POC Conf. Call 5-24-11 - Revision history

Rwalls: /* Annotations on parts of leaf */

2011-05-25T14:03:29Z

Annotations on parts of leaf

Rwalls: /* Annotations on parts of leaf */

2011-05-25T13:25:19Z

Annotations on parts of leaf

Rwalls: /* Review of leaf terms for Phenotype RCN meeting next week */

2011-05-25T13:01:09Z

Review of leaf terms for Phenotype RCN meeting next week

Rwalls: /* Review of leaf terms for Phenotype RCN meeting next week */

2011-05-25T12:51:47Z

Review of leaf terms for Phenotype RCN meeting next week

Cooperl: /* * Week of May 23-26th: */

2011-05-24T20:14:46Z

* Week of May 23-26th:

Cooperl: /* translation synonyms */

2011-05-24T19:33:13Z

translation synonyms

Cooperl: /* translation synonyms */

2011-05-24T19:32:45Z

translation synonyms

Cooperl: /* Annotations on parts of leaf */

2011-05-24T19:32:23Z

Annotations on parts of leaf

Cooperl: /* new relations in release */

2011-05-24T19:27:56Z

new relations in release

Cooperl: /* * Week of May 23-26th: */

2011-05-24T19:21:46Z

* Week of May 23-26th:

← Older revision		Revision as of 14:03, 25 May 2011
Line 63:		Line 63:

	''"If you are annotating to this term, please add an additional annotation to vascular leaf (PO:0009025) or non-vascular leaf (PO:0025075), depending on the species. All annotations for angiosperms, gymnosperms, and pteridophytes should go to vascular leaf and all annotations for bryophytes should go to non-vascular leaf."''		''"If you are annotating to this term, please add an additional annotation to vascular leaf (PO:0009025) or non-vascular leaf (PO:0025075), depending on the species. All annotations for angiosperms, gymnosperms, and pteridophytes should go to vascular leaf and all annotations for bryophytes should go to non-vascular leaf."''
		+
		+	''RW (after meeting): actually, there is a much longer list of terms that are part_of leaf, because the list on [[New_terms_and_obsolete_terms_for_May2011_release#List_of_terms_that_are_part_of_leaf]] was only for terms with annotations. The comment will need to go to all of the part_of descendents, and all of the is_a descendents, except vascular and non-vascular leaf and their descendents.''

	''We could also consider adding cross-product terms (pre- or post-compositionally).''		''We could also consider adding cross-product terms (pre- or post-compositionally).''

@@ Line 62: / Line 62: @@
 ''We should add a comment to each of the terms on the list saying:''
-''"If you are annotating to this term, please add an additional annotation to vascular leaf (PO:id) or non-vascular leaf (PO:id), depending on the species. All annotations for angiosperms, gymnosperms, and pteridophytes should go to vascular leaf and all annotations for bryophytes should go to non-vascular leaf."''
+''"If you are annotating to this term, please add an additional annotation to vascular leaf (PO:0009025) or non-vascular leaf (PO:0025075), depending on the species. All annotations for angiosperms, gymnosperms, and pteridophytes should go to vascular leaf and all annotations for bryophytes should go to non-vascular leaf."''
-''We could also consider adding cross-product terms (especially post-compositionally).''
+''We could also consider adding cross-product terms (pre- or post-compositionally).''
 ''We will not try to copy these annotations before this release -- leave at it is for now and they will be caught by TAIR or other for the next release.''
 ===translation synonyms===

← Older revision		Revision as of 13:01, 25 May 2011
Line 154:		Line 154:

	Possible new terms to add: lobe, tooth, mucro, areole, sinus, domatia, pinna, pinnule, others?		Possible new terms to add: lobe, tooth, mucro, areole, sinus, domatia, pinna, pinnule, others?
		+
		+	''There was some discussion of whether something like lobe or tooth is an entity in the PO, or a phenotype. For example, you could say "leaf margin lobed" as a phenotype. But then how to annotate expression to a lobe? You could put the the annotation on leaf margin, but the expression isn't really the whole margin, and may extend in past the margin into the lobe.''
		+
		+	''[http://sourceforge.net/tracker/index.php?func=detail&aid=3080925&group_id=76834&atid=835555 Tendril] is another structure we will need, but it has already been requested on SF.''

