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elserj [Thu, 5 Jan 2017 23:46:36 +0000 (23:46 +0000)]
Fix empty column 10, use col2 to fill it in.
svn path=/; revision=793
elserj [Thu, 5 Jan 2017 21:28:08 +0000 (21:28 +0000)]
Fix MGDB_REF reference links to MaizeGDB_REF
svn path=/; revision=792
elserj [Wed, 4 Jan 2017 21:20:41 +0000 (21:20 +0000)]
Change filename of genemodel to gene_model to be consistent
svn path=/; revision=791
elserj [Wed, 4 Jan 2017 21:19:55 +0000 (21:19 +0000)]
Insert missing tabs to end of some lines
svn path=/; revision=790
elserj [Tue, 3 Jan 2017 23:41:38 +0000 (23:41 +0000)]
Try to fix missing spaces in db object names (column 10)
svn path=/; revision=789
elserj [Tue, 3 Jan 2017 17:46:42 +0000 (17:46 +0000)]
Add new MaizeGDB assoc files.
svn path=/; revision=788
meiera [Thu, 29 Dec 2016 00:24:09 +0000 (00:24 +0000)]
Added all IRRI traits, version 1.0 for testing
svn path=/; revision=787
meiera [Tue, 20 Dec 2016 18:28:08 +0000 (18:28 +0000)]
added a new IRRI_GRIMS test association file.
svn path=/; revision=786
meiera [Mon, 17 Oct 2016 22:18:07 +0000 (22:18 +0000)]
fixed NA problem, and taxon change from GRIN to NCBI
svn path=/; revision=785
meiera [Fri, 14 Oct 2016 23:44:55 +0000 (23:44 +0000)]
fixed errors
svn path=/; revision=784
meiera [Fri, 14 Oct 2016 23:14:02 +0000 (23:14 +0000)]
Added new GRIN maize scrape from Samara for testing.
svn path=/; revision=783
cooperl [Thu, 29 Sep 2016 19:31:14 +0000 (19:31 +0000)]
Replaced deprecated EO term pest/pathogen/animal/plant environment EO:
0007124 pest/pathogen/animal/plant environment
with biotic plant treatment (EO:
0007357)
svn path=/; revision=782
cooperl [Thu, 29 Sep 2016 19:27:43 +0000 (19:27 +0000)]
Replaced deprecated EO term pest/pathogen/animal/plant environment EO:
0007124 pest/pathogen/animal/plant environment
with biotic plant treatment (EO:
0007357)
svn path=/; revision=781
cooperl [Sat, 3 Sep 2016 22:36:44 +0000 (22:36 +0000)]
Fixed annotations for grain number QTLs in rice: Changed from seed number TO:
0000445 to grain number TO:
0002759.
M to-associations/to_qtl_Oryza_Gramene.assoc
svn path=/; revision=780
elserj [Thu, 1 Sep 2016 00:52:25 +0000 (00:52 +0000)]
Replace Ensembl_Plants with EnsemblPlants to match the dbxref entry
svn path=/; revision=779
cooperl [Wed, 31 Aug 2016 18:36:14 +0000 (18:36 +0000)]
Updated the reference used in the SGN germplasm files from SGN_ref:861 (generic curator page) to PMID:
25428362
svn path=/; revision=778
meiera [Tue, 30 Aug 2016 23:15:03 +0000 (23:15 +0000)]
Changed database name in column 1 from cosmoss to cosmoss_PpV1.2
svn path=/; revision=777
elserj [Tue, 30 Aug 2016 23:05:31 +0000 (23:05 +0000)]
Remove bad references
svn path=/; revision=776
meiera [Tue, 30 Aug 2016 20:54:49 +0000 (20:54 +0000)]
Changed MaizeGDB: to MaizeGDB_REF: in column 6 to allow for correct URL link generation in AmiGO
svn path=/; revision=775
elserj [Fri, 26 Aug 2016 22:58:55 +0000 (22:58 +0000)]
continued fixes in evidence codes
svn path=/; revision=774
elserj [Fri, 26 Aug 2016 22:33:25 +0000 (22:33 +0000)]
Oops, should be changed to IMP, not ISM
svn path=/; revision=773
elserj [Fri, 26 Aug 2016 22:16:29 +0000 (22:16 +0000)]
Change evidence code from "SM" to "ISM". Assume was a mistake
svn path=/; revision=772
elserj [Fri, 26 Aug 2016 22:09:20 +0000 (22:09 +0000)]
Change evidence code from "NOT" to "IC". Assume was a typo. IC seems okay since Lol is a curator, and we inferred it.
