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meiera [Fri, 25 Sep 2015 17:08:18 +0000 (17:08 +0000)]
po_anatomy_gene_zea_MaizeGDB.assoc file was loaded into R and the deldupe() function was performed. The deldupe() function performs these operations: 1. Removes any line in the assoc file that has an exact duplicate (includes all 16 columns in step 1). 2. Identifies any lines in the association file that has relative duplicates (relative duplicates are rows where everything in columns 1 through 15 are exactly the same, but the row has different values in column 16.) 3. Removes any relative duplicate rows that contain "-" in column 16. 4. performs a check to see if the expected number of rows are removed.
svn path=/; revision=550
elserj [Fri, 18 Sep 2015 23:32:15 +0000 (23:32 +0000)]
Changed column 8 to have MaizeGDB: in the from part to fix how it shows up in AmiGO
svn path=/; revision=549
elserj [Fri, 18 Sep 2015 21:35:58 +0000 (21:35 +0000)]
Fix taxon id column to use NCBI ids rather than gramenes. Also, updated to latest from gramene release 39, which removed rice associations with no EO:XXXXXX numbers
svn path=/; revision=548
meiera [Wed, 16 Sep 2015 19:27:26 +0000 (19:27 +0000)]
revised the po_anatomy_stock_zea_MaizeGDB.assoc to include correct tab spacing.
svn path=/; revision=547
meiera [Wed, 16 Sep 2015 17:42:52 +0000 (17:42 +0000)]
revised column 1 of po_anatomy_stock_zea_MaizeGDB.assoc so the new MaizeGDB_stock Xref will be recognized.
svn path=/; revision=546
meiera [Sat, 12 Sep 2015 00:17:59 +0000 (00:17 +0000)]
Removed duplicate lines from TO_ontology_IMP_gene_Z.mays.assoc
svn path=/; revision=545
meiera [Sat, 12 Sep 2015 00:13:50 +0000 (00:13 +0000)]
Removed duplicate lines from TO_ontology_IMP_gene_M.truncatula.assoc
svn path=/; revision=544
meiera [Sat, 12 Sep 2015 00:07:17 +0000 (00:07 +0000)]
removed duplicate lines from GO_ontology_IMP_gene_M.truncatula.assoc
svn path=/; revision=543
meiera [Sat, 12 Sep 2015 00:01:17 +0000 (00:01 +0000)]
Removed duplicated lines from GO_ontology_IMP_gene_S.lycopersicum.assoc
svn path=/; revision=542
meiera [Fri, 11 Sep 2015 23:56:55 +0000 (23:56 +0000)]
removed duplicated lines from GO_ontology_IMP_gene_O.sativa.assoc
svn path=/; revision=541
cooperl [Fri, 11 Sep 2015 22:49:45 +0000 (22:49 +0000)]
Removed test_phenos folder and the go_gene_oryza_phenos.assoc.xls, as it has been replaced by go-associations/Test_PPPP_GO/GO_ontology_IMP_gene_O.sativa.assoc
svn path=/; revision=540
meiera [Fri, 11 Sep 2015 21:42:51 +0000 (21:42 +0000)]
renamed all the association files in the Test_PPPP_TO folder to be consistant with naming. Also fixed the spelling on the tomato association file in the test_PPPP_PO folder.
svn path=/; revision=539
meiera [Fri, 11 Sep 2015 21:36:53 +0000 (21:36 +0000)]
Renamed all association files in Test_PPPP_GO to be consistent with naming conventions.
svn path=/; revision=538
cooperl [Fri, 11 Sep 2015 21:31:26 +0000 (21:31 +0000)]
renamed the test-maizegdb-2015 folder to test-maizegdb
svn path=/; revision=537
cooperl [Fri, 11 Sep 2015 19:35:44 +0000 (19:35 +0000)]
Renamed test folder PO association files from test_PPPP to test_PPPP_PO to be consistent with the rest.
