Changes to the TO- Spring 2012 - Revision history

Cooperl at 19:36, 14 November 2013

2013-11-14T19:36:52Z

Cooperl: /* user requested: petiole traits */

2012-05-17T19:57:20Z

user requested: petiole traits

Cooperl: /* user requested: hypocotyl color */

2012-05-11T16:38:09Z

user requested: hypocotyl color

Cooperl: /* coleoptile trait terms */

2012-05-11T16:36:50Z

coleoptile trait terms

Cooperl: /* Requested cotyledon trait terms: */

2012-05-03T20:20:29Z

Requested cotyledon trait terms:

Cooperl: /* New children of anatomy and morphology trait (TO:0000017) */

2012-05-02T00:53:13Z

New children of anatomy and morphology trait (TO:0000017)

Cooperl: /* tuber traits */

2012-05-02T00:51:47Z

tuber traits

Cooperl: /* root anatomy and morphology trait (TO:0000043) */

2012-04-28T13:57:53Z

root anatomy and morphology trait (TO:0000043)

Cooperl: /* anatomy and morphology trait (TO:0000017) */

2012-04-27T18:41:36Z

anatomy and morphology trait (TO:0000017)

Cooperl: /* requested terms and suggested def'ns: */

2012-04-26T17:34:33Z

requested terms and suggested def'ns:

← Older revision		Revision as of 19:36, 14 November 2013
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	for more concise notes: [[Summary New TO Terms- Spring 2012]]		for more concise notes: [[Summary New TO Terms- Spring 2012]]

		+	Go back to the main [[Plant_Trait_Ontology]] wiki page
		+
		+	=To Do=
		+
		+	* seed weight (sensu Poaceae)TO:0000589: Average weights of full grain with the hull (seeds) obtained from a grass plant, representing the overall yield or produce from the field.
		+
		+	is_a seed weight (TO:0000181): A seed anatomy and morphology trait (TO:0000184) which is associated with the weight of a seed (PO:0009010).

−	~~Go back to the main [[Plant_Trait_Ontology]] wiki page~~

	=Changes to root term:=		=Changes to root term:=

@@ Line 275: / Line 275: @@
 ===user requested: petiole traits===
-From: Syngenta (see [https://docs.google.com/spreadsheet/ccc?key=0Ar1O1Y7eIKhsdDhtbTVITnNDVU1fWUVSYWo3OWZoZFE#gid=0 Crop Traits Google doc])
+From: AViel (see [https://docs.google.com/spreadsheet/ccc?key=0Ar1O1Y7eIKhsdDhtbTVITnNDVU1fWUVSYWo3OWZoZFE#gid=0 Crop Traits Google doc])
 cardinal organ part > stalk > petiole

