POC Conf. Call 9-15-10 - Revision history

Cooperl: /* Status and Update of Progress: PO Release */

2010-09-20T19:55:32Z

Status and Update of Progress: PO Release

Cooperl: /* Annotations that have no term associated with them */

2010-09-16T22:24:21Z

Annotations that have no term associated with them

Cooperl: /* Annotations that have no term associated with them */

2010-09-16T20:43:46Z

Annotations that have no term associated with them

Cooperl: /* Status and Update of Progress: PO Release */

2010-09-16T18:54:14Z

Status and Update of Progress: PO Release

Rwalls: /* Status and Update of Progress: PO Release */

2010-09-16T18:33:17Z

Status and Update of Progress: PO Release

Rwalls: /* Status and Update of Progress: PO Release */

2010-09-16T18:28:10Z

Status and Update of Progress: PO Release

Cooperl: /* Annotations that have no term associated with them */

2010-09-16T18:27:34Z

Annotations that have no term associated with them

Cooperl: /* Status and Update of Progress: PO Release */

2010-09-16T17:33:27Z

Status and Update of Progress: PO Release

Cooperl: /* Annotation File formats */

2010-09-15T23:13:44Z

Annotation File formats

Cooperl at 23:13, 15 September 2010

2010-09-15T23:13:10Z

← Older revision		Revision as of 19:55, 20 September 2010
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−	NM: '''"subterranean tuber axillary vegetative bud''' (PO:0025042): the term 'sprout' is often used by potato breeders. One example is the trait 'heat sprout rating' which measures new sprouts on the tuber. These range from 'swollen eyes' to 'chain tubers'. I'm not sure if 'tuber sprout' should be a synonym or a child term (develops from the axillary vegetative bud)"	+	NM: '''subterranean tuber axillary vegetative bud''' (PO:0025042): the term 'sprout' is often used by potato breeders. One example is the trait 'heat sprout rating' which measures new sprouts on the tuber. These range from 'swollen eyes' to 'chain tubers'. I'm not sure if 'tuber sprout' should be a synonym or a child term (develops from the axillary vegetative bud)"

	The 'sprouts' are buds (eyes) that begin to grow. Since they actually develop from an existing axillary vegetative bud, perhaps the term 'sprout' is more like a shoot than a bud?		The 'sprouts' are buds (eyes) that begin to grow. Since they actually develop from an existing axillary vegetative bud, perhaps the term 'sprout' is more like a shoot than a bud?

← Older revision		Revision as of 22:24, 16 September 2010
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	These ones are pretty straightforward- we recommended to TAIR to move them all to the new term 'collective leaf structure' PO:0025022		These ones are pretty straightforward- we recommended to TAIR to move them all to the new term 'collective leaf structure' PO:0025022

−	Response from TAIR (Tanya Berardini 8/16/10): - suggestion is fine, annotations should move if replacement term is in OBO stanza- it is.	+	Response from TAIR (Tanya Berardini 8/16/10): -suggestion is fine, annotations should move if replacement term is in OBO stanza- it is.

@@ Line 219: / Line 219: @@
 Suggested that this association be moved to male gametophyte (PO:0020091) or female gametophyte (PO:00290092) or to gametophytic phase (PO:0028003) and/or to to whole plant PO:0000003
-Note: It is already associated with the megagametophytic stage (PO:000721) and pollen developmental stage (PO:0001007) in the PDGSO.  ''Note:This comment appears to be an error''
+Note: It is already associated with the megagametophytic stage (PO:000721)''Note: This appears to be an error'' and pollen developmental stage (PO:0001007) in the PDGSO.
 ''Note: This annotation is concerning rice anthers so it should be moved to male gametophyte (PO:0020091) and to gametophytic phase (PO:0028003).''

← Older revision		Revision as of 18:54, 16 September 2010
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−	''We will add basal root as new term. New proposed definition: A root that develops from one of the of hypocotyl (which layer?). Will deal with synonyms and child terms of basal root in next round of revisions.''	+	''We will add basal root as new term. New proposed definition: A root that develops from one of the of hypocotyl (which layer?) or "A root that arises from a part of the hypocotyl" ?. Will deal with synonyms and child terms of basal root in next round of revisions.''

	''Decided to leave primary root named as is for now, keeping tap root as synonym, but will seek more outside input into what the best name should be. Will add comment: Is often the central axis of the root system.''		''Decided to leave primary root named as is for now, keeping tap root as synonym, but will seek more outside input into what the best name should be. Will add comment: Is often the central axis of the root system.''

