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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
elserj [Fri, 8 Jan 2016 01:48:46 +0000 (01:48 +0000)]
Add files created from iprscan
svn path=/; revision=693
cooperl [Fri, 8 Jan 2016 00:38:27 +0000 (00:38 +0000)]
Revised the ontology aspect from 'S' to 'A'
svn path=/; revision=692
elserj [Fri, 8 Jan 2016 00:28:34 +0000 (00:28 +0000)]
Change all "assigned by" for Jaiswal_group and jaiswallab to Jaiswal_lab to be consistent
svn path=/; revision=691
cooperl [Fri, 8 Jan 2016 00:23:27 +0000 (00:23 +0000)]
Revised the ontology aspect from 'N' to 'P'
svn path=/; revision=690
elserj [Thu, 7 Jan 2016 23:08:35 +0000 (23:08 +0000)]
Clean up go-associations folder. Move old gramene files to subfolder, they are not to be loaded in planteome, but want to keep history. Same with old jaiswallab files.
svn path=/; revision=689
meiera [Thu, 7 Jan 2016 19:22:08 +0000 (19:22 +0000)]
changed object name (column 10) to be the germplasm name (column 3) and changed annotations to TO:
0000181 to TO:
0000269
svn path=/; revision=688
elserj [Thu, 7 Jan 2016 06:44:37 +0000 (06:44 +0000)]
Add back extra tab to each line
svn path=/; revision=687
cooperl [Thu, 7 Jan 2016 04:29:46 +0000 (04:29 +0000)]
ommented out lines with CO_334:
0000010, as it is not a trait.
svn path=/; revision=686
meiera [Thu, 7 Jan 2016 04:15:02 +0000 (04:15 +0000)]
moved to_germplasm_lentil_Karthika from the test folder into the main folder
svn path=/; revision=685
meiera [Thu, 7 Jan 2016 04:11:48 +0000 (04:11 +0000)]
added GR: and the leading zeros to the DB ID number so that the Gramene links would work
svn path=/; revision=684
elserj [Thu, 7 Jan 2016 01:26:50 +0000 (01:26 +0000)]
Copy column 2 to column 10 so that "Object name" will show up on browser
svn path=/; revision=683
meiera [Thu, 7 Jan 2016 01:24:07 +0000 (01:24 +0000)]
changed "assayed_in" to "evaluation_location"
svn path=/; revision=682
meiera [Thu, 7 Jan 2016 00:45:03 +0000 (00:45 +0000)]
fixed assoc file to replace name with PI-number in cases where germplasm has no name in GRIN
svn path=/; revision=681
meiera [Wed, 6 Jan 2016 23:26:25 +0000 (23:26 +0000)]
modified annotation_Lentil.tsv
svn path=/; revision=680
elserj [Wed, 6 Jan 2016 23:05:40 +0000 (23:05 +0000)]
Replace "Gene" with "gene" to be consistent, and fix extra "-pgr" in column one of cassava file
svn path=/; revision=679
elserj [Wed, 6 Jan 2016 22:33:38 +0000 (22:33 +0000)]
Add extra tabs to lines to have 17 columns
svn path=/; revision=678
meiera [Wed, 6 Jan 2016 21:49:03 +0000 (21:49 +0000)]
fixed lentil annotation file to include "has_phenotype_variable()" in column16
svn path=/; revision=677
meiera [Wed, 6 Jan 2016 20:38:39 +0000 (20:38 +0000)]
Added lentil test folder. Added lentil data from Karthika in it's original format.
