name to response to low fluence red light and so on, just to be consistent and be explicit even though I think the existing terms are used without the red light attached to it in general. Can we just change the term name without any other changes? I mean without obsoleting the term? Since the definition remains the same, we can keep the same ID right?
Jen:
Do every one of those changes need to be in a separate sourceforge item? I understand already existing one such as root/trichome related. But others, I am not so sure. Is there a proposal to add anther development. I brought this up may be a year ago and I dont know what happened to the anther development term. All I know is it hasnt been added yet. Is there a reason why?
Again, I think the intiation of organ primordium parentage look good as you suggested. We can go ahead with the proposed changes. Why do we need a new sourceforge entry for this?
We have come up with new trichome patterning definition, parentage and synonyms and so we need to change all those to the term you just added.
Exact synonym: trichome spacing, trichome pattern formation.
(ps. Obsolete trichome intiation AND positive regulation of trichome initiation)
response to organic nitrogen ISA response to endogenous stimulus GO:0009719 Def: A change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of exposure to nitrogen, contained as amines in organic compounds such as amino acids and proteins. Ref:PMID: 9869419
response to low fluence blue light ISA response to blue light GO:0009637 Def: A change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of exposure to low fluence (threshold = 10(-1) micromol m-2) of blue light. Excitation of the Blue Low Fluence (BLF)-System induces the transcription of a number of nuclear and plastid coded genes. Ref: PMID:10398709
anthocyanin accumulation ISA response to photoperiodism GO:0009648 (since antho accumulation is photoregulated and in response to light) Def: The process(es) which control or direct the tissue specific accumulation of the pigment anthocyanin. Ref:TAIR:lr
root hair elongation ISA root morphogenesis GO:0010015 Def: Elongation of root hair cell of higher plants. Ref: TAIR:syr
radial microtubular system formation ISA male meiosis cytokinesis GO:0007112 and microtubule cytoskeleton organization and biogenesis GO:0000226 Def: Formation of radial microtubular systems during male meiotic cytokinesis in plants. Ref:TAIR:syr
rhamnogalacturonan I biosynthesis ISA pectin biosynthesis GO:0045489 Def: The formation from simpler components of rhamonogalacturonan I component of pectin, a rhamnose-rich pectic polysaccharide. Ref:TAIR:pz
phosphate ion sensing ISA detection of chemical substance GO:0009593 Def: The series of events by which a phosphate stimulus is received and converted into a molecular signal. Ref: TAIR:sm
differentiation of tapetal layer PART OF stamen development GO:0048443 (actually it should be anther development but the term doesnt exist in GO. Is there any plan to add anther development term Jen?) Def: The process by which a cell layer in the anther wall acquires the cellular and morphological characteristics of a tapetum. Ref: TAIR:lr
establishment and/or maintenance of transmembrane electrochemical gradient ISA transport GO: GO:0006810 Def: The specification, formation and maintenance of electrochemical gradient across the membrane. Ref:TAIR:sm and PMID: 1311852
(ps: should this also be a parent of hydrogen transport?)
initiation of organ primordium PART OF organogenesis GO:0009887 Def: Initiation of an organized group of cells to differentiate into an organ. Ref:TAIR:sm
organ senescence ISA senescence (sensu Magnoliophyta) GO:0010149 and parent for leaf senescence GO:0010150 Def: The process that occurs in a plant organ near the end of its active life that is associated with the dismantling of cell components and membranes, loss of functional chloroplasts, and an overall decline in metabolism. Ref:TAIR:sm
trichome patterning ISA pattern specification GO:0007389 PART OF trichome differentiation (sensu Magnoliophyta) GO:0010026 ISA cell-cell signaling involved in cell fate commitment GO:0045168 Def: The process of establishing the non-random spatial arrangement of trichomes on the surface and margin of a leaf. Process involves signaling between adjacent epidermal cells that results in differentiation of some epidermal cells into trichomes. Ref: ISBN:0865427429 and TAIR:tb
Exact synonym: trichome spacing, trichome pattern formation.
