POC Conf. Call 1-3-12 - Revision history

Cooperl at 19:44, 8 March 2012

2012-03-08T19:44:28Z

Rwalls: /* proposed solution */

2012-01-05T18:26:30Z

proposed solution

Rwalls: /* Resolving the issue about the existing synonyms of sporophyte dormant stage */

2012-01-05T14:51:21Z

Resolving the issue about the existing synonyms of sporophyte dormant stage

Rwalls: /* Review of PO terms for gametophyte/sporophyte dormant stage */

2012-01-05T13:49:44Z

Review of PO terms for gametophyte/sporophyte dormant stage

Rwalls: /* Review of PO terms for gametophyte/sporophyte dormant stage */

2012-01-05T13:33:40Z

Review of PO terms for gametophyte/sporophyte dormant stage

Rwalls: /* Mistake in the CL/PO coordination */

2012-01-04T16:31:21Z

Mistake in the CL/PO coordination

Rwalls: /* gametophyte/sporophyte senescent stage terms */

2012-01-04T16:23:38Z

gametophyte/sporophyte senescent stage terms

Rwalls: /* Senescence and aging in GO */

2012-01-04T16:12:12Z

Senescence and aging in GO

Rwalls: /* Updates to GO terms for Dormancy Process terms: */

2012-01-04T16:10:08Z

Updates to GO terms for Dormancy Process terms:

Rwalls: /* Resolving the issue about the existing synonyms of sporophyte dormant stage */

2012-01-04T16:00:25Z

Resolving the issue about the existing synonyms of sporophyte dormant stage

← Older revision		Revision as of 19:44, 8 March 2012
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−	~~Download recording link https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=60817692&rKey=e1ff945f72da8c95~~
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@@ Line 444: / Line 444: @@
 obsolete CL:0000610, with a consider link (not replaced by) to PO:0009002
-add an xref to PO:0009002 to CL:0000000 (just as we have for the other taxon-centric AOs).
+add an xref to PO:0009002 to CL:0000000 (just as has been done for the other taxon-centric AOs).
 Remove from CL: 'treat-xrefs-as-equivalent: PO'

@@ Line 166: / Line 166: @@
 ''During a seed dormant stage, does a seed need to be dormant? According to this definition, a seed is a dormant stage as soon as it starts to undergo dormancy initiation, and it stays in one until it has finished all of the dormancy breaking processes. There will be times when seeds are both maturing and in a dormant stage. This overlap of stages is universal, because the boundaries are not discrete.''
 ''Some seeds go dormant before the embryo develops cotyledons and other not. Also, the seed coat may go dormant before the embryo. We need to see what subtypes users need before we create too many specific terms.''
@@ Line 173: / Line 175: @@
 ''Seed dormancy is usually a one-off process, but many whole plants will go dormant many times (except for biennials).''
-''GO term should be added as a definition dbxref.
+''GO term should be added as a definition dbxref.''

@@ Line 118: / Line 118: @@
 ''We should add specific examples (species names) of what are resurrection plants. Examples for mosses: Andreas (look up), for sporophyte: Selaginella lepidophylla, Craterostigma plantagineum. Also, Polytrichum have annual growth marks, because they are dormant during the winter and aquatic ferns with sporocarps, where gametophytes are dormant. We can provide a number of examples illustrating not only the taxonomic diversity but the diversity of mechanisms.''
-''RW, after meeting: Polytrichum commune is a moss that is dessicated-dormant (PMCID: PMC343055). The boreal moss Polytrichum alpestre has shoot systems with annual growth segments due to a period of dormancy during the winter (JSTOR:3242212). All the examples of sporocarp dormancy that I could find had spores that had not germinated inside, but maybe DWS can supply another example. See SF tracker for new comments.''
+''RW, after meeting: Polytrichum commune is a moss that is dessicated-dormant (PMCID: PMC343055). The boreal moss Polytrichum alpestre has shoot systems with annual growth segments due to a period of dormancy during the winter (JSTOR:3242212). Spores are also in the gametophyte stage (according to our definition), so spore dormancy is a type of gametophyte dormancy. See SF tracker for new comments.''
 ===Resolving the issue about the existing synonyms of sporophyte dormant stage===

← Older revision		Revision as of 13:33, 5 January 2012
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	''We should add specific examples (species names) of what are resurrection plants. Examples for mosses: Andreas (look up), for sporophyte: Selaginella lepidophylla, Craterostigma plantagineum. Also, Polytrichum have annual growth marks, because they are dormant during the winter and aquatic ferns with sporocarps, where gametophytes are dormant. We can provide a number of examples illustrating not only the taxonomic diversity but the diversity of mechanisms.''		''We should add specific examples (species names) of what are resurrection plants. Examples for mosses: Andreas (look up), for sporophyte: Selaginella lepidophylla, Craterostigma plantagineum. Also, Polytrichum have annual growth marks, because they are dormant during the winter and aquatic ferns with sporocarps, where gametophytes are dormant. We can provide a number of examples illustrating not only the taxonomic diversity but the diversity of mechanisms.''
		+
		+	''RW, after meeting: Polytrichum commune is a moss that is dessicated-dormant (PMCID: PMC343055). The boreal moss Polytrichum alpestre has shoot systems with annual growth segments due to a period of dormancy during the winter (JSTOR:3242212). All the examples of sporocarp dormancy that I could find had spores that had not germinated inside, but maybe DWS can supply another example. See SF tracker for new comments.''

