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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
meiera [Sat, 12 Dec 2015 01:59:50 +0000 (01:59 +0000)]
Files should no longer be empty!!!
svn path=/; revision=577
meiera [Fri, 11 Dec 2015 23:57:18 +0000 (23:57 +0000)]
this time I actually added the gaf files.
svn path=/; revision=576
meiera [Fri, 11 Dec 2015 23:54:47 +0000 (23:54 +0000)]
Removed old test_rice_blast_annotation.tsv, and replaced with current 'blast_trait_annotation.tsv'. Also added annotation file for all other traits annotated via NSF.PROJECT.OBS experiment: https://npgsweb.ars-grin.gov/gringlobal/method.aspx?id=494436
svn path=/; revision=575
meiera [Wed, 25 Nov 2015 18:57:04 +0000 (18:57 +0000)]
Added a test_germplasm folder to store test annotation files for germplasm with annotations to traits in the TO
svn path=/; revision=574
elserj [Fri, 13 Nov 2015 22:29:41 +0000 (22:29 +0000)]
Replace GR_tax ids with corresponding NCBI ones
svn path=/; revision=573
elserj [Wed, 14 Oct 2015 23:41:57 +0000 (23:41 +0000)]
Remove all .txt files as they have been superceded by .gaf files. Fix header in all .gaf files (was missing "!"), and rename all files to .assoc. Files were originally downloaded from Gramene Sep 14 2014.
svn path=/; revision=572
elserj [Fri, 9 Oct 2015 20:03:11 +0000 (20:03 +0000)]
Updated zip file to have all association files in release #21
svn path=/; revision=571
elserj [Mon, 5 Oct 2015 18:51:03 +0000 (18:51 +0000)]
Replace references to "Ethan Johnson" and "Brian_Atkinson" to have "POC:" in front to make it clear who added the annotations
svn path=/; revision=570
elserj [Mon, 5 Oct 2015 17:00:41 +0000 (17:00 +0000)]
Change association to alt_id PO:
0007617 to PO:
0007616 (flowering stage)
svn path=/; revision=569
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