Plant Ontology Release #21 October 2015

Ontology Updates

Details of the Plant Ontology Release #21- Wiki page

Release Notes Archive

Number of Terms (not including obsoletes):

Total terms 1592
Total terms in Plant Anatomical Entity 1296
Total terms in Plant Structure Development Stage 296

 

Plant Ontology Database

 

Number of annotations:

Total number of annotations 2291235
Number of annotations NEW 37002
Total number of unique objects (genes, germplasms, QTLs) 150687
Number of unique objects NEW 8106

 

 

Total number of annotations by species:

Species Common name Annotations Total#
Arabidopsis thaliana thale cress 557020
Oryza sativa rice 104098
Physcomitrella patens moss 81885
Anisodus spp wild relative of tomato 2
Atropa spp nightshade 4
Capsicum spp peppers 54
Coffea spp coffee 8
Datura spp angel's trumpets, moonflowers 3
Hycoscyamus spp henbane 2
Nicotiana spp tobacco 41
Petunia spp petunia 55
Physalis spp groundcherry 4
Solanum lycopersicum tomato 19096
Solanum tuberosum potato 14
Solanum melongena eggplant 873
Solanum chmielewskii wild tomato 3
Solanum pennellii wild tomato 3
Fragaria vesca wild strawberry 9561
Picea abies Norway spruce 1
Picea glauca White spruce 2
Zea mays maize, corn 1512159
Gossypium hirsutum upland cotton 472
Vitis vinifera grape 3397
Glycine max soybean 2397
Medicago truncatula barrel medic 81

 

 

Number of annotations by source database:

Database Annotations Total#
TAIR Arabidopsis (thale cress) 551789
NASC Arabidopsis (thale cress) 1897
Gramene Oryza sativa (rice) 29868
Gramene Physcomitrella (moss) 10
MaizeGDB Zea mays (maize) 1494915
Jaiswal Lab Fragaria vesca (strawberry) 9561
Cosmoss Physcomitrella (moss) 81875
AgBase Gossypium hirsutum (upland cotton) 472
LIS Medicago trunculata (barrel medic) 81
MGCSC Zea mays (maize) 4932
POC Vitis (grape) 3675
POC Oryza sativa (rice - japonica subgroup) 89859
POC Picea (spruce) 3
Soybase Glycine max (soybean) 2364
SGN (individual species listed below) 20015
-Anisodus spp (wild relative of tomato) 2
-Atropa spp (nightshade) 4
-Capsicum spp (pepper) 54
-Coffea spp (coffee) 8
-Datura spp (angel's trumpets, moonflowers) 3
-Hyoscyamus spp (henbane) 2
-Nicotiana spp (tobacco) 41
-Petunia spp (petunia) 55
-Physalis spp (groundcherry) 4
-Solanum chmielewskii (wild tomato) 3
-Solanum insanum/Solanum melongena (eggplant) 873
-Solanum lycopersicum (tomato) 18949
-Solanum pennellii (wild tomato) 3
-Solanum tuberosum (potato) 14

 

 

Total number of individual object types by source database:

Database Object Type Object Types Total#
TAIR (Arabidopsis) protein 27336
TAIR (Arabidopsis) unknown 446
TAIR (Arabidopsis) miRNA 53
TAIR (Arabidopsis) RNA 280
TAIR (Arabidopsis) snRNA 8
TAIR (Arabidopsis) rRNA 4
TAIR (Arabidopsis) snoRNA 10
NASC (Arabidopsis) germplasm 1897
Jaiswal Lab (Fragaria) mRNA 3904
Gramene (rice) gene 1716
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
AgBase transcript 210
MGCSC stock 3609
LIS gene 32
POC gene 3732
POC gene_model 3457
POC miRNA 129
POC mRNA 29735
SoyBase QTL 2249

 

Total number of annotations by evidence code:

Evidence Code Annotations Total#
IC 20497
IDA 20770
IEA 1
IEP 2203797
IGI 1
IMP 40958
ISS 21
NAS 30
TAS 5357

 

Total number of object types by evidence code:

Object Type Evidence Code Object Type Total#
protein IDA 17613
protein IEP 531443
protein IMP 6
protein NAS 29
protein TAS 96
unknown IDA 9
unknown IEP 2381
miRNA IDA 24
miRNA IEP 520
RNA IEP 320
snRNA IEP 8
snoRNA IEP 10
rRNA IEP 4
germplasm IDA 3045
germplasm IMP 18393
gene IC 571
gene IDA 79
gene IEA 1
gene IEP 3908
gene IGI 1
gene IMP 11323
gene ISS 21
gene TAS 5261
QTL IC 19926
QTL IMP 6304
mRNA IEP 165021
gene_model IEP 1499971
stock IMP 4932
transcript IEP 210
gene product IEP 1
gene product NAS 1