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