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cooperl [Mon, 27 Sep 2010 21:28:04 +0000 (21:28 +0000)]
Edits to Gramene assoc files 9-27-10
The 15 annotations on PO:
0009003: sporophyte in
'po_anatomy_gene_oryza_gramene.assoc' were moved to PO:
0000003 whole
plant in the PSO.
Plus, the 15 from sporophyte were copied to
'po_growth_gene_oryza_gramene.assoc' and assigned to PO:
0028002
sprophytic stage.
po_anatomy_qtl_oryza_gramene.assoc
-In 'po_anatomy_qtl_oryza_gramene.assoc' moved the SDLVIG annotations
from sporophyte (PO:
0009003) to whole plant (PO:
0000003).
-In 'po_growth_qtl_oryza_gramene.assoc' the seedling vigor QTLs (SDLVIG)
are already assoc with seedling growth (PO:
0007131),
PO:
0009004: gametophyte 1
Source: Gramene
This annotation in 'po_growth_gene_oryza_gramene.assoc' was moved from
gametophyte (PO:
0009004) to male gametophyte (PO:
0020091)
Also, copied to 'po_growth_gene_oryza_gramene.assoc' and associated with
gametophytic phase (PO:
0028003).
Note: It is already associated with the megagametophytic stage
(PO:000721) ( This appears to be an error?) and pollen
developmental stage (PO:
0001007) in the PDGSO.
svn path=/; revision=105
cooperl [Tue, 21 Sep 2010 22:51:42 +0000 (22:51 +0000)]
Edits to 'po_anatomy_gene_arabidopsis_tair.assoc'
-PO:
0008034 leaf whorl replaced with PO:
0025022 collective leaf
structure (15,786)
-PO:
0008037 seedling replaced with PO:
0000003 whole plant (53)
-PO:
0009003 sporophyte replaced with PO:
0000003 whole plant (1)
Edits to 'po_temporal_gene_arabidopsis_tair.assoc'
-Added 53 annotations from PO:
0008037 seedling now on PO:
0007131
seedling growth stage
-Added 1 annotation from PO:
0009003 sporophyte now on PO:
0000003
sporophytic growth phase
Edits done by L. Cooper 9-21-10
svn path=/; revision=104
cooperl [Tue, 21 Sep 2010 17:52:19 +0000 (17:52 +0000)]
Edits to 'po_anatomy_gene_arabidopsis_tair.assoc' by L. Cooper
-Obsoleted term PO:
0008034 leaf whorl replaced with PO:
0025022 collective leaf
structure (15,786)
-Obsoleted term PO:
0008037 seedling replaced with PO:
0000003 whole plant (53)
-Obsoleted term PO:
0009003 sporophyte replaced with PO:
0000003 whole plant (1)
-saved as CSV txt file
svn path=/; revision=103
cooperl [Tue, 21 Sep 2010 17:15:55 +0000 (17:15 +0000)]
Updated files from TAIR
-This line, and those below, will be ignored--
M associations/po_temporal_gene_arabidopsis_tair.assoc
M associations/po_anatomy_gene_arabidopsis_tair.assoc
svn path=/; revision=102
liya [Thu, 24 Sep 2009 20:58:32 +0000 (20:58 +0000)]
gramene release30
svn path=/; revision=101
liya [Thu, 24 Sep 2009 20:58:18 +0000 (20:58 +0000)]
gramene release30
svn path=/; revision=100
liya [Thu, 24 Sep 2009 20:58:05 +0000 (20:58 +0000)]
gramene release30
svn path=/; revision=99
liya [Thu, 24 Sep 2009 20:57:48 +0000 (20:57 +0000)]
gramene release30
svn path=/; revision=98
shuly [Tue, 7 Apr 2009 02:24:12 +0000 (02:24 +0000)]
changed col 1 to MGCSC_genetic_stocks and col 6 to MGCSC_ref:
1232885
svn path=/; revision=97
shuly [Wed, 1 Apr 2009 22:14:39 +0000 (22:14 +0000)]
Changed annotation obkect type from stock to germplasm
svn path=/; revision=96
shuly [Wed, 1 Apr 2009 02:11:44 +0000 (02:11 +0000)]
release PO_0409
svn path=/; revision=95
