From 1e2649b2fda285b62fab3e1d49d590539f636fdf Mon Sep 17 00:00:00 2001 From: cooperl Date: Thu, 17 Mar 2016 19:55:15 +0000 Subject: [PATCH] Revised annotations to TO:0000079, with new terms for lemma and palea morphology. Fixed Xrefs to GR_REF. svn path=/; revision=702 --- to-associations/TO_IMP_gene_O.sativa.assoc | 66 +++++++++++----------- 1 file changed, 33 insertions(+), 33 deletions(-) diff --git a/to-associations/TO_IMP_gene_O.sativa.assoc b/to-associations/TO_IMP_gene_O.sativa.assoc index a6343e7..232fa4a 100644 --- a/to-associations/TO_IMP_gene_O.sativa.assoc +++ b/to-associations/TO_IMP_gene_O.sativa.assoc @@ -18,11 +18,11 @@ GR_gene GR:0060068 BC1 brittle culm TO:0000200 PMID:12953108 IMP T Os03g0416200 GR_gene GR:0060068 BC1 grain shattering TO:0000473 PMID:12953108 IMP T Os03g0416200 panicles brittle at green stage gene taxon:4530 20150417 Ethan Johnson GR_gene GR:0060068 BC1 grain shattering TO:0000473 PMID:12953108 IMP T Os03g0416200 panicles brittle at mature stage gene taxon:4530 20150417 Ethan Johnson !GR_gene GR:0060068 BC1 PMID:12953108 IMP Os03g0416200 low content of alpha-cellulose in cell wall gene taxon:4530 20150417 Ethan Johnson -GR_gene GR:0060070 BC3 stem strength TO:0000051 GR_gene:5651 IMP T Os02g0738900 weak culm gene taxon:4530 20150417 Ethan Johnson -GR_gene GR:0060070 BC3 brittle culm TO:0000200 GR_gene:5651 IMP T Os02g0738900 brittle culm gene taxon:4530 20150417 Ethan Johnson -GR_gene GR:0060070 BC3 panicle size TO:0006032 GR_gene:5651 IMP T Os02g0738900 short emergence of panicles gene taxon:4530 20150417 Ethan Johnson -GR_gene GR:0060070 BC3 panicle anatomy and morphology trait TO:0000847 GR_gene:5651 IMP T Os02g0738900 incomplete emergence of panicles gene taxon:4530 20150417 Ethan Johnson -!GR_gene GR:0060073 BC6 GR_gene:5933 IMP Os09g0422500 all parts of plant are extremely brittle gene taxon:4530 20150417 Ethan Johnson +GR_gene GR:0060070 BC3 stem strength TO:0000051 GR_REF5651 IMP T Os02g0738900 weak culm gene taxon:4530 20150417 Ethan Johnson +GR_gene GR:0060070 BC3 brittle culm TO:0000200 GR_REF:5651 IMP T Os02g0738900 brittle culm gene taxon:4530 20150417 Ethan Johnson +GR_gene GR:0060070 BC3 panicle size TO:0006032 GR_REF:5651 IMP T Os02g0738900 short emergence of panicles gene taxon:4530 20150417 Ethan Johnson +GR_gene GR:0060070 BC3 panicle anatomy and morphology trait TO:0000847 GR_REF:5651 IMP T Os02g0738900 incomplete emergence of panicles gene taxon:4530 20150417 Ethan Johnson +!GR_gene GR:0060073 BC6 GR_REF:5933 IMP Os09g0422500 all parts of plant are extremely brittle gene taxon:4530 20150417 Ethan Johnson GR_gene GR:0080018 BLE3 root length TO:0000227 PMID:16808934 IMP T Os05g0245300 short roots gene taxon:4530 20150417 Ethan Johnson GR_gene GR:0080018 BLE3 inflorescence branching TO:0000050 PMID:16808934 IMP T Os05g0245300 less branching gene taxon:4530 20150417 Ethan Johnson GR_gene GR:0080018 BLE3 plant height TO:0000207 PMID:16808934 IMP T Os05g0245300 Semi-dwarf gene taxon:4530 20150417 Ethan Johnson @@ -46,10 +46,10 @@ GR_gene GR:0060184 D1 panicle compactness and shape TO:0020001 