POC Conf. Call 2-14-12 - Revision history

Cooperl at 19:45, 8 March 2012

2012-03-08T19:45:35Z

Cooperl at 21:45, 21 February 2012

2012-02-21T21:45:53Z

Rwalls: /* PO terms for lateral meristems */

2012-02-16T20:56:48Z

PO terms for lateral meristems

Rwalls at 19:23, 16 February 2012

2012-02-16T19:23:18Z

Rwalls: /* PO terms for lateral meristems */

2012-02-16T19:21:53Z

PO terms for lateral meristems

Rwalls: /* PO terms for lateral meristems */

2012-02-16T13:50:40Z

PO terms for lateral meristems

Rwalls: /* Revisions of existing terms: */

2012-02-15T15:28:41Z

Revisions of existing terms:

Show changes

Rwalls: /* PO terms for lateral meristems */

2012-02-15T15:25:13Z

PO terms for lateral meristems

Rwalls: /* PO terms for lateral meristems */

2012-02-15T15:21:53Z

PO terms for lateral meristems

Rwalls: /* Questions Arising from the the Workshop */

2012-02-15T15:16:18Z

Questions Arising from the the Workshop

@@ Line 12: / Line 12: @@
 Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_1-31-12? ''none''
 Back to [[POC Meetings Minutes]]
 =News and Report from the Wood Ontology Meeting:=

@@ Line 3: / Line 3: @@
 In attendance:
-POC members: Laurel Cooper (OSU), Justin Elser (OSU), Justin Preece (OSU), Ramona Walls (NYBG), Dennis Stevenson (NYBG), Barry Smith (University at Buffalo, NY)
+POC members: ''Laurel Cooper (OSU), Justin Elser (OSU), Justin Preece (OSU), Ramona Walls (NYBG), Dennis Stevenson (NYBG), Barry Smith (University at Buffalo, NY)''
-Absent: Pankaj Jaiswal (OSU),  Marie Alejandra Gandolfo (Cornell University), Chris Mungall (Lawrence Berkeley National Lab)
+Absent: ''Pankaj Jaiswal (OSU),  Marie Alejandra Gandolfo (Cornell University), Chris Mungall (Lawrence Berkeley National Lab) ''
 Collaborators: none

@@ Line 178: / Line 178: @@
 '''cork cambium/phellogen (PO:0005599)'''
-'''revised def'n:''' A cambium (PO:0005597) that is part of a shoot axis periderm (PO:0005048) and produces phellem (PO:0004003) and phelloderm (PO:0005050).
+'''revised def'n:''' A cambium (PO:0005597) that is part of a periderm (PO:0005046) and produces phellem (PO:0004003) and phelloderm (PO:0005050).
 comment: Cork cambium is located between the phellem and phelloderm and produces phellem toward the outside and phelloderm toward the inside of a plant axis.

@@ Line 3: / Line 3: @@
 In attendance:
-POC members:
+POC members: Laurel Cooper (OSU), Justin Elser (OSU), Justin Preece (OSU), Ramona Walls (NYBG), Dennis Stevenson (NYBG), Barry Smith (University at Buffalo, NY)
 Collaborators: none
-Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_1-31-12?
+Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_1-31-12? ''none''
 Back to [[POC Meetings Minutes]]

← Older revision		Revision as of 19:21, 16 February 2012
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	comment: Contributes mainly to formation of the body of a stem (PO:0009047), but may also produce adventitious (shoot-borne) roots (PO:0000042). May be continuous or discontinuous with the primary thickening meristem (PO:0005039). Found in some monocot species of the Liliales and Asperigales.		comment: Contributes mainly to formation of the body of a stem (PO:0009047), but may also produce adventitious (shoot-borne) roots (PO:0000042). May be continuous or discontinuous with the primary thickening meristem (PO:0005039). Found in some monocot species of the Liliales and Asperigales.

−	''~~okay~~''	+	''There are also secondary thickening meristems in roots of some monocots (Cheadle 1937, JSTOR:2471543), so this should be lateral meristem, rather than a shoot lateral meristem.''