@@ Line 51: / Line 51: @@
 ''Seed coat is not part_of plant tissue, but is_a, which is correct, so no need to fix it.''
-''Re. definition of secondary xylem: should add that it develops from vascular cambium, and add develops_from relation. Fix typo in comment (tress).''
+''Re. definition of secondary xylem: should add that it develops from vascular cambium, and add develops_from relation. Fix typo in comment (tress). SF tracker: [https://sourceforge.net/tracker/?func=detail&aid=3067090&group_id=76834&atid=835555 secondary xylem]''
@@ Line 84: / Line 84: @@
 ''Decided to leave primary root named as is for now, keeping tap root as synonym, but will seek more outside input into what the best name should be.  Will add comment: Is often the central axis of the root system.''
-''Okay to add hyphen to shoot-borne root. We felt that adventitious root should not be a synonym, because some basal roots may be adventitious roots. Need to give adventitious roots further consideration, and maybe add as its own term for next round of revisions.''
+''Okay to add hyphen to shoot-borne root. Should add hyphens to other -borne terms in the ontology for consistency. We felt that adventitious root should not be a synonym, because some basal roots may be adventitious roots. Need to give adventitious roots further consideration, and maybe add as its own term for next round of revisions.''
 ''PJ: We also should discuss root terms with [http://www.biology.duke.edu/benfeylab/index.htm Phil Benfey (Duke)] and [http://gradeducation.lifesciences.cornell.edu/faculty/individual5367 Leon Kochian (Cornell)]. They are developing software for root type recognition. Should work to integrate PO with their software. Don't know if Rich is involved in discussions with them.''
@@ Line 105: / Line 105: @@
 ''Can have swollen eye as synonym of tuber axillary bud. Sprout should be added a synonym of axillary shoot or better yet, add new term subterranean tuber axillary shoot.''
-''Link to SF tracker for request for new term [subterranean tuber axillary bud https://sourceforge.net/tracker/index.php?func=detail&aid=3067097&group_id=76834&atid=835555''
+''Link to SF tracker for request for new term [https://sourceforge.net/tracker/index.php?func=detail&aid=3067097&group_id=76834&atid=835555 subterranean tuber axillary shoot]''

← Older revision		Revision as of 18:28, 16 September 2010
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	''Can have swollen eye as synonym of tuber axillary bud. Sprout should be added a synonym of axillary shoot or better yet, add new term subterranean tuber axillary shoot.''		''Can have swollen eye as synonym of tuber axillary bud. Sprout should be added a synonym of axillary shoot or better yet, add new term subterranean tuber axillary shoot.''
		+
		+	''Link to SF tracker for request for new term [subterranean tuber axillary bud https://sourceforge.net/tracker/index.php?func=detail&aid=3067097&group_id=76834&atid=835555''

@@ Line 176: / Line 176: @@
 Response from TAIR (Tanya Berardini 8/16/10):- suggestions are fine, annotations should move if replacement term is in OBO stanza
-Laurel added the ''consider'' relation to seedling growth stage in the PGDSO, as suggested by TB.
+''Laurel will add the ''consider'' relation to seedling growth stage in the PGDSO, but we need to clarify whether or not this works for TAIR's script.''
@@ Line 190: / Line 191: @@
 Response from TAIR (Tanya Berardini 8/16/10): - suggestion is fine, annotation should move if replacement term is in OBO stanza
-Laurel added the ''consider'' relation to sporophytic growth phase (PO:0028002) in the PGDSO, as suggested by TB.
+''Laurel will add the ''consider'' relation to seedling growth stage in the PGDSO, but we need to clarify whether or not this works for TAIR's script.''
@@ Line 217: / Line 219: @@
 Note: It is already associated with the megagametophytic stage (PO:000721) and pollen developmental stage (PO:0001007) in the PDGSO.  ''Note:This comment appears to be an error''
-''Note: This annotation is concerning rice anthers so it will be moved to male gametophyte (PO:0020091) and to gametophytic phase (PO:0028003).''
+''Note: This annotation is concerning rice anthers so it should be moved to male gametophyte (PO:0020091) and to gametophytic phase (PO:0028003).''

← Older revision		Revision as of 17:33, 16 September 2010
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−	''~~Should be~~ reproductive shoot system (which is a term we don't have at the moment).''	+	''perhaps we should have a reproductive shoot system? (which is a term we don't have at the moment).''

	''New proposed definition: A determinate reproductive shoot system that has as part at least one carpel or at least one stamen and does not contain any other determinate shoot system as a part.''		''New proposed definition: A determinate reproductive shoot system that has as part at least one carpel or at least one stamen and does not contain any other determinate shoot system as a part.''

← Older revision		Revision as of 23:13, 15 September 2010
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−	''Lol talked to Justin and Chris before meeting, and they say new format should work fine, so ~~TAIT~~ can send us the files in GAF 2.0''	+	''Lol talked to Justin and Chris before meeting, and they say new format should work fine, so TAIR can send us the files in GAF 2.0''

	==Priorities for the Next Round of Revisions==		==Priorities for the Next Round of Revisions==

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 Acceptance of the minutes from the 9-8-10 meeting? No changes or additions.
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 ==Other Items:==
 '''A.  Feedback page on Beta site fixed'''