← Older revision		Revision as of 16:38, 11 May 2012
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	Refer to: color (PATO:0000014); dark purple: PATO:0001259		Refer to: color (PATO:0000014); dark purple: PATO:0001259
		+
		+	''completed''
		+
		+	==[https://sourceforge.net/tracker/?func=detail&aid=3521779&group_id=76834&atid=835557 stem internode traits:] ==
		+	PO hierarchy: cardinal organ part > shoot internode > stem internode > hypocotyl (PO:0020100), mesocotyl (PO:0020037) and epicotyl (PO:0020035)
		+
		+	* shoot internode anatomy and morphology trait (TO:0000755): A cardinal organ part anatomy and morphology trait (TO:0000754) which is associated with a shoot internode (PO:0005005).
		+
		+	* stem internode anatomy and morphology trait (TO:0000756): A shoot internode anatomy and morphology trait (TO:0000755) which is associated with a stem internode (PO:0020142).
		+
		+	* hypocotyl anatomy and morphology trait (TO:0000757): A stem internode anatomy and morphology trait (TO:0000756) which is associated with a hypocotyl (PO:0020100).
		+
		+	* mesocotyl anatomy and morphology trait (TO:0000758): A stem internode anatomy and morphology trait (TO:0000756) which is associated with a mesocotyl (PO:0020037).
		+
		+
		+	Existing TO terms: these are currently children of ''shoot system anatomy and morphology trait''
		+
		+	* hypocotyl length (TO:0006065): A hypocotyl anatomy and morphology trait (TO:0000757) which is associated with the length of a hypocotyl (PO:0020100). Refer to length PATO:0000122
		+
		+	* mesocotyl length (TO:0000544): A mesocotyl anatomy and morphology trait (TO:0000758) which is associated with the length of a mesocotyl (PO:0020037). Refer to length PATO:0000122
		+
		+	''completed''
		+
		+	===user requested: petiole traits===
		+	From: Syngenta (see [https://docs.google.com/spreadsheet/ccc?key=0Ar1O1Y7eIKhsdDhtbTVITnNDVU1fWUVSYWo3OWZoZFE#gid=0 Crop Traits Google doc])
		+
		+	cardinal organ part > stalk > petiole
		+
		+	petiole (PO:0020038): A stalk of a leaf.
		+
		+	Add new terms:
		+
		+	stalk anatomy and morphology trait (TO:0000764): A cardinal organ part anatomy and morphology trait (TO:0000754) which is associated with a stalk (PO:0025066).
		+
		+	petiole anatomy and morphology trait (TO:0000765): A stalk anatomy and morphology trait (TO:0000764): which is associated with a petiole (PO:0020038).
		+
		+	Add new terms:
		+
		+	petiole length (TO:0000766): A petiole anatomy and morphology trait (TO:0000765)that is associated with the length of a petiole (PO:0020038). Refer to length PATO:0000122
		+
		+	petiole shape(TO:0000767): A petiole anatomy and morphology trait (TO:0000765) that is associated with the shape of a petiole (PO:0020038). Refer to shape PATO:0000052
		+
		+	petiole size (TO:0000768): A petiole anatomy and morphology trait (TO:0000765) that is associated with the size of a petiole (PO:0020038). Refer to size PATO:0000117

	''completed''		''completed''

← Older revision		Revision as of 16:36, 11 May 2012
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	Need new class: coleoptile anatomy and morphology trait (TO:0001007): A plant organ anatomy and morphology trait (TO:0000736) which is associated with a coleoptile (PO:0020033).		Need new class: coleoptile anatomy and morphology trait (TO:0001007): A plant organ anatomy and morphology trait (TO:0000736) which is associated with a coleoptile (PO:0020033).
		+
		+	''completed''
		+
		+	===user requested: hypocotyl color===
		+	From: Syngenta (see [https://docs.google.com/spreadsheet/ccc?key=0Ar1O1Y7eIKhsdDhtbTVITnNDVU1fWUVSYWo3OWZoZFE#gid=0 Crop Traits Google doc])
		+
		+	* seedling hypocotyl color (TO:0000759): A seedling hypocotyl anatomy and morphology trait (TO:0000769) which is associated with the color of a hypocotyl (PO:0020100). Refer to color PATO:0000014
		+
		+	''add comment: The color of a seedling hypocotyl (PO:0025291) during the hypocotyl emergence stage (PO:0007043).''
		+
		+	''completed''
		+
		+	''color of hypocotyl at or shortly after emergence: - green, green with bronze band, purple, dark purple. PATO terms for: green, green with bronze band, purple, dark purple. ''
		+
		+	* seedling hypocotyl green (TO:0000760): A seedling hypocotyl color trait (TO:0000759) where a hypocotyl (PO:0020100) is observed to have the quality color green (PATO:0000320).
		+
		+	Refer to: color (PATO:0000014); green (PATO:0000320)
		+
		+	* seedling hypocotyl green with bronze band (TO:0000761): A seedling hypocotyl color trait (TO:0000759) where a hypocotyl (PO:0020100) is observed to have the quality color green (PATO:0000320) with a bronze (PATO:0002363) band.
		+
		+	* seedling hypocotyl purple (TO:0000762): A seedling hypocotyl color trait (TO:0000759) where a hypocotyl (PO:0020100) is observed to have the quality color purple (PATO:0000951).
		+
		+	Refer to: color (PATO:0000014); purple: PATO:0000951
		+
		+	* seedling hypocotyl dark purple (TO:0000763): A seedling hypocotyl color trait (TO:0000759) where a hypocotyl (PO:0020100) is observed to have the quality color dark purple (PATO:0001259).
		+
		+	Refer to: color (PATO:0000014); dark purple: PATO:0001259

	''completed''		''completed''

@@ Line 192: / Line 192: @@
 refer to PATO size: PATO:0000117
-''completed''
+''these should all refer to the seedling cotyledon''
 ===[https://sourceforge.net/tracker/?func=detail&aid=3521755&group_id=76834&atid=835557 coleoptile trait terms]===