svn path=/; revision=676
elserj [Wed, 6 Jan 2016 18:21:38 +0000 (18:21 +0000)]
Move column 17 to column 11 and fix mac line endings
svn path=/; revision=675
elserj [Wed, 6 Jan 2016 18:14:20 +0000 (18:14 +0000)]
Fix missing tabs for column 17 and remove extra tabs on header line
svn path=/; revision=674
cooperl [Wed, 6 Jan 2016 18:10:29 +0000 (18:10 +0000)]
moved cassava data file with CO annotatins out of test folder and fixed column one- Genesys-pgr
svn path=/; revision=673
cooperl [Wed, 6 Jan 2016 17:48:42 +0000 (17:48 +0000)]
revisions to cassava: Moved BMS ids to synonym column (#11), replacing with object symbol again. Revised database name to be "Genesys-pgr" to match DBXref.
svn path=/; revision=672
cooperl [Wed, 6 Jan 2016 00:38:29 +0000 (00:38 +0000)]
Moved BMS ids to synonym column (#11), replacing with object symbol again. Revised database name to be "Genesys-pgr" to match DBXref.
svn path=/; revision=671
elserj [Tue, 5 Jan 2016 18:42:53 +0000 (18:42 +0000)]
Fix tab and spacing issues
svn path=/; revision=670
meiera [Mon, 4 Jan 2016 19:50:50 +0000 (19:50 +0000)]
Changed "Austin Meier" to "austin_meier" in z.mays gene assoc file.
svn path=/; revision=669
elserj [Mon, 4 Jan 2016 19:03:37 +0000 (19:03 +0000)]
This file is not needed as the species was the basis for the rest of the files.
svn path=/; revision=668
cooperl [Sun, 3 Jan 2016 02:08:09 +0000 (02:08 +0000)]
Modified Cassava Genesys assoc file- moved BMSid values to DB_Object_Id (col2) and copied germaplsm names to col 10: DB_Object_name
svn path=/; revision=667
elserj [Fri, 1 Jan 2016 20:43:53 +0000 (20:43 +0000)]
Added some of the gaf files created by projecting orthologs (from InParanoid) from Arabidopsis thaliana. Cant do all in the same commit as it fails because of space.
svn path=/; revision=666
elserj [Fri, 1 Jan 2016 20:43:29 +0000 (20:43 +0000)]
Added some of the gaf files created by projecting orthologs (from InParanoid) from Arabidopsis thaliana. Cant do all in the same commit as it fails because of space.
svn path=/; revision=665
elserj [Fri, 1 Jan 2016 20:43:07 +0000 (20:43 +0000)]
Added some of the gaf files created by projecting orthologs (from InParanoid) from Arabidopsis thaliana. Cant do all in the same commit as it fails because of space.
svn path=/; revision=664
elserj [Fri, 1 Jan 2016 20:41:26 +0000 (20:41 +0000)]
Added some of the gaf files created by projecting orthologs (from InParanoid) from Arabidopsis thaliana. Cant do all in the same commit as it fails because of space.
svn path=/; revision=663
elserj [Fri, 1 Jan 2016 20:40:40 +0000 (20:40 +0000)]
Added some of the gaf files created by projecting orthologs (from InParanoid) from Arabidopsis thaliana. Cant do all in the same commit as it fails because of space.
svn path=/; revision=662
elserj [Fri, 1 Jan 2016 20:40:13 +0000 (20:40 +0000)]
Added some of the gaf files created by projecting orthologs (from InParanoid) from Arabidopsis thaliana. Cant do all in the same commit as it fails because of space.
svn path=/; revision=661
elserj [Fri, 1 Jan 2016 20:39:10 +0000 (20:39 +0000)]
Added some of the gaf files created by projecting orthologs (from InParanoid) from Arabidopsis thaliana. Cant do all in the same commit as it fails because of space.
svn path=/; revision=660
elserj [Fri, 1 Jan 2016 20:38:47 +0000 (20:38 +0000)]
Added some of the gaf files created by projecting orthologs (from InParanoid) from Arabidopsis thaliana. Cant do all in the same commit as it fails because of space.
svn path=/; revision=659
elserj [Fri, 1 Jan 2016 20:38:26 +0000 (20:38 +0000)]
Added some of the gaf files created by projecting orthologs (from InParanoid) from Arabidopsis thaliana. Cant do all in the same commit as it fails because of space.
