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

From: Integrating phenotype ontologies across multiple species

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  
  1. 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.