POC Conf. Call 7-31-12 - Revision history

Cooperl at 18:33, 20 November 2013

2013-11-20T18:33:20Z

Cooperl: /* Update the Po webpages */

2012-08-13T17:30:26Z

Update the Po webpages

Cooperl: /* Complete outstanding user requests/SF tracker items */

2012-08-13T17:30:13Z

Complete outstanding user requests/SF tracker items

Cooperl: /* file naming and which variations of the file to create for each release */

2012-08-13T17:29:48Z

file naming and which variations of the file to create for each release

Rwalls: /* News since last meeting July 3rd */

2012-08-01T15:02:32Z

News since last meeting July 3rd

Rwalls: /* Continue major revision of PSDS */

2012-08-01T14:00:46Z

Continue major revision of PSDS

Rwalls: /* Continue major revision of PSDS */

2012-08-01T13:52:14Z

Continue major revision of PSDS

Rwalls: /* News since last meeting July 3rd */

2012-08-01T13:49:02Z

News since last meeting July 3rd

Cooperl: /* News since last meeting July 3rd */

2012-07-31T21:07:54Z

News since last meeting July 3rd

Cooperl: /* News since last meeting July 3rd */

2012-07-31T18:52:13Z

News since last meeting July 3rd

← Older revision		Revision as of 18:33, 20 November 2013
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	Absent:''Marie Alejandra Gandolfo (Cornell), Justin Preece (OSU), Chris Mungall (Lawrence Berkeley National Lab), Barry Smith (University at Buffalo, NY)''		Absent:''Marie Alejandra Gandolfo (Cornell), Justin Preece (OSU), Chris Mungall (Lawrence Berkeley National Lab), Barry Smith (University at Buffalo, NY)''
−
−

	Collaborators: none		Collaborators: none
−
−	~~Streaming recording link: https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=67050932&rKey=bc60932af8fc7983~~
−
−	~~Download recording link: https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=67050932&rKey=d3198c436914478b~~

← Older revision		Revision as of 17:30, 13 August 2012
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	See: [[Plant_Ontology_Web_Site_Update:_Winter_2012]]		See: [[Plant_Ontology_Web_Site_Update:_Winter_2012]]
		+
		+	''tabled for a future discussion''

	=Meeting reports=		=Meeting reports=

@@ Line 142: / Line 142: @@
 ==Complete outstanding user requests/SF tracker items==
-See the list at: [[http://wiki.plantontology.org/index.php/Items_for_future_meetings]]
+See the list at: [[Items_for_future_meetings]]
 ==Update the Po webpages==

← Older revision		Revision as of 17:29, 13 August 2012
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	see [[PO_Release_SOP_Page]]		see [[PO_Release_SOP_Page]]

		+	''tabled for a future discussion''

	==Complete outstanding user requests/SF tracker items==		==Complete outstanding user requests/SF tracker items==

@@ Line 32: / Line 32: @@
 ''We discussed the new terms and whether or not the names are appropriate or if they could be made less confusing.  We should review the names and definitions and make sure the child terms such as anther are in the appropriate class. BS suggested it might be helpful to ask Jose Mejino of the FMA to look at these.''
-''PJ was concerned that users would be confused by seeing, for example, two structures that are siblings, but one is also part of the other. BS: People who want to use ontologies (domain experts) often are put off by the complex modeling of the ontology. One way to deal with this is to create simpler user vies (e.g., using OntoFox).''
+''PJ was concerned that users would be confused by seeing, for example, two structures that are siblings, but one is also part of the other. BS: People who want to use ontologies (domain experts) often are put off by the complex modeling of the ontology. One way to deal with this is to create simpler user vies (e.g., using Ontodog).''
 * '''Please review the [[PO_Release_SOP_Page]]'''.  I revised and updated for the most recent release, but it is good to make sure we have not missed anything.
@@ Line 47: / Line 47: @@
 * PSDS invited paper- for Special Issue on "Functional Genomics and Systems Biology in the Post Genomics Era" that will be published in 2013 in Physiologia Plantarum.
 ''RW would like everyone to send her ideas as to what they would like to see in it.''
 ''Do we know if this is the end of October or the beginning?''
 ''Either way, in order to get it done by October, we need to have a draft done by September. The question is whether or not the PSDS is ready to write about. The upper level structure has been extensivly revised, but we still have a lot of changes to make to more specific terms.''