(ps. Obsolete trichome intiation AND positive regulation of trichome initiation)
somatic embryogenesis ISA embryonic development (sensu Magnoliophyta) GO:0009793 Def: Initiation of embryos from previously differentiated somatic cells. Ref: http://www.uwrf.edu/~dc01/somatlab.html
auxin conjugate metabolism part of auxin metabolism GO:0009850 Def: The chemical reaction involving auxin conjugate, a bound form of free auxin. Ref: TAIR:sm
S-methylmethionine biosynthesis ISA sulpur compound biosynthesis GO:0044272 Def: The formation of S-methyl-Methionine (SMM) from Methionine and S-adenosyl-Methionine (Ado-Met) catalyzed by Methionine (Met) S-methyltransferase (MMT). SMM can be reconverted to Met by donating a methyl group to homocysteine (homo-Cys), and concurrent operation of this reaction and that mediated by MMT sets up the SMM cycle. Ref: PMID:12692340
photosystem I assembly PART OF photosynthesis, light reaction GO:0019684 Def: Formation and assembly of photosystem I complex on thylakoid membrane. Ref: TAIR:sm
root hair initiation ISA trichoblast differentiation GO:0010054 Def: Initiation of root hair from root epidermal cell or trichoblast cell. Ref:TAIR:sm
auxin homeostasis ISA auxin metabolism GO:0009850 Def: Maintenance of endogenous concentration of primary auxin equilibrium, or constant level of auxin in a biological system by a number of biochemical processes including transport, biosynthesis, catabolism and conjugation. Ref: http://diss-epsilon.slu.se/archive/00000215/
UDP-rhamnose biosynthesis ISA rhamnose biosynthesis GO:0019300 Def: The formation from simpler components of UDP-L-rhamnose, a substance composed of rhamnose in glycosidic linkage with uridine diphosphate. Ref: PMID:15134748
nectary development PART OF flower development GO:0009908 Def: The process aimed at the progression of the floral nectaries over time, from its formation to the mature structure. Ref: TAIR:lr
glucose mediated signaling ISA hexose mediated signaling GO:0009757 Def: The process by which a change in the level of mono- and disaccharide glucose trigger the expression of genes controlling metabolic and developmental processes. Ref: TAIR:sm
(Ps. The term glucose is included in the definition for sugar mediated signaling. So, should this term also then be a child of sugar mediated signaling? Glucose is a hexose and hence I put this as a child of hexose mediated signaling.)
endomembrane organization ISA membrane organization and biogenesis GO:0016044 Def: The assembly and arrangement of endomembrane. Ref: TAIR:sm
NADH dehydrogenase complex (plastoquinone) assembly PART OF NADH dehydrogenase complex assembly (new) ISA protein complex assembly GO:0006461 Def: The formation of NADH:plastoquinone dehydrogenase complex, which is involved in the non-photochemical reduction of plastoquinones, as well as the cyclic electron transport around photosystem I. Ref: PMID 15608332
Original comment by: smundodi
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Hi Suparna,
Do every one of those changes need to be in a separate sourceforge item? I understand already existing one such as root/trichome related. But others, I am not so sure.
* For any terms that I can add directly I'll just do that. For those where I need to get back to you I'll open a new item. It's going to be too cluttered to discuss all these requests on one page.
Is there a proposal to add anther development. I brought this up may be a year ago and I dont know what happened to the anther development term. All I know is it hasnt been added yet. Is there a reason why?
* I'm not aware that you are waiting for that term. If you can find the sourceforge item and show me that I'd be grateful as I don't want people's requests to be disappearing down holes like that without finding out why. My understanding was that Tanya had requested all the flower development terms needed and that she was going to get back to me if she needed more. I'm not aware of any requests from you.
Again, I think the intiation of organ primordium parentage look good as you suggested. We can go ahead with the proposed changes. Why do we need a new sourceforge entry for this?
*I'll take a look and put it straight in if I can. I usually like to think proposals though and post them fully formed so people can comment before I commit them. Putting terms straight in without posting often results in bad terms and obsoletions.
We have come up with new trichome patterning definition, parentage and synonyms and so we need to change all those to the term you just added.
Exact synonym: trichome spacing, trichome pattern formation.
(ps. Obsolete trichome intiation AND positive regulation of trichome initiation)
* I'll take a look at that.
* If I have to open new items I'll send you the numbers.
Jen
Original comment by: jenclark
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Hi Suparna,
We were wondering whether anthocyanin accumulation could possibly go under organismal metabolism somewhere? Can you give us a bit more info about what's actually going on here? Jen reckons that light induces more anthocyanin to be made which is why it accumulates, and there isn't actually any transport occurring - is this right?
> Same for organ senescence. Should we add a organismal > senescence term?
Yes, that's a good solution actually...looking at the terms that are already there:
aging (synonym:senescence) ---[i] cell aging ---[i] determination of adult life span ---[p] menopause ---[i] senescence (sensu Magnoliophyta)
we could do this:
aging (synonym:senescence) ---[i] cell aging ---[i] organismal aging ------[i] determination of adult life span ------[p] menopause ------[i] senescence (sensu Magnoliophyta)
and then with organ senescence:
aging (synonym:senescence) ---[i] cell aging ---[i] organismal aging ------[i] organ senescence ---------[i] organ senescence (sensu Magnoliophyta)?? ------[i] determination of adult life span ------[p] menopause ------[i] senescence (sensu Magnoliophyta) ---------[i] organ senescence (sensu Magnoliophyta)??
