POC Conf. Call 3-15-11 - Revision history

Cooperl: /* Issues arising from last week's meeting: */

2011-03-21T21:00:35Z

Issues arising from last week's meeting:

Cooperl: /* Issues arising from last week's meeting: */

2011-03-21T20:59:36Z

Issues arising from last week's meeting:

Rwalls: /* Physcomitrella terms */

2011-03-16T13:36:47Z

Physcomitrella terms

Show changes

Rwalls at 13:31, 16 March 2011

2011-03-16T13:31:28Z

Rwalls: /* Cardinal organ parts */

2011-03-15T17:01:30Z

Cardinal organ parts

Rwalls: /* gametophytic perianth */

2011-03-15T16:52:07Z

gametophytic perianth

Rwalls: /* Gametangium, antheridium, archegonium and related terms */

2011-03-14T19:54:33Z

Gametangium, antheridium, archegonium and related terms

Rwalls: /* Gametangium, antheridium, archegonium and related terms */

2011-03-14T19:51:15Z

Gametangium, antheridium, archegonium and related terms

Rwalls: /* Gametangium, antheridium, archegonium and related terms */

2011-03-14T19:46:37Z

Gametangium, antheridium, archegonium and related terms

Rwalls: /* Gametangium, antheridium, archegonium and related terms */

2011-03-14T19:31:06Z

Gametangium, antheridium, archegonium and related terms

@@ Line 19: / Line 19: @@
 ''The conference call will take place on 3-17-11, at 4PM PDT.''
-''RW will look try to see if any other ontologies are using the has_part relation, and how they deal with it.  Will post possible alternative solutions on the [http://wiki.plantontology.org:8080/index.php/POC Technical Issues Page].''
+''RW will look try to see if any other ontologies are using the has_part relation, and how they deal with it.  Will post possible alternative solutions on the [[POC Technical Issues Page]].''
 =Physcomitrella terms=

@@ Line 17: / Line 17: @@
 Special technical meeting?
-''The confernce call will take place on 3-17-11, at 4PM PDT.''
+''The conference call will take place on 3-17-11, at 4PM PDT.''
-''RW will look try to see if any other ontologies are using the has_part relation, and how they deal with it.  Will post possible alternative solutions on the [http://wiki.plantontology.org:8080/index.php/POC_software_requests software request wiki page].''
+''RW will look try to see if any other ontologies are using the has_part relation, and how they deal with it.  Will post possible alternative solutions on the [http://wiki.plantontology.org:8080/index.php/POC Technical Issues Page].''
 =Physcomitrella terms=

@@ Line 1: / Line 1: @@
 '''POC meeting, Webex Conference Call; Date: Tuesday Mar 15th, 2011 10am (PST)'''
-In attendance:
+In attendance: Laurel Cooper (OSU), Ramona Walls (NYBG),  Justin Elser (OSU), Justin Preece (OSU)
-POC members:
+Absent: Pankaj Jaiswal (OSU), Marie Alejandra Gandolfo; (Cornell University) Chris Mungall (Lawrence Berkeley National Lab), Dennis Stevenson (NYBG), Barry Smith (University at Buffalo, NY)
-Collaborators:
+Collaborators: none
 =Issues arising from last week's meeting:=
 Special technical meeting?
 =Physcomitrella terms=
 ==[https://sourceforge.net/tracker/?func=detail&aid=3109542&group_id=76834&atid=835555 Gametangium, antheridium, archegonium and related terms]==

@@ Line 198: / Line 198: @@
 (Definition suggests that we should add a term for archegonium wall, is_a gametangium wall)
-*'''base'''
+*'''base''' (''save for next week'')
 Moss Ontology definition: The sterile bottom of the sporangium. Also called neck or if swollen apophysis or hypophysis. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition
@@ Line 211: / Line 211: @@
 Moss Ontology definition: A single or double circle of teeth inside the mouth of a moss sporangium. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition
 *'''peristome tooth'''
@@ Line 218: / Line 220: @@
 Proposed def: A cardinal organ part that is a lobe or tooth of the peristome.
-*'''theca'''
+*'''theca''' (''maybe save for next week'')
 Moss Ontology definition: The main body (urn) of a sporangium. Altered from Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition
@@ Line 291: / Line 293: @@
 Comment: Raises the sporophyte above the perichaetial bracts. Found in Sphagnum and Andreaea.
-* '''venter'''
+* '''venter''' (''save for next week'')
-*'''neck canal'''
+*'''neck canal''' (''save for next week'')
 =Upcoming meetings 2011:=

