Release Notes Archive

Plant Ontology Release #20 August 2013

Plant Ontology Database

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
-Lycopersicon esculentum (tomato)	18949
-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	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