POC Conf. Call 8-16-11 - Revision history

Rwalls: /* Syncing PO and CL */

2011-08-05T20:03:56Z

Syncing PO and CL

Rwalls: /* New terms for CL */

2011-08-05T20:03:08Z

New terms for CL

Rwalls: /* others= */

2011-08-05T19:44:56Z

others=

Rwalls: /* epidermal cells */

2011-08-05T19:43:09Z

epidermal cells

Rwalls at 19:39, 5 August 2011

2011-08-05T19:39:02Z

Cooperl at 17:01, 18 July 2011

2011-07-18T17:01:00Z

Cooperl: Created page with ''''POC meeting, Webex Conference Call; Date: Tuesday Aug 16th, 2011 10am (PDT)''' In attendance: POC members: Absent: Collaborators: Acceptance of the minutes from the …'

2011-07-07T15:33:39Z

Created page with ''''POC meeting, Webex Conference Call; Date: Tuesday Aug 16th, 2011 10am (PDT)''' In attendance: POC members: Absent: Collaborators: Acceptance of the minutes from the …'

New page

'''POC meeting, Webex Conference Call; Date: Tuesday Aug 16th, 2011 10am (PDT)'''

In attendance:

POC members:

Absent:

Collaborators:

Acceptance of the minutes from the [[POC_Conf._Call_8-2-11]]?

← Older revision		Revision as of 20:03, 5 August 2011
Line 12:		Line 12:
	Acceptance of the minutes from the [[POC_Conf._Call_8-2-11]]?		Acceptance of the minutes from the [[POC_Conf._Call_8-2-11]]?

−
−	~~=Syncing PO and CL=~~
−
−	~~CL plans to obsolete most of its plant cell types, and add xrefs to those for PO terms.~~
−
−	~~CL will provide bridge files as part of the CL release process.~~
−
−	~~==Problematic xrefs to CL terms from PO==~~
−
−	~~PO has xrefs to 46 CL terms. Most are fine. 9 are not under CL's category for plant cells, and a few are potentially problematic.~~
−
−	~~===plant cell===~~
−
−	~~PO:0009002 (plant cell) xref to CL:0000610 (plant cell).~~
−
−	~~CL defines plant cell as "A cell found in seeded plants."~~
−
−	~~Suggest that CL adopt PO's definition of plant cell.~~
−
−	~~===epidermal cells===~~
−	*PO:0004013 (epidermal cell) xref to CL:0000362 (epidermal cell)
−
−	~~CL:0000362 is_a squamose epithelial cell, is_a general ecto-epithelial cell~~
−
−	*PO:0000332 (epidermal pavement cell) xref to CL:0000400 (pavement cell)
−
−	~~CL:0000400 is_a epidermal cell~~
−
−	*PO:0000115 (socket cell) xref to CL:0000297 (socket cell)
−
−	~~CL:0000297 is_a epidermal cell, is_a supportive cell~~
−
−	*PO:0000282 (trichome) xref to CL:0000282 (trichome)
−
−	~~CL:0000282 is_a epidermal cell.~~
−
−	The xref from PO:0000282 to CL:0000282 should be on removed, and instead, there should be an xref from PO:0008030 (trichome cell) to CL:0000282. CL may want to obsolete CL:0000282 along with the other plant cell types, unless it is meant to refer to hairs on any type of organism.
−
−	~~===others===~~
−
−	*PO:0000423 (zygote) xref to CL:0000365 (zygote).
−
−	~~CL:0000365 is_a cell by lineage, is_a early embryonic cell. This is probably fine.~~
−
−	*PO:0004531 (sheath cell) xref to CL:0000618 (sheath cell).
−
−	~~CL:0000618 has no definition, but is_a columnar/cuboidal epithelial cell. Suggest we remove this xref and the CL obsolete the term.~~
−
−	*PO:0000263 (atrichoblast) xref to CL:0000332 (atrichoblast).
−
−	~~CL:0000332 is_a epidermal initial, is_a non-terminally differentiated cell (second is_a relation is redundant).~~
−
−	~~PO definition of atrichblast is: A root epidermal cell that is formed after asymmetric division of an epidermal initial and does not give rise to a root hair.~~
−
−	~~Suggest that CL obsolete CL:0000332, because it is a plant cell, and their definition is not up to date.~~
−
−	*PO:0004011 (initial cell) CL:0000034 stem cell CL:0000266 meristemoid PO:0000070 is_a cell, is_a cell by function
−
−	~~==PO cell types that should reference cell types in CL==~~
−
−	A few types of cells may fall are equivalent to remaining CL terms. If so, then they should have a general xref, then assert the general xrefs as relations using the header "treat-xrefs-as-equivalent: CL" (see [http://www.geneontology.org/GO.format.obo-1_4.shtml#S.1.4 obo format guidelines]).
−
−	~~PO:0009002 plant cell > CL:0000610 plant cell~~
−
−	~~PO:0000423 zygote > CL:0000365 zygote~~
−
−	~~==New terms for CL==~~
−
−	There are four terms in CL for which PO does not have equivalent terms, because it was set up for only angiosperms. Suggest we add terms like these when we work on the revisions of conducting tissue and cells. For now, Terry has removed the problematic xrefs from CL, will update them if we add new terms.
−
−	~~See [https://sourceforge.net/tracker/?func=detail&aid=3386970&group_id=76834&atid=835555 conducting cells for non-vascular plants].~~

