Abnormal Lab Fasting_Glucose_ABNORMAL OR Random_Glucose_ABNORMAL OR HBA1c_ABNORMAL YES Code_System A combined phenotype is a combination of corresponding single phenotypes (e.g., a combination of height and weight). Combined_Phenotype We define composite phenotypes as composite properties (e.g., combination of height and weight, BMI, SOFA score) of an organism or of one of its subsystems. A composite property is defined as a property that has single properties as parts. Composite_Phenotype 1 A derived phenotype is an additional property (e.g., BMI) derived from the corresponding phenotypes (e.g., height and weight). Derived_Phenotype decimal Fasting Glucose mg/dl 6 RTObservation 125 decimal SOME Fasting Glucose >= 125 mg/dl ABNORMAL decimal Hemoglobin A1c % 8 RTObservation 6.5 decimal SOME Hemoglobin A1c >= 6.5 % ABNORMAL Missing_Value_Phenotype_Class Non_restricted_Combined_Phenotype_Class Non_restricted_Derived_Phenotype_Class The extension (set of instances) of a non-restricted phenotype class is not restricted to a certain range of individual phenotypes, all instances are allowed. For example, the phenotype class ‘age’ instantiated by the ages of all living beings is non-restricted. Non_restricted_Phenotype_Class Non_restricted_Single_Phenotype_Class We consider a phenotype as a dependent individual (in sense of General Formal Ontology, GFO), for example, the weight of a specific person. Hereinafter, abstract instantiable entities that are instantiated by phenotypes are called phenotype classes. For instance, the abstract property ‘weight’ possesses individual weights as instances. Phenotype Phenotype_Category Abstract instantiable entities that are instantiated by phenotypes are called phenotype classes. Phenotype_Class decimal Random Glucose mg/dl 7 RTObservation 200 decimal SOME Random Glucose > 200 mg/dl ABNORMAL Restricted_Combined_Phenotype_Class Restricted_Derived_Phenotype_Class The extension (set of instances) of a restricted phenotype class is restricted to a certain range of individual phenotypes by defined conditions. For example, the phenotype class ‘young age’ instantiated by the ages of the young living beings (e.g., if the age is below 30 years) is restricted. A restricted phenotype class is a subclass of a non-restricted phenotype class (e.g., ‘young age’ is subclass of 'age'). Restricted_Phenotype_Class Restricted_Single_Phenotype_Class We define single phenotypes as single properties (e.g., age, weight, height) of an organism or of one of its subsystems. Single_Phenotype Single_Phenotype_Group decimal COUNT T1DM Diagnosis 1 RTCondition 0 decimal SOME T1DM Diagnosis = 0 NO 2 0 decimal SOME T1DM Diagnosis > 0 YES 1 decimal FIRST T1DM Medication 3 RTMedicationStatement T1DM Medication = MISSING VALUE NO 1 decimal SOME T1DM Medication = 1 YES T2DM_CAT true T2DM Case T1DM_Diagnosis_NO AND T2DM_Diagnosis_YES AND T1DM_Medication_YES AND T2DM_Medication_YES AND T2DM_precedes_T1DM_Medication_YES T2DM Case 1 1 T1DM_Diagnosis_NO AND T2DM_Diagnosis_YES AND T1DM_Medication_NO AND T2DM_Medication_YES T2DM Case 2 2 T1DM_Diagnosis_NO AND T2DM_Diagnosis_YES AND T1DM_Medication_NO AND T2DM_Medication_NO AND Abnormal_Lab_YES T2DM Case 3 3 T1DM_Diagnosis_NO AND T2DM_Diagnosis_NO AND T2DM_Medication_YES AND Abnormal_Lab_YES T2DM Case 4 4 T1DM_Diagnosis_NO AND T2DM_Diagnosis_YES AND T1DM_Medication_YES AND T2DM_Medication_NO AND T2DM_Diagnosis_by_Physician_YES T2DM Case 5 5 decimal COUNT T2DM Diagnosis 2 RTCondition 0 decimal SOME T2DM Diagnosis = 0 NO 2 0 decimal SOME T2DM Diagnosis > 0 YES 1 decimal COUNT T2DM Diagnosis by Physician 5 RTClinicalImpression 2 decimal SOME T2DM Diagnosis by Physician >= 2 >= 2 decimal FIRST T2DM Medication 4 RTMedicationStatement T2DM Medication = MISSING VALUE NO 1 decimal SOME T2DM Medication = 1 YES decimal GT($T1DM_Medication, $T2DM_Medication) T2DM precedes T1DM Medication 0 decimal SOME T2DM precedes T1DM Medication > 0 YES ICD-9-CM http://hl7.org/fhir/sid/icd-9-cm 250.00 http://hl7.org/fhir/sid/icd-9-cm|250.00 250.01 http://hl7.org/fhir/sid/icd-9-cm|250.01 