svn path=/; revision=658
elserj [Fri, 1 Jan 2016 20:37:44 +0000 (20:37 +0000)]
Added some of the gaf files created by projecting orthologs (from InParanoid) from Arabidopsis thaliana. Cant do all in the same commit as it fails because of space.
svn path=/; revision=657
elserj [Fri, 1 Jan 2016 20:37:26 +0000 (20:37 +0000)]
Added some of the gaf files created by projecting orthologs (from InParanoid) from Arabidopsis thaliana. Cant do all in the same commit as it fails because of space.
svn path=/; revision=656
elserj [Fri, 1 Jan 2016 20:37:02 +0000 (20:37 +0000)]
Added some of the gaf files created by projecting orthologs (from InParanoid) from Arabidopsis thaliana. Cant do all in the same commit as it fails because of space.
svn path=/; revision=655
elserj [Fri, 1 Jan 2016 20:36:45 +0000 (20:36 +0000)]
Added some of the gaf files created by projecting orthologs (from InParanoid) from Arabidopsis thaliana. Cant do all in the same commit as it fails because of space.
svn path=/; revision=654
elserj [Fri, 1 Jan 2016 20:36:23 +0000 (20:36 +0000)]
Added some of the gaf files created by projecting orthologs (from InParanoid) from Arabidopsis thaliana. Cant do all in the same commit as it fails because of space.
svn path=/; revision=653
elserj [Fri, 1 Jan 2016 20:35:50 +0000 (20:35 +0000)]
Added some of the gaf files created by projecting orthologs (from InParanoid) from Arabidopsis thaliana. Cant do all in the same commit as it fails because of space.
svn path=/; revision=652
elserj [Fri, 1 Jan 2016 20:34:45 +0000 (20:34 +0000)]
Added some of the gaf files created by projecting orthologs (from InParanoid) from Arabidopsis thaliana. Cant do all in the same commit as it fails because of space.
svn path=/; revision=651
elserj [Fri, 1 Jan 2016 20:33:36 +0000 (20:33 +0000)]
Added some of the gaf files created by projecting orthologs (from InParanoid) from Arabidopsis thaliana. Cant do all in the same commit as it fails because of space.
svn path=/; revision=650
elserj [Fri, 1 Jan 2016 20:32:12 +0000 (20:32 +0000)]
Added some of the gaf files created by projecting orthologs (from InParanoid) from Arabidopsis thaliana. Cant do all in the same commit as it fails because of space.
svn path=/; revision=649
elserj [Fri, 1 Jan 2016 19:58:15 +0000 (19:58 +0000)]
Fix missing tab in last column
svn path=/; revision=648
cooperl [Thu, 31 Dec 2015 23:34:38 +0000 (23:34 +0000)]
final edits to map CO-TO
svn path=/; revision=647
cooperl [Thu, 31 Dec 2015 23:26:07 +0000 (23:26 +0000)]
Removed lines to CO_334:
0000010- # of plants harvested. Metadata not trait.