svn path=/; revision=771
elserj [Fri, 26 Aug 2016 21:54:48 +0000 (21:54 +0000)]
Remove unnecessary extra info from colum 7 on a couple of lines
svn path=/; revision=770
cooperl [Thu, 25 Aug 2016 23:03:04 +0000 (23:03 +0000)]
Changed maizeGDB to MaizeGDB to be consistent
svn path=/; revision=769
cooperl [Thu, 25 Aug 2016 17:47:25 +0000 (17:47 +0000)]
Fixing filenames for consistency
svn path=/; revision=768
cooperl [Thu, 25 Aug 2016 17:45:42 +0000 (17:45 +0000)]
Fixing filenames for consistency
svn path=/; revision=767
elserj [Thu, 25 Aug 2016 16:35:32 +0000 (16:35 +0000)]
Replace GR_gene with gene to be consistent in object types
svn path=/; revision=766
elserj [Thu, 25 Aug 2016 16:31:58 +0000 (16:31 +0000)]
Remove extra characters at end of line
svn path=/; revision=765
cooperl [Mon, 22 Aug 2016 21:56:15 +0000 (21:56 +0000)]
Fixed DB:Curator_Name for consistency
M to-associations/to_gene_O.sativa_PPPP.assoc
svn path=/; revision=764
cooperl [Mon, 22 Aug 2016 18:41:58 +0000 (18:41 +0000)]
Fixed Curator names for consistency
svn path=/; revision=763
elserj [Fri, 19 Aug 2016 22:02:43 +0000 (22:02 +0000)]
Move eo_diversity files to sub folder, they are not ready to be loaded
svn path=/; revision=762
cooperl [Fri, 19 Aug 2016 21:49:42 +0000 (21:49 +0000)]
Fixed database names to be consistent
svn path=/; revision=761
elserj [Fri, 19 Aug 2016 21:48:14 +0000 (21:48 +0000)]
Change case of filename for consistency
svn path=/; revision=760
cooperl [Fri, 19 Aug 2016 21:28:38 +0000 (21:28 +0000)]
Fixing filenames for consistency
svn path=/; revision=759
cooperl [Fri, 19 Aug 2016 21:20:34 +0000 (21:20 +0000)]
Fixing filenames for consistency. Moved file with annotations to CO back to test folder for now
svn path=/; revision=758
cooperl [Fri, 19 Aug 2016 20:58:37 +0000 (20:58 +0000)]
Fixed missing column tab space.
svn path=/; revision=757
cooperl [Thu, 18 Aug 2016 23:43:46 +0000 (23:43 +0000)]
Fixing filenames for consistency
svn path=/; revision=756
cooperl [Thu, 18 Aug 2016 23:28:39 +0000 (23:28 +0000)]
Moving the CO cassava annotation file back to the test folder
svn path=/; revision=755
cooperl [Thu, 18 Aug 2016 23:26:32 +0000 (23:26 +0000)]
Fixing filenames for consistency
svn path=/; revision=754
cooperl [Thu, 18 Aug 2016 23:11:39 +0000 (23:11 +0000)]
Fixing filenames for consistency
svn path=/; revision=753
cooperl [Thu, 18 Aug 2016 23:05:59 +0000 (23:05 +0000)]
Fixed DB:Curator_Name for consistency
svn path=/; revision=752
cooperl [Thu, 18 Aug 2016 22:59:04 +0000 (22:59 +0000)]
Fixed DB:Curator_Name for consistency
M to-associations/to_gene_G.max_PPPP.assoc
M to-associations/to_gene_M.truncatula_PPPP.assoc
M to-associations/to_gene_S.lycopersicum_PPPP.assoc
M to-associations/to_gene_Z.mays_PPPP.assoc
M to-associations/to_gene_O.sativa_PPPP.assoc
svn path=/; revision=751
cooperl [Thu, 18 Aug 2016 22:50:27 +0000 (22:50 +0000)]
ng filenames for consistency
svn path=/; revision=750
cooperl [Thu, 18 Aug 2016 22:43:54 +0000 (22:43 +0000)]
Changed database name from GR to Gramene
svn path=/; revision=749
cooperl [Thu, 18 Aug 2016 22:38:06 +0000 (22:38 +0000)]
Changed database name from GR to Gramene
svn path=/; revision=748
cooperl [Thu, 18 Aug 2016 22:28:33 +0000 (22:28 +0000)]
Renaming merged file
svn path=/; revision=747
cooperl [Thu, 18 Aug 2016 22:26:49 +0000 (22:26 +0000)]
Combine the anatomy and growth versions of this file files, SVN history will be preserved from po_anatomy_gene_model_li_zea_mays.assoc
Removed separate growth file
svn path=/; revision=746
cooperl [Thu, 18 Aug 2016 22:17:05 +0000 (22:17 +0000)]
Changed database name from GR to Gramene
svn path=/; revision=745
cooperl [Thu, 18 Aug 2016 22:00:14 +0000 (22:00 +0000)]
Fixed Gramene gene format - should be GR:#######
svn path=/; revision=744
