Eliminating Zea/Poaceae terms from PO - Revision history

Cooperl at 01:22, 9 December 2011

2011-12-09T01:22:03Z

Cooperl: /* Annotations */

2011-12-09T01:21:19Z

Annotations

Cooperl: /* Annotations */

2011-10-13T05:28:10Z

Annotations

Cooperl: /* Plant G&D stages with Poaceae in the name: */

2011-10-12T20:58:10Z

Plant G&D stages with Poaceae in the name:

Cooperl at 20:41, 12 October 2011

2011-10-12T20:41:10Z

Rwalls: /* lemma, palea */

2011-10-04T18:44:22Z

lemma, palea

Rwalls: /* ovary and parts */

2011-09-27T15:07:26Z

ovary and parts

Rwalls: /* flower meristem (PO:0000229) */

2011-09-27T14:23:47Z

flower meristem (PO:0000229)

Rwalls: /* lemma, palea */

2011-09-27T13:22:08Z

lemma, palea

Rwalls: /* PO:0006318 Poaceae floret (71) */

2011-09-15T19:11:13Z

PO:0006318 Poaceae floret (71)

← Older revision		Revision as of 01:22, 9 December 2011
Line 11:		Line 11:
	See [[list of Poaceae/Zea terms with annotations]]		See [[list of Poaceae/Zea terms with annotations]]

−	~~During the release-this is the list of ids that amigo had problems with:These are alt ids~~
−	*PO:0006318
−	*PO:0006329
−	*PO:0006384
−	*PO:0006441
−	*PO:0006442
−	*PO:0006444
−	*PO:0006445
−	*PO:0006446
−	*PO:0006449
−	*PO:0006450
−	*PO:0006451
−	*PO:0006452
−	*PO:0006455
−	*PO:0006456
−	*PO:0006457
−	*PO:0006462
−	*PO:0006463
−	*PO:0006464
−	*PO:0006465
−	*PO:0006472
−	*PO:0006497
−	*PO:0006508
−
−	~~The all seem to be from the file po_anatomy_gene_oryza_gramene.assoc and po_anatomy_qtl_oryza_gramene.assoc.~~

	=Existing terms=		=Existing terms=

← Older revision		Revision as of 01:21, 9 December 2011
Line 10:		Line 10:

	See [[list of Poaceae/Zea terms with annotations]]		See [[list of Poaceae/Zea terms with annotations]]
		+
		+	During the release-this is the list of ids that amigo had problems with:These are alt ids
		+	*PO:0006318
		+	*PO:0006329
		+	*PO:0006384
		+	*PO:0006441
		+	*PO:0006442
		+	*PO:0006444
		+	*PO:0006445
		+	*PO:0006446
		+	*PO:0006449
		+	*PO:0006450
		+	*PO:0006451
		+	*PO:0006452
		+	*PO:0006455
		+	*PO:0006456
		+	*PO:0006457
		+	*PO:0006462
		+	*PO:0006463
		+	*PO:0006464
		+	*PO:0006465
		+	*PO:0006472
		+	*PO:0006497
		+	*PO:0006508
		+
		+	The all seem to be from the file po_anatomy_gene_oryza_gramene.assoc and po_anatomy_qtl_oryza_gramene.assoc.

	=Existing terms=		=Existing terms=

@@ Line 3: / Line 3: @@
 =Annotations=
-If one term is merged with another, the IDs merge too. This means any annotations should automatically move to the target term, but we should double check it.
+If one term is merged with another, one of the IDs becomes a synonym (alt_id:PO:XXXXXXX) under the ID of the target term.
-''PJ and JE say that the associations will not automatically go with the alternate ID. This means that the association files will have to be edited, so the new target ID is in column 5. RW will make a list the lines in the association files can be fixed.''
+However, the  annotations do not automatically move to the target term, they have to be moved manually.
 See [[list of Poaceae/Zea terms with annotations]]

← Older revision		Revision as of 20:58, 12 October 2011
Line 580:		Line 580:

	See SF tracker for [http://sourceforge.net/tracker/?func=detail&aid=3324099&group_id=76834&atid=835555 3 infloresence visible]		See SF tracker for [http://sourceforge.net/tracker/?func=detail&aid=3324099&group_id=76834&atid=835555 3 infloresence visible]
		+
		+	Merged Poaceae inflorescence visible (PO:0007012) into 3 inflorescence detectable phase (PO:0007047) and made booting (PO:0007014) a subtype of IL.00 inflorescence just visible phase (PO:0007006)

	==Plant G&D stages with Zea in the name:==		==Plant G&D stages with Zea in the name:==

← Older revision		Revision as of 20:41, 12 October 2011
Line 1:		Line 1:
		+	Back to [[Summary_of_Changes to PO October 2011]]
		+
	=Annotations=		=Annotations=

