POC Conf. Call 3-22-11 - Revision history

Cooperl: /* POC 'Technical Issues' Conf Call 3-17-11: */

2011-03-28T22:25:13Z

POC 'Technical Issues' Conf Call 3-17-11:

Cooperl: /* has_parts problem */

2011-03-28T22:12:19Z

has_parts problem

Cooperl: /* has_parts problem */

2011-03-28T22:11:21Z

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Cooperl: /* POC 'Technical Issues' Conf Call 3-17-11 */

2011-03-28T22:10:29Z

POC 'Technical Issues' Conf Call 3-17-11

Cooperl: /* has_parts problem */

2011-03-28T22:07:47Z

has_parts problem

Cooperl at 22:04, 28 March 2011

2011-03-28T22:04:16Z

Cooperl: /* has_parts problem */

2011-03-28T22:01:58Z

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Cooperl: /* has_parts problem */

2011-03-28T22:01:17Z

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Cooperl: /* has_parts problem */

2011-03-28T22:00:09Z

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Cooperl: /* has_parts problem */

2011-03-28T21:50:23Z

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@@ Line 11: / Line 11: @@
-=POC 'Technical Issues' Conf Call 3-17-11:=
+=POC 'Technical Issues' Conf Call 3-17-11 Problems discussed:=
 Updates from the "Technical Issues" Conference call meeting we had on Thursday Mar 17th.
@@ Line 51: / Line 51: @@
 ''LC: [http://www.gramene.org/plant_ontology/ontology_browse.html#tax Gramene's taxonomic ontology] is limited in its scope- focuses on the Poaceae (Gramineae) family of plant taxonomy only''
-==Problem of Annotations and the has_part relationships==
+==Annotations and the has_part relationships==
 =Items carried over from last week's meeting:  Physcomitrella terms=

@@ Line 28: / Line 28: @@
 '''1.''' Confirm that the reciprocal part_of and has_part relations were what was actually cause the problem with loading the obo file onto our browser. To do this, we should:
-      '''a)''' Try loading the file without the reciprocal relations but with some has_part relations onto the beta browser with annotations (this will require an editted a version of the live file, since the annotation files currently match the live file),
+      '''a)''' Try loading the file without the reciprocal relations but with some has_part relations onto the beta browser with annotations (this will require an edited a version of the live file, since the annotation files currently match the live file)
       '''b)''' Try loading a version of the file that has maybe one or two reciprocal relations, but no annotations on to the dev browser (to see if the reciprocal relations cause a problem when there are no annotations).
@@ Line 36: / Line 38: @@
       '''a)''' remove all reciprocal relations from the ontology file, that is, only use part_of or has_part, but not both
-      '''b)''' include reciprocal relations when they are appropriate, but write a script that searches the files for reciprocal relations and removes the has_part relation from classes that have both.
+     '''b)''' include reciprocal relations when they are appropriate, but write a script that searches the files for reciprocal relations and removes the has_part relation from classes that have both.
 '''3.'''  For cases where a class has two children that differ in structural characteristics and also occur in separate taxa, we should create the children, but not propagate the part_of children from the parent to the specific children (i.e., what we did for leaf and what have talked about for microsporangium).

@@ Line 38: / Line 38: @@
        '''b)''' include reciprocal relations when they are appropriate, but write a script that searches the files for reciprocal relations and removes the has_part relation from classes that have both.
-'''3.''' For cases where a class has two children that differ in structural characteristics and also occur in separate taxa, we should create the children, but not propagate the part_of children from the parent to the specific children (i.e., what we did for leaf and what have talked about for microsporangium).
+'''3.'''  For cases where a class has two children that differ in structural characteristics and also occur in separate taxa, we should create the children, but not propagate the part_of children from the parent to the specific children (i.e., what we did for leaf and what have talked about for microsporangium).
-In these cases, we should add '''"only_in_taxon"''' relations to the specific children. Then we can use the only_in_taxon relations in a script that will examine the annotation for the part_of children of the parent class and assign them to the child class if they come from the correct taxon.
+In these cases, we could add '''"only_in_taxon"''' relations to the specific children. Then we can use the only_in_taxon relations in a script that will examine the annotation for the part_of children of the parent class and assign them to the child class if they come from the correct taxon.
-''We should send CM an example file with the only_in_taxon relations so that he can send us an example of how the script would work''
+''Action item: We should send CM an example file with the only_in_taxon relations so that he can send us an example of how the script would work''
@@ Line 48: / Line 48: @@
 ''LC: [http://www.gramene.org/plant_ontology/ontology_browse.html#tax Gramene's taxonomic ontology] is limited in its scope- focuses on the Poaceae (Gramineae) family of plant taxonomy only''
 ==Problem of Annotations and the has_part relationships==

← Older revision		Revision as of 22:10, 28 March 2011
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−	=POC 'Technical Issues' Conf Call 3-17-11=	+	=POC 'Technical Issues' Conf Call 3-17-11:=
	Updates from the "Technical Issues" Conference call meeting we had on Thursday Mar 17th.		Updates from the "Technical Issues" Conference call meeting we had on Thursday Mar 17th.

← Older revision		Revision as of 22:07, 28 March 2011
Line 48:		Line 48:

	''LC: [http://www.gramene.org/plant_ontology/ontology_browse.html#tax Gramene's taxonomic ontology] is limited in its scope- focuses on the Poaceae (Gramineae) family of plant taxonomy only''		''LC: [http://www.gramene.org/plant_ontology/ontology_browse.html#tax Gramene's taxonomic ontology] is limited in its scope- focuses on the Poaceae (Gramineae) family of plant taxonomy only''
		+
		+
		+	==Problem of Annotations and the has_part relationships==

	=Items carried over from last week's meeting: Physcomitrella terms=		=Items carried over from last week's meeting: Physcomitrella terms=

@@ Line 47: / Line 47: @@
 ''We may be able to use Gramene's taxonomic ontology (check if it is for all plants) rather than editing the slim CM et al. created for GO.''
-''LC: Gramene's taxonomic ontology (
+''LC: [http://www.gramene.org/plant_ontology/ontology_browse.html#tax Gramene's taxonomic ontology] is limited in its scope
 =Items carried over from last week's meeting:  Physcomitrella terms=