PO/CL Conference call 08-30-11 - Revision history

Cooperl: /* plant cell */

2013-10-22T00:31:02Z

plant cell

Rwalls: /* Equivalent cell types in PO and CL */

2011-08-31T21:42:48Z

Equivalent cell types in PO and CL

Rwalls: /* Equivalent cell types in PO and CL */

2011-08-31T21:04:06Z

Equivalent cell types in PO and CL

Rwalls: /* plant cell */

2011-08-30T21:27:42Z

plant cell

Rwalls: /* epidermal cells */

2011-08-30T21:27:03Z

epidermal cells

Rwalls at 21:26, 30 August 2011

2011-08-30T21:26:22Z

Rwalls: /* Problematic xrefs to CL terms from PO */

2011-08-30T21:15:53Z

Problematic xrefs to CL terms from PO

Rwalls: /* Problematic xrefs to CL terms from PO */

2011-08-30T21:07:40Z

Problematic xrefs to CL terms from PO

Rwalls: /* Syncing PO and CL */

2011-08-30T21:04:08Z

Syncing PO and CL

Rwalls: /* PO cell types that should reference cell types in CL */

2011-08-30T20:48:15Z

PO cell types that should reference cell types in CL

← Older revision		Revision as of 00:31, 22 October 2013
Line 53:		Line 53:

	''PO will remove xref to CL:0000610.''		''PO will remove xref to CL:0000610.''
		+
		+	''Note: as of 2013, CL:0000610 has been obsoleted''

	===zygote===		===zygote===

@@ Line 137: / Line 137: @@
 PO:0004010 meristem is a subtype of CL:0000034 stem cell.
-PO will add CL:0000034 as a general xref to PO:0004010, then assert the general xrefs as genus-differentia, using the header "treat-xrefs-as-genus-differntia: CL part_of NCBITaxon:(need to get id for land plants)"
+PO will add CL:0000034 as a general xref to PO:0004010, then assert the general xrefs as genus-differentia, using the header "treat-xrefs-as-genus-differntia: CL part_of NCBITaxon:3193 (Embryophyta)"
 See [http://www.geneontology.org/GO.format.obo-1_4.shtml#S.1.4 obo format guidelines].

@@ Line 133: / Line 133: @@
 =Equivalent cell types in PO and CL=
-Based on the decisions above, the only equivalent terms in PO and CL are for plant cell (PO:0009002 and CL:0000610). CL will add PO:0009002 as xref, and use "treat-xrefs-as-equivalent:PO"
+Based on the decisions above, the only equivalent terms in PO and CL are for plant cell (PO:0009002 and CL:0000610). CL will add PO:0009002 as xref, and use "treat-xrefs-as-equivalent: PO"
 PO:0004010 meristem is a subtype of CL:0000034 stem cell.
-PO will add CL:0000034 as a general xref to PO:0004010, then assert the general xrefs as genus-differentia, using the header "treat-xrefs-as-genus-differntia:CL"
+PO will add CL:0000034 as a general xref to PO:0004010, then assert the general xrefs as genus-differentia, using the header "treat-xrefs-as-genus-differntia: CL part_of NCBITaxon:(need to get id for land plants)"
 See [http://www.geneontology.org/GO.format.obo-1_4.shtml#S.1.4 obo format guidelines].

← Older revision		Revision as of 21:27, 30 August 2011
Line 48:		Line 48:


−	''For now, CL will keep CL:0000610 (but use PO's definition, instead of the current one) and add an xref to PO:0009002. Cl will add header to treat PO xrefs as equivalent.''	+	''For now, CL will keep CL:0000610 (but use PO's definition, instead of the current one) and add an xref to PO:0009002. CL will add header to treat PO xrefs as equivalent.''

	''If CL were to use PO:0009002 as the primary id (by Mireoting it or other mechanism), it would not show up in CL basic.''		''If CL were to use PO:0009002 as the primary id (by Mireoting it or other mechanism), it would not show up in CL basic.''

@@ Line 93: / Line 93: @@
 The xref from PO:0000282 to CL:0000282 should be on removed, because CL:0000282 really corresponds to PO:0008030 (trichome cell).
-''It is not clear from the CL definition if CL:0000282 refers to a hair in any organism or only to plant trichomes. If it refers to plant trichome cells only, then CL should obsolete CL:0000282 along with the other plant cell types. Should look at how GO treats trichome cells.''
+It is not clear from the CL definition if CL:0000282 refers to a hair in any organism or only to plant trichomes. If it refers to plant trichome cells only, then CL should obsolete CL:0000282 along with the other plant cell types. Should look at how GO treats trichome cells.
 ===others===

