POC Conf. Call 3-20-12 - Revision history

Cooperl: /* Apache update: */

2012-04-06T22:58:50Z

Apache update:

Cooperl: /* icons for new relations */

2012-03-27T19:17:21Z

icons for new relations

Cooperl: /* Proposed terms and definitions */

2012-03-23T01:33:41Z

Proposed terms and definitions

Cooperl: /* Proposed terms and definitions */

2012-03-23T01:32:51Z

Proposed terms and definitions

Cooperl: /* Proposed terms and definitions */

2012-03-23T01:28:11Z

Proposed terms and definitions

Cooperl: /* Proposed terms and definitions */

2012-03-23T01:09:03Z

Proposed terms and definitions

Cooperl: /* Proposed terms and definitions */

2012-03-23T00:55:54Z

Proposed terms and definitions

Cooperl: /* Proposed terms and definitions */

2012-03-23T00:18:30Z

Proposed terms and definitions

Cooperl: /* Proposed terms and definitions */

2012-03-22T23:51:34Z

Proposed terms and definitions

Cooperl: /* Proposed terms and definitions */

2012-03-22T23:39:18Z

Proposed terms and definitions

@@ Line 31: / Line 31: @@
 ==Apache update:==
-JE has managed to port the website code to work with Apache2.  Please check http://beta.plantontology.org (no port 8080).
+JE has ported the website code to work with Apache2.  Please check http://beta.plantontology.org (no port 8080).
 Question: Should we wait until after the release to update? Probably could update with only minor disruption, but there could be unforeseen difficulties.  Most of it could be done in parallel to minimize downtime however.

@@ Line 130: / Line 130: @@
 * derives_by_manipulation_from icon is present but not working in dev browser? Although it is working on live
-''This may a result of RW changed the id to make it match the new name. JE will see if he can fix this.''
+''This is a result of when RW changed the id to make it match the new name. JE will see if he can fix this.''
 ''also:''
 ''* We will add 'cultured leaf cell synonym''
 ''* definitions for the relations have been removed from the OBO file, add a link in the comments sections to the wiki definitions page.''

@@ Line 458: / Line 458: @@
 Comment: This terms is used only for seed plants. The actual point of emergence from the seed coat (PO:0009088) may not be observed if the seed is underneath a growth medium.
 ''We also have the existing term which still needs to be worked on: seedling shoot emergence stage (PO:0007030): Shoot or leaf breaks through soil surface. ''
 for more stage information: [http://www.jki.bund.de/fileadmin/dam_uploads/_veroeff/bbch/BBCH-Skala_englisch.pdf BBCH scale]

@@ Line 414: / Line 414: @@
 ==Proposed terms and definitions==
 * sporophyte development stage (PO:0028002): A whole plant development stage (PO:0007033) that has as primary participant a whole plant (PO:0000003) during the interval between fertilization (or apogamy) and death.
 * sporophyte vegetative stage (PO:0007134): A sporophyte development stage (PO:0028002) that occurs during the interval between the first division of a plant zygote (PO:0000423) and the formation of a sporangium (PO:0025094).
 * seedling development stage (PO:0007131): A sporophyte vegetative stage (PO:0007134) that succeeds the seed germination stage (PO:0007057) and terminates with the development of the first adult vascular leaf (PO:0006340).

← Older revision		Revision as of 01:28, 23 March 2012
Line 453:		Line 453:
	* epicotyl emergence stage (PO:0007054): A seedling development stage (PO:0007131) during which the epicotyl (PO:0020035) emerges from the seed coat (PO:0009088).		* epicotyl emergence stage (PO:0007054): A seedling development stage (PO:0007131) during which the epicotyl (PO:0020035) emerges from the seed coat (PO:0009088).

−	Comment: This ~~terms~~ is used only for seed plants. ~~During this phase, only the first true foliage leaf or pair of leaves is visible.~~ Occurs in plants with hypogeal germination. The actual point of emergence from the seed coat (PO:0009088) may not be observed if the seed is underneath a growth medium.	+	Comment: This term is used only for seed plants. Occurs in plants with hypogeal germination such as pea (pisum sativum). The actual point of emergence from the seed coat (PO:0009088) may not be observed if the seed is underneath a growth medium.