PMID:12237405 IMP GR_gene GR:0060184 D1 glume width TO:0020034 PMID:12237405 IMP T Os05g0333200 small glume gene taxon:4530 20150420 Ethan Johnson GR_gene GR:0060184 D1 glume anatomy and morphology trait TO:0000869 PMID:12237405 IMP T Os05g0333200 round glumes gene taxon:4530 20150420 Ethan Johnson GR_gene GR:0060184 D1 basal internode diameter TO:0000132 PMID:12237405 IMP T Os05g0333200 thick internodes gene taxon:4530 20150420 Ethan Johnson -GR_gene GR:0060192 D10 plant height TO:0000207 GR_gene:5792 IMP T Os01g0746400 dwarf gene taxon:4530 20150420 Ethan Johnson -GR_gene GR:0060192 D10 tiller number TO:0000346 GR_gene:5792 IMP T Os01g0746400 profuse tillers gene taxon:4530 20150420 Ethan Johnson -!GR_gene GR:0060192 D10 GR_gene:5792 IMP Os01g0746400 slender tillers gene taxon:4530 20150420 Ethan Johnson -GR_gene GR:0060192 D10 panicle size TO:0006032 GR_gene:5792 IMP T Os01g0746400 small panicles gene taxon:4530 20150420 Ethan Johnson +GR_gene GR:0060192 D10 plant height TO:0000207 GR_REF:5792 IMP T Os01g0746400 dwarf gene taxon:4530 20150420 Ethan Johnson +GR_gene GR:0060192 D10 tiller number TO:0000346 GR_REF:5792 IMP T Os01g0746400 profuse tillers gene taxon:4530 20150420 Ethan Johnson +!GR_gene GR:0060192 D10 GR_REF:5792 IMP Os01g0746400 slender tillers gene taxon:4530 20150420 Ethan Johnson +GR_gene GR:0060192 D10 panicle size TO:0006032 GR_REF:5792 IMP T Os01g0746400 small panicles gene taxon:4530 20150420 Ethan Johnson GR_gene GR:0060193 D11 plant height TO:0000207 PMID:15705958 IMP T Os04g0469800 semidwarf gene taxon:4530 20150420 Ethan Johnson GR_gene GR:0060193 D11 stem internode anatomy and morphology trait TO:0000756 PMID:15705958 IMP T Os04g0469800 second internode reduced gene taxon:4530 20150420 Ethan Johnson GR_gene GR:0060193 D11 panicle length TO:0000040 PMID:15705958 IMP T Os04g0469800 long panicles gene taxon:4530 20150420 Ethan Johnson @@ -146,8 +146,8 @@ GR_gene GR:0080037 LSI2 growth and development trait TO:0000357 PMID:17625566 IM GR_gene GR:0080037 LSI2 pericarp color TO:0000707 PMID:17625566 IMP T Os03g0107300 grain discoloration gene taxon:4530 20150427 Ethan Johnson !GR_gene GR:0080037 LSI2 PMID:17625566 IMP Os03g0107300 low silicon in shoot gene taxon:4530 20150427 Ethan Johnson !GR_gene GR:0080037 LSI2 PMID:17625566 IMP Os03g0107300 low silicon in hull gene taxon:4530 20150427 Ethan Johnson -GR_gene GR:0080015 MADS1 lemma and palea anatomy and morphology trait TO:0000079 PMID:16146529 IMP T Os03g0215400 leafy lemma gene taxon:4530 20150427 Ethan Johnson -GR_gene GR:0080015 MADS1 lemma and palea anatomy and morphology trait TO:0000079 PMID:16146529 IMP T Os03g0215400 leafy palea gene taxon:4530 20150427 Ethan Johnson +GR_gene GR:0080015 MADS1 lemma morphology trait TO:1000023 PMID:16146529 IMP T Os03g0215400 leafy lemma gene taxon:4530 20150427 cooperl +GR_gene GR:0080015 MADS1 palea morphology trait TO:1000024 PMID:16146529 IMP T Os03g0215400 leafy palea gene taxon:4530 20150427 cooperl !GR_gene GR:0080015 MADS1 PMID:16146529 IMP Os03g0215400 open hull gene taxon:4530 20150427 Ethan Johnson GR_gene GR:0080015 