@@ Line 817: / Line 817: @@
 ====lemma, palea====
-I made these are part of spikelet, not part of floret (because they are bracts, and bracts by definition are not part of a flower). Therefore, the comment refers to specific types of spikelets, rather than florets.
+Lemma and palea are part_of spikelet floret, but an annotation can also be made to the more specific floret type.
-''If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding spikelet type, if known. Choose the most specific term possible from: ear spikelet (PO:0006320), ear pedicellate spikelet (PO:0006348), ear sessile spikelet (PO:0006349), tassel spikelet (PO:0006309), tassel pedicellate spikelet (PO:0006312), tassel sessile spikelet (PO:0006311).''
+''Found in Poaceae such as Zea mays. A lemma and a palea enclose an individual floret while glumes subtend a pair of florets. Lemma/palea is part_of spikelet floret, but if you are annotating to this structure for Zea mays or other similar grasses, an annotation can also be made to the more specific floret type, if known. Choose the most specific term possible from: ear floret (PO:0006354), lower floret of pedicellate spikelet of ear (PO:0006353), lower floret of sessile spikelet of ear (PO:0006351), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352), tassel floret (PO:0006310), lower floret of pedicellate spikelet of tassel (PO:0006313), lower floret of sessile spikelet of tassel (PO:0006315), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316).''
 ====flower meristem (PO:0000229)====

← Older revision		Revision as of 15:07, 27 September 2011
Line 833:		Line 833:
	For ovary and its parts, in the comment, I only included the types of florets that normally have fully developed gynoecia:		For ovary and its parts, in the comment, I only included the types of florets that normally have fully developed gynoecia:

−	'''Terms:''' PO:0020006 funicle, PO:0020022 inner integument, PO:0020021 integument, PO:0006043 integument epidermis, PO:0020023 outer integument, PO:0006045 outer integument epidermis, PO:0006044 inner integument epidermis, PO:0006506 chalaza, PO:0020001 ovary placenta~~, PO:0009073 stigma, PO:0006061 stigma epidermis~~, PO:0000245 degenerate megaspore, PO:0000244 functional megaspore, PO:0020019 megaspore, PO:0000431 megasporocyte, PO:0020020 nucellus, PO:0009072 ovary, PO:0006063 ovary epidermis, PO:0020003 ovule, micropyle (PO:0020025), PO:0020102 portion of transmitting tissue	+	'''Terms:''' PO:0020006 funicle, PO:0020022 inner integument, PO:0020021 integument, PO:0006043 integument epidermis, PO:0020023 outer integument, PO:0006045 outer integument epidermis, PO:0006044 inner integument epidermis, PO:0006506 chalaza, PO:0020001 ovary placenta, PO:0000245 degenerate megaspore, PO:0000244 functional megaspore, PO:0020019 megaspore, PO:0000431 megasporocyte, PO:0020020 nucellus, PO:0009072 ovary, PO:0006063 ovary epidermis, PO:0020003 ovule, micropyle (PO:0020025), PO:0020102 portion of transmitting tissue

← Older revision		Revision as of 14:23, 27 September 2011
Line 826:		Line 826:


−	''In Zea mays and other grasses, the floret meristem is part of a spikelet and develops into a specific type of floret. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the spikelet type that the meristem is part of. Choose the most specific term possible from: spikelet (PO:0009051), ear spikelet (PO:0006320), ear pedicellate spikelet (PO:0006348), ear sessile spikelet (PO:0006349), tassel spikelet (PO:0006309), tassel pedicellate spikelet (PO:0006312), tassel sessile spikelet (PO:0006311). An additional annotation can ~~also~~ be added for the type of floret the meristem will develop into~~. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), lower floret of pedicellate spikelet of ear (PO:0006353)~~, ~~lower floret of sessile spikelet of ear (PO:0006351), upper floret of pedicellate spikelet of ear (PO:0006350)~~, upper floret of sessile spikelet of ear (PO:0006352), tassel floret (PO:0006310), lower floret of pedicellate spikelet of tassel (PO:0006313), lower floret of sessile spikelet of tassel (PO:0006315), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316).''	+	''In Zea mays and other grasses, the floret meristem is part of a spikelet and develops into a specific type of floret. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the spikelet type that the meristem is part of. Choose the most specific term possible from: spikelet (PO:0009051), ear spikelet (PO:0006320), ear pedicellate spikelet (PO:0006348), ear sessile spikelet (PO:0006349), tassel spikelet (PO:0006309), tassel pedicellate spikelet (PO:0006312), tassel sessile spikelet (PO:0006311).''
		+
		+	An additional annotation can be added for the type of floret the meristem will develop into, if we had a develops_into relation, but we don't!

	====ovary and parts====		====ovary and parts====

@@ Line 441: / Line 441: @@
 ===PO:0006318	Poaceae floret (71)===
-Merge into floret
+'''x''' Merge into floret
 ===PO:0006329	Poaceae floret meristem (1)===