svn path=/; revision=536
elserj [Fri, 11 Sep 2015 18:44:47 +0000 (18:44 +0000)]
Changed Test_GO folder to Test_PPPP_GO
svn path=/; revision=535
elserj [Fri, 11 Sep 2015 18:43:51 +0000 (18:43 +0000)]
Changed Test_TO folder to Test_PPPP_TO
svn path=/; revision=534
johnseth [Thu, 10 Sep 2015 23:40:26 +0000 (23:40 +0000)]
added TEST_TO folder containing .assoc files for maize, medicago, rice,
soybean, tomato
svn path=/; revision=533
johnseth [Thu, 10 Sep 2015 23:38:59 +0000 (23:38 +0000)]
added TEST_GO file containing .assoc files for Maize, medicago,rice,
soybean, tomato, arabidopsis
svn path=/; revision=532
meiera [Fri, 28 Aug 2015 22:42:25 +0000 (22:42 +0000)]
Added go-association/ directory, and moved all go-associations from the [poc] branch into it. All files were moved except for compressed .gz files.
svn path=/; revision=531
meiera [Fri, 28 Aug 2015 22:29:33 +0000 (22:29 +0000)]
created to-associations/ folder, and moved all to.assoc files from the [poc] branch to here. They are now duplicated on the svn
svn path=/; revision=530
meiera [Fri, 28 Aug 2015 22:26:01 +0000 (22:26 +0000)]
Added an eo-association folder to the associations branch. Moved all eo-association*.assoc files into it. They are now duplicated in both [poc] and associations/ within the SVN"
svn path=/; revision=529
cooperl [Thu, 27 Aug 2015 01:27:49 +0000 (01:27 +0000)]
Adding test folder for new MaizeGDB association files
svn path=/; revision=528
meiera [Wed, 26 Aug 2015 23:36:41 +0000 (23:36 +0000)]
changed the + to a space in plant_ontology_qtl_glycine_soybase.assoc because the + cases amigo to crash.
svn path=/; revision=527
meiera [Wed, 26 Aug 2015 21:39:40 +0000 (21:39 +0000)]
replaced all spaces with '+' so they would work as IDs in the URL xref
svn path=/; revision=526
meiera [Wed, 26 Aug 2015 21:00:15 +0000 (21:00 +0000)]
Modified the second column of the plant_ontology_qtl_glycine_soybase.assoc file to have correct verbose ID for lookup in SOY_QTL database
svn path=/; revision=525
johnseth [Fri, 21 Aug 2015 23:19:25 +0000 (23:19 +0000)]
removed PO_ontology_IMP_gene_oryza.assoc
svn path=/; revision=524
johnseth [Fri, 21 Aug 2015 23:18:14 +0000 (23:18 +0000)]
renamed test_PPPP/PO_ontology_IMP_gene_G.max.assoc,/PO_ontology_IMP_gene_M.truncatula.assoc,/PO_ontology_IMP_gene_S.lycopersum.assoc
svn path=/; revision=523
johnseth [Fri, 21 Aug 2015 23:14:52 +0000 (23:14 +0000)]
added pubmed IDs to
/PO_anatomy_IMP_gene_arabidopsis.assoc,/PO_ontology_IMP_gene_Z.mays.assoc,/PO_ontology_IMP_gene_medicago.assoc,/PO_ontology_IMP_gene_solanum.assoc,/PO_ontology_IMP_gene_soybean.assoc
and renamed
PO _ontology_IMP_gene_Z.mays.assoc
svn path=/; revision=522
meiera [Fri, 21 Aug 2015 18:50:07 +0000 (18:50 +0000)]
Fixed a typo in the taxonID column of PO_ontology_IMP_gene_soybean.assoc file.
svn path=/; revision=521
meiera [Fri, 21 Aug 2015 18:46:46 +0000 (18:46 +0000)]
Updated the Taxon column to add "taxon:" before the taxonID number
svn path=/; revision=520
johnseth [Fri, 21 Aug 2015 18:39:41 +0000 (18:39 +0000)]
revised column 13, added "taxon" before actual id for/PO_anatomy_IMP_gene_arabidopsis.assoc,/PO_ontology_IMP_gene_maize.assoc,/PO_ontology_IMP_gene_medicago.assoc
svn path=/; revision=519
meiera [Fri, 21 Aug 2015 17:26:21 +0000 (17:26 +0000)]
Added leading zeros back to Database ID column.