@@ Line 164: / Line 164: @@
 ===[https://sourceforge.net/tracker/?func=detail&aid=3185171&group_id=76834&atid=835555 gametophytic perianth]===
-Proposed def'n:  A collective phyllome structure that consists of two or more of the most distal parachaetal bracts on an axis that are fused laterally and surround the calyptra.
+Proposed def'n:  A collective phyllome structure that consists of two or more of the most distal parachaetal bracts on a gametophore axis that are fused laterally and surround the calyptra.
 Should it be surrounds the capsule, in case no calyptra is present?
@@ Line 171: / Line 171: @@
 Comment: The gametophytic perianth is not the same structure as a perianth (PO:0009058) in angiosperms.
 ===[https://sourceforge.net/tracker/?func=detail&aid=3185175&group_id=76834&atid=835555 seta]===

@@ Line 49: / Line 49: @@
 '''[http://sourceforge.net/tracker/index.php?func=detail&aid=3030032&group_id=76834&atid=835555 embryo sac egg cell]''' (PO:0025123): An egg cell that is produced by a megagametophyte.
-'''antheridium sperm cell''' (PO:0025120): A sperm cell that is produced by an antheridium.
+'''[http://sourceforge.net/tracker/index.php?func=detail&aid=3030033&group_id=76834&atid=835555 antheridium sperm cell]''' (PO:0025120): A sperm cell that is produced by an antheridium.
-'''pollen sperm cell''' (PO:0025121): A sperm cell that is produced by a microgametophyte.
+'''[http://sourceforge.net/tracker/index.php?func=detail&aid=3030033&group_id=76834&atid=835555 pollen sperm cell]''' (PO:0025121): A sperm cell that is produced by a microgametophyte.
 Having both sets of egg and sperms cells is redundant. They were put in to satisfy the part_of relations. We could get around this by using has_part relations.

@@ Line 45: / Line 45: @@
 We also have the terms:
-'''archegonium egg cell''' (PO:0025122): An egg cell that is produced by an archegonium.
+'''[http://sourceforge.net/tracker/index.php?func=detail&aid=3030032&group_id=76834&atid=835555 archegonium egg cell]''' (PO:0025122): An egg cell that is produced by an archegonium.
-'''embryo sac egg cell''' (PO:0025123): An egg cell that is produced by a megagametophyte.
+'''[http://sourceforge.net/tracker/index.php?func=detail&aid=3030032&group_id=76834&atid=835555 embryo sac egg cell]''' (PO:0025123): An egg cell that is produced by a megagametophyte.
 '''antheridium sperm cell''' (PO:0025120): A sperm cell that is produced by an antheridium.

← Older revision		Revision as of 19:46, 14 March 2011
Line 54:		Line 54:

	Having both sets of egg and sperms cells is redundant. They were put in to satisfy the part_of relations. We could get around this by using has_part relations.		Having both sets of egg and sperms cells is redundant. They were put in to satisfy the part_of relations. We could get around this by using has_part relations.
		+
		+
		+	Here is an image of the current PO, showing only female parts:
		+
		+	[[File:egg_cell1.jpg]]
		+
		+	-Maybe having reciprocal part_of and has_part relations is causing a problem?
		+
		+	Here is how it would look using has_part relations:
		+
		+	[[File:egg_cell2.jpg]]
		+
		+	In this image, archegonium egg cell and embryo sac egg cell have been merged with egg cell. May also want to merge embryo sac with female gametophyte. It is the only child of female gametophyte, suggesting they are redundant.

	==apical cell==		==apical cell==

@@ Line 24: / Line 24: @@
 Current definitions:
-'''plant gametangium''' (PO:0025124): A cardinal organ part (?) that is part of a whole plant in the gametophytic phase and produces gametes.
+'''plant gametangium''' (PO:0025124): A cardinal organ part (or an organ?) that is part of a whole plant in the gametophytic phase and produces gametes.
 '''antheridium''' (PO:0025125): A gametangium that produces antheridium sperm cells.