Integrating phenotype ontologies across multiple species

Table 4 Examples of equivalence mappings between pre-composed phenotype classes and EQ descriptions

Phenotype class	Bearer (E)	Quality (PATO)	Towards (E2)	Qualifier
MP
Decreased diameter of femur	Femur	Decreased diameter
MP:0008152	MA:0001359	PATO:0001715
Spherocytosis	Erythrocyte	Spherical
MP:0002812	CL:0000232	PATO:0001499
Abnormal spleen iron level	Spleen	Concentration of	Iron	Abnormal
MP:0008739	MA:0000141	PATO:0000033	CHEBI:18248	PATO:0000460
Situs inversus	Visceral organ system	Inverted
MP:0002766	MA:0000019	PATO:0000625
Delayed kidney development	Kidney development	Delayed
MP:0000528	GO:0001822	PATO:0000502
Truncated notochord	TS20 notochord	Truncated
MP:0004714	EMAP:4109	PATO:0000936
Motor neuron degeneration	CL:0000100 motor neuron	Degenerate
MP:0000938		PATO:0000639
Axon degeneration	Axon	Degenerate
MP:0005405	GO:0030424	PATO:0000639
Loss of basal ganglion neurons	Basal ganglia	Has fewer parts of type	Neuron
MP:0003242	MA:0000184	PATO:0002001	CL:0000540
Abnormal Purkinje cell dendrite morphology	Dendrite of Purkinje cell	Morphology		Abnormal
MP:0008572	GO:0030425^part_of(CL:0000121)	PATO:0000051		PATO:0000460
HP
Hypoplastic uterus	Uterus	Hypoplastic
HP:0000013	FMA:17558	PATO:0000645
Abnormality of vision	Visual perception	Quality		Abnormal
HP:0000504	GO:0007601	PATO:0000001		PATO:0000460
Narrow pelvis	Pelvis	Decreased width
HP:0003275	FMA:9578	PATO:0000599
WP
Shruken intestine	Intestine	Shrunken
WBPhenotype:0000086	WBbt:0005772	PATO:0000585
TO
Leaf area	Leaf	Area
TO:0000540	PO:0009025	PATO:0001323
Auxin sensitivity	Whole plant	Sensitivity	Auxin
TO:000163	PO:0000003	PATO:0000085	CHEBI:22676

Examples of pre-composed terms from four phenotype ontologies together with their logical definitions expressed as EQ expressions. The phenotype category can be seen by the ontologies used. Basic anatomical phenotypes use an anatomical ontology, unspecified abnormality can be seen in the final column. The one example of a compositional anatomical class (Purkinje cell dendrite is written as an OBO intersection expression. Processual phenotypes use the GO process ontology, and relational qualities have the E2 column filled in. PO, Plant Ontology (anatomical structure); WBbt, Worm anatomy ontology.

ISSN: 1474-760X