@@ Line 467: / Line 467: @@
 for more stage information: [http://www.jki.bund.de/fileadmin/dam_uploads/_veroeff/bbch/BBCH-Skala_englisch.pdf BBCH scale]
-Could also add terms for feeder emergence for some gymnosperms.
+Comment from DWS: Could also add terms for feeder emergence for some gymnosperms.
-For all of the above terms, need to check existing synonyms and move or copy them as needed.
+''The feeder is apparently a structure in some gymnosperm seeds, e.g. Gnetum which is involved in the mobilization of food reserves from the endosperm. Forms at the junction of the hypocotyl and the radicle.  See Govil 2007 Gymnosperms: ISBN:81-8283-0540''
 =[http://sourceforge.net/tracker/?func=detail&aid=3502954&group_id=76834&atid=835555 non-hair root epidermal cell]=

← Older revision		Revision as of 00:55, 23 March 2012
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−	''We also have the existing term: seedling shoot emergence stage (PO:0007030): Shoot or leaf breaks through soil surface~~. Which still needs to be worked on~~.''	+	''We also have the existing term which still needs to be worked on: seedling shoot emergence stage (PO:0007030): Shoot or leaf breaks through soil surface. ''

@@ Line 445: / Line 445: @@
 Comment: May occur simultaneously with coleoptile emergence from the growth medium. This terms is used only for seed plants.
 * cotyledon emergence stage (PO:0007049): A seedling development stage (PO:0007131) during which the cotyledon (PO:0020030) emerges from the seed coat (PO:0009088).
-Comment: This terms is used only for seed plants.
+Comment: This term is used only for seed plants. The actual point of emergence from the seed coat (PO:0009088) may not be observed if the seed is underneath a growth medium, especially in plants with with hypogeal germination.
-* epicotyl emergence stage (PO:0007054): A seedling development stage (PO:0007131) during which the seedling epicotyl (PO:0025293) emerges from the seed coat (PO:0009088).
+Comment: This terms is used only for seed plants. During this phase, only the first true foliage leaf or pair of leaves is visible. Occurs in plants with hypogeal germination. The actual point of emergence from the seed coat (PO:0009088) may not be observed if the seed is underneath a growth medium.
-* hypocotyl emergence stage (PO:0007043): A seedling development stage (PO:0007131) during which the seedling hypocotyl (PO:0025291) emerges from the surface of the growth medium.
+Comment: This terms is used only for seed plants. The actual point of emergence from the seed coat (PO:0009088) may not be observed if the seed is underneath a growth medium.
-''Do we want to keep  a corresponding stage for hypocotyl emergence from the growth media to distinguish plants with hypogeal and epigeal germination?''
+''We also have the existing term: seedling shoot emergence stage (PO:0007030): Shoot or leaf breaks through soil surface. Which still needs to be worked on.''
-''* seedling shoot emergence stage (PO:0007030): A seedling development stage (PO:0007131) Shoot or leaf breaks through soil surface.''
+for more stage information: [http://www.jki.bund.de/fileadmin/dam_uploads/_veroeff/bbch/BBCH-Skala_englisch.pdf BBCH scale]
 Could also add terms for feeder emergence for some gymnosperms.

@@ Line 438: / Line 438: @@
-* coleoptile emergence stage (PO:0007045): A seedling development stage (PO:0007131) during which the coleoptile (PO:0025287) emerges from the seed coat (PO:0009088).
+* coleoptile emergence stage (PO:0007045): A sporophyte vegetative stage (PO:0007134) during which the coleoptile (PO:0020033) emerges from the seed coat (PO:0009088).
 part_of seed germination stage, occurs in Poaceae and possibly other monocots
-This cannot be both a seedling development stage and part of the seed germination stage
+''Made this a sporophyte vegetative stage, since it cannot be both a seedling development stage and part of the seed germination stage.''
 Comment: May occur simultaneously with coleoptile emergence from the growth medium. This terms is used only for seed plants.