MADS1 stamen number TO:0000225 PMID:16146529 IMP T Os03g0215400 reduced stamen number gene taxon:4530 20150427 Ethan Johnson GR_gene GR:0080015 MADS1 carpel number TO:0006013 PMID:16146529 IMP T Os03g0215400 increased carpel number gene taxon:4530 20150427 Ethan Johnson @@ -255,21 +255,21 @@ GR_gene GR:0060882 SHL4 shoot system growth and development trait TO:0000654 PMI !GR_gene GR:0060882 SHL4 PMID:10409508 IMP Os03g0449200 scutellum normal gene taxon:4530 20150501 Ethan Johnson !GR_gene GR:0060882 SHL4 PMID:10409508 IMP Os03g0449200 radicle normal gene taxon:4530 20150501 Ethan Johnson GR_gene GR:0060882 SHL4 root development trait TO:0000656 PMID:10409508 IMP T Os03g0449200 roots grow normally gene taxon:4530 20150501 Ethan Johnson -GR_gene GR:0060883 SHO1 shoot apical meristem development TO:0006020 GR_gene:1477 IMP T Os04g0509300 malformed shoot apical meristem gene taxon:4530 20150501 Ethan Johnson -GR_gene GR:0060883 SHO1 plastochron TO:0000735 GR_gene:1477 IMP T Os04g0509300 short plastochron gene taxon:4530 20150501 Ethan Johnson -GR_gene GR:0060883 SHO1 leaf shape TO:0000492 GR_gene:1477 IMP T Os04g0509300 aberrant leaves gene taxon:4530 20150501 Ethan Johnson -GR_gene GR:0060883 SHO1 leaf number TO:0000241 GR_gene:1477 IMP T Os04g0509300 increased leaf production gene taxon:4530 20150501 Ethan Johnson -GR_gene GR:0060883 SHO1 leaf shape TO:0000492 GR_gene:1477 IMP T Os04g0509300 leaves thread-like (short/narrow) gene taxon:4530 20150501 Ethan Johnson -GR_gene GR:0060883 SHO1 shoot apical meristem development TO:0006020 GR_gene:1477 IMP T Os04g0509300 shoot apical meristem flat gene taxon:4530 20150501 Ethan Johnson -GR_gene GR:0060883 SHO1 cell cycle trait TO:0000728 GR_gene:1477 IMP T Os04g0509300 disorganized cell division in shoot meristem gene taxon:4530 20150501 Ethan Johnson -GR_gene GR:0060936 SL1 lemma and palea anatomy and morphology trait TO:0000079 GR_gene:6472 IMP T Os01g0129200 degenerated lemma gene taxon:4530 20150501 Ethan Johnson -GR_gene GR:0060936 SL1 lemma and palea anatomy and morphology trait TO:0000079 GR_gene:6472 IMP T Os01g0129200 degenerated palea gene taxon:4530 20150501 Ethan Johnson -GR_gene GR:0060936 SL1 sterility or fertility trait TO:0000392 GR_gene:6472 IMP T Os01g0129200 stamen nonfunctional gene taxon:4530 20150501 Ethan Johnson -GR_gene GR:0060936 SL1 male sterility TO:0000437 GR_gene:6472 IMP T Os01g0129200 male sterile gene taxon:4530 20150501 Ethan Johnson -GR_gene GR:0060936 SL1 stamen anatomy and morphology trait TO:0000215 GR_gene:6472 IMP T Os01g0129200 stamens malformed gene taxon:4530 20150501 Ethan Johnson -GR_gene GR:0060936 SL1 reproductive homeotic development trait TO:0002613 GR_gene:6472 IMP T Os01g0129200 stamens transformed to pistils gene taxon:4530 20150501 Ethan Johnson -GR_gene GR:0060936 SL1 floret anatomy and morphology trait TO:0000274 GR_gene:6472 IMP T Os01g0129200 Mutant floret has 3 ovaries gene taxon:4530 20150501 Ethan Johnson -GR_gene GR:0060936 SL1 fertility related trait TO:0000420 GR_gene:6472 IMP T Os01g0129200 female fertile gene taxon:4530 20150501 Ethan