	'''2. Within ‘leaf’ subsection of PO, find terms where database cross-references to taxonomic nodes within RegNum would be useful for delimiting which taxa the term applies to. Find appropriate IDs within RegNum that could be used as dbxrefs for these PO terms.'''		'''2. Within ‘leaf’ subsection of PO, find terms where database cross-references to taxonomic nodes within RegNum would be useful for delimiting which taxa the term applies to. Find appropriate IDs within RegNum that could be used as dbxrefs for these PO terms.'''

← Older revision		Revision as of 12:51, 25 May 2011
Line 168:		Line 168:

	Could also get non-vascular leaf characters from glossaries in Parihar, Schofeld, Crum, etc..		Could also get non-vascular leaf characters from glossaries in Parihar, Schofeld, Crum, etc..
		+
		+	''We reviewed list of leaf descriptors from Harris and Harris that LC had converted to a spread sheet. We could also use images from Lawrence's "Vascular Plant Anatomy," since they are older and past copyright. We also discussed the possibility of using something like [http://www.morphobank.org/ Morphobank] or Delta to construct character matrix based on PO terms. These allow you to insert images into cells. (Could even use Mesquite).''
		+
		+	''Need to set up a matrix with PO terms in first column, different characters across the other columns, then character states in each cell.
		+
		+	''We will probably need to create an ontology of phenotypic descriptors for plants that is maintained by PO. It should be based on PATO. PATO could host it, but they may not be able to get the terms in fast enough.''

@@ Line 122: / Line 122: @@
 ''PJ suggested we should have a count of the terms associated with the new relations and provide a few examples
 '''* update on PO page, Facebook'''
 ==Review of leaf terms for Phenotype RCN meeting next week==

@@ Line 72: / Line 72: @@
 -SVN folder has been created and the translation files are in it.
--''we have a file of the Spanish synonyms, including ASCII characters for almost all the terms in the release, but the script to add them to the OBO file is not ready. ''These can go in the next release''
+-''we have a file of the Spanish synonyms, including ASCII characters for almost all the terms in the release, but the script to add them to the OBO file is not ready. ''
 -''File of the Japanese synonyms is based on the live version (Jan 2011 release, Version #14)''
 =Timeline for release:=

← Older revision		Revision as of 19:32, 24 May 2011
Line 67:		Line 67:

	''We will not try to copy these annotations before this release -- leave at it is for now and they will be caught by TAIR or other for the next release.''		''We will not try to copy these annotations before this release -- leave at it is for now and they will be caught by TAIR or other for the next release.''
		+
		+
		+	===translation synonyms===
		+	-SVN folder has been created and the translation files are in it.
		+
		+	-we have a file of the Spanish synonyms, including ASCII characters for almost all the terms in the release, but the script to add them to the OBO file is not ready. ''These can go in the next release''
		+
		+	-File of the Japanese synonyms is based on the live version (Jan 2011 release, Version #14)

	=Timeline for release:=		=Timeline for release:=

← Older revision		Revision as of 19:27, 24 May 2011
Line 48:		Line 48:

	''Be sure web page is updated too.''		''Be sure web page is updated too.''
		+
		+	''relation icons will be stored on the SVN in the icons folder''

	===Annotations on parts of leaf===		===Annotations on parts of leaf===

@@ Line 94: / Line 94: @@
 ===* Week of May 23-26th:===
-*fix any final issues that have come up:
+'''*fix any final issues that have come up:'''
 ''-add comments to the part_of children of leaf to remind users to annotate to either vascular or non-vascular leaf''
@@ Line 110: / Line 110: @@
 ''PJ suggested we should have a count of the terms associated with the new relations and provide a few examples
-* update on PO page, Facebook
+'''* update on PO page, Facebook'''
-'''-Release on live browser by the end of this week'''
+'''* Release on live browser by the end of this week'''
 ==Review of leaf terms for Phenotype RCN meeting next week==