POC Conf. Call 4-17-12 - Revision history

Cooperl: /* bud areole and lamina areole */

2012-11-29T22:49:57Z

bud areole and lamina areole

Cooperl: /* Separate Aspect Files on Bioportal */

2012-06-10T16:34:01Z

Separate Aspect Files on Bioportal

Cooperl: /* Separate Aspect Files on Bioportal */

2012-06-10T16:32:01Z

Separate Aspect Files on Bioportal

Cooperl: /* add top-level plant ontology term */

2012-04-23T02:19:18Z

add top-level plant ontology term

Cooperl: /* Crop Ontology Workshop */

2012-04-23T02:11:12Z

Crop Ontology Workshop

Cooperl: /* add top-level plant ontology term */

2012-04-23T01:46:07Z

add top-level plant ontology term

Rwalls at 19:06, 18 April 2012

2012-04-18T19:06:38Z

Rwalls: /* New items for the July 2012 Release */

2012-04-18T19:02:58Z

New items for the July 2012 Release

Rwalls: /* primordium */

2012-04-18T19:01:59Z

primordium

Rwalls: /* bud areole and lamina areole */

2012-04-18T18:42:52Z

bud areole and lamina areole

@@ Line 102: / Line 102: @@
 ''Download ontologies page must be updated for the next release, along with tutorials''
-==[https://sourceforge.net/tracker/index.php?func=detail&aid=3438986&group_id=76834&atid=835555 bud areole and lamina areole]==
+==[https://sourceforge.net/tracker/index.php?func=detail&aid=3438986&group_id=76834&atid=835555 areole bud and lamina areole]==
 At the POC meeting on 11-8-11 we to add a term for areole, refering to a type of bud in cacti. However, this term is also used to refer to a part of a leaf (or other phyllome) lamina. The term for lamina areole was requested by one of our Arabidopsis users (Dora).

← Older revision		Revision as of 16:34, 10 June 2012
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	''Ask BioPortal to stop serving them now. Bioportal should only server plant_ontology.obo (or does it serve plant_ontology_assert.obo?)''		''Ask BioPortal to stop serving them now. Bioportal should only server plant_ontology.obo (or does it serve plant_ontology_assert.obo?)''
		+
		+	*Need to check with Gramene and TAIR and SGN to see if they are still using those files
		+
		+	* note that these are derived from the plant _ontology assert_basic file.

	==[https://sourceforge.net/tracker/index.php?func=detail&aid=3479039&group_id=76834&atid=835555 add top-level plant ontology term]==		==[https://sourceforge.net/tracker/index.php?func=detail&aid=3479039&group_id=76834&atid=835555 add top-level plant ontology term]==

@@ Line 52: / Line 52: @@
 ''On recording: Alert users that we will stop supplying these files after release 18.''
-''Ask BioPortal to stop serving them now. Bioportal should only server plant_ontoloyg.obo (or does it serve plant_ontology_assert.obo?)''
+''Ask BioPortal to stop serving them now. Bioportal should only server plant_ontology.obo (or does it serve plant_ontology_assert.obo?)''
 ==[https://sourceforge.net/tracker/index.php?func=detail&aid=3479039&group_id=76834&atid=835555 add top-level plant ontology term]==

← Older revision		Revision as of 02:19, 23 April 2012
Line 92:		Line 92:

	''PJ and JE will look at options- one would be for JE to write a script to add in a top level term "entity" that gets added after each commit.''		''PJ and JE will look at options- one would be for JE to write a script to add in a top level term "entity" that gets added after each commit.''
		+
		+	''One solution would be for them to load the separate aspect files.''

	''We still need to revisit the issue of changing names of all the files, if that is something we want to do. (see last week's minutes).''		''We still need to revisit the issue of changing names of all the files, if that is something we want to do. (see last week's minutes).''