Johnson +GR_gene GR:0060883 SHO1 shoot apical meristem development TO:0006020 GR_REF:1477 IMP T Os04g0509300 malformed shoot apical meristem gene taxon:4530 20150501 Ethan Johnson +GR_gene GR:0060883 SHO1 plastochron TO:0000735 GR_REF:1477 IMP T Os04g0509300 short plastochron gene taxon:4530 20150501 Ethan Johnson +GR_gene GR:0060883 SHO1 leaf shape TO:0000492 GR_REF:1477 IMP T Os04g0509300 aberrant leaves gene taxon:4530 20150501 Ethan Johnson +GR_gene GR:0060883 SHO1 leaf number TO:0000241 GR_REF:1477 IMP T Os04g0509300 increased leaf production gene taxon:4530 20150501 Ethan Johnson +GR_gene GR:0060883 SHO1 leaf shape TO:0000492 GR_REF:1477 IMP T Os04g0509300 leaves thread-like (short/narrow) gene taxon:4530 20150501 Ethan Johnson +GR_gene GR:0060883 SHO1 shoot apical meristem development TO:0006020 GR_REF:1477 IMP T Os04g0509300 shoot apical meristem flat gene taxon:4530 20150501 Ethan Johnson +GR_gene GR:0060883 SHO1 cell cycle trait TO:0000728 GR_REF:1477 IMP T Os04g0509300 disorganized cell division in shoot meristem gene taxon:4530 20150501 Ethan Johnson +GR_gene GR:0060936 SL1 lemma morphology trait TO:1000023 GR_REF:6472 IMP T Os01g0129200 degenerated lemma gene taxon:4530 20150501 Ethan Johnson +GR_gene GR:0060936 SL1 palea morphology trait TO:1000024 GR_REF:6472 IMP T Os01g0129200 degenerated palea gene taxon:4530 20150501 Ethan Johnson +GR_gene GR:0060936 SL1 sterility or fertility trait TO:0000392 GR_REF:6472 IMP T Os01g0129200 stamen nonfunctional gene taxon:4530 20150501 Ethan Johnson +GR_gene GR:0060936 SL1 male sterility TO:0000437 GR_REF:6472 IMP T Os01g0129200 male sterile gene taxon:4530 20150501 Ethan Johnson +GR_gene GR:0060936 SL1 stamen anatomy and morphology trait TO:0000215 GR_REF:6472 IMP T Os01g0129200 stamens malformed gene taxon:4530 20150501 Ethan Johnson +GR_gene GR:0060936 SL1 reproductive homeotic development trait TO:0002613 GR_REF:6472 IMP T Os01g0129200 stamens transformed to pistils gene taxon:4530 20150501 Ethan Johnson +GR_gene GR:0060936 SL1 floret anatomy and morphology trait TO:0000274 GR_REF:6472 IMP T Os01g0129200 Mutant floret has 3 ovaries gene taxon:4530 20150501 Ethan Johnson +GR_gene GR:0060936 SL1 fertility related trait TO:0000420 GR_REF:6472 IMP T Os01g0129200 female fertile gene taxon:4530 20150501 Ethan Johnson GR_gene GR:0060897 SLR shoot system anatomy and morphology trait TO:0000077 PMID:11340177 IMP T Os03g0707600 slender shoots gene taxon:4530 20150501 Ethan Johnson GR_gene GR:0060897 SLR internode length TO:0000145 PMID:11340177 IMP T Os03g0707600 basal internodes elongated gene taxon:4530 20150501 Ethan Johnson GR_gene GR:0060897 SLR root number TO:0000084 PMID:11340177 IMP T Os03g0707600 reduced root number gene taxon:4530 20150501 Ethan Johnson @@ -279,13 +279,13 @@ GR_gene GR:0080036 SNB floral bract number TO:0006026 PMID:17144896 IMP T Os07g GR_gene GR:0080036 SNB bract anatomy and morphology trait TO:0000815 PMID:17144896 IMP T Os07g0235800 rudimentary bract gene taxon:4530 20150501 Ethan Johnson GR_gene GR:0080036 SNB phyllotaxy TO:0006014 PMID:17144896 IMP T Os07g0235800 