POC Conf. Call 10-26-10 - Revision history

Cooperl at 18:46, 29 October 2010

2010-10-29T18:46:16Z

Cooperl: /* stylar ridge */

2010-10-29T17:53:16Z

stylar ridge

Cooperl: /* stylar ridge */

2010-10-29T17:52:05Z

stylar ridge

Cooperl: /* stylar ridge */

2010-10-29T17:51:42Z

stylar ridge

Rwalls: /* Dehiscence zone */

2010-10-27T13:09:49Z

Dehiscence zone

Rwalls: /* stylar ridge */

2010-10-27T13:02:30Z

stylar ridge

Rwalls: /* Upcoming meetings 2010-2011: */

2010-10-27T12:16:37Z

Upcoming meetings 2010-2011:

Rwalls: /* Other Items: */

2010-10-27T12:15:23Z

Other Items:

Rwalls: /* Pollen tube */

2010-10-27T12:14:08Z

Pollen tube

Rwalls: /* New children for portion of plant tissue */

2010-10-27T12:06:06Z

New children for portion of plant tissue

← Older revision		Revision as of 18:46, 29 October 2010
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−	Acceptance of the minutes from the 10-20-10 meeting? no changes	+	Acceptance of the minutes from the 10-20-10 meeting? ''no changes''

@@ Line 88: / Line 88: @@
 ''These definitions were accepted, but have to be modified slightly to use Zea gynoecium ridge, instead of gynoecial ridge (sensu Zea).''
-''We need to put a comment on these terms that they have multiple inheritance because we are dealing with an entity at a certain stage in its developlment. Need re-examine this once we know how we are going to deal with developmental stages for gynoecium.''
+''We need to put a comment on these terms that they have multiple inheritance because we are dealing with an entity at a certain stage in its development. Need re-examine this once we know how we are going to deal with developmental stages for gynoecium.''
 ''Updated names and definitions for all terms will be posted on SourceForge tracker.''

@@ Line 64: / Line 64: @@
 gynoecial ridge (sensu Zea): A gynoecial ridge (sensu Poaceae)  that is a gynoecium of an ear floret in the early stages of development. is_a gynoecial ridge (sensu Poaceae) and is_a gynoecium of ear floret
-''BS suggested that we get away from the use of sensu terms (GO has gotten rid of them). We will need a top level term 'gynoecium ridge' that can be parent to the new terms 'Poaceae gynoecium ridge' and 'Zea gynoecium ridge'. However, this does not get rid of the taxon specific terms, and we will need to examine whether or not all of the taxon specific terms in the PO are necessary (do they actually have features that distinguish them from the more general parent?). BS also suggested that rather than renaming terms that has sensu in their name, we obsolete them and make new terms. Sent a paper by [http://dx.doi.org/10.1016/j.jbi.2007.07.007  Kusnierczyk] on linking species to GO using NCBO taxon ontology, which we can use a a guide for how to deal with species specific concepts.''
+''BS suggested that we get away from the use of sensu terms (GO has gotten rid of them). We will need a top level term 'gynoecium ridge' that can be parent to the new terms 'Poaceae gynoecium ridge' and 'Zea gynoecium ridge'. However, this does not get rid of the taxon specific terms, and we will need to examine whether or not all of the taxon specific terms in the PO are necessary (do they actually have features that distinguish them from the more general parent?). BS also suggested that rather than renaming terms that has sensu in their name, we obsolete them and make new terms. Sent a paper by [http://dx.doi.org/10.1016/j.jbi.2007.07.007  Kusnierczyk, 2008] on linking species to GO using NCBO taxon ontology, which we can use a a guide for how to deal with species specific concepts.''
 ''Chris also contributed an additional, related reference detailing the GO implementation based on Kusnierczyk's formalism : [http://www.biomedcentral.com/1471-2105/11/530/ Deegan et al, 2010]''

