valuesets 0.3.1__py3-none-any.whl

valuesets/schema/medical/clinical.yaml

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+name: clinical
+title: Clinical and Medical Value Sets
+description: 'Value sets for clinical and medical domains including blood types, anatomical systems, medical specialties,
+  drug routes, and diagnostic categories.
+
+  '
+id: https://w3id.org/valuesets/medical/clinical
+imports:
+- linkml:types
+prefixes:
+  linkml: https://w3id.org/linkml/
+  NCIT: http://purl.obolibrary.org/obo/NCIT_
+  UBERON: http://purl.obolibrary.org/obo/UBERON_
+  HP: http://purl.obolibrary.org/obo/HP_
+  DOID: http://purl.obolibrary.org/obo/DOID_
+  CHEBI: http://purl.obolibrary.org/obo/CHEBI_
+  SNOMED: http://snomed.info/id/
+  LOINC: http://loinc.org/
+  ICD10: http://purl.bioontology.org/ontology/ICD10/
+  RxNorm: http://purl.bioontology.org/ontology/RXNORM/
+  valuesets: https://w3id.org/valuesets/
+default_prefix: valuesets
+slots:
+  blood_type:
+    description: ABO and Rh blood group classifications
+    range: BloodTypeEnum
+  anatomical_system:
+    description: Major anatomical systems of the body
+    range: AnatomicalSystemEnum
+  medical_specialty:
+    description: The medical specialty classification
+    range: MedicalSpecialtyEnum
+  drug_route:
+    description: The drug route classification
+    range: DrugRouteEnum
+  vital_sign:
+    description: The vital sign classification
+    range: VitalSignEnum
+  diagnostic_test_type:
+    description: The diagnostic test type classification
+    range: DiagnosticTestTypeEnum
+  symptom_severity:
+    description: The symptom severity classification
+    range: SymptomSeverityEnum
+  allergy_type:
+    description: The allergy type classification
+    range: AllergyTypeEnum
+  vaccine_type:
+    description: The vaccine type classification
+    range: VaccineTypeEnum
+  bmi_classification:
+    description: The bmi classification classification
+    range: BMIClassificationEnum
+enums:
+  BloodTypeEnum:
+    description: ABO and Rh blood group classifications
+    permissible_values:
+      A_POSITIVE:
+        description: Blood type A, Rh positive
+        meaning: SNOMED:278149003
+        annotations:
+          abo: A
+          rh: positive
+          can_receive: A+, A-, O+, O-
+          can_donate: A+, AB+
+      A_NEGATIVE:
+        description: Blood type A, Rh negative
+        meaning: SNOMED:278152006
+        annotations:
+          abo: A
+          rh: negative
+          can_receive: A-, O-
+          can_donate: A+, A-, AB+, AB-
+      B_POSITIVE:
+        description: Blood type B, Rh positive
+        meaning: SNOMED:278150003
+        annotations:
+          abo: B
+          rh: positive
+          can_receive: B+, B-, O+, O-
+          can_donate: B+, AB+
+      B_NEGATIVE:
+        description: Blood type B, Rh negative
+        meaning: SNOMED:278153001
+        annotations:
+          abo: B
+          rh: negative
+          can_receive: B-, O-
+          can_donate: B+, B-, AB+, AB-
+      AB_POSITIVE:
+        description: Blood type AB, Rh positive (universal recipient)
+        meaning: SNOMED:278151004
+        annotations:
+          abo: AB
+          rh: positive
+          can_receive: all types
+          can_donate: AB+
+          special: universal recipient
+      AB_NEGATIVE:
+        description: Blood type AB, Rh negative
+        meaning: SNOMED:278154007
+        annotations:
+          abo: AB
+          rh: negative
+          can_receive: A-, B-, AB-, O-
+          can_donate: AB+, AB-
+      O_POSITIVE:
+        description: Blood type O, Rh positive
+        meaning: SNOMED:278147001
+        annotations:
+          abo: O
+          rh: positive
+          can_receive: O+, O-
+          can_donate: A+, B+, AB+, O+
+      O_NEGATIVE:
