Plant Ontology Release 19 - December 2012

Release Notes Archive

Plant Ontology Release #19 December 2012

Plant Ontology Database

Release 19

Ontology updates

Number of terms:

Total terms (not including obsoletes) 1509
Total children terms in Plant Anatomical Entity (not including obsoletes) 1221
Total children terms in Plant Structure Development Stage (not including obsoletes) 286

Associations / Annotations

Number of associations/annotations:

Total number of associations 2258615
Number of associations NEW 82703
Total number of unique objects (genes, germplasms, QTLs) 142344
Number of unique objects NEW 31384

Number of associations by source database:

Database Associations Total#
TAIR Arabidopsis (mouse-ear cress) 532476
NASC Arabidopsis (mouse-ear cress) 1897
Gramene Oryza sativa (rice) 29871
Gramene Physcomitrella 20
MaizeGDB Zea mays (maize) 1495156
Jaiswal Lab Fragaria vesca (strawberry) 9561
Cosmoss Physcomitrella 81875
AgBase Gossypium hirsutum (upland cotton) 262
MGCSC 5070
POC Vitis (grape) 3397
POC Oryza sativa (rice - japonica subgroup) 73951
POC Picea (spruce) 3
SGN (individual species listed below) 20016
-Anisodus acutangulus 2
-Atropa baetica 4
-Capsicum annuum (pepper) 54
-Coffea arabica (coffee) 8
-Datura strumonium (jimson weed) 3
-Hyoscyamus niger (black henbane) 2
-Lycopersicon esculentum (tomato) 18950
-Nicotiana tabacum (tobacco) 41
-Petunia hybrida (hybrid petunia) 55
-Physalis spp 4
-Solanum chmielewskii 3
-Solanum insanum/Solanum melongena (eggplant) 873
-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 24548
TAIR (Arabidopsis) 224
TAIR (Arabidopsis) miRNA 41
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 1428
POC miRNA 128
POC mRNA 29735

Total number of associations by evidence code:

Evidence Code Associations Total#
IC 18101
IDA 20611
IEA 1
IEP 2172624
IGI 1
IMP 42230
ISS 21
NAS 30
TAS 5358

Total number of object types by evidence code:

Object Type Evidence Code Object Type Total#
protein IDA 17456
protein IEP 512886
protein IMP 6
protein NAS 29
protein TAS 96
IDA 9
IEP 2105
miRNA IDA 22
miRNA IEP 497
RNA IEP 41
gene_product IEP 1
gene_product NAS 1
snoRNA IEP 1
germplasm IDA 3045
germplasm IMP 18393
gene IC 571
gene IDA 79
gene IEA 1
gene IEP 3911
gene IGI 1
gene IMP 7387
gene ISS 21
gene TAS 5262
QTL IC 17530
QTL IMP 6304
mRNA IEP 165021
gene_model IEP 1487963
stock IMP 5070