shuly [Wed, 1 Apr 2009 02:00:08 +0000 (02:00 +0000)]
Not loaded to PO DB
svn path=/; revision=94
shuly [Wed, 1 Apr 2009 01:55:45 +0000 (01:55 +0000)]
po_growth_phenotype_melongena_sgn.assoc To po_growth_germplasm_S.melongena_sgn.assoc
svn path=/; revision=93
shuly [Wed, 1 Apr 2009 01:54:53 +0000 (01:54 +0000)]
po_growth_phenotype_lycopersicum_sgn.assoc To po_growth_germplasm_S.lycopersicum_sgn.assoc
svn path=/; revision=92
shuly [Wed, 1 Apr 2009 01:53:39 +0000 (01:53 +0000)]
Renamed po_growth_gene_lycopersicum_sgn.assoc To po_growth_gene_S.lycopersicum_sgn.assoc
svn path=/; revision=91
shuly [Wed, 1 Apr 2009 01:52:24 +0000 (01:52 +0000)]
Renamed po_anatomy_phenotype_melongena_sgn.assoc To po_anatomy_germplasm_S.melongena_sgn.assoc
svn path=/; revision=90
shuly [Wed, 1 Apr 2009 01:51:08 +0000 (01:51 +0000)]
Renamed po_anatomy_phenotype_lycopersicum_sgn.assoc To po_anatomy_germplasm_S.lycopersicum_sgn.assoc
svn path=/; revision=89
shuly [Wed, 1 Apr 2009 01:48:51 +0000 (01:48 +0000)]
Renamed po_anatomy_gene_tuberosum_sgn.assoc To po_anatomy_gene_S.tuberosum_sgn.assoc
svn path=/; revision=88
shuly [Wed, 1 Apr 2009 01:47:39 +0000 (01:47 +0000)]
renamed po_anatomy_gene_tabacum_sgn.assoc To po_anatomy_gene_N.tabacum_sgn.assoc
svn path=/; revision=87
shuly [Wed, 1 Apr 2009 01:45:51 +0000 (01:45 +0000)]
Renamed po_anatomy_gene_lycopersicum_sgn.assoc To po_anatomy_gene_S.lycopersicum_sgn.assoc
svn path=/; revision=86
shuly [Wed, 1 Apr 2009 01:44:13 +0000 (01:44 +0000)]
Renamed po_anatomy_gene_Capsicum_sgn.assoc to po_anatomy_gene_C.annuum_sgn.assoc
svn path=/; revision=85
shuly [Wed, 1 Apr 2009 01:41:10 +0000 (01:41 +0000)]
renamed po_anatomy_gene_Hyoscyamus_sgn.assoc to po_anatomy_gene_H.niger_sgn.assoc
svn path=/; revision=84
shuly [Wed, 1 Apr 2009 01:25:00 +0000 (01:25 +0000)]
*** empty log message ***
svn path=/; revision=83
shuly [Wed, 1 Apr 2009 01:15:54 +0000 (01:15 +0000)]
removed MaizeGDB: from second column, DB Object ID
svn path=/; revision=82
shuly [Tue, 31 Mar 2009 23:45:42 +0000 (23:45 +0000)]
Removed NULL
svn path=/; revision=81
polaccom [Fri, 27 Mar 2009 21:32:12 +0000 (21:32 +0000)]
new file of Maize stocks with phenotypes associated to PO anatomy terms
new file of Maieze stocks available from the coop (MGCSC)
svn path=/; revision=80
polaccom [Fri, 27 Mar 2009 21:26:49 +0000 (21:26 +0000)]
updated references to first report or gene list for each locus and added a few more loci
:wq
; ------------------------------------------------------------------
updated references and addes a few more associations
:wq
q\VS: ----------------------------------------------------------------------
svn path=/; revision=79
liya [Mon, 23 Feb 2009 20:02:52 +0000 (20:02 +0000)]
gramene release29
svn path=/; revision=78
donghui [Thu, 12 Feb 2009 23:09:58 +0000 (23:09 +0000)]
updated by Donghui 02-12-2009, assoociation files generated on 02-10-2009
svn path=/; revision=77
donghui [Wed, 5 Nov 2008 17:48:32 +0000 (17:48 +0000)]
updated: po_temporal has 1740 lines
po_anatomy has 18314 lines
svn path=/; revision=76
donghui [Mon, 13 Oct 2008 18:12:50 +0000 (18:12 +0000)]
grow-081010.txt po_temporal_gene_arabidopsis_tair.assoc
stru-081010.txt po_anatomy_gene_arabidopsis_tair.assoc
previous version incorrect (temporal file has only 3 lines).