	=Next meeting scheduled for Tuesday, Aug 23rd, 2011 at 10am PDT/1pm EDT=		=Next meeting scheduled for Tuesday, Aug 23rd, 2011 at 10am PDT/1pm EDT=

← Older revision		Revision as of 20:03, 5 August 2011
Line 69:		Line 69:

	*PO:0004011 (initial cell) CL:0000034 stem cell CL:0000266 meristemoid PO:0000070 is_a cell, is_a cell by function		*PO:0004011 (initial cell) CL:0000034 stem cell CL:0000266 meristemoid PO:0000070 is_a cell, is_a cell by function
		+
		+	==PO cell types that should reference cell types in CL==
		+
		+	A few types of cells may fall are equivalent to remaining CL terms. If so, then they should have a general xref, then assert the general xrefs as relations using the header "treat-xrefs-as-equivalent: CL" (see [http://www.geneontology.org/GO.format.obo-1_4.shtml#S.1.4 obo format guidelines]).
		+
		+	PO:0009002 plant cell > CL:0000610 plant cell
		+
		+	PO:0000423 zygote > CL:0000365 zygote

	==New terms for CL==		==New terms for CL==

@@ Line 50: / Line 50: @@
 The xref from PO:0000282 to CL:0000282 should be on removed, and instead, there should be an xref from PO:0008030 (trichome cell) to CL:0000282. CL may want to obsolete CL:0000282 along with the other plant cell types, unless it is meant to refer to hairs on any type of organism.
-==others===
+===others===
 *PO:0000423 (zygote) xref to CL:0000365 (zygote).
-CL:0000365 is_a cell by lineage, is_a early embryonic cell. I think this is fine.
+CL:0000365 is_a cell by lineage, is_a early embryonic cell. This is probably fine.
 *PO:0004531 (sheath cell) xref to CL:0000618 (sheath cell).
@@ Line 69: / Line 69: @@
 *PO:0004011 (initial cell)	CL:0000034 stem cell	CL:0000266 meristemoid	PO:0000070	is_a cell, is_a cell by function
 ==New terms for CL==

@@ Line 36: / Line 36: @@
 CL:0000362 is_a squamose epithelial cell, is_a general ecto-epithelial cell
-*PO:0000332 (epidermal pavement cell) xref to CL:0000400			is_a epidermal cell
+*PO:0000332 (epidermal pavement cell) xref to CL:0000400 (pavement cell)
-PO:0000115	socket cell	CL:0000297			is_a epidermal cell, is_a supportive cell
+CL:0000400 is_a epidermal cell
-PO:0000282	trichome	CL:0000282			is_a epidermal cell; xref to CL should be on trichome cell
+*PO:0000115 (socket cell) xref to CL:0000297 (socket cell)
 ==others===

← Older revision		Revision as of 19:39, 5 August 2011
Line 12:		Line 12:
	Acceptance of the minutes from the [[POC_Conf._Call_8-2-11]]?		Acceptance of the minutes from the [[POC_Conf._Call_8-2-11]]?

