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#22 various vascular system terms
Hi Pankaj and Chih-wei,
I would like to propose the following vascular system terms. Please comment.
1) embryo vascular system PMID 16543410
2) stigma vascular system PMID 15665497
3) filament vascular system PMID 15665497
4) anther vascular system PMID 17257168
5) hypocotyl vascular system PMID 17041031
Thanks!
Donghui
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Hi, Pankaj and Chih-wei,
We could replace the two previously requested term: stigma vein, filament vein with stigma vascular system, filament vascular system.
Additionally, I suggest we create a term: root vascular system and remove my previous request root vein.
I'm wondering if any of you are working on the vascular system terms.
Thanks!
Donghui
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Hi Donghui,
Is it ok for you to use carpel vascular system PO:0005019 and stamen vascular system PO:0005018 for stigma, filament and anther, respectively? or you prefer more specific ones? please let us know.
We will create new PO for embryo vascular system and hypocotyl vascular system.
chih-wei
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Chih-wei,
Thank you for the quick response. I would prefer the more specific terms to be created. For example, in PMID 17257168, page 813, ''expression of SUS5 and SUS6 is also vascular in cotyledons, leaves, petals, anthers and roots (figure 3b)''. It would be more appropriate to annotate SUS to 'anther vascular system' instead of 'stamen vascular system' as the latter may imply expression in filament as well. This is also the case for the other vascular system terms we requested.
Thank you for working on these terms!
Donghui
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Sorry for being picky on this. I saw that picture earlier. The author has used the term 'anther' in a casual way. If you look at the flower picture, it is noticeable that there is a blue strand running along the length of the filament, with a bright blue spot appearing in the anther. It is most likely the distal end of the stamen vascular system that ends at the junction of the anther and filament and not necessarily in anther. I may be wrong, but I don't think there is a vsacular system/tissue in anther. Also most of the genes that are expressed in vascular system of one organ are expressed ubiquitously in the vascular system often independent of its site. As is noticeable in this artcile the gene is expressed everywhere.
Therefore I think Chih-wei's suggestion of using stamen VS is fine as it covers all the vascular tissue in the stamen.
Pankaj
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Pankaj,
Thank you for the comments. My thoughts:
1) As curators, we merely curate the paper, it is not our responsibilty to make a judgement on whether the results are valid or not unless there is an obvious error. I believe this have generally being agreed upon by the curators. So, if the authors wrote in the paper that the gene is expressed in ather vascular system, it is our responsiblity to capture this information based on what was reported.
2) It's a different matter, however, if domain experts like you reckon that there is no vascular system in anther. If that's the case, I can use stamen vascular system instead.
best
Donghui
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Hi Donghui,
This is my opinion: vascular system is made up of pholem and xylem to conduct nutrients and water through the plants. It's very difficult to find a vascular system discontinued from other parts within a certain tissue or organ type. For example, in the stamen if you do cross-sectioning in the anthers and you will find a vascular bundle in the center which joints to filaments, this is also true in carpel,i.e the vascular system is continuous through the carpel. So I think it's more accurate to use stamen vascular system or if you prefer we will create "filament vascular system".
In Pubmed ID: 15665497, the authors stated "In flowers, GUS expression was found in the vascular bundle of the stamen filament and in the stigma, where the filament joins the pistil"(Fig. 3e, page 224). I am fine with stamen filament, but totally uncomfortable and do not understand what authors meant by saying " in the stigma, where the filament joins the pistil", it's not correct in terms of structural description, and also the GUS stain is very blurry in the picture. This is the main reason I think it's safe to use carpel vascular system in this case, rather than create "stigma vascular system.
Let us know if this make sense to you.
Chih-Wei
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Hi, Chih-Wei and Pankaj,
Thank you for the explanation. I am ok with the term 'stamen vascular system'. Based on Chih-Wei's comments that vascular system is continous, would it be more appropriate to renames the terms: vascular system in stamen, vascular system in hypotocol etc?
Please go ahead to create the remaining vascular system terms I requested: stigma vs, hypotocol vs, embryo vs. Thanks!
Donghui
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Hi Donghui,
I apologize for the delay of adding these terms. These terms are added to the database now.
Chih-Wei
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Please find the new terms with PO ID.
[Term]
id: PO:0008011
name: embryo vascular system
namespace: plant_structure
def: "Vascular system of embryo" [GR:cwt]
is_a: PO:0000034 ! vascular system
relationship: part_of PO:0009009 ! embryo
[Term]
id: PO:0008012
name: stigma vascular system
namespace: plant_structure
def: "Vascular system of stigma" [GR:cwt]
relationship: part_of PO:0005019 ! carpel vascular system
[Term]
id: PO:0008013
name: anther vascular system
namespace: plant_structure
def: "Vascular system of the anther" [GR:cwt]
relationship: part_of PO:0005018 ! stamen vascular system
[Term]
id: PO:0008014
name: filament vascular system
namespace: plant_structure
def: "Vascular system of filament in the stamen" [GR:cwt]
relationship: part_of PO:0005018 ! stamen vascular system
[Term]
id: PO:0008015
name: hypocotyl vascular system
namespace: plant_structure
def: "Vascular system of the hypocotyl" [GR:cwt]
is_a: PO:0000034 ! vascular system
relationship: part_of PO:0020100 ! hypocotyl