donghui 2008-10-13
svn path=/; revision=75
donghui [Tue, 7 Oct 2008 21:16:23 +0000 (21:16 +0000)]
updated 081007
stru-081006.txt
grow-08006.txt
donghui
svn path=/; revision=74
liya [Tue, 30 Sep 2008 19:20:32 +0000 (19:20 +0000)]
gramene release28
svn path=/; revision=73
liya [Fri, 18 Apr 2008 08:53:58 +0000 (08:53 +0000)]
gramene release 27
svn path=/; revision=72
shuly [Mon, 7 Apr 2008 22:23:41 +0000 (22:23 +0000)]
changed phenotype to germplasm
svn path=/; revision=71
shuly [Wed, 2 Apr 2008 22:24:32 +0000 (22:24 +0000)]
SGN annotations
svn path=/; revision=70
donghui [Wed, 19 Mar 2008 22:24:16 +0000 (22:24 +0000)]
Updated on 03-19-2008 by Donghui
: ----------------------------------------------------------------------
svn path=/; revision=69
donghui [Wed, 19 Mar 2008 20:42:32 +0000 (20:42 +0000)]
Updated by Donghui 03/19/2008
-----------------------------------------------------------------
svn path=/; revision=68
donghui [Wed, 12 Dec 2007 23:15:22 +0000 (23:15 +0000)]
updated 2007-12-11 by Donghui:
`----------------------------------------------------------------------
svn path=/; revision=67
shuly [Fri, 2 Nov 2007 15:02:24 +0000 (15:02 +0000)]
removed space from taxon field
svn path=/; revision=66
polaccom [Thu, 27 Sep 2007 22:35:58 +0000 (22:35 +0000)]
This file adds new rows, the allele responsible for the association to gene by phenotype and replaces the uninformative previous generic ref with the record, similar to the NASC associations files. IN cases of multiple alleles for a row, the one with a stock at the Maize Genetics Cooperation Stock Center is preferred. (Mary SchaefferSep 2007)
svn path=/; revision=65
liya [Thu, 30 Aug 2007 14:53:16 +0000 (14:53 +0000)]
gramene release 26
svn path=/; revision=64
donghui [Wed, 18 Jul 2007 16:05:44 +0000 (16:05 +0000)]
updated association files by donghui 07-18-2007
svn path=/; revision=63
liya [Wed, 7 Mar 2007 14:54:02 +0000 (14:54 +0000)]
update GR db source to GR_gene and GR_QTL
svn path=/; revision=62
liya [Wed, 28 Feb 2007 21:43:05 +0000 (21:43 +0000)]
update SM evidence code to IMP due to POC without SM
svn path=/; revision=61
donghui [Wed, 28 Feb 2007 18:10:38 +0000 (18:10 +0000)]
updated by Donghui
svn path=/; revision=60
liya [Wed, 28 Feb 2007 17:18:04 +0000 (17:18 +0000)]
gramene release 24
svn path=/; revision=59
donghui [Tue, 16 Jan 2007 22:23:33 +0000 (22:23 +0000)]
updated 2007-01-15 by donghui
:CVS: ----------------------------------------------------------------------
svn path=/; revision=58
donghui [Tue, 16 Jan 2007 22:09:52 +0000 (22:09 +0000)]
updated by donghui on 2007-01-15.
eCVS: ----------------------------------------------------------------------
svn path=/; revision=57
liya [Mon, 6 Nov 2006 16:43:59 +0000 (16:43 +0000)]
gramene release23
svn path=/; revision=56
katica [Tue, 31 Oct 2006 00:50:06 +0000 (00:50 +0000)]
Update of PSO associations from tair, 5086 lines, dated at 061027 (ki).
svn path=/; revision=55
katica [Tue, 31 Oct 2006 00:46:46 +0000 (00:46 +0000)]
update of associations from TAIR for Growth and Dev stages, total lines 397, updated by ki (dated 061027).