← Older revision		Revision as of 14:00, 1 August 2012
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	''BFO 2.0 addresses whether or not sites have histories the way material entities do.''		''BFO 2.0 addresses whether or not sites have histories the way material entities do.''
		+
		+	''We need to make sure, as we revise, that the PSDS terms correspond to the PAE terms (some upper level re-organization has already been done to align them).''
		+
		+	''Annotations of development stages:''
		+
		+	''PJ suggested that annotating directly to development stage should be required. We have mechanisms to move annotations back and forth between PAEs and PSDSs, based on ontology relations, but at this point, when people download annotation directly from the server (rather than via Amigo), they do not aggregate based on ontology relations.''
		+
		+	''Another issue is that the annotations only move to the generic term (e.g., an annotation to leaf may go to generic leaf development stage, but it would go to the more specific stage of development of the leaf.''
		+
		+	''Mysql queries also only give direct annotations.''
		+
		+	''Ultimately, we would like to have tools that suggest development stages, when annotator searches for a structure, or vice versa.''

	==file naming and which variations of the file to create for each release==		==file naming and which variations of the file to create for each release==

@@ Line 118: / Line 118: @@
 >PO:0007615 : flower development stage [48067]
+''BFO 2.0 addresses whether or not sites have histories the way material entities do.''
 ==file naming and which variations of the file to create for each release==

@@ Line 31: / Line 31: @@
 ''We discussed the new terms and whether or not the names are appropriate or if they could be made less confusing.  We should review the names and definitions and make sure the child terms such as anther are in the appropriate class. BS suggested it might be helpful to ask Jose Mejino of the FMA to look at these.''
 * '''Please review the [[PO_Release_SOP_Page]]'''.  I revised and updated for the most recent release, but it is good to make sure we have not missed anything.
@@ Line 39: / Line 41: @@
 ''Need to post notices on PO home page and facebook and could send something out on po-announce as well.''
 * PAE paper is being revised-consolidated all the comments from everyone and updating to match the release. Will go out again to everyone this week.
@@ Line 44: / Line 47: @@
 * PSDS invited paper- for Special Issue on "Functional Genomics and Systems Biology in the Post Genomics Era" that will be published in 2013 in Physiologia Plantarum.
 ''Do we know if this is the end of October or the beginning?''
-''RW would like everyone to send her ideas as to what they would like to see in it.''
+''PJ: The PAE paper could also go into Phys. Plantarum instead.''
 =Plans for the next release=

@@ Line 30: / Line 30: @@
 A new term, collective plant structure (PO:0025497), was created to describe collections of plant structures and to serve as parent term to collective plant organ structure (PO:0025007) and collective organ part structure (PO:0025269). Note that collective plant organ structure (PO:0025007) was formerly named "collective plant structure" (the same name as the new upper-level term), but was renamed for clarity.
-''We discussed the new terms and whether or not the names are appropriate or if they could be made less confusing.  We should review the names and definitions and make sure the child terms such as anther are in the appropriate class. ''
+''We discussed the new terms and whether or not the names are appropriate or if they could be made less confusing.  We should review the names and definitions and make sure the child terms such as anther are in the appropriate class. BS suggested it might be helpful to ask Jose Mejino of the FMA to look at these.''
 * '''Please review the [[PO_Release_SOP_Page]]'''.  I revised and updated for the most recent release, but it is good to make sure we have not missed anything.

← Older revision		Revision as of 18:52, 31 July 2012
Line 44:		Line 44:

	* PSDS invited paper- for Special Issue on "Functional Genomics and Systems Biology in the Post Genomics Era" that will be published in 2013 in Physiologia Plantarum.		* PSDS invited paper- for Special Issue on "Functional Genomics and Systems Biology in the Post Genomics Era" that will be published in 2013 in Physiologia Plantarum.
		+
		+	''Do we know if this is the end of October or the beginning?''

	''RW would like everyone to send her ideas as to what they would like to see in it.''		''RW would like everyone to send her ideas as to what they would like to see in it.''