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.

Mungall et al. Genome Biology 2010 11:R2   doi:10.1186/gb-2010-11-1-r2

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