svn path=/; revision=646
cooperl [Thu, 31 Dec 2015 23:15:28 +0000 (23:15 +0000)]
Adding cassava trait file with TO annotations
svn path=/; revision=645
meiera [Thu, 31 Dec 2015 22:13:39 +0000 (22:13 +0000)]
moved "isolated_from_germplasm" relation from column 16 to column 8 (with/from)
svn path=/; revision=644
meiera [Thu, 31 Dec 2015 21:37:26 +0000 (21:37 +0000)]
removed empty test folders
svn path=/; revision=643
meiera [Thu, 31 Dec 2015 21:35:16 +0000 (21:35 +0000)]
changed names to include database "GRIN"
svn path=/; revision=642
meiera [Thu, 31 Dec 2015 21:31:47 +0000 (21:31 +0000)]
added rice and lentil germplasm assoc files to main folder from test folder
svn path=/; revision=641
meiera [Thu, 31 Dec 2015 21:30:49 +0000 (21:30 +0000)]
moved rice and lentil germplasm assoc files out of test folder for loading
svn path=/; revision=640
cooperl [Thu, 31 Dec 2015 21:23:12 +0000 (21:23 +0000)]
Moved the TO_IMP files from PPPP to main folder
svn path=/; revision=639
cooperl [Thu, 31 Dec 2015 21:16:21 +0000 (21:16 +0000)]
Changed Assigned by from POC:Ethan_Johnson to Ethan Johnson to be consistent
svn path=/; revision=638
meiera [Thu, 31 Dec 2015 21:12:32 +0000 (21:12 +0000)]
added the !gaf-version: 2.0 first line back.≈
svn path=/; revision=637
meiera [Thu, 31 Dec 2015 21:05:42 +0000 (21:05 +0000)]
moved "isolated_from_germplasm(Nipponbare)" to column 8 in po_growth_gene_oryza_poc.assoc
svn path=/; revision=636
cooperl [Thu, 31 Dec 2015 21:03:32 +0000 (21:03 +0000)]
Changed aspect code from S to A
svn path=/; revision=635
cooperl [Thu, 31 Dec 2015 20:58:12 +0000 (20:58 +0000)]
Fixed typo on line #91
svn path=/; revision=634
elserj [Thu, 31 Dec 2015 20:56:25 +0000 (20:56 +0000)]
Fix gaf-version header
svn path=/; revision=633
cooperl [Thu, 31 Dec 2015 20:43:50 +0000 (20:43 +0000)]
Changed object type "Protein" to "protein"
svn path=/; revision=632
cooperl [Thu, 31 Dec 2015 20:21:19 +0000 (20:21 +0000)]
Removed spaces after object type "gene"
svn path=/; revision=631
elserj [Thu, 31 Dec 2015 20:11:04 +0000 (20:11 +0000)]
Change expressed_under relation to in_presence_of
svn path=/; revision=630
elserj [Thu, 31 Dec 2015 20:09:14 +0000 (20:09 +0000)]
Change taxon id to one that works
svn path=/; revision=629
cooperl [Thu, 31 Dec 2015 20:03:55 +0000 (20:03 +0000)]
Fixed 'stock" to "germplasm"
svn path=/; revision=628
cooperl [Thu, 31 Dec 2015 19:57:14 +0000 (19:57 +0000)]
Fixed Ethan Johnson! assigned by column.
svn path=/; revision=627
cooperl [Thu, 31 Dec 2015 19:47:27 +0000 (19:47 +0000)]
Removed NA from Col8
svn path=/; revision=626
cooperl [Thu, 31 Dec 2015 19:31:41 +0000 (19:31 +0000)]
Fixed Gene- should be "gene"
svn path=/; revision=625
cooperl [Thu, 31 Dec 2015 19:24:17 +0000 (19:24 +0000)]
Fixed Aspect code
svn path=/; revision=624
cooperl [Thu, 31 Dec 2015 19:03:35 +0000 (19:03 +0000)]
Commented out line with missing TO term
svn path=/; revision=623
elserj [Thu, 31 Dec 2015 02:58:16 +0000 (02:58 +0000)]
Add gaf-version header since these files are gaf 2.0
svn path=/; revision=622
elserj [Thu, 31 Dec 2015 02:41:31 +0000 (02:41 +0000)]
Remove version header as this isn't actually a gaf 2.0 file
svn path=/; revision=621
meiera [Thu, 31 Dec 2015 02:30:48 +0000 (02:30 +0000)]
added "GRIN" to column 6 of lentil assoc file.
svn path=/; revision=620
elserj [Thu, 31 Dec 2015 02:14:31 +0000 (02:14 +0000)]
Added PMID to column 6
svn path=/; revision=619
elserj [Thu, 31 Dec 2015 01:17:58 +0000 (01:17 +0000)]
Fix missing columns
svn path=/; revision=618
cooperl [Thu, 31 Dec 2015 01:12:43 +0000 (01:12 +0000)]
-commented out lines with missing data.
