POC Conf. Call 5-25-10 - Revision history

Cooperl at 18:26, 27 May 2010

2010-05-27T18:26:41Z

Cooperl: /* Agenda: */

2010-05-26T23:30:37Z

Agenda:

Rwalls at 15:30, 26 May 2010

2010-05-26T15:30:11Z

Rwalls at 15:06, 26 May 2010

2010-05-26T15:06:26Z

Rwalls: added comment to TraitNet item

2010-05-26T15:05:30Z

added comment to TraitNet item

Rwalls at 15:03, 26 May 2010

2010-05-26T15:03:29Z

Rwalls at 14:57, 26 May 2010

2010-05-26T14:57:39Z

Rwalls at 14:54, 26 May 2010

2010-05-26T14:54:07Z

Cooperl at 19:36, 25 May 2010

2010-05-25T19:36:35Z

Cooperl: /* Agenda: */

2010-05-25T19:21:09Z

Agenda:

@@ Line 3: / Line 3: @@
 In attendance: POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU),Dennis Stevenson (NYBG),  Alejandra Gandolfo, (Cornell University), Barry Smith (University at Buffalo, NY)
-Collaborators: Rex Nelson-SOYbase, USDA-ARS, Ames, Iowa, Rosemary Shrestha- Generation Challenge Program, CIMMYT, Mexico
+Collaborators: Rex Nelson-SOYBase, USDA-ARS, Ames, Iowa, Rosemary Shrestha- Generation Challenge Program, CIMMYT, Mexico
 Absent: Chris Mungall (Lawrence Berkeley National Lab)

@@ Line 188: / Line 188: @@
 (2) develops_from zygote (see comment above) Usually
 (3) embryo contained_in archegonium (works for land plants, not charophytes (doi: 10.1111/j.1469-8137.2009.03054.x)
 ==4. Upcoming Conferences and Meetings: Updates==

← Older revision		Revision as of 15:30, 26 May 2010
Line 41:		Line 41:


−	''Tuber flesh: We decided that we should make a term for storage parenchyma tissue, with children tuber storage parenchyma, and grandchildren aerial tuber storage parenchyma tissue and subterranean tuber storage parenchyma tissue. (Using the prefix portion of in each case). Tuber flesh can be a synonym of tuber storage parenchyma tissue. There will also be specific terms for each part of the tuber flesh, which will have part_of relationships to subterranean tuber storage parenchyma tissue.''	+	''Tuber flesh: We decided that we should make a term for storage parenchyma tissue, with children tuber storage parenchyma, and grandchildren aerial tuber storage parenchyma tissue and subterranean tuber storage parenchyma tissue. (Using the prefix portion of in each case). Tuber flesh can be a synonym of tuber storage parenchyma tissue. There will also be specific terms for each part of the tuber flesh (medulla, perimedulla, cortex), which will have part_of relationships to subterranean tuber storage parenchyma tissue.''

	''Tuber eye: This is really a vegetative axillary meristem. Can make term tuber vegetative axillary meristem, with children for aerial and subterranean tubers.''		''Tuber eye: This is really a vegetative axillary meristem. Can make term tuber vegetative axillary meristem, with children for aerial and subterranean tubers.''

← Older revision		Revision as of 15:06, 26 May 2010
Line 46:		Line 46:

	''Tuber epidermis: In potatoes, the skin is actually two layers, an epidermis underlain by a periderm (bark) (need to check references on this). We can make terms tuber periderm and tuber epidermis, with children for aerial and subterranean tubers. Epidermis should be used for species (like monocots) that have no secondary growth, and also for young tubers, before the periderm has developed. These terms should probably be children of shoot periderm and shoot epidermis.''		''Tuber epidermis: In potatoes, the skin is actually two layers, an epidermis underlain by a periderm (bark) (need to check references on this). We can make terms tuber periderm and tuber epidermis, with children for aerial and subterranean tubers. Epidermis should be used for species (like monocots) that have no secondary growth, and also for young tubers, before the periderm has developed. These terms should probably be children of shoot periderm and shoot epidermis.''
		+
		+	''We will need to make a new subset for terms that are used by people who study potatoes.''

← Older revision		Revision as of 15:05, 26 May 2010
Line 126:		Line 126:

	A semantic web-based application tool developed by the group would be used to coordinate the clarification of the definitions, and define a hierarchal structure and relatedness between the plant trait concepts. It was decided to build the ontology using the OWL language rather than the OBO standard. Besides the ontology, it was decided that a semantic based registry of databases relevant to ecologists would be developed to showcase the usefulness of working with data in a semantic framework.		A semantic web-based application tool developed by the group would be used to coordinate the clarification of the definitions, and define a hierarchal structure and relatedness between the plant trait concepts. It was decided to build the ontology using the OWL language rather than the OBO standard. Besides the ontology, it was decided that a semantic based registry of databases relevant to ecologists would be developed to showcase the usefulness of working with data in a semantic framework.
		+
		+	''Ramona will meet with Dan and Farshid on Friday. Will put them in contact with Pankaj if they have further questions.''