(I've put a question mark by the sensu terms because I'm not sure if these are warranted or not). From a quick scan of the literature, it looks like organ senescence is used in relation to mammals, particularly humans, do describe the loss of function of organs that occurs with aging (and disease, but we're not interested in that), sometimes menopause actually (uterus senescence I suppose) so we could possibly make this a child.
Original comment by: jl242
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19 years ago Logged In: YES user_id=436423
Just replying to my bit, on the low-fluence light terms: Yes, we can just rename the existing terms, and add the proposed new ones.
m
Original comment by: mah11
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19 years ago Logged In: YES user_id=614564
Jane,
Here is a pdf for the article from where the annotation for anthocyanin accumulation was derived.
http://tesuque.stanford.edu:8080/pub/pdfs/1357.pdf
light seem to induce the synthesis of anthocyanin but according to the above paper, it looks like, there is a process involved that detemines where anthocyanin accumulates. I am not an expert in this field either and couldn't really find much information on the exact process(:
Some other tid bits from this url: http://www.biomedcentral.com/1471-2229/5/7/abstract
By uncoupling the effect of light on anthocyanin accumulation, we have found light to induce the fusion of anthocyanin-containing vacuoles, the coalescence of anthocyanic vacuolar inclusion (AVI)-like structures contained, and the spread of anthocyanins from the inclusions into the vacuolar sap.
Suparna
Original comment by: smundodi
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Hi Jen,
My answers to your questions have 2 stars ** just so you know where to look.
-Do every one of those changes need to be in a separate sourceforge item? I understand already existing one such as root/trichome related. But others, I am not so sure.
* For any terms that I can add directly I'll just do that. For those where I need to get back to you I'll open a new item. It's going to be too cluttered to discuss all these requests on one page.
** I always send all the items sourceforge before addint them to GO mainly for the reason you mentioned. I thought that is what we are doing here. I have been getting feedback from you guys and that gets incorporated when I add those terms. I still don't understand what is new this time. I prefer to keep them in one sourceforge entry as I add them all at the same time unless any item needs any additional discussion.
-Is there a proposal to add anther development. I brought this up may be a year ago and I dont know what happened to the anther development term. All I know is it hasnt been added yet. Is there a reason why?
* I'm not aware that you are waiting for that term. If you can find the sourceforge item and show me that I'd be grateful as I don't want people's requests to be disappearing down holes like that without finding out why. My understanding was that Tanya had requested all the flower development terms needed and that she was going to get back to me if she needed more. I'm not aware of any requests from you.
** I guess they are not anther development terms afterall. Instead they are flower development terms such as petal, sepal, stamen etc. I got confused. I can wait for you to add anther development term if you are planning on doing so, before I add the 'differentiation of tapetal layer'.That way it will be under the right parentage.
-Again, I think the intiation of organ primordium parentage look good as you suggested. We can go ahead with the proposed changes. Why do we need a new sourceforge entry for this?
*I'll take a look and put it straight in if I can. I usually like to think proposals though and post them fully formed so people can comment before I commit them. Putting terms straight in without posting often results in bad terms and obsoletions.
** We add the terms to sourceforge for the same reasons you mentioned above. We like your suggestion of organ primordium parentage and so I plan on adding the new structure as you suggested.
-We have come up with new trichome patterning definition, parentage and synonyms and so we need to change all those to the term you just added.
Exact synonym: trichome spacing, trichome pattern formation.
(ps. Obsolete trichome intiation AND positive regulation of trichome initiation)
* I'll take a look at that.
** In addition to changing the definition, we also need to obsolete few terms which are all listed. I can change this too as I add the other terms. Let me know.
Cheers, Suparna
* If I have to open new items I'll send you the numbers.
Original comment by: smundodi
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I'll answer Suparna by e-mail.
Jen
Original comment by: jenclark
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Please see the following items for discussion of the relevant terms requested in this item.
[ 1247046 ] trichome patterning [ 1012287 ] root hair related terms [ 1247346 ] somatic embryogenesis [ 1247348 ] initiation of organ primordium [ 1247349 ] differentiation of tapetal layer
Thanks,
Jen
Original comment by: jenclark
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Hi Suparna - right, think we've got this sorted out. The problem is that we need to get all the proper higher level terms in place before adding this - it's always the way!
Basically, we already have a 'pigmentation' term, but this refers to the laying down of pigment during development, whereas what we're talking about is the accumulation of pigment in response to some external stimulus, in this case light. [Note that we made the term a child of 'response to light' rather than 'photoperiodism' because it seems to be the intensity of light that's important rather than the duration]. So what we decided to do is make a generic 'pigmentation' term with children 'developmental pigmentation' and 'pigment accumulation (in response to external stimulus)' - see below.
Also, Jen tells me that anthocyanin accumulation can occur in the absence of light (e.g. it's genetic in snapdragons), so I made the term end '....in response to light'. Finally, I made a term that was pertinent to accumulation in tissues, which goes under organismal physiological process and another for cellular.