@@ Line 64: / Line 64: @@
 gynoecial ridge (sensu Zea): A gynoecial ridge (sensu Poaceae)  that is a gynoecium of an ear floret in the early stages of development. is_a gynoecial ridge (sensu Poaceae) and is_a gynoecium of ear floret
-''BS suggested that we get away from the use of sensu terms (GO has gotten rid of them). We will need a top level term 'gynoecium ridge' that can be parent to the new terms 'Poaceae gynoecium ridge' and 'Zea gynoecium ridge'. However, this does not get rid of the taxon specific terms, and we will need to examine whether or not all of the taxon specific terms in the PO are necessary (do they actually have features that distinguish them from the more general parent?). BS also suggested that rather than renaming terms that has sensu in their name, we obsolete them and make new terms. Sent a paper by Kusnierczyk on linking species to GO using NCBO taxon ontology, which we can use a a guide for how to deal with species specific concepts.''
+''BS suggested that we get away from the use of sensu terms (GO has gotten rid of them). We will need a top level term 'gynoecium ridge' that can be parent to the new terms 'Poaceae gynoecium ridge' and 'Zea gynoecium ridge'. However, this does not get rid of the taxon specific terms, and we will need to examine whether or not all of the taxon specific terms in the PO are necessary (do they actually have features that distinguish them from the more general parent?). BS also suggested that rather than renaming terms that has sensu in their name, we obsolete them and make new terms. Sent a paper by [http://dx.doi.org/10.1016/j.jbi.2007.07.007  Kusnierczyk] on linking species to GO using NCBO taxon ontology, which we can use a a guide for how to deal with species specific concepts.''
 ''We will test this strategy for the gynoecium ridge terms and see how it works out. Later, maybe extend it to other existing sensu terms.''

← Older revision		Revision as of 13:09, 27 October 2010
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	''This definition should be reworded to parallel the definition of dehiscence zone. Will open SourceForge tracker for this definition.''		''This definition should be reworded to parallel the definition of dehiscence zone. Will open SourceForge tracker for this definition.''

		+	''Some discussion of whether or not there should be a common parent for abscission zone and dehiscence zone. Decided not to add it.''

	GO defines abscission and dehiscence separately:		GO defines abscission and dehiscence separately:

← Older revision		Revision as of 13:02, 27 October 2010
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−	*Suggest new parent terms '''gynoecial ridge (sensu Zea)''', and '''gynoecial ridge (~~sensue~~ Poaceae)'''	+	*Suggest new parent terms '''gynoecial ridge (sensu Zea)''', and '''gynoecial ridge (sensu Poaceae)'''

	New proposed definitions:		New proposed definitions:

@@ Line 339: / Line 339: @@
 Pankaj will give the introductory talk on general use of ontologies, GO, genomics, etc, and Ramona will present the talk on the Plant Ontology.
-'''Ramona's abstract has been circulated, thanks for everyone's comments'''
+''Ramona's abstract has been circulated, thanks for everyone's comments. RW and PJ will submit abstracts this week.''
 ==Next meeting scheduled for: Fri, Nov 4th, from NYBG, 10am PDT (1pm EDT)==

@@ Line 258: / Line 258: @@
 *See [http://wiki.plantontology.org:8080/index.php/POC_Meeting_and_Workshop_Nov_4th_to_6th,_NYBG,_Bronx,_NY Wiki page] for more details.
 '''Links to images through PlantSystematics.org'''
 *Goal is to add links between PO terms and images on [http://www.plantsystematics.org/ PlantSystematics.org].

← Older revision		Revision as of 12:14, 27 October 2010
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	'''pollen tube''' (PO:0006345): A microgametophytic cell that develops from the tube cell and forms a tubular extension of the pollen grain. Comment: carries the male gametes to into or near the ovule.		'''pollen tube''' (PO:0006345): A microgametophytic cell that develops from the tube cell and forms a tubular extension of the pollen grain. Comment: carries the male gametes to into or near the ovule.
		+
		+
		+	''We had limited time to discuss this item. Agreed that the term microgametophytic cell was probably not appropriate, terms should just be child of plant cell. Some discussion of whether or not there should be a general term for tube cell, that includes other cells like trichomes that have tubular extensions. Will discuss more later.''

	==Other Items:==		==Other Items:==

@@ Line 155: / Line 155: @@
 Proposed new def: A portion of plant tissue composed of a layer of cells in the abscission zone that have lignin and suberin depositions and are found on the axial side of the break or exposed surface of abscission.
@@ Line 162: / Line 165: @@
 Proposed new def: A portion of plant tissue composed of a group of cells that covers the apical meristem of the root.
@@ Line 176: / Line 182: @@
 Comment from Dennis: Zone of elongation in roots at least refers to longitudinal expansion not radial. The new definition will not work. Also, those cells have
 enlarging vacuoles so the cytoplasm actually becomes less dense. Suggest waiting until Dennis and Alejandra are present to work on this definition.
@@ Line 213: / Line 221: @@
 Proposed new def: A portion of plant tissue that is part of a root and contains hemispherically shaped aggregation of mitotically and metabolically inactive cells positioned behind the root cap.
 ===[https://sourceforge.net/tracker/?func=detail&aid=3093226&group_id=76834&atid=835555 Pollen tube]===