cooperl [Thu, 18 Aug 2016 21:38:15 +0000 (21:38 +0000)]
Fixed Gramene gene format - should be GR:#######
svn path=/; revision=743
cooperl [Thu, 18 Aug 2016 21:11:00 +0000 (21:11 +0000)]
Fixed DB:Curator_Name for consistency
svn path=/; revision=742
cooperl [Thu, 18 Aug 2016 20:48:53 +0000 (20:48 +0000)]
Fixing filenames for consistency
svn path=/; revision=741
cooperl [Thu, 18 Aug 2016 20:14:20 +0000 (20:14 +0000)]
Fixing filenames for consistency
svn path=/; revision=740
cooperl [Thu, 18 Aug 2016 19:54:37 +0000 (19:54 +0000)]
Fixed DB:Curator_Name for consistency
svn path=/; revision=739
cooperl [Thu, 18 Aug 2016 19:42:34 +0000 (19:42 +0000)]
Fixed DB:Curator_Name for consistency
svn path=/; revision=738
elserj [Thu, 18 Aug 2016 19:40:41 +0000 (19:40 +0000)]
Run dos2unix to fix weird line endings
svn path=/; revision=737
cooperl [Thu, 18 Aug 2016 19:31:06 +0000 (19:31 +0000)]
Fixed DB:Curator_Name for consistency
svn path=/; revision=736
cooperl [Thu, 18 Aug 2016 19:00:59 +0000 (19:00 +0000)]
Fixing filenames for consistency
svn path=/; revision=735
cooperl [Thu, 18 Aug 2016 18:56:33 +0000 (18:56 +0000)]
iFixing filenames for consistency
svn path=/; revision=734
cooperl [Thu, 18 Aug 2016 18:54:54 +0000 (18:54 +0000)]
Fixing filenames for consistency
svn path=/; revision=733
cooperl [Thu, 18 Aug 2016 18:47:00 +0000 (18:47 +0000)]
Fixing filenames for consistency
svn path=/; revision=732
cooperl [Thu, 18 Aug 2016 18:17:22 +0000 (18:17 +0000)]
Fixing filenames for consistency
svn path=/; revision=731
cooperl [Thu, 18 Aug 2016 18:07:51 +0000 (18:07 +0000)]
Changed object type from transcript to mRNA
svn path=/; revision=730
meiera [Wed, 17 Aug 2016 23:38:41 +0000 (23:38 +0000)]
removed individual trait files. These have been combined into a single file: to_germplasm_rice_IRRI3K.assoc
svn path=/; revision=729
meiera [Wed, 17 Aug 2016 23:28:31 +0000 (23:28 +0000)]
concatenated all IRRI3K OryzaSNP assocication files into to_germplasm_rice_IRRI3K.assoc
svn path=/; revision=728
elserj [Wed, 17 Aug 2016 23:06:54 +0000 (23:06 +0000)]
Combine all anatomy and growth SGN files, rename to just po_*. SVN history will be preserved from po_anatomy_*.
svn path=/; revision=727
elserj [Wed, 17 Aug 2016 22:55:10 +0000 (22:55 +0000)]
Change all references of genemodel back to gene_model to be consistent
svn path=/; revision=726
elserj [Wed, 17 Aug 2016 22:46:18 +0000 (22:46 +0000)]
Fix wrong column 10. Had genemodel rather then the db object name in some lines near the end of the file(s).
svn path=/; revision=725
cooperl [Wed, 17 Aug 2016 22:37:10 +0000 (22:37 +0000)]
Fixing filename to be consistent with the file contents.
svn path=/; revision=724
elserj [Wed, 17 Aug 2016 18:17:57 +0000 (18:17 +0000)]
Fix missing dash in header
svn path=/; revision=723
elserj [Wed, 17 Aug 2016 16:52:47 +0000 (16:52 +0000)]
Fix missing column 10 by inputting column 3
svn path=/; revision=722
cooperl [Tue, 16 Aug 2016 23:42:10 +0000 (23:42 +0000)]
Renamed po_growth_gene_model_li_zea_mays.assoc to po_growth_genemodel_li_zea_mays.assoc for consistency
svn path=/; revision=721
cooperl [Tue, 16 Aug 2016 23:38:27 +0000 (23:38 +0000)]
Removed extraneous dashes and Fixed spelling of gene model 'gene_model >> genemodel' for consistency
svn path=/; revision=720
cooperl [Tue, 16 Aug 2016 23:36:03 +0000 (23:36 +0000)]
Fixed spelling of gene model 'gene_model >> genemodel' for consistency
svn path=/; revision=719
cooperl [Tue, 16 Aug 2016 23:31:27 +0000 (23:31 +0000)]
Renamed po_anatomy_gene_model_li_zea_mays.assoc to po_anatomy_genemodel_li_zea_mays.assoc for consistency
svn path=/; revision=718
cooperl [Tue, 16 Aug 2016 23:19:12 +0000 (23:19 +0000)]
Fixed spelling of genemodel, to be consistent and removed the extraneous dashes.