svn path=/; revision=617
meiera [Thu, 31 Dec 2015 00:59:01 +0000 (00:59 +0000)]
updated headers of gaf files to include "!gaf-version: 2.0\n"
svn path=/; revision=616
cooperl [Thu, 31 Dec 2015 00:52:19 +0000 (00:52 +0000)]
-commented out lines with missing data.
svn path=/; revision=615
cooperl [Thu, 31 Dec 2015 00:31:23 +0000 (00:31 +0000)]
Commented out lines with missing data.
svn path=/; revision=614
meiera [Thu, 31 Dec 2015 00:25:19 +0000 (00:25 +0000)]
Added lentil germplasm annotation file created from data downloaded from GRIN
svn path=/; revision=613
elserj [Thu, 31 Dec 2015 00:25:14 +0000 (00:25 +0000)]
Fix extra bracket in column 16
svn path=/; revision=612
cooperl [Thu, 31 Dec 2015 00:24:36 +0000 (00:24 +0000)]
- Removed test file Test_PPPP_TO/TO_IMP_gene_O.sativa-new.assoc
- modified Test_PPPP_TO/TO_IMP_gene_Z.mays.assoc to nromalize line endings
- Commented out lines with missing data in 'Test_PPPP_TO/TO_IMP_gene_O.sativa.assoc'
svn path=/; revision=611
elserj [Thu, 31 Dec 2015 00:22:04 +0000 (00:22 +0000)]
Fix broken relations in column 16 and missing columns
svn path=/; revision=610
elserj [Thu, 31 Dec 2015 00:05:21 +0000 (00:05 +0000)]
Add extra tabs to last line that were missing
svn path=/; revision=609
elserj [Wed, 30 Dec 2015 23:53:45 +0000 (23:53 +0000)]
Add tab to get 17 columns
svn path=/; revision=608
elserj [Wed, 30 Dec 2015 23:42:00 +0000 (23:42 +0000)]
Changed taxon id to one that works for Physcomitrella
svn path=/; revision=607
elserj [Wed, 30 Dec 2015 23:18:10 +0000 (23:18 +0000)]
Add gaf-version header and fix number of columns
svn path=/; revision=606
meiera [Wed, 30 Dec 2015 22:43:03 +0000 (22:43 +0000)]
Changed aspect column to "T" from "TO". Should be last change.
svn path=/; revision=605
elserj [Wed, 30 Dec 2015 22:24:04 +0000 (22:24 +0000)]
Add gaf version header
svn path=/; revision=604
elserj [Wed, 30 Dec 2015 20:34:13 +0000 (20:34 +0000)]
Fix all loading errors, which included adding version headers, commenting out lines with nothing in column 2, remove Windows line endings and random spaces, and added extra tabs
svn path=/; revision=603
meiera [Wed, 30 Dec 2015 20:04:02 +0000 (20:04 +0000)]
updated rice germplasm annotation file, removed individual annotation files.
svn path=/; revision=602
meiera [Wed, 30 Dec 2015 20:03:08 +0000 (20:03 +0000)]
updated new annotation files, added them to the concatenated file.
svn path=/; revision=601
elserj [Wed, 30 Dec 2015 20:00:34 +0000 (20:00 +0000)]
Remove unnecessary tabs from last column
svn path=/; revision=600
elserj [Wed, 30 Dec 2015 19:55:07 +0000 (19:55 +0000)]
Fix loding errors in AmiGO2
svn path=/; revision=599
elserj [Wed, 30 Dec 2015 19:29:19 +0000 (19:29 +0000)]
Remove extra columns from header
svn path=/; revision=598
elserj [Wed, 30 Dec 2015 19:08:21 +0000 (19:08 +0000)]
Add "taxon:" to taxon column
svn path=/; revision=597
projects / associations / .git / log