+        description: Blood type O, Rh negative (universal donor)
+        meaning: SNOMED:278148006
+        annotations:
+          abo: O
+          rh: negative
+          can_receive: O-
+          can_donate: all types
+          special: universal donor
+  AnatomicalSystemEnum:
+    description: Major anatomical systems of the body
+    permissible_values:
+      CARDIOVASCULAR:
+        title: Heart and blood vessels
+        aliases:
+        - cardiovascular system
+        meaning: UBERON:0004535
+        annotations:
+          components: heart, arteries, veins, capillaries
+      RESPIRATORY:
+        title: Lungs and airways
+        aliases:
+        - respiratory system
+        meaning: UBERON:0001004
+        annotations:
+          components: lungs, trachea, bronchi, diaphragm
+      NERVOUS:
+        title: Brain, spinal cord, and nerves
+        aliases:
+        - nervous system
+        meaning: UBERON:0001016
+        annotations:
+          components: brain, spinal cord, nerves
+      DIGESTIVE:
+        title: GI tract and accessory organs
+        aliases:
+        - digestive system
+        meaning: UBERON:0001007
+        annotations:
+          components: mouth, esophagus, stomach, intestines, liver, pancreas
+      MUSCULOSKELETAL:
+        title: Bones, muscles, and connective tissue
+        aliases:
+        - musculoskeletal system
+        meaning: UBERON:0002204
+        annotations:
+          components: bones, muscles, tendons, ligaments, cartilage
+      INTEGUMENTARY:
+        title: Skin and related structures
+        aliases:
+        - integumental system
+        meaning: UBERON:0002416
+        annotations:
+          components: skin, hair, nails, glands
+      ENDOCRINE:
+        title: Hormone-producing glands
+        aliases:
+        - endocrine system
+        meaning: UBERON:0000949
+        annotations:
+          components: pituitary, thyroid, adrenals, pancreas
+      URINARY:
+        title: Kidneys and urinary tract
+        aliases:
+        - renal system
+        meaning: UBERON:0001008
+        annotations:
+          components: kidneys, ureters, bladder, urethra
+      REPRODUCTIVE:
+        title: Reproductive organs
+        aliases:
+        - reproductive system
+        meaning: UBERON:0000990
+        annotations:
+          components: gonads, ducts, external genitalia
+      IMMUNE:
+        title: Immune and lymphatic system
+        aliases:
+        - immune system
+        meaning: UBERON:0002405
+        annotations:
+          components: lymph nodes, spleen, thymus, bone marrow
+      HEMATOLOGIC:
+        title: Blood and blood-forming organs
+        aliases:
+        - hematopoietic system
+        meaning: UBERON:0002390
+        annotations:
+          components: blood, bone marrow, spleen
+  MedicalSpecialtyEnum:
+    title: Medical specialties and subspecialties
+    permissible_values:
+      ANESTHESIOLOGY:
+        title: Anesthesia and perioperative medicine
+      CARDIOLOGY:
+        title: Heart and cardiovascular diseases
+      DERMATOLOGY:
+        title: Skin diseases
+      EMERGENCY_MEDICINE:
+        title: Emergency and acute care
+      ENDOCRINOLOGY:
+        title: Hormonal and metabolic disorders
+      FAMILY_MEDICINE:
+        title: Primary care for all ages
+      GASTROENTEROLOGY:
+        title: Digestive system disorders
+      HEMATOLOGY:
+        title: Blood disorders
+      INFECTIOUS_DISEASE:
+        title: Infectious diseases
+      INTERNAL_MEDICINE:
+        title: Adult internal medicine
+      NEPHROLOGY:
+        title: Kidney diseases
+      NEUROLOGY:
+        title: Nervous system disorders
+      OBSTETRICS_GYNECOLOGY:
+        title: Women's health and childbirth
+      ONCOLOGY:
+        title: Cancer treatment
+      OPHTHALMOLOGY:
+        title: Eye diseases
