Sunday Sept 11th, 2011 - Revision history

Cooperl: /* Next steps for the PO: */

2011-09-16T19:07:49Z

Next steps for the PO:

Cooperl: /* Discussion of the Pheno RCN */

2011-09-16T18:50:09Z

Discussion of the Pheno RCN

Cooperl: /* Next steps for the PO: */

2011-09-16T18:48:47Z

Next steps for the PO:

Rwalls: /* Discussion of the Pheno RCN */

2011-09-13T17:45:59Z

Discussion of the Pheno RCN

Rwalls: /* Discussion of the Pheno RCN */

2011-09-13T16:47:28Z

Discussion of the Pheno RCN

Rwalls: /* Discussion of the Pheno RCN */

2011-09-13T16:46:39Z

Discussion of the Pheno RCN

Rwalls: /* banner, wing and keel */

2011-09-13T15:49:18Z

banner, wing and keel

Rwalls: /* Images in the PO */

2011-09-13T15:47:16Z

Images in the PO

Rwalls: /* banner, wing and keel */

2011-09-13T15:44:03Z

banner, wing and keel

Rwalls: /* banner, wing and keel */

2011-09-13T15:42:15Z

banner, wing and keel

← Older revision		Revision as of 19:07, 16 September 2011
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	GO model genome and Gramene		GO model genome and Gramene
−

	Cathy Wu- Protein Ontology- use their pipeline?		Cathy Wu- Protein Ontology- use their pipeline?

← Older revision		Revision as of 18:50, 16 September 2011
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	''Discussion of the Ellis book on leaf architecture. It is appropriate for draft ontology of leaf characters, even though it may be missing characters that are needed for non-dicot leaves.		''Discussion of the Ellis book on leaf architecture. It is appropriate for draft ontology of leaf characters, even though it may be missing characters that are needed for non-dicot leaves.
−

	''Some discussion of how to deal with continuous characters. There is no good solution with current ontology development, but one can use the general quality (character or trait), e.g., "leaf apex angle quality", with a comment "Use this term if you want to score an exact numerical value for leaf apex angle." Subtypes of general qualities (characters) are categorical character states, e.g., "leaf apex angle equal to or less than 45 degrees", with exact synonym "acute leaf apex angle".''		''Some discussion of how to deal with continuous characters. There is no good solution with current ontology development, but one can use the general quality (character or trait), e.g., "leaf apex angle quality", with a comment "Use this term if you want to score an exact numerical value for leaf apex angle." Subtypes of general qualities (characters) are categorical character states, e.g., "leaf apex angle equal to or less than 45 degrees", with exact synonym "acute leaf apex angle".''

@@ Line 8: / Line 8: @@
 =Next steps for the PO:=
-PJ: presented at NSF as part of the Gramene application
+PJ: presented the PO at  NSF as part of the Gramene application
-As part of publication process of paper
+As part of publication process of paper authors will be encouraged/required to annotate to the PO and GO and ...?, Initially starting with Plant cell
-- text mining:associate to GO, PO and TO
+*text mining: associate to GO, PO and TO *[http://www.textpresso.org/ Textpresso]
 expression, phenotype, interactions
-Cathy Wu- protein Ontology- use their pipeline
 Freelance annotators @ Plant Cell (soon Plant Physiology)
@@ Line 24: / Line 32: @@
 allergies, food, symbionts, toxins, ecology, pathogens
-BS: Need to find money for Plant Disease Ontology:
+''BS: Need to find money for development of the Plant Disease Ontology''
 Infectious Disease Ontology (IDO): human disease, need to be able to link to the PDO

← Older revision		Revision as of 17:45, 13 September 2011
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−	''Some discussion of how to deal with continuous characters. There is no good solution with current ontology development, but one can use the general quality (character or trait), e.g., "leaf apex angle quality", with a comment "Use this term if you want to score an exact numerical value for leaf apex angle." Subtypes of qualities are ~~all~~ categorical character ~~state~~, e.g., "leaf apex angle equal to or less than 45 degrees", with exact synonym "acute leaf apex angle".''	+	''Some discussion of how to deal with continuous characters. There is no good solution with current ontology development, but one can use the general quality (character or trait), e.g., "leaf apex angle quality", with a comment "Use this term if you want to score an exact numerical value for leaf apex angle." Subtypes of general qualities (characters) are categorical character states, e.g., "leaf apex angle equal to or less than 45 degrees", with exact synonym "acute leaf apex angle".''