svn path=/; revision=54
katica [Thu, 31 Aug 2006 21:13:49 +0000 (21:13 +0000)]
removed annotations to the obsolete term "columella", total lines 4842, file generated on 060830 (KI).
svn path=/; revision=53
katica [Mon, 28 Aug 2006 20:50:42 +0000 (20:50 +0000)]
Update of associations from TAIR for growth and dev stages ontology, 388 lines, dated 060825 (ki)
svn path=/; revision=52
katica [Mon, 28 Aug 2006 20:39:27 +0000 (20:39 +0000)]
Update of PSO associations from tair,4837 lines, dated at 060825 (ki)
svn path=/; revision=51
liya [Wed, 23 Aug 2006 21:03:53 +0000 (21:03 +0000)]
gramene release 22
svn path=/; revision=50
liya [Fri, 19 May 2006 20:27:01 +0000 (20:27 +0000)]
gramene release 21
svn path=/; revision=49
katica [Tue, 9 May 2006 17:14:12 +0000 (17:14 +0000)]
*** empty log message ***
svn path=/; revision=48
liya [Tue, 7 Mar 2006 20:58:24 +0000 (20:58 +0000)]
Gramene release 20
svn path=/; revision=47
liya [Tue, 7 Mar 2006 18:56:17 +0000 (18:56 +0000)]
Gramene release 20
svn path=/; revision=46
liya [Tue, 7 Mar 2006 03:52:28 +0000 (03:52 +0000)]
Gramene release20
svn path=/; revision=45
shuly [Fri, 3 Feb 2006 20:37:00 +0000 (20:37 +0000)]
revised evidence code from NAS to IMP
svn path=/; revision=44
shuly [Fri, 3 Feb 2006 20:28:00 +0000 (20:28 +0000)]
annotations from NASC
svn path=/; revision=43
shuly [Thu, 22 Sep 2005 03:45:06 +0000 (03:45 +0000)]
Substituted by the po_temporal_gene_arabidopsis_tair.assoc file.
svn path=/; revision=42
katica [Wed, 21 Sep 2005 02:43:44 +0000 (02:43 +0000)]
removed associations to tair terms, 183 lines total
svn path=/; revision=41
katica [Fri, 16 Sep 2005 22:20:16 +0000 (22:20 +0000)]
added associations to both, growth and dev stages terms, total 186 lines.
svn path=/; revision=40
katica [Fri, 16 Sep 2005 18:03:52 +0000 (18:03 +0000)]
added new gene asssociations, total 2,051 lines.
svn path=/; revision=39
shuly [Thu, 21 Apr 2005 16:38:12 +0000 (16:38 +0000)]
in po_anatomy_gene_arabidopsis_tair.assoc
svn path=/; revision=38
shuly [Thu, 21 Apr 2005 16:34:38 +0000 (16:34 +0000)]
Katica's updates
svn path=/; revision=37
shuly [Thu, 21 Apr 2005 16:11:35 +0000 (16:11 +0000)]
*** empty log message ***
svn path=/; revision=36
shuly [Thu, 21 Apr 2005 16:09:13 +0000 (16:09 +0000)]
*** empty log message ***
svn path=/; revision=35
shuly [Thu, 21 Apr 2005 16:08:53 +0000 (16:08 +0000)]
*** empty log message ***
svn path=/; revision=34
shuly [Thu, 21 Apr 2005 16:06:51 +0000 (16:06 +0000)]
*** empty log message ***
svn path=/; revision=33
shuly [Thu, 21 Apr 2005 04:10:24 +0000 (04:10 +0000)]
renamed to po_anatomy_stock_zea_MaizeGDB.assoc
svn path=/; revision=32
shuly [Thu, 21 Apr 2005 04:09:29 +0000 (04:09 +0000)]
renamed to po_anatomy_phenotype_zea_MaizeGDB.assoc
svn path=/; revision=31
shuly [Thu, 21 Apr 2005 04:08:09 +0000 (04:08 +0000)]
po_anatomy_gene_zea_MaizeGDB.assoc
svn path=/; revision=30
shuly [Thu, 21 Apr 2005 04:05:32 +0000 (04:05 +0000)]
renamed to po_anatomy_gene_oryza_gramene.assoc
svn path=/; revision=29
shuly [Thu, 21 Apr 2005 04:03:18 +0000 (04:03 +0000)]
renamed to po_anatomy_gene_arabidopsis_tair.assoc
svn path=/; revision=28
shuly [Thu, 21 Apr 2005 03:55:20 +0000 (03:55 +0000)]
renamed file to po_growth_gene_arabidopsis_tair.assoc
svn path=/; revision=27
pankaj [Wed, 20 Apr 2005 20:33:55 +0000 (20:33 +0000)]
Gramene's association file to POC growth stahe ontology
svn path=/; revision=26
katica [Wed, 13 Apr 2005 18:56:36 +0000 (18:56 +0000)]
updated gene associations to PO anatomy terms. 1486 lines.
