Table 4 |
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|
Examples of equivalence mappings between pre-composed phenotype classes and EQ descriptions |
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|
Phenotype class |
Bearer (E) |
Quality (PATO) |
Towards (E2) |
Qualifier |
|
|
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|
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. |
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|
Mungall et al. Genome Biology 2010 11:R2 doi:10.1186/gb-2010-11-1-r2 |
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