← Older revision		Revision as of 00:53, 2 May 2012
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	*new term and def'n: '''branch anatomy and morphology trait''' (TO:0000740): A shoot axis anatomy and morphology trait (TO:0000739) which is associated with a branch (PO:0025073).		*new term and def'n: '''branch anatomy and morphology trait''' (TO:0000740): A shoot axis anatomy and morphology trait (TO:0000739) which is associated with a branch (PO:0025073).
		+
		+
		+
		+	''need to check these now that we have changed the definition of tuber:''

	*new term and def'n: '''tuber anatomy and morphology trait ''' (TO:0000741): A branch anatomy and morphology trait (TO:0000740) which is associated with a tuber (PO:0004543).		*new term and def'n: '''tuber anatomy and morphology trait ''' (TO:0000741): A branch anatomy and morphology trait (TO:0000740) which is associated with a tuber (PO:0004543).

@@ Line 58: / Line 58: @@
 Terms requested by Syngenta (in bold):
-'''tuber''' (PO:0004543): An enlarged storage branch (PO:0025073)
+'''tuber''' (PO:0004543): An enlarged storage branch (PO:0025073)''- needs to be updated''
 probably should be: subterranean tuber (PO:0004547): A tuber (PO:0004543) that is below ground

← Older revision		Revision as of 13:57, 28 April 2012
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	''note issue with children: adventitious root traits: in the PO adventitious root is a broad synonym of shoot-borne root and also basal root, depending where it arises from.''		''note issue with children: adventitious root traits: in the PO adventitious root is a broad synonym of shoot-borne root and also basal root, depending where it arises from.''
		+	=plant organ anatomy and morphology traits (TO:0000736)=
		+	* [https://sourceforge.net/tracker/?func=detail&aid=3521426&group_id=76834&atid=835557 phyllome anatomy and morphology trait (TO:0000747)]
		+
		+	PO hierarchy: plant organ > phyllome >leaf > vascular leaf > cotyledon
		+
		+	make children of new class: plant organ anatomy and morphology trait (TO:0000736): An anatomy and morphology trait (TO:0000017) which is associated with a plant organ (PO:0009008).
		+
		+	Add new classes:
		+	* '''phyllome anatomy and morphology trait (TO:0000747):''' A plant organ anatomy and morphology trait (TO:0000736) which is associated with a phyllome (PO:0006001).
		+
		+	* existing class: '''leaf anatomy and morphology trait (TO:0000419):''' Traits associated with changes in the anatomy or structure of the leaf and its parts.
		+
		+	this refers only to vascular leaves, there are 625 annotations on Gramene for this class
		+
		+	propose we rename to '''vascular''' leaf anatomy and morphology trait (TO:0000419). this will make it clear that it is specific to vascular leaves. See revised def'n below. This will allow all the existing children to stay on the vlamt and won't mess up the annotations as TO# will stay the same.
		+
		+	* new term: '''leaf anatomy and morphology trait (TO:0000748)''': A phyllome anatomy and morphology trait (TO:0000747) which is associated with a leaf (PO:0025034).
		+
		+	*'''vascular leaf anatomy and morphology trait (TO:0000419):''' revised def'n: A leaf anatomy and morphology trait (TO:0000748) which is associated with a vascular leaf (PO:0009025).
		+
		+	*'''cotyledon anatomy and morphology trait (TO:0000749):''' A vascular leaf anatomy and morphology trait (TO:0000419) which is associated with a cotyledon (PO:0020030).
		+
		+	''completed''
		+
		+	==Requested [https://sourceforge.net/tracker/?func=detail&aid=3521436&group_id=76834&atid=835557 cotyledon trait terms]:==
		+	From: Syngenta (see [https://docs.google.com/spreadsheet/ccc?key=0Ar1O1Y7eIKhsdDhtbTVITnNDVU1fWUVSYWo3OWZoZFE#gid=0 Crop Traits Google doc])
		+
		+
		+	PO term: cotyledon (PO:0020030): A vascular leaf (PO:0009025) formed at the first shoot node (PO:0005004) of a plant embryo (PO:0009009) or a seedling (PO:0000003).
		+
		+	* cotyledon color(TO:0000750): A cotyledon anatomy and morphology trait (TO:0000749) which is associated with the shape of a cotyledon(PO:0020030).
		+	refer to PATO color: PATO:0000014
		+
		+	* cotyledon number (TO:0000751): A cotyledon anatomy and morphology trait (TO:0000749) which is associated with the number of cotyledons (PO:0020030).
		+	refer to PATO count: PATO:0000070
		+
		+	* cotyledon size (TO:0000752): A cotyledon anatomy and morphology trait (TO:0000749) which is associated with the size of a cotyledon(PO:0020030).
		+	refer to PATO size: PATO:0000117
		+
		+	''completed''
		+
		+	===[https://sourceforge.net/tracker/?func=detail&aid=3521755&group_id=76834&atid=835557 coleoptile trait terms]===
		+
		+	PO hierarchy: plant organ > coleoptile >embryo coleoptile (PO:00252860 and seedling coleoptile (PO:0025287)
		+
		+	Add new terms:
		+	coleoptile anatomy and morphology trait (TO:0000753) : A plant organ anatomy and morphology trait (TO:0000736) which is associated with a coleoptile (PO:0020033).
		+
		+
		+	Move existing TO terms and refine:
		+
		+	* coleoptile color (TO:0000244) def: "Measure of color of the coleoptile in the germinating seedling." [GR:pj]
		+	synonym: "COLCL" RELATED
		+
		+	is_a: TO:0000064 ! embryo related trait
		+
		+	is_a: TO:0000736 ! plant organ anatomy and morphology trait
		+
		+	new definition: A coleoptile anatomy and morphology trait (TO:0000753) which is associated with the color of a coleoptile (PO:0020033).
		+	refer to: color PATO:0000014
		+
		+
		+
		+	* coleoptile length (TO:0001007) def: "Measurement of the length of the coleoptile in the germinating seed." [GR:pj]
		+
		+	is_a: TO:0000736 ! plant organ anatomy and morphology trait
		+
		+	new definition:A coleoptile anatomy and morphology trait (TO:0000753) which is associated with the length of a coleoptile (PO:0020033).
		+	refer to: length PATO:0000122
		+
		+	Need new class: coleoptile anatomy and morphology trait (TO:0001007): A plant organ anatomy and morphology trait (TO:0000736) which is associated with a coleoptile (PO:0020033).
		+
		+	''completed''