svn path=/; revision=25
katica [Tue, 12 Apr 2005 22:57:07 +0000 (22:57 +0000)]
Arabidopsis annotations to POC growth stages. 75 lines, 04-11-05.
svn path=/; revision=24
shuly [Tue, 22 Feb 2005 17:47:46 +0000 (17:47 +0000)]
Changed wrong acc from PO:
0005368 to PO:
0005360
svn path=/; revision=23
shuly [Fri, 18 Feb 2005 19:24:57 +0000 (19:24 +0000)]
Wrong file name - shouldn't have the .txt suffix in first place
svn path=/; revision=22
shuly [Fri, 18 Feb 2005 19:23:02 +0000 (19:23 +0000)]
Rename file name to have the po_prefix
svn path=/; revision=21
shuly [Fri, 18 Feb 2005 19:20:08 +0000 (19:20 +0000)]
Rename file name to have the po_ prefix
svn path=/; revision=20
shuly [Fri, 18 Feb 2005 19:15:04 +0000 (19:15 +0000)]
Fix by Katica - fixed wrong acc
svn path=/; revision=19
shuly [Fri, 18 Feb 2005 19:12:56 +0000 (19:12 +0000)]
Changed name from gene_association.tair_arabosopsis to have the po_ prefix
svn path=/; revision=18
shuly [Fri, 18 Feb 2005 19:08:10 +0000 (19:08 +0000)]
Removed wrong acc: PO:0000NA
svn path=/; revision=17
shuly [Fri, 18 Feb 2005 19:01:02 +0000 (19:01 +0000)]
Canged name from phenotype_association.gramene_oryza to po_gene_association.gramene_oryza
svn path=/; revision=16
shuly [Fri, 18 Feb 2005 18:34:06 +0000 (18:34 +0000)]
Rest - renamed the file to test_tair_txt
svn path=/; revision=15
shuly [Fri, 14 Jan 2005 23:14:41 +0000 (23:14 +0000)]
Added associations.
Added object type 'gene'.
svn path=/; revision=14
shuly [Fri, 10 Dec 2004 03:26:09 +0000 (03:26 +0000)]
added gene_sequenced instead of gene to the association type
svn path=/; revision=13
katica [Fri, 10 Dec 2004 02:52:42 +0000 (02:52 +0000)]
replaced gene by gene_sequenced
svn path=/; revision=12
katica [Fri, 10 Dec 2004 01:46:06 +0000 (01:46 +0000)]
corrected carriage returns in the file
svn path=/; revision=11
katica [Fri, 10 Dec 2004 01:44:38 +0000 (01:44 +0000)]
Initial load
svn path=/; revision=10
polaccom [Mon, 6 Dec 2004 17:10:51 +0000 (17:10 +0000)]
Mary - updated object type to 'gene'; update the db reference with a general
reference to describe how the IMP associations are made in MaizeGDB, and a
second for certain of the Neuffer mutant collection.
svn path=/; revision=9
shuly [Sun, 5 Dec 2004 03:25:15 +0000 (03:25 +0000)]
Shuly - fixed format:
added missing empty columns, changed object type from 'gene' to 'gene_sequenced'
svn path=/; revision=8
polaccom [Fri, 3 Dec 2004 19:56:17 +0000 (19:56 +0000)]
format of file altered
svn path=/; revision=7
polaccom [Fri, 3 Dec 2004 19:54:04 +0000 (19:54 +0000)]
format of file altered only
svn path=/; revision=6
projects / associations / .git / log