		+
		+	=Syncing PO and CL=
		+
		+	CL plans to obsolete most of its plant cell types, and add xrefs to those for PO terms.
		+
		+	CL will provide bridge files as part of the CL release process.
		+
		+	==Problematic xrefs to CL terms from PO==
		+
		+	PO has xrefs to 46 CL terms. Most are fine. 9 are not under CL's category for plant cells, and a few are potentially problematic.
		+
		+	===plant cell===
		+
		+	PO:0009002 (plant cell) xref to CL:0000610 (plant cell).
		+
		+	CL defines plant cell as "A cell found in seeded plants."
		+
		+	Suggest that CL adopt PO's definition of plant cell.
		+
		+	===epidermal cells===
		+	*PO:0004013 (epidermal cell) xref to CL:0000362 (epidermal cell)
		+
		+	CL:0000362 is_a squamose epithelial cell, is_a general ecto-epithelial cell
		+
		+	*PO:0000332 (epidermal pavement cell) xref to CL:0000400 is_a epidermal cell
		+
		+	PO:0000115 socket cell CL:0000297 is_a epidermal cell, is_a supportive cell
		+
		+	PO:0000282 trichome CL:0000282 is_a epidermal cell; xref to CL should be on trichome cell
		+
		+
		+
		+	==others===
		+
		+	*PO:0000423 (zygote) xref to CL:0000365 (zygote).
		+
		+	CL:0000365 is_a cell by lineage, is_a early embryonic cell. I think this is fine.
		+
		+	*PO:0004531 (sheath cell) xref to CL:0000618 (sheath cell).
		+
		+	CL:0000618 has no definition, but is_a columnar/cuboidal epithelial cell. Suggest we remove this xref and the CL obsolete the term.
		+
		+	*PO:0000263 (atrichoblast) xref to CL:0000332 (atrichoblast).
		+
		+	CL:0000332 is_a epidermal initial, is_a non-terminally differentiated cell (second is_a relation is redundant).
		+
		+	PO definition of atrichblast is: A root epidermal cell that is formed after asymmetric division of an epidermal initial and does not give rise to a root hair.
		+
		+	Suggest that CL obsolete CL:0000332, because it is a plant cell, and their definition is not up to date.
		+
		+	*PO:0004011 (initial cell) CL:0000034 stem cell CL:0000266 meristemoid PO:0000070 is_a cell, is_a cell by function
		+
		+
		+	==New terms for CL==
		+
		+	There are four terms in CL for which PO does not have equivalent terms, because it was set up for only angiosperms. Suggest we add terms like these when we work on the revisions of conducting tissue and cells. For now, Terry has removed the problematic xrefs from CL, will update them if we add new terms.
		+
		+	See [https://sourceforge.net/tracker/?func=detail&aid=3386970&group_id=76834&atid=835555 conducting cells for non-vascular plants].

	=Next meeting scheduled for Tuesday, Aug 23rd, 2011 at 10am PDT/1pm EDT=		=Next meeting scheduled for Tuesday, Aug 23rd, 2011 at 10am PDT/1pm EDT=

← Older revision		Revision as of 17:01, 18 July 2011
Line 11:		Line 11:

	Acceptance of the minutes from the [[POC_Conf._Call_8-2-11]]?		Acceptance of the minutes from the [[POC_Conf._Call_8-2-11]]?
		+
		+
		+	=Next meeting scheduled for Tuesday, Aug 23rd, 2011 at 10am PDT/1pm EDT=