POC Conf. Call 5-11-10 - Revision history

Rwalls at 11:35, 12 May 2010

2010-05-12T11:35:26Z

Rwalls at 11:33, 12 May 2010

2010-05-12T11:33:00Z

Rwalls at 11:28, 12 May 2010

2010-05-12T11:28:53Z

Cooperl at 21:52, 11 May 2010

2010-05-11T21:52:01Z

Cooperl at 21:51, 11 May 2010

2010-05-11T21:51:39Z

Rwalls at 11:33, 11 May 2010

2010-05-11T11:33:17Z

Rwalls at 11:26, 11 May 2010

2010-05-11T11:26:54Z

Cooperl at 21:11, 10 May 2010

2010-05-10T21:11:15Z

Cooperl at 21:05, 10 May 2010

2010-05-10T21:05:01Z

Cooperl at 21:01, 10 May 2010

2010-05-10T21:01:26Z

← Older revision		Revision as of 11:35, 12 May 2010
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−	''4. Upcoming Conferences and Meetings: Updates'''	+	'''4. Upcoming Conferences and Meetings:''' Updates
		+
		+	''There was no discussion of upcoming conferences and meeting (other than the CL meeting).''
		+

@@ Line 87: / Line 87: @@
 ''Barry gave some background on what the CL is trying to accomplish. Said that the Bard et al. 2005 paper is largely out of date. They are currently aiming to have an ontology where each term has a single parent, based on structural properties of cells. Shared a paper that describes an ontology for dendritic cells (http://www.biomedcentral.com/1471-2105/10/70/abstract/) and provides an example of how the CL is trying to structure their entire ontology. Suggested that the PO should try to find cell types that are very general, based on their structure, and submit those to CL. We discussed parenchymatic cells as a cell type that is unique to plants and epidermal cells as a cell type that is shared by plants and animals (at least in name), but actually represents two different types of cells.''
 ''There was general agreement that plant cell types should be defined and curated by, and annotated in, the PO, but it was not clear if upper level terms that appear in the CL would have CL or PO id's. We will need to discuss this at the meeting.''
@@ Line 104: / Line 106: @@
 Note that we may need to define parthenocarpy at some point (or put in a dbx ref for it).
 Dbx ref to parthenogenesis: Medical subject heading Ontology D010312
 '''2.  Embryo''' (See SF Tracker: [https://sourceforge.net/tracker/?func=detail&aid=2982384&group_id=76834&atid=835555/ embryo])
 '''Current def'n:''' A young sporophyte contained within a seed. [source: APWeb:Glossary, GR:pj]

← Older revision		Revision as of 11:28, 12 May 2010
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	* In addition to cell by organism, the CL also lists cells by type. Right now, it gamete is the only haploid plant cell, but this leaves out all the cells in gametophytes. May also want to add triploid cells of endosperm under polyploid cell.''		* In addition to cell by organism, the CL also lists cells by type. Right now, it gamete is the only haploid plant cell, but this leaves out all the cells in gametophytes. May also want to add triploid cells of endosperm under polyploid cell.''

		+
		+	''Barry gave some background on what the CL is trying to accomplish. Said that the Bard et al. 2005 paper is largely out of date. They are currently aiming to have an ontology where each term has a single parent, based on structural properties of cells. Shared a paper that describes an ontology for dendritic cells (http://www.biomedcentral.com/1471-2105/10/70/abstract/) and provides an example of how the CL is trying to structure their entire ontology. Suggested that the PO should try to find cell types that are very general, based on their structure, and submit those to CL. We discussed parenchymatic cells as a cell type that is unique to plants and epidermal cells as a cell type that is shared by plants and animals (at least in name), but actually represents two different types of cells.''
		+
		+	''There was general agreement that plant cell types should be defined and curated by, and annotated in, the PO, but it was not clear if upper level terms that appear in the CL would have CL or PO id's. We will need to discuss this at the meeting.''

← Older revision		Revision as of 21:52, 11 May 2010
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	Acceptance of the minutes from last weeks meeting? All in favor?		Acceptance of the minutes from last weeks meeting? All in favor?
		+
	''There were no additions, deletions or changes to last weeks minutes.''		''There were no additions, deletions or changes to last weeks minutes.''

@@ Line 1: / Line 1: @@
 POC meeting, Webex Conference Call; Date: May 11th, 2010 10am (PDT)
 Acceptance of the minutes from last weeks meeting? All in favor?
+''There were no additions, deletions or changes to last weeks minutes.''
 == Agenda: ==

← Older revision		Revision as of 11:33, 11 May 2010
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−	-- [http://plantontology.org/amigo/go.cgi?action=~~minus_node~~&search_constraint=terms&query=PO:~~0000423~~&session_id=5918b1272559194 current PO browser with all cell types expanded]	+	-- [http://plantontology.org/amigo/go.cgi?action=plus_node&depth=1&search_constraint=terms&query=PO:0000274&session_id=5918b1272559194 current PO browser with all cell types expanded]

	-- [http://dev.plantontology.org:8080/amigo/go.cgi?action=plus_node&depth=1&search_constraint=terms&query=PO:0025029&session_id=7712b1273499903 dev PO browser with possible new organization for plant cell types]		-- [http://dev.plantontology.org:8080/amigo/go.cgi?action=plus_node&depth=1&search_constraint=terms&query=PO:0025029&session_id=7712b1273499903 dev PO browser with possible new organization for plant cell types]

