POC Conf. Call 11-10-10 - Revision history

Cooperl: /* Restructuring of PGDSO */

2010-11-29T22:03:32Z

Restructuring of PGDSO

Cooperl: /* Next meeting scheduled for Weds, Nov. 17th, 2010 at 10am PST */

2010-11-11T17:50:51Z

Next meeting scheduled for Weds, Nov. 17th, 2010 at 10am PST

Cooperl: /* Restructuring of PGDSO */

2010-11-11T17:50:10Z

Restructuring of PGDSO

Cooperl at 17:35, 11 November 2010

2010-11-11T17:35:38Z

Cooperl: /* New Item: Collaboration with Physco group to cover mosses in PO */

2010-11-11T17:22:13Z

New Item: Collaboration with Physco group to cover mosses in PO

Cooperl: /* Trichomes (Approval of changes from 11-5 and 11-6) */

2010-11-11T17:21:12Z

Trichomes (Approval of changes from 11-5 and 11-6)

Cooperl: /* Trichomes (Approval of changes from 11-5 and 11-6) */

2010-11-11T17:20:44Z

Trichomes (Approval of changes from 11-5 and 11-6)

Cooperl: /* Restructuring of PGDSO */

2010-11-11T17:15:37Z

Restructuring of PGDSO

Cooperl: /* Restructuring of PGDSO */

2010-11-11T17:10:37Z

Restructuring of PGDSO

Rwalls: /* Trichomes (Approval of changes from 11-5 and 11-6) */

2010-11-11T12:50:50Z

Trichomes (Approval of changes from 11-5 and 11-6)

@@ Line 57: / Line 57: @@
 '''Suggested New "working" Structure of the PGDSO:'''
-*The root term, plant growth and development stage, would be renamed 'plant life cycle process' (a continuant).
+*The root term, plant growth and development stage, would be renamed 'plant life cycle process' (an "Occurrent").
 The top level structure would have three branches, as below
@@ Line 71: / Line 71: @@
-''We reviewed this proposed structure, and decided to experiment with how it will work for existing PGDSO terms. Barry suggested that his goal was to have all PO terms in one of two branches: plant structures (plant anatomical entity = independent continuant) and plant processes (plant life cycle process = occurant)''
+''We reviewed this proposed structure, and decided to experiment with how it will work for existing PGDSO terms. Barry suggested that his goal was to have all PO terms in one of two branches: plant structures (plant anatomical entity = independent continuant) and plant processes (plant life cycle process = occurent)''
 ''Lol and Ramona will work on moving all of the ~120 terms from the PGDSO into one of the three new plant life cycle process branches, to see where they can fit. Can delete existing relations for those terms, but will still be able to compare to old structure by comparing dev to live browser. Will schedule a meeting with Barry next week to go over any problems or issues that may come up, then present the results to the whole group on our meeting on Dec. 1''

← Older revision		Revision as of 17:50, 11 November 2010
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	=Next meeting scheduled for Weds, Nov. 17th, 2010 at 10am PST=		=Next meeting scheduled for Weds, Nov. 17th, 2010 at 10am PST=
		+
		+	Alejandra gone from Nov 19-Dec 9th.

@@ Line 34: / Line 34: @@
 - Barry gave a brief presentation of the structure of the Basic Formal Ontology (BFO), and how it is divided into occurants and continuants, with dependent and independent continuants. (see ppt [[File:BFO_for_Plants.pdf]]
-- The PSO covers independent occurants. He suggested that the life cycle of a plant is a continuant that contains phases, with landmarks or transitions between those phases.  He felt that the current structure, based on stages as continuants, was not correct.
+''-In the PSO, plant structures (plant anatomical entities) are Independent Continuants (corresponding to the GO cellular component) and the plant processes (plant life cycle process) are the occurrents, corresponding to the GO Biological processes.  He felt that the current structure, based on stages as continuants, was not correct.''
 '''Points of discussion:'''

@@ Line 11: / Line 11: @@
 Acceptance of the minutes from the [[Friday, November 5th]] and [[Saturday, November 6th]] meeting?
 ''There were no additions, deletions or changes to the minutes of the last meeting.''
 '''Agenda:'''

← Older revision		Revision as of 17:22, 11 November 2010
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−	''Pankaj will respond to Rensing (copy to po-internal). Lol will invite Rensing or someone from Physco group to present at the PO workshop at PAG.''	+	''Pankaj will respond to Rensing (copy to po-internal). Lol will invite Rensing or someone from Physco group to present at the PO workshop at PAG. We will not do a meeting at this time.''