svn path=/; revision=518
elserj [Fri, 21 Aug 2015 17:08:16 +0000 (17:08 +0000)]
Remove empty lines from end of file
svn path=/; revision=517
johnseth [Fri, 21 Aug 2015 16:47:16 +0000 (16:47 +0000)]
revised the PO_anatomy_IMP_gene_arabidopsis.assoc
svn path=/; revision=516
johnseth [Thu, 20 Aug 2015 23:44:03 +0000 (23:44 +0000)]
revised column 1 of PO_ontology_IMP_gene_soybean.assoc
svn path=/; revision=515
johnseth [Thu, 20 Aug 2015 18:54:49 +0000 (18:54 +0000)]
revised column 1 of PO_ontology_IMP_gene_soybean.assoc
svn path=/; revision=514
johnseth [Wed, 19 Aug 2015 21:38:53 +0000 (21:38 +0000)]
made revisions to column 4 and last rows of the test_PPPP/PO_anatomy_IMP_gene_arabidopsis.assoc,/PO_ontology_IMP_gene_maize.assoc,/PO_ontology_IMP_gene_medicago.assoc,/PO_ontology_IMP_gene_solanum.assoc,/PO_ontology_IMP_gene_soybean.assoc
svn path=/; revision=513
meiera [Wed, 19 Aug 2015 20:54:40 +0000 (20:54 +0000)]
corrected errors in test_PPPP/PO_anatomy_IMP_gene_arabidopsis.assoc,/PO_ontology_IMP_gene_maize.assoc,/PO_ontology_IMP_gene_soybean.assoc
~
svn path=/; revision=512
meiera [Wed, 19 Aug 2015 19:58:49 +0000 (19:58 +0000)]
revised database column in /PO_ontology_IMP_gene_soybean.assoc
svn path=/; revision=511
meiera [Wed, 19 Aug 2015 19:05:18 +0000 (19:05 +0000)]
removed headers from /PO_anatomy_IMP_gene_arabidopsis.assoc
:
M test_PPPP/PO_anatomy_IMP_gene_arabidopsis.assoc
svn path=/; revision=510
meiera [Wed, 19 Aug 2015 18:59:44 +0000 (18:59 +0000)]
added directory test_PPPP containing /PO_anatomy_IMP_gene_arabidopsis.assoc,/PO_ontology_IMP_gene_maize.assoc,/PO_ontology_IMP_gene_medicago.assoc,/PO_ontology_IMP_gene_oryza.assoc,/PO_ontology_IMP_gene_solanum.assoc,/PO_ontology_IMP_gene_soybean.assoc
svn path=/; revision=509
elserj [Mon, 27 Jul 2015 22:30:54 +0000 (22:30 +0000)]
Fixed some more spacing problems.
svn path=/; revision=508
elserj [Mon, 27 Jul 2015 19:40:35 +0000 (19:40 +0000)]
Fixed extra spaces in PO id column. Needed for AmiGO2 load
svn path=/; revision=507
elserj [Fri, 26 Jun 2015 23:01:53 +0000 (23:01 +0000)]
Fixed spacing issues in file. Can't have spaces between relationship and parantheses. Fixed in anticipation of migration to AmiGO2
svn path=/; revision=506
tair [Thu, 25 Jun 2015 18:33:01 +0000 (18:33 +0000)]
Undoing commit of bad data merge
svn path=/; revision=505
tair [Thu, 25 Jun 2015 18:09:18 +0000 (18:09 +0000)]
TAIR monthly commit
svn path=/; revision=504
elserj [Tue, 21 Apr 2015 22:23:19 +0000 (22:23 +0000)]
Fixed spacing issues in assoc files. Most were in col 16, but some in col 5 as well. AmiGO2 does not like the spaces and fails on load. Fixed in anticipation of migration to AmiGO2 for planteome.
svn path=/; revision=503
tair [Sat, 2 Aug 2014 08:10:42 +0000 (08:10 +0000)]
TAIR weekly commit
svn path=/; revision=502
tair [Sat, 2 Aug 2014 08:09:45 +0000 (08:09 +0000)]
TAIR weekly commit
svn path=/; revision=501
tair [Fri, 1 Aug 2014 08:29:34 +0000 (08:29 +0000)]
TAIR weekly commit
svn path=/; revision=500
tair [Fri, 1 Aug 2014 08:26:59 +0000 (08:26 +0000)]
TAIR weekly commit
svn path=/; revision=499
tair [Sat, 26 Jul 2014 08:28:57 +0000 (08:28 +0000)]
TAIR weekly commit
svn path=/; revision=498
tair [Sat, 19 Jul 2014 08:28:13 +0000 (08:28 +0000)]
TAIR weekly commit
svn path=/; revision=497
tair [Sat, 19 Jul 2014 08:25:41 +0000 (08:25 +0000)]
TAIR weekly commit
svn path=/; revision=496
elserj [Tue, 1 Jul 2014 22:14:12 +0000 (22:14 +0000)]
Some lines had the worng aspect entered (column 9)
svn path=/; revision=495
tair [Mon, 10 Feb 2014 19:50:31 +0000 (19:50 +0000)]
Final checkin of free TAIR data as of August 31, 2013
svn path=/; revision=494
cooperl [Sun, 20 Oct 2013 22:42:14 +0000 (22:42 +0000)]
Fixed typo in name and remove header line.