svn path=/; revision=717
elserj [Tue, 16 Aug 2016 23:04:06 +0000 (23:04 +0000)]
Replace empty column 10 with gene ID from column 3
svn path=/; revision=716
cooperl [Tue, 16 Aug 2016 21:41:34 +0000 (21:41 +0000)]
Fixed the dbxref to MaizeGDB references to work with new link. And removed the extraneous dashes.
svn path=/; revision=715
cooperl [Tue, 16 Aug 2016 21:22:12 +0000 (21:22 +0000)]
Fixed the dbxref to MaizeGDB references to work with new link. Updated in the db-xrefs.yaml file on GitHub.
svn path=/; revision=714
elserj [Tue, 16 Aug 2016 16:16:24 +0000 (16:16 +0000)]
Fix missing columns.
svn path=/; revision=713
elserj [Fri, 12 Aug 2016 05:48:48 +0000 (05:48 +0000)]
Try againt at filtering out duplicate lines. Use pipe rather than comma, and put AGI_LocusCode prefix so that they linkout.
svn path=/; revision=712
elserj [Tue, 9 Aug 2016 22:57:45 +0000 (22:57 +0000)]
Replace all ortholog GO annotation files so that lines with everything the same except for the "with" column are combined.
svn path=/; revision=711
meiera [Fri, 10 Jun 2016 18:45:58 +0000 (18:45 +0000)]
Added back all the OryzaSNP.assoc files without special characters in the filenames.
svn path=/; revision=710
meiera [Fri, 10 Jun 2016 18:33:23 +0000 (18:33 +0000)]
Removed old oryzasnp assoc files. These will be replaced with properly named ones.
svn path=/; revision=709
meiera [Fri, 10 Jun 2016 16:45:43 +0000 (16:45 +0000)]
Fixed to remove spaces in the ID column
svn path=/; revision=708
meiera [Fri, 10 Jun 2016 16:26:26 +0000 (16:26 +0000)]
Added traits from OryzaSNP database.
svn path=/; revision=707
meiera [Tue, 5 Apr 2016 21:25:52 +0000 (21:25 +0000)]
modified test file for further testing
svn path=/; revision=706
meiera [Tue, 5 Apr 2016 17:42:47 +0000 (17:42 +0000)]
a test of columns 3 and 10, for display purposes.
svn path=/; revision=705
meiera [Wed, 23 Mar 2016 18:23:27 +0000 (18:23 +0000)]
First try for the automatically generated GRIMS database of IRRI germplasm. First trait was awn color. Currently annotated to the TO term. Just testing display, and errors.
svn path=/; revision=704
cooperl [Thu, 17 Mar 2016 20:12:27 +0000 (20:12 +0000)]
Fixed typo in the GR_REF columns.
svn path=/; revision=703
cooperl [Thu, 17 Mar 2016 19:55:15 +0000 (19:55 +0000)]
Revised annotations to TO:
0000079, with new terms for lemma and palea morphology. Fixed Xrefs to GR_REF.
svn path=/; revision=702
elserj [Wed, 9 Mar 2016 20:10:47 +0000 (20:10 +0000)]
Fix extra tab character in column 4 and add header line
svn path=/; revision=701
elserj [Wed, 9 Mar 2016 17:47:12 +0000 (17:47 +0000)]
Add test IRRI assoc files from Austin
svn path=/; revision=700
elserj [Wed, 24 Feb 2016 23:20:44 +0000 (23:20 +0000)]
Replace all object types (column 12) of Gene with gene to match other files for consistency
svn path=/; revision=699
elserj [Wed, 24 Feb 2016 22:55:40 +0000 (22:55 +0000)]
Change Protein to protein in object types (column 12) to match other files
svn path=/; revision=698
elserj [Wed, 27 Jan 2016 01:16:44 +0000 (01:16 +0000)]
Filter out duplicate lines
svn path=/; revision=697
elserj [Fri, 8 Jan 2016 17:31:40 +0000 (17:31 +0000)]
Fix tab issues
svn path=/; revision=696
meiera [Fri, 8 Jan 2016 02:19:01 +0000 (02:19 +0000)]
fixed Gramene database numbers, so links will work.
svn path=/; revision=695
elserj [Fri, 8 Jan 2016 02:07:47 +0000 (02:07 +0000)]
Move to_diversity files out of main folder as they are not to be loaded at this point.
svn path=/; revision=694
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