@@ Line 131: / Line 131: @@
 ''PO should not reference CL:0000266, because it is an animal cell.  Will remove xrefs. See below about xref for meristematic cell.''
-===PO cell types that should reference cell types in CL===
+=Equivalent cell types in PO and CL=
-Based on the decisions above, the only equivalent terms in PO and CL are plant cel If so, then they should have a general xref, then assert the general xrefs as equivalent using the header "treat-xrefs-as-genus-differntia: CL" (see [http://www.geneontology.org/GO.format.obo-1_4.shtml#S.1.4 obo format guidelines]).
+Based on the decisions above, the only equivalent terms in PO and CL are for plant cell (PO:0009002 and CL:0000610). CL will add PO:0009002 as xref, and use "treat-xrefs-as-equivalent:PO"
-PO:0009002 plant cell > CL:0000610 plant cell (''but maybe CL will use PO id'')
+PO:0004010 meristem is a subtype of CL:0000034 stem cell.
-PO:0000423 zygote > CL:0000365 zygote
+PO will add CL:0000034 as a general xref to PO:0004010, then assert the general xrefs as genus-differentia, using the header "treat-xrefs-as-genus-differntia:CL"
-PO:0004011/PO:0000070 intial cell/meristemoid > CL:0000266 meristemoid
+See [http://www.geneontology.org/GO.format.obo-1_4.shtml#S.1.4 obo format guidelines].
 ==New terms for CL==

@@ Line 35: / Line 35: @@
 * Here is what CM said about the xrefs to CL: "Hmm, have to figure out what to do about the CL xrefs. I think all the ones that have been obsoleted should be translated to alt_ids. If we have one remaining, PO:0009002, keep the xref and add a header: treat-xrefs-as-equivalent: CL".
 ===plant cell===
@@ Line 61: / Line 62: @@
 We should keep this xref. See below on treating xrefs as equivalent terms.
-''We don't need to name this "plant zygote" because it is really the same thing across organisms.''
+We don't need to name this "plant zygote" because it is really the same thing across organisms.
-''This is okay.''
 ===epidermal cells===
-''POC agreed to the suggestions below, but need to confirm with CL that or interpretation of their terms is correct.''
+''CL has already obsoleted socket cell, pavement cell, and trichome. PO will remove all of the xrefs listed below.''
 *PO:0004013 (epidermal cell) xref to CL:0000362	(epidermal cell)
@@ Line 101: / Line 103: @@
 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).
@@ Line 109: / Line 114: @@
 Suggest that CL obsolete CL:0000332, because it is a plant cell, and their definition is not up to date. We will remove xref. PO:0000263 will be imported into CL when they bridge to plant cell types.
 *PO:0004011/PO:0000070 (initial cell) xref to CL:0000034 (stem cell) and CL:0000266 (meristemoid)
@@ Line 121: / Line 129: @@
 Based on these definitions, PO:0004011/PO:0000070 is a better match to CL:0000266. Furthermore, meristemoid is an exact synonym of initial cell.
-We should remove the xref to CL:0000034 and keep the xref to CL:0000266. See below on treating xrefs as equivalent terms.
+''PO should not reference CL:0000266, because it is an animal cell.  Will remove xrefs. See below about xref for meristematic cell.''
 ===PO cell types that should reference cell types in CL===
-A few types of cells are equivalent to remaining CL terms. If so, then they should have a general xref, then assert the general xrefs as equivalent 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]).
+Based on the decisions above, the only equivalent terms in PO and CL are plant cel If so, then they should have a general xref, then assert the general xrefs as equivalent using the header "treat-xrefs-as-genus-differntia: 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 (''but maybe CL will use PO id'')

@@ Line 33: / Line 33: @@
 * Nine of the xrefs are not under CL's category for plant cells, and require special attention (see below).
-''Here is what CM said about the xrefs to CL: "Hmm, have to figure out what to do about the CL xrefs. I think all the ones that have been obsoleted should be translated to alt_ids. If we have one remaining, PO:0009002, keep the xref and add a header: treat-xrefs-as-equivalent: CL".''
+* Here is what CM said about the xrefs to CL: "Hmm, have to figure out what to do about the CL xrefs. I think all the ones that have been obsoleted should be translated to alt_ids. If we have one remaining, PO:0009002, keep the xref and add a header: treat-xrefs-as-equivalent: CL".
@@ Line 44: / Line 44: @@
 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 probably use PO:0009002 as the primary number, and either obsolete CL:0000610 or merge it into PO:0009002.''
+From PO meeting: ''CL should probably use PO:0009002 as the primary number, and either obsolete CL:0000610 or merge it into PO:0009002.''
 ===zygote===

@@ Line 12: / Line 12: @@
 CL will provide bridge files as part of the CL release process.
-''-- Is this accurate?''
 ==New subset for CL==
@@ Line 20: / Line 23: @@
 This subset will need to be updated whenever we add new cell types.
-''Details on how CL will create and maintain bridge file?''
+''In the future OORT will be able to generate subsets like this automatically. For now, PO can maintain it mannually, since it is already done.''
 =Problematic xrefs to CL terms from PO=

← Older revision		Revision as of 20:48, 30 August 2011
Line 125:		Line 125:

	''This is okay for zygote and meristemoid. Maybe CL should get rid of CL:0000610.''		''This is okay for zygote and meristemoid. Maybe CL should get rid of CL:0000610.''
		+
		+	PO:0004010 meristem > CL:0000034
		+
		+	Treat xrefs as g-d

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