Plant Ontology Release #20 August 2013

Plant Ontology Release 20 - August 2013

Release Notes Archive

 

Release 20

 

Ontology updates

 

Number of terms:

Total terms (not including obsoletes) 1554
Total children terms in Plant Anatomical Entity (not including obsoletes) 1263
Total children terms in Plant Structure Development Stage (not including obsoletes) 289

 

 

Associations / Annotations

 

Number of associations/annotations:

Total number of associations 2254233
Number of associations NEW N/A
Total number of unique objects (genes, germplasms, QTLs) 142581
Number of unique objects NEW 237

 

 

Number of associations by source database:

Database Associations Total#
TAIR Arabidopsis (mouse-ear cress) 532679
NASC Arabidopsis (mouse-ear cress) 1897
Gramene Oryza sativa (rice) 29867
Gramene Physcomitrella 10
MaizeGDB Zea mays (maize) 1495156
Jaiswal Lab Fragaria vesca (strawberry) 9561
Cosmoss Physcomitrella 81875
AgBase Gossypium hirsutum (upland cotton) 472
MGCSC 5070
POC Vitis (grape) 3675
POC Oryza sativa (rice - japonica subgroup) 73952
POC Picea (spruce) 3
SGN (individual species listed below) 20015
-Anisodus acutangulus 2
-Atropa baetica 4
-Capsicum annuum (pepper) 54
-Coffea arabica (coffee) 8
-Datura strumonium (jimson weed) 3
-Hyoscyamus niger (black henbane) 2
-Nicotiana tabacum (tobacco) 41
-Petunia hybrida (hybrid petunia) 55
-Physalis spp 4
-Solanum chmielewskii 3
-Solanum insanum/Solanum melongena (eggplant) 873
-Solanum lycopersicum (tomato) 18949
-Solanum pennellii 3
-Solanum tuberosum (potato) 14

 

Total number of individual object types by source database:

Database Object Type Object Types Total#
TAIR (Arabidopsis) protein 24568
TAIR (Arabidopsis)   224
TAIR (Arabidopsis) miRNA 42
TAIR (Arabidopsis) RNA 2
TAIR (Arabidopsis) gene_product 2
TAIR (Arabidopsis) snoRNA 1
NASC (Arabidopsis) germplasm 1897
Jaiswal Lab (Fragaria) mRNA 3904
Gramene (rice) gene 1715
Gramene (rice) QTL 8558
Gramene (Physcomitrella Patens) gene 5
Cosmoss (Physcomitrella Patens) mRNA 25593
MaizeGDB (maize) gene 780
MaizeGDB (maize) gene_model 35323
SGN gene 216
SGN germplasm 4503
AgBase protein 132
MGCSC stock 3609
POC gene 1508
POC miRNA 129
POC mRNA 29735

 

Total number of associations by evidence code:

Evidence Code Associations Total#
IC 18101
IDA 20694
IEA 1
IEP 2172755
IGI 1
IMP 37438
ISS 21
NAS 30
TAS 5357

 

Total number of object types by evidence code:

Object Type Evidence Code Object Type Total#
protein IDA 17539
protein IEP 513004
protein IMP 6
protein NAS 29
protein TAS 96
  IDA 9
  IEP 2105
miRNA IDA 22
miRNA IEP 501
RNA IEP 41
gene_product IEP 1
gene_product NAS 1
snoRNA IEP 1
germplasm IDA 3045
germplasm IMP 18385
gene IC 571
gene IDA 79
gene IEA 1
gene IEP 3908
gene IGI 1
gene IMP 7665
gene ISS 21
gene TAS 5261
QTL IC 17530
QTL IMP 6304
mRNA IEP 165021
gene_model IEP 1487963
stock IMP 5070
transcript IEP 210