Table 7.

Inferred relevant phenotypes for nephrocalcinosis, stage 5 chronic kidney disease, and calcium oxalate nephrolithiasis generated by HPOEmb-Orphanet and HPOSim with seven conventional similarity measurements. (Phenotypes in bold indicate they are relevant to a corresponding PH-related phenotype according to the domain expert’s feedback.)

Methods	Nephrocalcinosis	Stage 5 chronic kidney disease	Calcium oxalate nephrolithiasis
HPOEmb-Orphanet	Medullary nephrocalcinosis Decreased numbers of nephrons Hyperechogenic kidneys Renal atrophy Nephrosclerosis	Chronic kidney disease Secondary hyperparathyroidism Renal insufficiency Polyarticular arthritis Synovitis	Renal calcium wasting Hypercalciuria Parietal bossing Obtuse angle of mandible Parathyroid hyperplasia
HPOSim-Resnik	Overbite Abnormal glomerular filtration rate Severe periodontitis Premature loss of permanent teeth Agenesis of incisor	Stage 5 chronic kidney disease Chronic kidney disease Renal insufficiency Acute kidney injury Glomerulonephritis	Calcium oxalate nephrolithiasis Calcium nephrolithiasis Nephrolithiasis Uric acid nephrolithiasis Xanthine nephrolithiasis
HPOSim-JC	Ulnar claw Central hypothyroidism Mucopolysacchariduria Abnormality of the 5th metacarpal Percussion myotonia	Renal insufficiency Stage 5 chronic kidney disease Abnormal renal physiology Abnormality of the urinary system physiology Abnormality of the kidney	Delayed calcaneal ossification Mask-like facies Abnormal atrial septum morphology Nephrosclerosis Schizencephaly
HPOSim-Lin	Orthostatic tachycardia Childhood onset short-limb short stature Odontoma Finger symphalangism Acute necrotizing encephalopathy	Stage 5 chronic kidney disease Chronic kidney disease Renal insufficiency Abnormal renal physiology Abnormality of the urinary system physiology	Impaired pursuit initiation and maintenance Thenar muscle atrophy Decreased urinary urate Urocanic aciduria Elevated urinary catecholamines
HPOSim-ICE	Foam cells Abnormality of the fallopian tube Increased mean platelet volume Aplasia/Hypoplasia of the fibula Congenital nonbullous ichthyosiform erythroderma	Stage 5 chronic kidney disease Chronic kidney disease Renal insufficiency Abnormal renal physiology Nephrotic syndrome	Irregular myelin loops Fused cervical vertebrae Precocious puberty in males Hemiparesis Abnormality of forebrain morphology
HPOSim-RL	Colon cancer Abnormality of the seventh cranial nerve Facial hypertrichosis Progressive flexion contractures Mandibular aplasia	Stage 5 chronic kidney disease Chronic kidney disease Renal insufficiency Abnormal renal physiology Nephrotic syndrome	Rib segmentation abnormalities Cerebral calcification Vacuolated lymphocytes Increased urinary sulfite Abnormality of brainstem morphology
HPOSim-GIC	Short nail Abnormal autonomic nervous system physiology Leiomyosarcoma Abnormal platelet membrane protein expression Dilated vestibule of the inner ear	Stage 5 chronic kidney disease Acute kidney injury Chronic kidney disease Renal insufficiency Nephrotic syndrome	Hypermobility of distal interphalangeal joints Duodenal atresia Delayed peripheral myelination Curved linear dimple below the lower lip Spastic tetraplegia
HPOSim-Wang	Ulnar claw Corneal stromal edema Central hypothyroidism Mucopolysacchariduria Abnormal blistering of the skin	Stage 5 chronic kidney disease Chronic kidney disease Renal insufficiency Abnormal renal physiology Acute kidney injury	Delayed calcaneal ossification Radial metaphyseal irregularity Mask-like facies Abnormal atrial septum morphology Nephrosclerosis