bracts in alternative phyllotaxy gene taxon:4530 20150501 Ethan Johnson GR_gene GR:0080036 SNB anatomy and morphology trait TO:0000017 PMID:17144896 IMP T Os07g0235800 interfered with subsequent floral architecture gene taxon:4530 20150501 Ethan Johnson -GR_gene GR:0060900 SP1 panicle length TO:0000040 GR_gene:1712 IMP T Os11g0235200 short panicle gene taxon:4530 20150501 Ethan Johnson -GR_gene GR:0060900 SP1 primary branch number TO:0000547 GR_gene:1712 IMP T Os11g0235200 absence of primary branches in lower part of ear axis gene taxon:4530 20150501 Ethan Johnson -GR_gene GR:0060900 SP1 spikelets per panicle length TO:0000565 GR_gene:1712 IMP T Os11g0235200 spikelets per panicle decreased gene taxon:4530 20150501 Ethan Johnson -GR_gene GR:0060900 SP1 primary branch number TO:0000547 GR_gene:1712 IMP T Os11g0235200 primary branches per panicle reduced gene taxon:4530 20150501 Ethan Johnson -GR_gene GR:0060900 SP1 secondary branch number TO:0000557 GR_gene:1712 IMP T Os11g0235200 secondary branches per primary branch reduced gene taxon:4530 20150501 Ethan Johnson -GR_gene GR:0060900 SP1 relative spikelet number TO:0001033 GR_gene:1712 IMP T Os11g0235200 number of spikelets per primary branch reduced gene taxon:4530 20150501 Ethan Johnson -GR_gene GR:0060900 SP1 relative spikelet number TO:0001033 GR_gene:1712 IMP T Os11g0235200 number of spikelets per secondary branch reduced gene taxon:4530 20150501 Ethan Johnson +GR_gene GR:0060900 SP1 panicle length TO:0000040 GR_REF:1712 IMP T Os11g0235200 short panicle gene taxon:4530 20150501 Ethan Johnson +GR_gene GR:0060900 SP1 primary branch number TO:0000547 GR_REF:1712 IMP T Os11g0235200 absence of primary branches in lower part of ear axis gene taxon:4530 20150501 Ethan Johnson +GR_gene GR:0060900 SP1 spikelets per panicle length TO:0000565 GR_REF:1712 IMP T Os11g0235200 spikelets per panicle decreased gene taxon:4530 20150501 Ethan Johnson +GR_gene GR:0060900 SP1 primary branch number TO:0000547 GR_REF:1712 IMP T Os11g0235200 primary branches per panicle reduced gene taxon:4530 20150501 Ethan Johnson +GR_gene GR:0060900 SP1 secondary branch number TO:0000557 GR_REF:1712 IMP T Os11g0235200 secondary branches per primary branch reduced gene taxon:4530 20150501 Ethan Johnson +GR_gene GR:0060900 SP1 relative spikelet number TO:0001033 GR_REF:1712 IMP T Os11g0235200 number of spikelets per primary branch reduced gene taxon:4530 20150501 Ethan Johnson +GR_gene GR:0060900 SP1 relative spikelet number TO:0001033 GR_REF:1712 IMP T Os11g0235200 number of spikelets per secondary branch reduced gene taxon:4530 20150501 Ethan Johnson GR_gene GR:0080031 SPK protein content TO:0000598 PMID:8325505 IMP T Os10G0539600 decreased amount of proteins gene taxon:4530 20150501 Ethan Johnson GR_gene GR:0080031 SPK protein composition related trait TO:0000490 PMID:8325505 IMP T Os10G0539600 altered protein composition gene taxon:4530 20150501 Ethan Johnson GR_gene GR:0080031 SPK endosperm storage protein content TO:0002653 PMID:8325505 IMP T Os10G0539600 lacks seed storage gene taxon:4530 20150501 Ethan Johnson -- 2.34.1