250.02 http://hl7.org/fhir/sid/icd-9-cm|250.02 250.03 http://hl7.org/fhir/sid/icd-9-cm|250.03 250.11 http://hl7.org/fhir/sid/icd-9-cm|250.11 250.13 http://hl7.org/fhir/sid/icd-9-cm|250.13 250.20 http://hl7.org/fhir/sid/icd-9-cm|250.20 250.21 http://hl7.org/fhir/sid/icd-9-cm|250.21 250.22 http://hl7.org/fhir/sid/icd-9-cm|250.22 250.23 http://hl7.org/fhir/sid/icd-9-cm|250.23 250.30 http://hl7.org/fhir/sid/icd-9-cm|250.30 250.31 http://hl7.org/fhir/sid/icd-9-cm|250.31 250.32 http://hl7.org/fhir/sid/icd-9-cm|250.32 250.33 http://hl7.org/fhir/sid/icd-9-cm|250.33 250.40 http://hl7.org/fhir/sid/icd-9-cm|250.40 250.41 http://hl7.org/fhir/sid/icd-9-cm|250.41 250.42 http://hl7.org/fhir/sid/icd-9-cm|250.42 250.43 http://hl7.org/fhir/sid/icd-9-cm|250.43 250.50 http://hl7.org/fhir/sid/icd-9-cm|250.50 250.51 http://hl7.org/fhir/sid/icd-9-cm|250.51 250.52 http://hl7.org/fhir/sid/icd-9-cm|250.52 250.53 http://hl7.org/fhir/sid/icd-9-cm|250.53 250.60 http://hl7.org/fhir/sid/icd-9-cm|250.60 250.61 http://hl7.org/fhir/sid/icd-9-cm|250.61 250.62 http://hl7.org/fhir/sid/icd-9-cm|250.62 250.63 http://hl7.org/fhir/sid/icd-9-cm|250.63 250.70 http://hl7.org/fhir/sid/icd-9-cm|250.70 250.71 http://hl7.org/fhir/sid/icd-9-cm|250.71 250.72 http://hl7.org/fhir/sid/icd-9-cm|250.72 250.73 http://hl7.org/fhir/sid/icd-9-cm|250.73 250.80 http://hl7.org/fhir/sid/icd-9-cm|250.80 250.81 http://hl7.org/fhir/sid/icd-9-cm|250.81 250.82 http://hl7.org/fhir/sid/icd-9-cm|250.82 250.83 http://hl7.org/fhir/sid/icd-9-cm|250.83 250.90 http://hl7.org/fhir/sid/icd-9-cm|250.90 250.91 http://hl7.org/fhir/sid/icd-9-cm|250.91 250.92 http://hl7.org/fhir/sid/icd-9-cm|250.92 250.93 http://hl7.org/fhir/sid/icd-9-cm|250.93 LOINC http://loinc.org 1558-6 http://loinc.org|1558-6 17855-8 http://loinc.org|17855-8 17856-6 http://loinc.org|17856-6 2339-0 http://loinc.org|2339-0 2345-7 http://loinc.org|2345-7 4548-4 http://loinc.org|4548-4 4549-2 http://loinc.org|4549-2 RxNorm http://www.nlm.nih.gov/research/umls/rxnorm 10633 http://www.nlm.nih.gov/research/umls/rxnorm|10633 139825 http://www.nlm.nih.gov/research/umls/rxnorm|139825 139953 http://www.nlm.nih.gov/research/umls/rxnorm|139953 16681 http://www.nlm.nih.gov/research/umls/rxnorm|16681 173 http://www.nlm.nih.gov/research/umls/rxnorm|173 217360 http://www.nlm.nih.gov/research/umls/rxnorm|217360 2404 http://www.nlm.nih.gov/research/umls/rxnorm|2404 25789 http://www.nlm.nih.gov/research/umls/rxnorm|25789 274332 http://www.nlm.nih.gov/research/umls/rxnorm|274332 274783 http://www.nlm.nih.gov/research/umls/rxnorm|274783 30009 http://www.nlm.nih.gov/research/umls/rxnorm|30009 314684 http://www.nlm.nih.gov/research/umls/rxnorm|314684 33738 http://www.nlm.nih.gov/research/umls/rxnorm|33738 352385 http://www.nlm.nih.gov/research/umls/rxnorm|352385 400008 http://www.nlm.nih.gov/research/umls/rxnorm|400008 4815 http://www.nlm.nih.gov/research/umls/rxnorm|4815 4821 http://www.nlm.nih.gov/research/umls/rxnorm|4821 51428 http://www.nlm.nih.gov/research/umls/rxnorm|51428 5856 http://www.nlm.nih.gov/research/umls/rxnorm|5856 593411 http://www.nlm.nih.gov/research/umls/rxnorm|593411 60548 http://www.nlm.nih.gov/research/umls/rxnorm|60548 6809 http://www.nlm.nih.gov/research/umls/rxnorm|6809 72610 http://www.nlm.nih.gov/research/umls/rxnorm|72610 73044 http://www.nlm.nih.gov/research/umls/rxnorm|73044 84108 http://www.nlm.nih.gov/research/umls/rxnorm|84108 86009 http://www.nlm.nih.gov/research/umls/rxnorm|86009 T2DM case selection algorithm https://www.smith.care/phenoman/t2dm_case_selection_algorithm t2dm_case_1 https://www.smith.care/phenoman/t2dm_case_selection_algorithm|t2dm_case_1 t2dm_case_2 https://www.smith.care/phenoman/t2dm_case_selection_algorithm|t2dm_case_2 t2dm_case_3 https://www.smith.care/phenoman/t2dm_case_selection_algorithm|t2dm_case_3 t2dm_case_4 https://www.smith.care/phenoman/t2dm_case_selection_algorithm|t2dm_case_4 t2dm_case_5 https://www.smith.care/phenoman/t2dm_case_selection_algorithm|t2dm_case_5 t2dm_case_calculated https://www.smith.care/phenoman/t2dm_case_selection_algorithm|t2dm_case_calculated