	===Resolving the issue about the existing synonyms of sporophyte dormant stage===		===Resolving the issue about the existing synonyms of sporophyte dormant stage===

← Older revision		Revision as of 16:31, 4 January 2012
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	PO cell would be a subtype of either cell (CL:0000000) or multicellular organism cell (new) depending on how plant is defined (viridiplantae versus embryophyta). ''PO defines plant as viridiplantae, so we should use CL:0000000.''		PO cell would be a subtype of either cell (CL:0000000) or multicellular organism cell (new) depending on how plant is defined (viridiplantae versus embryophyta). ''PO defines plant as viridiplantae, so we should use CL:0000000.''
		+
		+	''Discussed the use of ex situ or in situ. Perhaps they used ex environment and ex vivo instead, to deal with the two different meanings of ex situ.''
		+
		+	''BS: The CL should be restricted to those terms that apply to cells in general, and used for cross products to cells that occur in particular organism. PO could then use the CL to talk about plant cells ex vivo, etc.''

	==proposed solution==		==proposed solution==

@@ Line 242: / Line 242: @@
 Suggest adding to comment of sporophyte reproductive stage: The sporophyte senescent stage always succeeds the sporophyte reproductive stage in monocarpic plants.
 '''gametophyte senescent stage (PO:0025343):''' A gametophyte development stage during which a gametophyte participates in multicellular organism senescence (GO:0010259).
@@ Line 250: / Line 252: @@
 ===Senescence and aging in GO===
-''Should these terms have process at the end of the name. Maybe yes for clarity and consistency, but most of us agreed that it was somewhat redundant in the name. CM felt that the GO editors probably wouldn't go for it.''
+''Should these terms have process at the end of the name? Maybe yes for clarity and consistency, but most of us agreed that it was somewhat redundant in the name. CM felt that the GO editors probably wouldn't go for it.''
@@ Line 273: / Line 277: @@
 Comment:  Cell aging may occur when a cell has temporarily stopped dividing through cell cycle arrest  (GO:0007050) or when a cell has permanently stopped dividing, in which case it is undergoing cellular senescence (GO:0090398). May precede cell death (GO:0008219) and succeed cell maturation (GO:0048469).
-'''cellular senescence (GO:0090398)
+''Can remove clause "after a cell has stopped dividing" from the definition, because the comment covers it.''
 Current definition: A cell aging process stimulated in response to cellular stress, whereby normal cells lose the ability to divide through irreversible cell cycle arrest. Source: GOC:BHF
@@ Line 341: / Line 353: @@
 Note that there is an open tracker for [https://sourceforge.net/tracker/index.php?func=detail&aid=3425355&group_id=36855&atid=440764 flower senescence]. RW will add a comment to that tracker that it is not a type of organ senescence, because a flower is not a plant organ. Also, although the term flower senescence is used, it is not really the whole flower that senesces, but the petals or tepals.
 See also PO SF tracker for [https://sourceforge.net/tracker/?func=detail&aid=3464416&group_id=76834&atid=835555 floral organ].

← Older revision		Revision as of 16:12, 4 January 2012
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	===Senescence and aging in GO===		===Senescence and aging in GO===
		+	''Should these terms have process at the end of the name. Maybe yes for clarity and consistency, but most of us agreed that it was somewhat redundant in the name. CM felt that the GO editors probably wouldn't go for it.''
		+
		+
	We discussed these new definitions for GO last week. The following changes were suggested on the [https://sourceforge.net/tracker/?func=detail&aid=3468945&group_id=36855&atid=440764 GO SourceForge tracker]:		We discussed these new definitions for GO last week. The following changes were suggested on the [https://sourceforge.net/tracker/?func=detail&aid=3468945&group_id=36855&atid=440764 GO SourceForge tracker]:

@@ Line 68: / Line 68: @@
 From RW: I think the taxon restriction should be for Embryophyta, but I will check into '''whether or not the term bud is used for green algae'''.
 RW noted: "You could add an xref: bud dormancy process (GO:0010162 has_participant bud (PO:0000055)."
@@ Line 147: / Line 149: @@
 Seems like they should be synonyms of seed dormant stage, but we do not have a term for that, which is why they probably got stuck here.
@@ Line 161: / Line 167: @@
 ''Some seeds go dormant before the embryo develops cotyledons and other not. Also, the seed coat may go dormant before the embryo. We need to see what subtypes users need before we create too many specific terms.''
-''We will probably need terms like embryo dormant stage (is_a sporophyte dormant stage, maybe part_of seed dormancy, but ferns, etc. can also have dormant embryos) and seed coat dormant stage at some point.''
+''We should add a term for embryo dormant stage (is_a sporophyte dormant stage, maybe part_of seed dormancy, but ferns, etc. can also have dormant embryos). Maybe later we can add seed coat dormant stage if it is needed.''
 ''Seed dormancy is usually a one-off process, but many whole plants will go dormant many times (except for biennials).''

← Older revision		Revision as of 16:00, 4 January 2012
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	''We agreed that this term should be added.''		''We agreed that this term should be added.''
		+
		+	''During a seed dormant stage, does a seed need to be dormant? According to this definition, a seed is a dormant stage as soon as it starts to undergo dormancy initiation, and it stays in one until it has finished all of the dormancy breaking processes. There will be times when seeds are both maturing and in a dormant stage. This overlap of stages is universal, because the boundaries are not discrete.''
		+
		+	''Some seeds go dormant before the embryo develops cotyledons and other not. Also, the seed coat may go dormant before the embryo. We need to see what subtypes users need before we create too many specific terms.''
		+
		+	''We will probably need terms like embryo dormant stage (is_a sporophyte dormant stage, maybe part_of seed dormancy, but ferns, etc. can also have dormant embryos) and seed coat dormant stage at some point.''
		+
		+	''Seed dormancy is usually a one-off process, but many whole plants will go dormant many times (except for biennials).''
		+

	These synonyms should be moved here (or gotten rid of):		These synonyms should be moved here (or gotten rid of):