svn path=/; revision=493
cooperl [Fri, 18 Oct 2013 22:29:39 +0000 (22:29 +0000)]
Added 2 new files of associations to developing maize leaves from Li et al,2010
svn path=/; revision=492
cooperl [Sat, 28 Sep 2013 00:13:33 +0000 (00:13 +0000)]
Added a folder to put the Leaf development annotations in to test.
svn path=/; revision=491
elserj [Wed, 28 Aug 2013 23:05:43 +0000 (23:05 +0000)]
run mac2unix again
svn path=/; revision=490
cooperl [Wed, 28 Aug 2013 23:03:01 +0000 (23:03 +0000)]
Fixed object symbol column.
svn path=/; revision=489
cooperl [Wed, 28 Aug 2013 22:20:21 +0000 (22:20 +0000)]
Fixed space in curator name.
svn path=/; revision=488
elserj [Wed, 28 Aug 2013 21:27:17 +0000 (21:27 +0000)]
Had to run mac2unix to fix the mac line breaks. Made the file only have one line until fixed
svn path=/; revision=487
cooperl [Wed, 28 Aug 2013 18:54:47 +0000 (18:54 +0000)]
Fixed suffix for filename
svn path=/; revision=486
cooperl [Wed, 28 Aug 2013 18:50:28 +0000 (18:50 +0000)]
Renaming SoyBase QTL test file.
svn path=/; revision=485
cooperl [Wed, 28 Aug 2013 18:46:57 +0000 (18:46 +0000)]
Removed the new file fix continuity.
svn path=/; revision=484
cooperl [Wed, 28 Aug 2013 18:45:08 +0000 (18:45 +0000)]
SoyBase QTL annotation file was updated- corrected columns and PO Ids to obsolete term: sporophyte (PO:
0009003).
svn path=/; revision=483
cooperl [Wed, 28 Aug 2013 18:35:42 +0000 (18:35 +0000)]
Fixing name
svn path=/; revision=482
cooperl [Wed, 28 Aug 2013 18:34:00 +0000 (18:34 +0000)]
Renaming the test file of SoyBase QTL annotations.
svn path=/; revision=481
elserj [Wed, 21 Aug 2013 21:18:09 +0000 (21:18 +0000)]
Updated to associations files in release #20
svn path=/; revision=480
cooperl [Mon, 12 Aug 2013 18:36:32 +0000 (18:36 +0000)]
Adding new association file for Soybase QTLs for Rex Nelson.
svn path=/; revision=479
elserj [Mon, 29 Jul 2013 05:48:36 +0000 (05:48 +0000)]
Changed obsoleted term PO:
0007617 to PO:
0007616
svn path=/; revision=478
tair [Sat, 27 Jul 2013 20:15:28 +0000 (20:15 +0000)]
TAIR weekly commit
svn path=/; revision=477
tair [Sat, 27 Jul 2013 19:49:36 +0000 (19:49 +0000)]
TAIR weekly commit
svn path=/; revision=476
cooperl [Thu, 25 Jul 2013 23:09:37 +0000 (23:09 +0000)]
emoved extra GR: from the Gramene files.
svn path=/; revision=475
cooperl [Wed, 24 Jul 2013 20:11:55 +0000 (20:11 +0000)]
Removed the working copies of the rice IMP files since it has been moved to the main folder.
svn path=/; revision=474
cooperl [Wed, 24 Jul 2013 19:03:47 +0000 (19:03 +0000)]
Removed some extra spaces in the DB_object_ID
svn path=/; revision=473
cooperl [Wed, 24 Jul 2013 18:58:19 +0000 (18:58 +0000)]
emoved annotations to DSG1 as we do not have a GR:id for those.