@@ Line 141: / Line 141: @@
 ''New proposed def.: A portion of meristem (PO:0009013) tissue located parallel to the sides of a plant axis (PO:0025004), the cells of which undergo periclinal and anticlinal (tangential?) division.''
-''New comment: Participates in lateral growth (request has been made for lateral growth in GO) of a  shoot axis (PO:0025029) or root (PO:0009005). Contrast with apical meristem (PO:0020144) or intercalary meristem (PO:0006073).''
+''New comment: Participates in lateral growth (request has been made for lateral growth in GO) of a  shoot axis (PO:0025029) or root (PO:0009005), leading to an increase in the cross-sectional area. Contrast with apical meristem (PO:0020144) or intercalary meristem (PO:0006073).''
 ''Add lateral meristem part_of plant axis.''
@@ Line 174: / Line 174: @@
 ''No one likes "gives off" or "girth".''
-''New proposed comment: A vascular cambium produces cells in both directions by periclinal division, leading to an increase in the cross sectional area of a plant axis (PO:0025004).''
+''New proposed comment: A vascular cambium produces cells in both directions by periclinal division, leading to an increase in the cross-sectional area of a plant axis (PO:0025004).''

@@ Line 188: / Line 188: @@
 '''primary thickening meristem (PO:0005039)'''
-Esau defines it as originating in the apical meristem, but [http://www.jstor.org/stable/4354165 . Rudall's review] shows that in some species, it is discontinuous with the SAM.
+Esau defines it as originating in the apical meristem, but [http://www.jstor.org/stable/4354165 Rudall's review] shows that in some species, it is discontinuous with the SAM.
 '''revised def'n:''' A shoot lateral meristem (PO:0006344) that is part of a stem (PO:0009047) and has a parts multiple layers of meristematic cells (PO:0004010) located near the shoot apical meristem (PO:0020148).
@@ Line 243: / Line 243: @@
 This should be called '''inflorescence branch meristem''', and be a subtype of inflorescence meristem (PO:0000230), which should in turn be an apical meristem.
@@ Line 249: / Line 251: @@
 This should be called '''ear inflorescence branch meristem''', and be a subtype of inflorescence branch meristem (PO:0009105). Will need to add XP definitions to the different types of meristems so that they don't have dual parentage (e.g., ear inflorescence meristem XP of is_a inflorescence meristem and part_of ear inflorescence).
-'''revised def'n:''' An inflorescence branch meristem that gives rise to a branch of an ear inflorescence.
+'''revised def.:''' An inflorescence branch meristem that gives rise to a branch of an ear inflorescence.
 ==Primary and secondary growth, etc.==

@@ Line 145: / Line 145: @@
 ''Add lateral meristem part_of plant axis.''
-''May want to add periclinal, anticlinal cell division to GO.''
+''May want to add periclinal, anticlinal cell division to GO (or maybe just add periclinal and anticlinal to PATO).''
 ''Definition of intercalary meristem need a little work too, to distinguish it from lateral meristem.''
@@ Line 174: / Line 174: @@
 ''No one likes "gives off" or "girth".''
-''New proposed comment: Vascular cambium produced cells in both directions by periclinal division, leading to an increase in the cross sectional area of a plant axis (PO:0025004).''
+''New proposed comment: A vascular cambium produces cells in both directions by periclinal division, leading to an increase in the cross sectional area of a plant axis (PO:0025004).''

← Older revision		Revision as of 15:16, 15 February 2012
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	* How are we going to deal with terms that contain adjectives; such as 'storied cambium', 'early wood', 'late wood' etc? These are commonly used terms in this community and we need them.		* How are we going to deal with terms that contain adjectives; such as 'storied cambium', 'early wood', 'late wood' etc? These are commonly used terms in this community and we need them.
		+
		+	''BS raised the concern that having terms with adjectives can cause problems with multiple inheritance -- two different ways of classifying wood leads to two different parents. Suggest that we put all the adjectives in a phenotype ontology to which we can refer.''
		+
		+	''However, there are instances where the terms need to be in the PO, particularly for adjectives that are used only for particular plant structures (like epigynous flower). On the other hand, some adjectives can be used for many different structures (like variegated), and terms like "variegated leaf" probably shouldn't go in the PO. Adjectives like "storied" are somewhere in between -- it can apply multiple tissue types, but not hundreds of them. We will need to examine these terms on a case by case basis.''
		+
		+	''BS, best practice: Terms like "septate" should go into PATO, and we include terms for fiber types and instruct people how to post compose terms as they need them. Some communities would eventually create compound terms like "septate phloem fiber", but they will not live in PO.''
		+
		+	''We will probably not be able to live up to this best practice, but at a minimum, when we do add terms with synonyms, we should introduce the synonym into PATO and add xrefs to them.''
		+
		+	''Note, latewood and earlywood should be one word.''
		+

	* How do we want to approach the TO terms, since this is a complex area and officially outside the mandate of the PO?		* How do we want to approach the TO terms, since this is a complex area and officially outside the mandate of the PO?