POC Conf. Call 12-22-10 - Revision history

Rwalls: /* Upcoming meetings 2011: */

2010-12-23T20:30:03Z

Upcoming meetings 2011:

2010-12-23T20:29:07Z

Musa requests still needing to be resolved:

2010-12-23T20:28:03Z

Issues arising from new terms:

2010-12-23T20:25:48Z

Completed Musa requests:

2010-12-23T20:24:04Z

PGDSO Terms without is_a parents

2010-12-23T20:23:16Z

Issues arising from last week's agenda

2010-12-23T20:20:35Z

Issues arising from last week's agenda

2010-12-23T20:06:33Z

Issues arising from new terms:

2010-12-23T20:04:23Z

Musa requests still needing to be resolved:

2010-12-23T19:54:45Z

Issues arising from new terms:

← Older revision		Revision as of 20:30, 23 December 2010
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	Dennis will speak in place of Angelica. PJ invited two other speakers. Gavin Kennedy will talk about the ontology application in large scale phenomics projects. Rudi Appels will speak on crop genomics and phenomics. Ramona has contacted these speakers to get their information and abstract; waiting for responses from them.		Dennis will speak in place of Angelica. PJ invited two other speakers. Gavin Kennedy will talk about the ontology application in large scale phenomics projects. Rudi Appels will speak on crop genomics and phenomics. Ramona has contacted these speakers to get their information and abstract; waiting for responses from them.

−	'''We received permission to use the 6th time slot for a discussion session, but need to have a commitment that someone will lead the discussion. ~~Should this be~~ PJ ~~or RW?'~~''	+	''We received permission to use the 6th time slot for a discussion session, but need to have a commitment that someone will lead the discussion. PJ will do it.''

@@ Line 195: / Line 195: @@
 Below is a list of the requested terms, with definitions and is a or part of relations from Rosemary, followed by suggestions and/or proposed definitions for PO format.
-''We still have a lot of work to do on these, so we will split the SF tracker up into 3 ind ones and hopefully be able to complete it next week.''
+''We still have a lot of work to do on these, so we will split the SF tracker up into 3 ind ones and hopefully be able to complete it next week. Will make a separate tracker for inflorescence and infructescence.''
 ===Musa flower terms===

@@ Line 181: / Line 181: @@
 ''All present agreed that canal should be a plant anatomical space, BS: check FMA ''
-''new proposed def'n: A canal along the petiole.  Comment may be open or enclosed, can occur on the upper (adaxial) surface''
+''new proposed def'n: A canal that is part of a petiole.  Comment: May occur on the abaxial or adaxial surface or be internal.''
 *'''Fused tepal''': Added a new term to PO that is a cross-product of PO tepal and PATO fused (PATO:0000642).

@@ Line 134: / Line 134: @@
 *'''cigar leaf (PO:0025130)''':  Although it is a phenotype, we added the term for Musa subset. May apply to other species as well, especially in monocots. is_a vascular leaf.
-''We had discussion to clarify a vascular leaf;  MAG: Is this redundant? when is a leaf not vascular?  Moss leaves lack vascular tissue''
+''We had discussion to clarify a vascular leaf;  MAG: Is this redundant? when is a leaf not vascular?  Moss leaves lack vascular tissue and so are non-vascular leaves. Megaphylls and microphylls are both vascular leaves. We will revisit the whole ontological structure of leaf at a future date.''
 *'''petiole margin edge''': Should just use petiole margin (PO:0025010)

@@ Line 115: / Line 115: @@
 All are part of leaf trichome development stage. Probably should be is_a trichome development stage, to be consistent with existing structure (may change in alter revisions)
-''All were in favor of making this change, RW will post the resulting def'ns (make a SF tracker?) and send them to BS''
+''All were in favor of making this change, RW will post the resulting def'ns and make a SF tracker and send them to BS''
 =User requests still open on SourceForge=

← Older revision		Revision as of 20:23, 23 December 2010
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	What about structures that are present in embryos but may also be present after germination (e.g., hypocotyl)?		What about structures that are present in embryos but may also be present after germination (e.g., hypocotyl)?

−	''BS: Avoid dual parentage if possible, this is a problem that many ontologies are dealing with. We decided for now to just include the embryonic plant structures that are only present in the embryo.''	+	''BS: Avoid dual parentage if possible, this is a problem that many ontologies are dealing with. We decided for now to just include the embryonic plant structures that are only present in the embryo. This excludes terms like hypocotyl. May need to change some relations that are part_of to has_part (e.g., embryonic axis has part hypocotyl, rather than hypocotyl part_of embryonic axis.''

← Older revision		Revision as of 20:20, 23 December 2010
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	''comment: May have sinuous anticlinal cell walls that overall give a jigsaw like appearance to the leaf epidermis, not associated with a stomatal complex or trichome.''		''comment: May have sinuous anticlinal cell walls that overall give a jigsaw like appearance to the leaf epidermis, not associated with a stomatal complex or trichome.''
		+
		+	''Will add disjoint_from relations to trichome cell, guard cell, and subsidiary cell.''
		+
	''Note: the terms 'long cell', 'short cell' are children of 'leaf pavement cell' and 'papilla cell' is_a 'pavement cell'.		''Note: the terms 'long cell', 'short cell' are children of 'leaf pavement cell' and 'papilla cell' is_a 'pavement cell'.

← Older revision		Revision as of 20:04, 23 December 2010
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	Below is a list of the requested terms, with definitions and is a or part of relations from Rosemary, followed by suggestions and/or proposed definitions for PO format.		Below is a list of the requested terms, with definitions and is a or part of relations from Rosemary, followed by suggestions and/or proposed definitions for PO format.
		+
		+	''We still have a lot of work to do on these, so we will split the SF tracker up into 3 ind ones and hopefully be able to complete it next week.''

	===Musa flower terms===		===Musa flower terms===

@@ Line 167: / Line 167: @@
 ===Issues arising from new terms:===
-*'''Petiole canal:''' The upper (adaxial) canal along the petiole. part_of CO_125.0000057 ! petiole
+*'''petiole canal:''' The upper (adaxial) canal along the petiole. part_of CO_125.0000057 ! petiole
 Added term 'adaxial petiole': A cardinal organ part that is the adaxial portion of petiole. Comment: Adaxial petiole may be concave or form a canal. Narrow synonym: petiole canal.
@@ Line 175: / Line 175: @@
 Now that we have plant anatomical space, maybe we should add petiole canal as a space?  See tracker for [http://sourceforge.net/tracker/index.php?func=detail&aid=3109646&group_id=76834&atid=835555 canal]
 *'''Fused tepal''': Added a new term to PO that is a cross-product of PO tepal and PATO fused (PATO:0000642).