@@ Line 37: / Line 37: @@
 ''may move this stuff to this page: [[anatomy and morphology related trait (TO:0000017)]]''
-''need to post comment on SF-remove "related from names''
+''Can we just use "anatomy trait"?  It would make all these names less cumbersome. ''
 ===[https://sourceforge.net/tracker/?func=detail&aid=3519674&group_id=76834&atid=835557 New children of anatomy and morphology trait (TO:0000017)]===

← Older revision		Revision as of 17:34, 26 April 2012
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	''done: 4-20-12''		''done: 4-20-12''
		+
		+	==[https://sourceforge.net/tracker/?func=detail&aid=3520729&group_id=76834&atid=835557 root anatomy and morphology trait (TO:0000043)]==
		+	current def'n: Traits associated with changes in the anatomy or structure of the root and its parts.
		+
		+	propose revised def'n: root anatomy and morphology trait (TO:0000043): A plant axis anatomy and morphology trait (TO:0000738) that is associated with the root (PO:0025025).
		+
		+	''Is a child of the new class: plant axis anatomy and morphology trait (TO:0000738)''
		+
		+	root (PO:0025025): A plant axis that is part of a root system. [source: POC:curators]
		+
		+	PO Comment: Commonly thought of as one of the three basic parts of the seed plant body. A plant stucture (''organ'') that is usually underground and does not bear leaves and only rarely shoots, is usually more or less positively geotropic, is endogenous in origin, indeterminate in growth and often with secondary thickening.
		+
		+	PO hierarchy: plant organ > plant axis > shoot axis > root
		+
		+	PO Children of root:
		+	*PO:0020127: primary root
		+	*PO:0020121: lateral root
		+	*PO:0000045: embryo root
		+	*PO:0025002: basal root (broad: adventitious root)
		+	*PO:0000042: shoot-borne root (broad: adventitious root)
		+
		+	''note issue with children: adventitious root traits: in the PO adventitious root is a broad synonym of shoot-borne root and also basal root, depending where it arises from.''