Changed assigned by from PO:Laurel_Cooper to POC:Laurel_Cooper
Changed GR to GR_gene as DB in Col #1
Renamed file po_ontology_IMP_gene_oryza_poc.assoc
svn path=/; revision=472
cooperl [Wed, 24 Jul 2013 18:06:40 +0000 (18:06 +0000)]
Renamed cotton transcript anatomy file and moved to main folder.
svn path=/; revision=471
cooperl [Wed, 24 Jul 2013 18:03:43 +0000 (18:03 +0000)]
Renamed cotton transcript anatomy file and moved to main folder.
svn path=/; revision=470
cooperl [Wed, 24 Jul 2013 17:06:25 +0000 (17:06 +0000)]
Changed annotation from seed trichomes (PO:
0004511) to plant protoplasts (PO:
0000006), and fixed DB_Object_name- col#10.
svn path=/; revision=469
cooperl [Wed, 24 Jul 2013 00:25:12 +0000 (00:25 +0000)]
Removed the extra GR: from the Rice_phenos annotation file.
svn path=/; revision=468
elserj [Mon, 22 Jul 2013 23:30:56 +0000 (23:30 +0000)]
Added tsv version of association file
svn path=/; revision=467
cooperl [Mon, 22 Jul 2013 22:34:30 +0000 (22:34 +0000)]
Updated the "assigned _by" and removed colored lines.-
-This line, and those below, will be ignored--
M test_phenos/go_gene_oryza_phenos.assoc.xls
M test_phenos/po_gene_oryza_phenos.assoc.xls
svn path=/; revision=466
tair [Sat, 20 Jul 2013 20:17:12 +0000 (20:17 +0000)]
TAIR weekly commit
svn path=/; revision=465
tair [Sat, 20 Jul 2013 19:52:29 +0000 (19:52 +0000)]
TAIR weekly commit
svn path=/; revision=464
tair [Sat, 13 Jul 2013 20:13:58 +0000 (20:13 +0000)]
TAIR weekly commit
svn path=/; revision=463
tair [Sat, 13 Jul 2013 19:51:19 +0000 (19:51 +0000)]
TAIR weekly commit
svn path=/; revision=462
tair [Sat, 6 Jul 2013 20:38:02 +0000 (20:38 +0000)]
TAIR weekly commit
svn path=/; revision=461
tair [Sat, 6 Jul 2013 20:06:51 +0000 (20:06 +0000)]
TAIR weekly commit
svn path=/; revision=460
tair [Fri, 28 Jun 2013 20:37:17 +0000 (20:37 +0000)]
TAIR weekly update
svn path=/; revision=459
tair [Fri, 28 Jun 2013 20:36:23 +0000 (20:36 +0000)]
TAIR weekly update
svn path=/; revision=458
moorel [Tue, 11 Jun 2013 21:47:21 +0000 (21:47 +0000)]
Added annotations to growth stages for the rice phenotype data set.
svn path=/; revision=457
moorel [Wed, 29 May 2013 19:43:01 +0000 (19:43 +0000)]
changed the gramene ID for DSG1 to be GR:xxxxxxx until we can replace
with a real gramene ID.
svn path=/; revision=456
moorel [Tue, 28 May 2013 21:34:56 +0000 (21:34 +0000)]
Added correct gene names from the gramene site to the PO annotation
file.
svn path=/; revision=455
moorel [Tue, 28 May 2013 18:23:21 +0000 (18:23 +0000)]
Added PubMed IDs for GO annotations and added correct Aspects for GO
annotations. Flagged DSG1 gene lines in green to indicate a problem with
the GR ID.
svn path=/; revision=454
moorel [Thu, 23 May 2013 21:55:48 +0000 (21:55 +0000)]
Added Gramene database IDs for literature unavailable on PubMed.
svn path=/; revision=453
cooperl [Thu, 23 May 2013 21:48:04 +0000 (21:48 +0000)]
Saved the GO file as .xls for editting.
svn path=/; revision=452
moorel [Thu, 23 May 2013 21:33:50 +0000 (21:33 +0000)]
Added all available PMIDs to the PO rice phenotype annotations.
svn path=/; revision=451
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