@@ Line 24: / Line 24: @@
 *incorporate phenotypic information about these cell types and is thus far more comprehensive in its cellular detail than these other resources
 *provide organism-independent knowledge as well as cell-type unique identifiers (ID) that can be incorporated into any database holding cell-type-associated knowledge
-*expected us cataloging phenotypes and gene expression patterns
+*expected use cataloging phenotypes and gene expression patterns
 [http://obofoundry.org/wiki/index.php/Cell_Ontology_Workshop_2010#Agenda Cell Type Ontology Workshop]

@@ Line 31: / Line 31: @@
 *Laurel and Ramona will attend and will give a 10-15 minute presentation
 Points:
-Basic goals of PO
+Basic goals of PO:
 *to encompass all plants
@@ Line 41: / Line 39: @@
 *machine-readable definitions
 *separation of ''in vitro'' and ''in vivo'' plant cell terms
 *plant cell organization mirrors organization of plant structure with cell types that are specific to sporophytes, gametophytes and whole plant (can occur in gametophyte or sporophyte):
@@ Line 52: / Line 51: @@
 whole plant cell is_a plant cell that can occur in a gametophyte or sporophyte; example: axial cell
 -- [http://plantontology.org/amigo/go.cgi?action=minus_node&search_constraint=terms&query=PO:0000423&session_id=5918b1272559194 current PO browser with all cell types expanded]
@@ Line 65: / Line 61: @@
 *If CL is going to use PO terms, definitions, and structures, should they use our ID numbers (see below:)?
-*Should there be hyperlinks to the PO browser from the CL?
+*Should there be hyper links to the PO browser from the CL?
 - [http://www.obofoundry.org/wiki/index.php/Identifiers From OBO foundry Identifiers wiki page]:
@@ Line 74: / Line 70: @@
-From last week:
+General Comments:
-* Laurel, Ramona and Rex had a brief discussion about plant cells at the end of the meeting.  Rex said he made the list of terms that were in the PO but not the CL by going through the two ontologies term by term. Ramona said there do not appear to be any terms that are in the CL but not the PO, but we need to check systematically.''
+* The two ontologies have similar structure (at least under 'plant cell'), with a few differences, probably changes that were made after terms were imported into the CL. It might be better to have a more hierarchical structure so there are not so many direct children of plant cell.
-* The two ontologies have similar structure, with a few differences, probably changes that were made after terms were imported into the CL. It might be better to have a more hierarchical structure so there are not so many direct children of plant cell.''
+* In addition to cell by organism, the CL also lists cells by type. Right now, it gamete is the only haploid plant cell, but this leaves out all the cells in gametophytes. May also want to add triploid cells of endosperm under polyploid cell.''

@@ Line 61: / Line 61: @@
 *Should we aim for complete '''redundancy between cells in PO and plant cells in CL'''?
-(List of PO plant cell types that are not in the Cell.obo file (thanks Rex!)) Do we want to request that these terms be included in the CL?
+List of PO plant cell types that are not in the Cell.obo file (thanks Rex!) Do we want to request that these terms be included in the CL?
 *If CL is going to use PO terms, definitions, and structures, should they use our ID numbers (see below:)?
@@ Line 81: / Line 81: @@
 * In addition to cell by organism, the CL also lists cells by type. Right now, it gamete is the only haploid plant cell, but this leaves out all the cells in gametophytes. May also want to add triploid cells of endosperm under polyploid cell.''

@@ Line 143: / Line 143: @@
 '''* Bio-Ontologies 2010: Semantic Applications in Life Sciences.''' July 9th and 10th, 2010, Boston, Mass. Satellite Interest Group (SIG) meeting preceding the International Society for Computational Biology (ISCB). Laurel, Ramona are registered.
--Flash updates, up to 1 page: (short talks (5 min) giving the salient new developments on existing public ontologies) -Poster abstracts, up to 1 page (posters will be up for 2 days, with at least 1 poster session) Poster authors can also do a flash update.
+Our one page write up has been selected for a 'flash update talk' along with the poster.  Final revisions need to be submitted by Friday May 14th.
 '''* American Society of Plant Biology (ASPB) July 31-Aug 4th 2010, Montreal, Quebec, Canada.''' Laurel, Pankaj going,
@@ Line 162: / Line 159: @@
 Dennis and Alejandra are already planning to attend IBC2011 and speak in other symposia.
-Ramona circulated a proposal that was submitted on Thursday April 29th and contacted the organizers about whether or not it is possible to get a room with internet for outreach activities.
+Ramona circulated a proposal that was submitted on Thursday April 29th and contacted the organizers about whether or not it is possible to get a room with Internet for outreach activities.
 Pankaj will be co-organizer with Ramona.  Laurel and Ramona are interested in going and speaking if funds are available.
@@ Line 177: / Line 174: @@
-'''8. Next meeting scheduled for Tuesday May 25th at 10am PDT.'''
+'''8. Next meeting scheduled for '''Tuesday May 25th at 10am PDT'''.'''