← Older revision		Revision as of 15:03, 26 May 2010
Line 45:		Line 45:
	''Tuber eye: This is really a vegetative axillary meristem. Can make term tuber vegetative axillary meristem, with children for aerial and subterranean tubers.''		''Tuber eye: This is really a vegetative axillary meristem. Can make term tuber vegetative axillary meristem, with children for aerial and subterranean tubers.''

−	''Tuber epidermis: In potatoes, the skin is actually a periderm (bark)~~, so we~~ can make ~~a term~~ tuber periderm, with children for aerial and subterranean tubers. ~~We will also need the term tuber epidermis,~~ for species (like monocots) that have no secondary growth, and also for young tubers, before the periderm has developed. These terms should probably be children of shoot periderm and shoot epidermis.''	+	''Tuber epidermis: In potatoes, the skin is actually two layers, an epidermis underlain by a periderm (bark) (need to check references on this). We can make terms tuber periderm and tuber epidermis, with children for aerial and subterranean tubers. Epidermis should be used for species (like monocots) that have no secondary growth, and also for young tubers, before the periderm has developed. These terms should probably be children of shoot periderm and shoot epidermis.''

@@ Line 39: / Line 39: @@
 ''We looked at a diagram of the [http://www.geochembio.com/biology/organisms/potato/#tuber potato tuber anatomy] online and saw that the 'flesh' is actually several different layers.  There was discussion about how the users would be able to know where the annotations would go. There is a similar issue for the epidermis, which in mature potatoes is actually periderm.''
 ''Tuber flesh: We decided that we should make a term for storage parenchyma tissue, with children tuber storage parenchyma, and grandchildren aerial tuber storage parenchyma tissue and subterranean tuber storage parenchyma tissue. (Using the prefix portion of in each case). Tuber flesh can be a synonym of tuber storage parenchyma tissue. There will also be specific terms for each part of the tuber flesh, which will have part_of relationships to subterranean tuber storage parenchyma tissue.''
@@ Line 44: / Line 45: @@
 ''Tuber eye: This is really a vegetative axillary meristem. Can make term tuber vegetative axillary meristem, with children for aerial and subterranean tubers.''
-Tuber epidermis: In potatoes, the skin is actually a periderm (bark)
+''Tuber epidermis: In potatoes, the skin is actually a periderm (bark), so we can make a term tuber periderm, with children for aerial and subterranean tubers. We will also need the term tuber epidermis, for species (like monocots) that have no secondary growth, and also for young tubers, before the periderm has developed.  These terms should probably be children of shoot periderm and shoot epidermis.''

@@ Line 38: / Line 38: @@
 ''PJ, RN: the ontology must be understandable to the users like  plant breeders''
-''We looked at a diagram of the [http://www.geochembio.com/biology/organisms/potato/#tuber potato tuber anatomy] online and saw that the 'flesh' is actually several different layers.  There was discussion about how the users would be able to know where the annotations would go.
+''We looked at a diagram of the [http://www.geochembio.com/biology/organisms/potato/#tuber potato tuber anatomy] online and saw that the 'flesh' is actually several different layers.  There was discussion about how the users would be able to know where the annotations would go. There is a similar issue for the epidermis, which in mature potatoes is actually periderm.''
 There is a similar issue for the epidermis, which is actually periderm.''

@@ Line 185: / Line 185: @@
-'''4. Upcoming Conferences and Meetings:''' Updates
+==4. Upcoming Conferences and Meetings: Updates==
@@ Line 241: / Line 241: @@
-* Annotation workshops to be held at NYBG in fall 2010. Date TBD. Will invite outside experts, scientists, students and postdocs.
+* Workshop to be held at NYBG in fall 2010. Will invite outside experts, scientists, students and postdocs.
 '''8. Next meeting scheduled for '''Tuesday June 1st at 10am PDT'''.'''

← Older revision		Revision as of 19:21, 25 May 2010
Line 217:		Line 217:

	Annotation workshop with Gramene is scheduled for '''Saturday July 31, 8am-12pm'''. more details TBA		Annotation workshop with Gramene is scheduled for '''Saturday July 31, 8am-12pm'''. more details TBA
		+
		+
		+	* '''Botanical Society of America (BSA)- July 31-Aug 4th 2010. Providence, Rhode Island.''' Ramona presenting, Dennis attending, 15 minute oral presentation, Abstract submitted 3/26/10.