POC Conf. Call 8-23-11 - Revision history

Cooperl at 19:38, 8 March 2012

2012-03-08T19:38:31Z

2011-08-24T15:18:43Z

tassel and ear

2011-08-23T23:16:59Z

others

2011-08-23T23:11:27Z

tassle and ear

2011-08-23T23:08:00Z

Conference report

2011-08-23T20:50:12Z

2011-08-23T20:33:31Z

Update on addition of new MaizeGDB Annotations

2011-08-23T20:17:07Z

epidermal cells

2011-08-23T20:16:46Z

Problematic xrefs to CL terms from PO

2011-08-23T20:15:35Z

plant cell

← Older revision		Revision as of 19:38, 8 March 2012
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	Acceptance of the minutes from the [[POC_Conf._Call_8-2-11]]? ''There were no changes, additions, or deletions.''		Acceptance of the minutes from the [[POC_Conf._Call_8-2-11]]? ''There were no changes, additions, or deletions.''

−	~~[https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=56620957&rKey=e7a67bf8374c8519 link to Webex recording of the meeting]~~

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 We don't want to get rid of tassel and ear at this point (although they could just be synonyms of inflorescence). "Ear" is only used in maize.  "Cob" is a synonym of inflorescence, used for sorghum.
-No one was comfortable with the name "functionally male (or female) inflorescence, because of the implications.
+No one was comfortable with the name "functionally male (or female) inflorescence", because it suggests that both male and female flowers are present, but only one type is functional.
 We will use the names "tassle inflorescence" and "ear inflorescence".

@@ Line 177: / Line 177: @@
 ===others===
 ''We agreed to the suggestions below, but will set up a call with CL to go over them. For example, need to make sure that sheath cell really was supposed to refer to a type of plant cell and that this is not some kind of animal cell called a sheath cell. Need to talk to them about trichomes or hair cells too. Should look at how GO treats them.''
 *PO:0004531 (sheath cell) xref to CL:0000618 (sheath cell).
@@ Line 202: / Line 204: @@
 We should remove the xref to CL:0000034 and keep the xref to CL:0000266. See below on treating xrefs as equivalent terms.
 ===PO cell types that should reference cell types in CL===

@@ Line 84: / Line 84: @@
 It is documented in the SVN site and SourceForge, but that information is not so easy to find after some point. Better to have the information in the obo file.  PJ: there are ways to document changes in obo, but it is not standard format. PJ is asking them to make modified_on and modified_by part of the standard obo format.
-==tassle and ear==
+==tassel and ear==
-We don't want to get rid of tassle and ear at this point (although they could just be synonyms of inflorescence). "Ear" is only used in maize.  "Cob" is a synonym of inflorescence, used for sorghum.
+We don't want to get rid of tassel and ear at this point (although they could just be synonyms of inflorescence). "Ear" is only used in maize.  "Cob" is a synonym of inflorescence, used for sorghum.
-No one was comforatable with the name "functionally male (or female) inflorescence, because of the implications.
+No one was comfortable with the name "functionally male (or female) inflorescence, because of the implications.
-We will use the names "tassle infloresce" and "ear inflorescence".
+We will use the names "tassle inflorescence" and "ear inflorescence".
 ==strawberry structures==

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 [http://my.aspb.org/?page=Meetings_Annual Plant Biology 2011]
-Gramene and Plant Ontology hosted a [http://outreach.gramene.org/gramene-outreach/index.php/ASPB_2011_Workshop Data Curation Workshop] again, focusing on pathway curations.
+Gramene and Plant Ontology hosted a [http://outreach.gramene.org/gramene-outreach/index.php/ASPB_2011_Workshop Data Curation Workshop] again, focusing on Gramene tools and the PO.
 LC and PJ presented a [http://abstracts.aspb.org/pb2011/public/P21/P21013.html PO poster].
-TAIR/PMN (Kate Dreher) is organizing an [[Plant_Biology_2011_Outreach_Booth]] and we are invited to take part.  We are hosting the website.
+TAIR/PMN (Kate Dreher) organized a [[Plant_Biology_2011_Outreach_Booth]]and we took part, we hosted the website.
 =Update on addition of new MaizeGDB Annotations=

← Older revision		Revision as of 20:50, 23 August 2011
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	Acceptance of the minutes from the [[POC_Conf._Call_8-2-11]]? ''There were no changes, additions, or deletions.''		Acceptance of the minutes from the [[POC_Conf._Call_8-2-11]]? ''There were no changes, additions, or deletions.''
		+
		+	[https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=56620957&rKey=e7a67bf8374c8519 link to Webex recording of the meeting]

@@ Line 52: / Line 52: @@
 Got rid of 29 Zea/Poaceae specific terms by merging them into the their parent terms. See list of merged terms [http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/plant_ontology.obo?view=log here].
-Merged terms were those needed to accomodate the new MaizeGDB annotations, mostly anther and its parts, and silk/style.
+Merged terms were those needed to accommodate the new MaizeGDB annotations, mostly anther and its parts, and silk/style.
 This doesn't seem to cause any problems with loading the file. Still need to test how it will affect moving the annotations for the merged terms (they should automatically move with the merge).

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 PO:0004013 should be renamed plant epidermal cell (?). Remove xref to CL terms. PO:0004013 will be imported into CL with other plant cell types.
 *PO:0000332 (epidermal pavement cell) xref to CL:0000400 (pavement cell)
 CL:0000400 is_a epidermal cell. CL should obsolete this term, and PO should remove xref. PO:0000332 will be imported into CL with other plant cell types.
 *PO:0000115 (socket cell) xref to CL:0000297 (socket cell)
 CL:0000297 is_a epidermal cell, is_a supportive cell. CL should obsolete this term, and PO should remove xref. PO:0000115 will be imported into CL with other plant cell types.
 *PO:0000282 (trichome) xref to CL:0000282 (trichome)

@@ Line 118: / Line 118: @@
 *Most are accurate and reference CL plant cell types. '''Suggest that we delete these xrefs, because CL is going to obsolete those terms.'''
-* Nine of the xrefs are not under CL's category for plant cells, and require special attention:
+* Nine of the xrefs are not under CL's category for plant cells, and require special attention (see below).
 ===plant cell===

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 Suggest that CL adopt PO's definition of plant cell. We should keep this xref. See below on treating xrefs as equivalent terms.
-''CL should obsolete CL:0000610 and use PO:0009002.''
+''CL should probably obsolete CL:0000610 and use PO:0009002.''
 ===zygote===