	=Upcoming meetings 2010-2011:=		=Upcoming meetings 2010-2011:=

← Older revision		Revision as of 17:21, 11 November 2010
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−	We have the term [http://sourceforge.net/tracker/index.php?func=detail&aid=3031668&group_id=76834&atid=835555 trichome cell (PO:0008031)], part_of trichome, has no is_a parent. Suggest that it is_ a epidermal cell. It can have the child unicellular trichome, but then we could also use trichome cell to describe individual cells that are part of a multicellular trichome.	+	We have the term [http://sourceforge.net/tracker/index.php?func=detail&aid=3031668&group_id=76834&atid=835555 trichome cell (PO:0008031)], part_of trichome, has no is_a parent.
		+
		+	Suggest that it is_ a epidermal cell. It can have the child unicellular trichome, but then we could also use trichome cell to describe individual cells that are part of a multicellular trichome.

	To deal with the term trichome branch (PO:0008031), we will need the new term multicellular trichome branch cell, is_a trichome cell. We will put a comment under unicellular trichome that the branches of a branched unicellular trichome are part of GO.		To deal with the term trichome branch (PO:0008031), we will need the new term multicellular trichome branch cell, is_a trichome cell. We will put a comment under unicellular trichome that the branches of a branched unicellular trichome are part of GO.

← Older revision		Revision as of 17:20, 11 November 2010
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−	We have the term trichome cell (PO:0008031), part_of trichome, has no is_a parent. Suggest that it is_ a epidermal cell. It can have the child unicellular trichome, but then we could also use trichome cell to describe individual cells that are part of a multicellular trichome.	+	We have the term [http://sourceforge.net/tracker/index.php?func=detail&aid=3031668&group_id=76834&atid=835555 trichome cell (PO:0008031)], part_of trichome, has no is_a parent. Suggest that it is_ a epidermal cell. It can have the child unicellular trichome, but then we could also use trichome cell to describe individual cells that are part of a multicellular trichome.

	To deal with the term trichome branch (PO:0008031), we will need the new term multicellular trichome branch cell, is_a trichome cell. We will put a comment under unicellular trichome that the branches of a branched unicellular trichome are part of GO.		To deal with the term trichome branch (PO:0008031), we will need the new term multicellular trichome branch cell, is_a trichome cell. We will put a comment under unicellular trichome that the branches of a branched unicellular trichome are part of GO.

← Older revision		Revision as of 17:15, 11 November 2010
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	''Note from BS: Keep in mind where there might be potential overlaps with the GO- we will need to figure out how to split the process terms, ie: will they reside in the PO or in GO? Make a list as we go along.''		''Note from BS: Keep in mind where there might be potential overlaps with the GO- we will need to figure out how to split the process terms, ie: will they reside in the PO or in GO? Make a list as we go along.''
		+
		+	''-Stage term names need to be rewritten as nouns, for example: "whole plant in the phase where 1 leaf is visible'''
		+
		+	''-Complex terms could be rendered using post coordination; ie: 'on the fly' for users, but some may need to have actual PO IDs in order to accommodate annotations.''

	==Trichomes (Approval of changes from 11-5 and 11-6)==		==Trichomes (Approval of changes from 11-5 and 11-6)==

@@ Line 72: / Line 72: @@
 ''Lol and Ramona will work on moving all of the ~120 terms from the PGDSO into one of the three new plant life cycle process branches, to see where they can fit. Can delete existing relations for those terms, but will still be able to compare to old structure by comparing dev to live browser. Will schedule a meeting with Barry next week to go over any problems or issues that may come up, then present the results to the whole group on our meeting on Dec. 1''
-Note from BS: Keep in mind where there might be potential overlaps with the GO- we will need to figure out
+''Note from BS: Keep in mind where there might be potential overlaps with the GO- we will need to figure out how to split the process terms, ie: will they reside in the PO or in GO? Make a list as we go along.''
 ==Trichomes (Approval of changes from 11-5 and 11-6)==

← Older revision		Revision as of 12:50, 11 November 2010
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	''new def: A portion of plant tissue that forms an outgrowth from the epidermis and is not sclerified.''		''new def: A portion of plant tissue that forms an outgrowth from the epidermis and is not sclerified.''

−	''Can't use epidermal tissue, instead develops from an epidermal cell. (~~note to self for RW: is there~~ a term similar to trichoblast for shoot trichome development~~? will look into this and update minutes tomorrow~~)''	+	''Can't use epidermal tissue, instead develops from an epidermal cell. (could not find a term similar to trichoblast for shoot trichome development)''