POC Conf. Call 1-4-11 - Revision history

Cooperl: /* Completion of Changes for the Next Release: */

2011-01-06T19:30:04Z

Completion of Changes for the Next Release:

2011-01-06T19:17:25Z

sensu terms

2011-01-06T19:14:46Z

sensu terms

2011-01-06T19:14:09Z

sensu terms

2011-01-06T19:13:37Z

sensu terms

2011-01-06T18:00:05Z

inflorescence and infructescence branch orders, secondary inflorescence

2011-01-06T17:54:12Z

Completion of Changes for the Next Release:

2011-01-06T17:50:16Z

TIPS proposal

2011-01-06T17:50:02Z

TIPS proposal

2011-01-06T17:49:35Z

@@ Line 15: / Line 15: @@
 ==Completion of Changes for the Next Release:==
 '''
-Timeline and Plan for Upcoming Release:'''
+'''*Timeline and Plan for Upcoming Release:'''
-**
 - We completed all the changes discussed last week, and the merged plant_ontology.obo file was loaded on the *Beta* browser (Thanks Justin E!)

@@ Line 109: / Line 109: @@
 Action:
 ''Old terms [floret (sensu Poaceae), florest meristem (sensu Poaceae), and gynoecium (sensu Poaceae)] should be unobsoleted, then new terms (Poaceae floret, Poaceae floret meristem, and Poaceae gynoecium) should be merged with the old terms, so old number is primary number. Primary name will be changed to new names.''
@@ Line 125: / Line 127: @@
 ''RW forwarded an additional paper that describes the method.[http://www.sciencedirect.com/science/article/B6WHD-4PJ04XX-2/2/e07badd44d5dec559ae7a8ff5dfafa99 Kusnierczyk, 2008]''
 * Elizabeth Arnaud confirmed we should use ''Musa'' as their terms encompass banana and plantain

@@ Line 122: / Line 122: @@
 ''We had a further discussion of the method GO uses to associated terms with taxa. That method has the advantage of automatically including any term from a sub-clade in the set of terms for a larger clade. PJ asked how this information is encoded in the obo file.''
-''LC posted a link to one of the GO-taxonomy in the chat:[http://www.biomedcentral.com/1471-2105/11/530 Deegan et al; 2010]''
+''LC posted a link to one of the GO-taxonomy papers in the chat:[http://www.biomedcentral.com/1471-2105/11/530 Deegan et al; 2010]''
-''RW will forward paper that describes the method.[http://www.sciencedirect.com/science/article/B6WHD-4PJ04XX-2/2/e07badd44d5dec559ae7a8ff5dfafa99 Kusnierczyk, 2008]''
+''RW forwarded an additional paper that describes the method.[http://www.sciencedirect.com/science/article/B6WHD-4PJ04XX-2/2/e07badd44d5dec559ae7a8ff5dfafa99 Kusnierczyk, 2008]''

@@ Line 121: / Line 121: @@
 ''We had a further discussion of the method GO uses to associated terms with taxa. That method has the advantage of automatically including any term from a sub-clade in the set of terms for a larger clade. PJ asked how this information is encoded in the obo file.''
 ''LC posted a link to one of the GO-taxonomy in the chat:[http://www.biomedcentral.com/1471-2105/11/530 Deegan et al; 2010]''
 ''RW will forward paper that describes the method.[http://www.sciencedirect.com/science/article/B6WHD-4PJ04XX-2/2/e07badd44d5dec559ae7a8ff5dfafa99 Kusnierczyk, 2008]''

@@ Line 112: / Line 112: @@
 ''Old terms [floret (sensu Poaceae), florest meristem (sensu Poaceae), and gynoecium (sensu Poaceae)] should be unobsoleted, then new terms (Poaceae floret, Poaceae floret meristem, and Poaceae gynoecium) should be merged with the old terms, so old number is primary number. Primary name will be changed to new names.''
-''There was a general discussion of taxon-specific terms and subsets. We agreed that in principle they should use scientific rather than common names, and that subset names should agree with term names. This means, for example, that the subset for maize should be the subset for ''Zea mays''. Also, since terms like "Zea anther" are referring only to anthers in Zea mays, and not in all Zea species, they should have names like "Zea mays anther." However, since we have on our agenda to try to get away from terms with taxon names in them, I (RW) will not change the names until we decide on a final policy on how to deal with these terms.''
+''There was a general discussion of taxon-specific terms and subsets. We agreed that in principle they should use scientific rather than common names, and that subset names should agree with term names. This means, for example, that the subset for maize should be the subset for ''Zea mays spp. mays''.''
 ''We decided that there should be a page on the PO wiki (under developers guidelines) with guidelines on when terms should be obsoleted, detroyed, or merged.''

← Older revision		Revision as of 18:00, 6 January 2011
Line 95:		Line 95:


−	''Comment from Justin P (from chat)~~:from Justin Preece to Everyone~~:''	+	''Comment from Justin Preece (from chat):''
	''something to chew on: just have a single inflorescence branch term, and perhaps use a PATO xref term to represent DEGREE of ordinality (1st, 2nd, 3rd...Nth), and use that to characterize any annotations. what you lose with this approach is the ability to reason up and down the PO on the basis of ordinality parentage, but it's a cleaner way to represent an infinite number of ordinal inflorescence branches. it depends on whether the priority is annotative accuracy or reasoning capacity.''		''something to chew on: just have a single inflorescence branch term, and perhaps use a PATO xref term to represent DEGREE of ordinality (1st, 2nd, 3rd...Nth), and use that to characterize any annotations. what you lose with this approach is the ability to reason up and down the PO on the basis of ordinality parentage, but it's a cleaner way to represent an infinite number of ordinal inflorescence branches. it depends on whether the priority is annotative accuracy or reasoning capacity.''

@@ Line 17: / Line 17: @@
 '''
 Timeline and Plan for Upcoming Release:'''
+**
-- We completed all the changes discussed last week, and the merged plant_ontology.obo file was loaded on the Beta browser (Thanks Justin E!)
+- We completed all the changes discussed last week, and the merged plant_ontology.obo file was loaded on the *Beta* browser (Thanks Justin E!)
 *Internal review before full release:
@@ Line 30: / Line 30: @@
 List of things to fix:
-''Beta browser is not working, so everyone in the group should go over file on dev brower before the release. RW will make final changes on Wednesday, then LC will put the file up on the dev browser for viewing after Wednesday afternoon.''
+''*Beta browser is not working, so everyone in the group should go over file on dev brower before the release. RW will make final changes on Wednesday, then LC will put the file up on the dev browser for viewing after Wednesday afternoon.''
 ==Issues arising from last week's meeting:==

@@ Line 120: / Line 120: @@
 ==TIPS proposal==
 An abstract/proposal was been submitted to Trends in Plant Science on Dec 31st, 2010.  It was sent out to everyone by email.
 =Upcoming meetings 2011:=

← Older revision		Revision as of 17:49, 6 January 2011
Line 10:		Line 10:


−	Acceptance of the minutes from the [[POC Conf. Call 12-28-10]]?	+	Acceptance of the minutes from the [[POC Conf. Call 12-28-10]]? ''There were no additions, deletions or changes to the minutes of the last meeting.''