@@ Line 220: / Line 220: @@
 For more information see the wiki page: [[Crop_Ontology_Workshop_at_OSU,_2012]]
-We are looking at the tentative dates of either: June 11-13th or Aug 6th to 8th
+Dates TBA: probably  Aug 6th to 8th or in Sept.
 The focus of the workshop will be on mostly development stages and traits for the crop plants

@@ Line 56: / Line 56: @@
 ==[https://sourceforge.net/tracker/index.php?func=detail&aid=3479039&group_id=76834&atid=835555 add top-level plant ontology term]==
-I suggest we make a root term "plant entity'  This would be consistent with BFO and avoid the problems above.
+This is in reference to the issues raised by NM of SGN:
 from RW:
@@ Line 83: / Line 85: @@
 ''SGN currently has to run script to strip out cross-aspect relations (has_participant and participates_in).''
-''PJ does not want to add an upper-level terms, because in some applications, only the upper-level term will show up, so it won't be clear that there are two different branches.''
+''PJ does not want to add an upper-level terms, because in some applications, only the upper-level term will show up, so it won't be clear that there are two different branches.  We will look into how other sites are handling the cross-aspect relations and  ''
 ''PJ suggested creating another file that strips out cross-aspect relations and presenting them as a bridge file.''
@@ Line 89: / Line 91: @@
 ''Create another file called something like "plant_ontology_assert_no_hp or pi.obo" (will need to work out name and provide this on the download page. Alternative is to automatically generate a separate file that inserts a top level term and provide that to SGN.''
-''JE should write a script to add in a top level term "entity" that gets added after each commit.'
+''PJ and JE will look at options- one would be for JE to write a script to add in a top level term "entity" that gets added after each commit.''
-''We still need to work on names of all the files (see last week's minutes).''
+''We still need to revisit the issue of changing names of all the files, if that is something we want to do. (see last week's minutes).''
 ''Download ontologies page must be updated for the next release, along with tutorials''

@@ Line 3: / Line 3: @@
 In attendance:
-POC members:
+POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Justin Preece (OSU), Pankaj Jaiswal (OSU), Justin Elser (OSU), Marie Alejandra Gandolfo (Cornell).
 Collaborators: none

← Older revision		Revision as of 19:02, 18 April 2012
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	Page set up with goals and priorities etc.		Page set up with goals and priorities etc.
		+
		+	''Need to update tutorials and dowload page on PO website.''

	=Upcoming meetings and Presentations 2012:=		=Upcoming meetings and Presentations 2012:=

@@ Line 158: / Line 158: @@
 See for example [http://jxb.oxfordjournals.org/content/58/5/1083.long PMID:17272833] and [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2751957/?tool=pubmed PMID:19717616], two of the PO annotations for flower primordium, which are really referring to floral organ primordia.
-There a number of annotations on flower primordium that will have to be moved.
+''There a number of annotations on flower primordium that will have to be moved.''
 ''Okay. Also checked this with Amy Litt at NYBG, and she said it made sense to her.''
@@ Line 171: / Line 171: @@
 '''proposed definition, primordium (PO:0025127):''' A ''plant organ/plant structure/portion of meristem tissue'' in an early stage of development after a protoderm has begun to develop and before anatomical structure morphogenisis (GO:0009653).
-''new proposed def.: A portion of meristem tissue (PO:0009013) that
+''new proposed def.: A portion of meristem tissue (PO:0009013) that has been committed to the formation of a particular plant structure.''
 ===subtypes of primordium===

← Older revision		Revision as of 18:42, 18 April 2012
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	''Comment: Found in Cactaceae. Appears as a cluster of spine leaves. May be covered in trichomes (PO:0000282). In species with tubercles (PO:0025352), the areole bud is often found at the distal end of the tubercle. The areole bud originates in a leaf axil (PO:0009023) of a leaf that becomes a tubercle but is displaced to the tip of a tubercle through elongation of the tubercle.''		''Comment: Found in Cactaceae. Appears as a cluster of spine leaves. May be covered in trichomes (PO:0000282). In species with tubercles (PO:0025352), the areole bud is often found at the distal end of the tubercle. The areole bud originates in a leaf axil (PO:0009023) of a leaf that becomes a tubercle but is displaced to the tip of a tubercle through elongation of the tubercle.''
		+
		+	''Could add subset for Cactaceae.''

	==[http://sourceforge.net/tracker/index.php?func=detail&aid=3081059&group_id=76834&atid=835555 primordium]==		==[http://sourceforge.net/tracker/index.php?func=detail&aid=3081059&group_id=76834&atid=835555 primordium]==