+      ORTHOPEDICS:
+        title: Musculoskeletal disorders
+      OTOLARYNGOLOGY:
+        title: Ear, nose, and throat
+      PATHOLOGY:
+        title: Disease diagnosis through lab analysis
+      PEDIATRICS:
+        title: Children's health
+      PSYCHIATRY:
+        title: Mental health disorders
+      PULMONOLOGY:
+        title: Lung and respiratory diseases
+      RADIOLOGY:
+        title: Medical imaging
+      RHEUMATOLOGY:
+        title: Joint and autoimmune diseases
+      SURGERY:
+        title: Surgical procedures
+      UROLOGY:
+        title: Urinary and male reproductive system
+  DrugRouteEnum:
+    title: Routes of drug administration
+    permissible_values:
+      ORAL:
+        title: By mouth
+        aliases:
+        - Oral Route of Administration
+        meaning: NCIT:C38288
+        annotations:
+          abbreviation: PO
+          absorption: GI tract
+      INTRAVENOUS:
+        title: Into a vein
+        aliases:
+        - Intravenous Route of Administration
+        meaning: NCIT:C38276
+        annotations:
+          abbreviation: IV
+          onset: immediate
+      INTRAMUSCULAR:
+        title: Into muscle
+        aliases:
+        - Intramuscular Route of Administration
+        meaning: NCIT:C28161
+        annotations:
+          abbreviation: IM
+          sites: deltoid, gluteus, vastus lateralis
+      SUBCUTANEOUS:
+        title: Under the skin
+        aliases:
+        - Subcutaneous Route of Administration
+        meaning: NCIT:C38299
+        annotations:
+          abbreviation: SC, SubQ
+          absorption: slow
+      TOPICAL:
+        title: On the skin surface
+        aliases:
+        - Topical Route of Administration
+        meaning: NCIT:C38304
+        annotations:
+          forms: cream, ointment, gel
+      INHALATION:
+        title: By breathing in
+        aliases:
+        - Inhalation Route of Administration
+        meaning: NCIT:C38216
+        annotations:
+          devices: inhaler, nebulizer
+      RECTAL:
+        title: Into the rectum
+        aliases:
+        - Rectal Route of Administration
+        meaning: NCIT:C38295
+        annotations:
+          forms: suppository, enema
+      INTRANASAL:
+        title: Into the nose
+        aliases:
+        - Nasal Route of Administration
+        meaning: NCIT:C38284
+        annotations:
+          forms: spray, drops
+      TRANSDERMAL:
+        title: Through the skin
+        aliases:
+        - Transdermal Route of Administration
+        meaning: NCIT:C38305
+        annotations:
+          forms: patch
+      SUBLINGUAL:
+        title: Under the tongue
+        aliases:
+        - Sublingual Route of Administration
+        meaning: NCIT:C38300
+        annotations:
+          absorption: rapid
+      EPIDURAL:
+        title: Into epidural space
+        aliases:
+        - Intraepidermal Route of Administration
+        meaning: NCIT:C38243
+        annotations:
+          use: anesthesia, analgesia
+      INTRATHECAL:
+        title: Into spinal fluid
+        aliases:
+        - Intraventricular Route of Administration
+        meaning: NCIT:C38277
+        annotations:
+          use: CNS drugs
+      OPHTHALMIC:
+        title: Into the eye
+        aliases:
+        - Ophthalmic Route of Administration
+        meaning: NCIT:C38287
+        annotations:
+          forms: drops, ointment
+      OTIC:
+        title: Into the ear
+        aliases:
+        - Auricular Route of Administration
+        meaning: NCIT:C38192
+        annotations:
+          forms: drops
+  VitalSignEnum:
+    title: Standard vital signs
+    permissible_values:
+      HEART_RATE:
+        title: Heart beats per minute
+        meaning: LOINC:8867-4
+        annotations:
+          normal_range: 60-100 bpm
+          units: beats/min
