POC Conf. Call 4-14-11 - Revision history

Rwalls: /* Removing the part_of relationships to whole plant? */

2011-04-19T18:35:30Z

Removing the part_of relationships to whole plant?

2011-04-18T21:56:20Z

Adding mutual disjoint from relations among top-level PAO terms

2011-04-18T21:54:15Z

Adding mutual disjoint from relations among top-level PAO terms

2011-04-18T21:49:12Z

Removing the part_of relationships to whole plant?

2011-04-18T21:48:08Z

part_of children of whole plant

2011-04-18T21:17:05Z

plant embryo (PO:0009009)

2011-04-18T20:12:50Z

plant embryo (PO:0009009)

2011-04-18T20:07:11Z

cultured embryos

2011-04-18T20:01:17Z

plant embryo (PO:0009009)

2011-04-18T18:44:54Z

plant embryo (PO:0009009)

@@ Line 58: / Line 58: @@
 ''For the terms in the list below, we will remove the part_of relations to whole plant, since "Plant structure already gives you the info you need and it is part of the definition, so you do not need to assert this relationship, it can be inferred (BS)''
 plant structure (PO:0009011): An anatomical structure that is or was part of a plant, or was derived from a part of a plant. [source: CARO:0000003, POC:curators]
@@ Line 97: / Line 99: @@
 ''Response: We have 14 direct is_a children of vascular system: for anther, cotyledon*, embryo*, filament, hypocotyl*, leaf lamina, petiole, phyllome, root, scutellar*, shoot axis, shoot system*, stigma. (I think filament vs should be part_of anther VS)''.
-''Do all of these satisfy the part_of whole plant rule? What is these organs are no longer part of a whole plant?''
+''Do all of these satisfy the part_of whole plant rule? What if these organs are no longer part of a whole plant?''

← Older revision		Revision as of 21:56, 18 April 2011
Line 135:		Line 135:
	PO:0009007 : portion of plant tissue		PO:0009007 : portion of plant tissue

−	vascular system	+	''PO:0000034:vascular system (should also be included in this list)''

← Older revision		Revision as of 21:49, 18 April 2011
Line 56:		Line 56:

	''We discussed whether or not having the part_of relationship to whole plant was incorrect and/or redundant. Consensus was that the definitions were sufficient as stated. Since not every instance of plant cell, plant tissue, etc. is part of a whole plant, it is not correct to use the part_of relation.''		''We discussed whether or not having the part_of relationship to whole plant was incorrect and/or redundant. Consensus was that the definitions were sufficient as stated. Since not every instance of plant cell, plant tissue, etc. is part of a whole plant, it is not correct to use the part_of relation.''
		+
		+	''For the terms in the list below, we will remove the part_of relations to whole plant, since "Plant structure already gives you the info you need and it is part of the definition, so you do not need to assert this relationship, it can be inferred (BS)''

	plant structure (PO:0009011): An anatomical structure that is or was part of a plant, or was derived from a part of a plant. [source: CARO:0000003, POC:curators]		plant structure (PO:0009011): An anatomical structure that is or was part of a plant, or was derived from a part of a plant. [source: CARO:0000003, POC:curators]

@@ Line 101: / Line 101: @@
 ''shoot xylem and shoot phloem and all the lower terms: - is this the current situation?''
-''We decided that the VS would have to stay as a part of the whole plant, as a result of the way it is defined. For the rest in the list above, we will remove the part_of relations to whole plant, since "Plant structure already gives you the info you need and it is part of the definition, so you do not need to assert this relationship, it can be inferred(BS)''
+''We decided that the VS would have to stay as a part of the whole plant, as a result of the way it is defined.''
 *removed part_of relationship between plant cell and POPT in dev version #1066

← Older revision		Revision as of 21:17, 18 April 2011
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	'''Proposed definition of plant embryo:''' A whole plant in the early part of a sporophytic phase after the first cell division.		'''Proposed definition of plant embryo:''' A whole plant in the early part of a sporophytic phase after the first cell division.

−	Comment: An embryo is generally formed after the first division of a zygote, but in the case of adventitious embryos, somatic embryos, embryos that arise through apogamy, and cultured haploid embryos, it is formed after the division of a single cell that is not a zygote. In seed plants, the embryonic phase ends with germination. In non-seed plants and cultured embryos of seed plants, the end of the embryonic phase is less clearly defined and varies among taxa.	+	Comment: An embryo is generally formed after the first division of a zygote, but in the case of adventitious embryos, somatic embryos, embryos that arise through apogamy and cultured haploid embryos, it is formed after the division of a single cell that is not a zygote. In seed plants, the embryonic phase ends with germination. In non-seed plants and cultured embryos of seed plants, the end of the embryonic phase is less clearly defined and varies among taxa.

@@ Line 282: / Line 282: @@
 ''BS: The word 'early' is quite vague, can we say pre-seedling stage?''
-''PJ: need to have terms for: zygotic embryo- the one in the seed and also haploid embryo- child of cultured embryo.  Do they ever form in nature?  Check one''
+''PJ: need to have terms for: zygotic embryo- the one in the seed and also haploid embryo- child of cultured embryo.  Do they ever form in nature?  Check on''
 ==cultured embryos==

@@ Line 289: / Line 289: @@
 Current Def’n:  In vitro isolated and maintained mature or immature zygotic embryos, somatic embryos or haploid embryos (derived from male gametophyte). [source: TAIR:ki]
+''Italic text''
 Comment: None
@@ Line 300: / Line 300: @@
 parentage: is_a plant embryo (PO:0009009) and is_a in vitro plant structure
@@ Line 308: / Line 309: @@
 Proposed def’n: A plant somatic embryo that is grown or maintained in vitro.
-is_a: plant somatic embryo??
+is_a: plant embryo
-''If cultured plant embryo is to be a child of embryo, we will need to adjust definition of embryo.  Should talk to Melissa Haendel about how they handle haploid and diploid embryos in Zebrafish.''
+'' from 4-12-11: If cultured plant embryo is to be a child of embryo, we will need to adjust definition of embryo.  Should talk to Melissa Haendel about how they handle haploid and diploid embryos in Zebrafish.''
 See new proposed definition of embryo above.

@@ Line 270: / Line 270: @@
 adventitious embryo (PO:0004537): Embryo derived directly from nucellus cells without involving embryo sac cells
-Prposed revised def'n:
+'' need to revise the def'n:''
@@ Line 279: / Line 282: @@
 ''BS: The word 'early' is quite vague, can we say pre-seedling stage?''
-PJ: need to have a zygotic embryo- the one in the seed
+''PJ: need to have terms for: zygotic embryo- the one in the seed and also haploid embryo- child of cultured embryo.  Do they ever form in nature?  Check one''
 ==cultured embryos==