Note that I probably haven't included all possible relationships (gets a bit confusing) - I'll do that when making the terms.
biological process ---[i] pigmentation ; GO:new ------[i] pigmentation during development ; GO:0048066 ---------[i] cuticle pigmentation ; GO:0048067 synonym: cuticle pigmentation during development ---------[i] etc. ---------[p] pigment metabolism during developmental pigmentation ------[p] pigment metabolism during pigmentation ---------[i] pigment metabolism during developmental pigmentation ---------[i] pigment metabolism during pigment accumulation ---[i] pigment accumulation synonym: pigment accumulation in response to external stimulus ------[i] etc. (see below)
development ---[p] pigmentation during development ; GO:0048066 ------[i] etc.
response to external stimulus ---[i] pigment accumulation synonym: pigment accumulation in response to external stimulus ------[p] pigment metabolism during pigment accumulation ---------[i] pigment biosynthesis during pigment accumulation ------[i] pigment accumulation in response to light ---------[i] pigment accumulation in tissues in response to light ------------[i] anthocyanin accumulation in tissues in response to light ------[i] pigment accumulation in tissues synonym: organismal pigment accumulation ---------[i] pigment accumulation in tissues in response to light ------------[i] anthocyanin accumulation in tissues in response to light ------[i] cellular pigment accumulation
organismal physiological process ---[i] pigment accumulation in tissues synonym: organismal pigment accumulation
response to light ---[i] pigment accumulation in response to light
pigment metabolism ------[p] pigment metabolism during pigment accumulation
Original comment by: jl242
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Hi Jane,
You guys really worked this tree out. jen is right is saying that anthocyanin accumulation could happen even in the absence of light. pH can effect the transport of this pigment into vacuole as well. So, the structure looks fine as you suggested. I think it will be better if you added these terms to GO just to avoid one more level of mistakes.Would you mind? Thanx
Suparna
Original comment by: smundodi
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Hi Suparna - no problem, I'll add those terms. Will post the new ids when I'm done.
cheers,
jane
Original comment by: jl242
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Okay, have added all those accumulation terms. New ids:
pigmentation ; GO:0043473 pigment metabolism during pigmentation ; GO:0043474 pigment metabolism during pigment accumulation ; GO:0043475 pigment accumulation ; GO:0043476 pigment biosynthesis during pigment accumulation ; GO:0043477 pigment accumulation in response to light ; GO:0043478 pigment accumulation in tissues in response to light ; GO:0043479 pigment accumulation in tissues ; GO:0043480 anthocyanin accumulation in tissues in response to light ; GO:0043481 cellular pigment accumulation ; GO:0043482 anthocyanin biosynthesis during anthocyanin accumulation ; GO:0043483
Original comment by: jl242
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Are those '... in response to light' terms all specific for UV light (as the defs suggest)? I will change the term string if so.
Original comment by: girlwithglasses
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Yes, all UV...
Original comment by: jl242
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commented
19 years ago Logged In: YES user_id=614564
Is it necessary to change the term string to "uv"? What other types of light are we dealing with here? I don't really see the need.
Suparna
Original comment by: smundodi
gocentral
commented
19 years ago Logged In: YES user_id=473796
It could be infra red light or visible light, and there isn't anything in the term name or parentage to specify which kind of light it is.
Original comment by: girlwithglasses
gocentral
commented
19 years ago Logged In: YES user_id=614564
Sorry, I forgot about those.
I also noticed that, GO:0043483 has an alias 'ANTHOCYANIN BIOSYNTHESIS DURING ANTHOCYANIN ACCUMULATION IN TISSUES IN RESPONSE TO LIGHT' but definition doesn't talk about the light stimulus. I think the UV stimulus should be mentioned in the definition for this.
Suparna
Original comment by: smundodi
gocentral
commented
18 years ago Logged In: YES user_id=614564
Looks like most of the outstanding items on this thread are taken care of except for the root hair related terms, which I assume Jen is working on or will work on..
Suparna
Original comment by: smundodi
gocentral
commented
18 years ago Original comment by: smundodi
gocentral
commented
18 years ago Logged In: YES user_id=614564
Looks like most of the outstanding items on this thread are taken care of except for the root hair related terms, which I assume Jen is working on or will work on..
Suparna
Original comment by: smundodi
gocentral
commented
18 years ago Logged In: YES user_id=473796
I've altered that def for you.
Original comment by: girlwithglasses
Hi,
I have attached a file with 23 process terms from TAIR. Please let me know if you have any comments on these. Thanx
Suparna
Reported by: smundodi
Original Ticket: "geneontology/ontology-requests/2728":https://sourceforge.net/p/geneontology/ontology-requests/2728