	=Plans for upcoming Release=		=Plans for upcoming Release=

@@ Line 40: / Line 40: @@
 =Discussion of the Pheno RCN=
-- Ellis book is appropriate for draft ontology of leaf characters, even though it may be missing some characters that are needed for non-dicot leaves.
+''Discussion of the Ellis book on leaf architecture. It is appropriate for draft ontology of leaf characters, even though it may be missing characters that are needed for non-dicot leaves.
-- Some discussion of how to deal with continuous characters. There is no good solution with current ontology development, but one can use the general quality (character or trait), e.g., "leaf apex angle quality", with a comment "Use this term if you want to score an exact numerical value for leaf apex angle." Subtypes of qualities are all categorical character state, e.g., "leaf apex angle equal to or less than 45 degrees", with exact synonym "acute leaf apex angle".
+''Some discussion of how to deal with continuous characters. There is no good solution with current ontology development, but one can use the general quality (character or trait), e.g., "leaf apex angle quality", with a comment "Use this term if you want to score an exact numerical value for leaf apex angle." Subtypes of qualities are all categorical character state, e.g., "leaf apex angle equal to or less than 45 degrees", with exact synonym "acute leaf apex angle".''
 =Plans for upcoming Release=

← Older revision		Revision as of 16:46, 13 September 2011
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	- Ellis book is appropriate for draft ontology of leaf characters, even though it may be missing some characters that are needed for non-dicot leaves.		- Ellis book is appropriate for draft ontology of leaf characters, even though it may be missing some characters that are needed for non-dicot leaves.
		+
		+
		+	- Some discussion of how to deal with continuous characters. There is no good solution with current ontology development, but one can use the general quality (character or trait), e.g., "leaf apex angle quality", with a comment "Use this term if you want to score an exact numerical value for leaf apex angle." Subtypes of qualities are all categorical character state, e.g., "leaf apex angle equal to or less than 45 degrees", with exact synonym "acute leaf apex angle".

	=Plans for upcoming Release=		=Plans for upcoming Release=

← Older revision		Revision as of 15:49, 13 September 2011
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	''New proposed name: '''keel'''''		''New proposed name: '''keel'''''
		+
		+	''We need to reword the definition of corolla (and other collective phyllome structures), because technically, the keel is a corolla (it consists of two or more petals). New definition should be the maximal set of petals or whatever in a flower.''

@@ Line 276: / Line 276: @@
-Some have 8 slides, some have 16. More than 3000 slides.
+''Some slides have 8 images, some have 16. More than 3000 slides.''
-Make each image and xml file so metadata is associated.
+''Make each image and xml file so metadata is associated.''
-Phil Bourne nano-publishing UCSD
+''Some discussion of copyright issues. PO material must be open access (according to grant), but users need to get credit for their photos. PJ suggested putting a watermark on the images with the credit for the photographer, then people can contact photographer for image without water mark if they want to use it.''

@@ Line 249: / Line 249: @@
 is_a collective phyllome structure, part_of corolla
 '''keel petal:''' A petal that is one of the two lowest petals of a papilionaceous corolla.
-Comment: The keel petals are usually larger than the adjacent wing petals. They are often partially fused to each other.
+Comment: The keel petals are usually larger than the adjacent wing petals. They are often partially fused to each other. Each petal is shaped like half a boat and projects toward the front of the flower.
-----
+''Okay to add '''keel petal'''.''
 ===[https://sourceforge.net/tracker/?func=detail&aid=3165984&group_id=76834&atid=835555 phyllode]===

← Older revision		Revision as of 15:42, 13 September 2011
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	Synonyms vexillum (exact), standard (broad)		Synonyms vexillum (exact), standard (broad)
		+
		+	''Okay to add '''banner petal'''.''


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	Comment: The wing petals are usually much smaller than the banner petal and the corolla keel. Found in the flowers of some Fabaceae.		Comment: The wing petals are usually much smaller than the banner petal and the corolla keel. Found in the flowers of some Fabaceae.
		+
		+	''Okay to add '''wing petal'''.''