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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
elserj [Wed, 30 Dec 2015 19:02:27 +0000 (19:02 +0000)]
Remove gaf-version tag from header, file isn't actually 2.0
svn path=/; revision=596
elserj [Wed, 30 Dec 2015 05:26:37 +0000 (05:26 +0000)]
Change Physcomitrella taxon id to one that works
svn path=/; revision=595
elserj [Wed, 30 Dec 2015 02:27:18 +0000 (02:27 +0000)]
Messed up adding the "taxon:", it shouldn't have been on the header line, caused the warnings about how many columns there were to come back.
svn path=/; revision=594
elserj [Wed, 30 Dec 2015 01:40:28 +0000 (01:40 +0000)]
Removed extra column 18, added gaf-version header and fixed taxon column (13) to have "taxon:"
svn path=/; revision=593
elserj [Wed, 30 Dec 2015 01:03:20 +0000 (01:03 +0000)]
Added gaf-version header line to make warnings go away when loading in Amigo.
svn path=/; revision=592
meiera [Wed, 30 Dec 2015 00:50:50 +0000 (00:50 +0000)]
Removed individual annotation files, replaced them with concatenated version- to_germplasm_rice.assoc
svn path=/; revision=591
cooperl [Tue, 29 Dec 2015 22:29:49 +0000 (22:29 +0000)]
Removed lines in TO_IMP_gene_O.sativa.assoc and saved as TO_IMP_gene_O.sativa-new.assoc
svn path=/; revision=590
cooperl [Tue, 29 Dec 2015 21:49:28 +0000 (21:49 +0000)]
Adding cassava data files for reference
svn path=/; revision=589
cooperl [Tue, 29 Dec 2015 21:09:53 +0000 (21:09 +0000)]
Adding cassava germaplsm annotations from Genesys
svn path=/; revision=588
cooperl [Tue, 29 Dec 2015 20:33:30 +0000 (20:33 +0000)]
Fixed file names for TO_PPPP files
D Test_PPPP_TO/TO_ontology_IMP_gene_G.max.assoc
A + Test_PPPP_TO/TO_IMP_gene_O.sativa.assoc
D Test_PPPP_TO/TO_ontology_IMP_gene_M.truncatula.assoc
D Test_PPPP_TO/TO_ontology_IMP_gene_S.lycopersicum.assoc
A + Test_PPPP_TO/TO_IMP_gene_G.max.assoc
D Test_PPPP_TO/TO_ontology_IMP_gene_Z.mays.assoc
A + Test_PPPP_TO/TO_IMP_gene_M.truncatula.assoc
D Test_PPPP_TO/TO_ontology_IMP_gene_O.sativa.assoc
A + Test_PPPP_TO/TO_IMP_gene_S.lycopersicum.assoc
A + Test_PPPP_TO/TO_IMP_gene_Z.mays.assoc
svn path=/; revision=587
cooperl [Tue, 29 Dec 2015 20:24:07 +0000 (20:24 +0000)]
changed aspect to T from branch identifiers in PPPP TO files
svn path=/; revision=586
cooperl [Tue, 29 Dec 2015 04:54:09 +0000 (04:54 +0000)]
Added a couple missing TO annotations.
svn path=/; revision=585
meiera [Mon, 28 Dec 2015 20:57:27 +0000 (20:57 +0000)]
added test files to test column 9 (Aspect). Added DB object name as the germplasm name
svn path=/; revision=584
meiera [Mon, 28 Dec 2015 19:06:08 +0000 (19:06 +0000)]
Added blast annotation file back
svn path=/; revision=583
meiera [Mon, 28 Dec 2015 19:05:30 +0000 (19:05 +0000)]
removed blast annotation file testing the use of column8.
svn path=/; revision=582
cooperl [Thu, 17 Dec 2015 18:01:35 +0000 (18:01 +0000)]
Adding test folder for cassava annotations
svn path=/; revision=581
meiera [Thu, 17 Dec 2015 02:34:11 +0000 (02:34 +0000)]
changed from_country annotation to column 8, and left has_phenotype_score in column 16
svn path=/; revision=580
meiera [Mon, 14 Dec 2015 20:01:10 +0000 (20:01 +0000)]
Removed '\n' from protein_trait_annotation.tsv
svn path=/; revision=579
meiera [Mon, 14 Dec 2015 18:33:07 +0000 (18:33 +0000)]
Fixed line errors in files. Testing column 8 in blast2_trait_annotation.tsv
svn path=/; revision=578
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