+      BLOOD_PRESSURE_SYSTOLIC:
+        title: Systolic blood pressure
+        meaning: LOINC:8480-6
+        annotations:
+          normal_range: <120 mmHg
+          units: mmHg
+      BLOOD_PRESSURE_DIASTOLIC:
+        title: Diastolic blood pressure
+        meaning: LOINC:8462-4
+        annotations:
+          normal_range: <80 mmHg
+          units: mmHg
+      RESPIRATORY_RATE:
+        title: Breaths per minute
+        meaning: LOINC:9279-1
+        annotations:
+          normal_range: 12-20 breaths/min
+          units: breaths/min
+      TEMPERATURE:
+        title: Body temperature
+        meaning: LOINC:8310-5
+        annotations:
+          normal_range: 36.5-37.5°C
+          units: °C or °F
+      OXYGEN_SATURATION:
+        title: Blood oxygen saturation
+        meaning: LOINC:2708-6
+        annotations:
+          normal_range: 95-100%
+          units: '%'
+      PAIN_SCALE:
+        title: Pain level (0-10)
+        meaning: LOINC:38208-5
+        annotations:
+          scale: 0-10
+          type: subjective
+  DiagnosticTestTypeEnum:
+    title: Types of diagnostic tests
+    permissible_values:
+      BLOOD_TEST:
+        title: Blood sample analysis
+        aliases:
+        - Biopsy Procedure
+        meaning: NCIT:C15189
+        annotations:
+          samples: serum, plasma, whole blood
+      URINE_TEST:
+        title: Urine sample analysis
+        aliases:
+        - Tissue Factor
+        annotations:
+          types: urinalysis, culture, drug screen
+      IMAGING_XRAY:
+        title: X-ray imaging
+        aliases:
+        - X-Ray
+        meaning: NCIT:C17262
+        annotations:
+          radiation: 'yes'
+      IMAGING_CT:
+        title: Computed tomography scan
+        aliases:
+        - Computed Tomography
+        meaning: NCIT:C17204
+        annotations:
+          radiation: 'yes'
+      IMAGING_MRI:
+        title: Magnetic resonance imaging
+        aliases:
+        - Magnetic Resonance Imaging
+        meaning: NCIT:C16809
+        annotations:
+          radiation: 'no'
+      IMAGING_ULTRASOUND:
+        title: Ultrasound imaging
+        aliases:
+        - Ultrasound Imaging
+        meaning: NCIT:C17230
+        annotations:
+          radiation: 'no'
+      IMAGING_PET:
+        title: Positron emission tomography
+        aliases:
+        - Positron Emission Tomography
+        meaning: NCIT:C17007
+        annotations:
+          uses: radiotracer
+      ECG:
+        title: Electrocardiogram
+        aliases:
+        - Electroencephalography
+        meaning: NCIT:C38054
+        annotations:
+          measures: heart electrical activity
+      EEG:
+        title: Electroencephalogram
+        aliases:
+        - Djibouti
+        annotations:
+          measures: brain electrical activity
+      BIOPSY:
+        title: Tissue sample analysis
+        aliases:
+        - Biopsy Procedure
+        meaning: NCIT:C15189
+        annotations:
+          invasive: 'yes'
+      ENDOSCOPY:
+        title: Internal visualization
+        aliases:
+        - Endoscopic Procedure
+        meaning: NCIT:C16546
+        annotations:
+          types: colonoscopy, gastroscopy, bronchoscopy
+      GENETIC_TEST:
+        title: DNA/RNA analysis
+        aliases:
+        - Genetic Testing
+        meaning: NCIT:C15709
+        annotations:
+          types: karyotype, sequencing, PCR
+  SymptomSeverityEnum:
+    title: Severity levels for symptoms
+    permissible_values:
+      ABSENT:
+        title: No symptoms
+        aliases:
+        - Blood group B
+        annotations:
+          grade: '0'
+      MILD:
+        title: Mild symptoms, minimal impact
+        meaning: HP:0012825
+        annotations:
+          grade: '1'
+          impact: minimal daily activity limitation
+      MODERATE:
+        title: Moderate symptoms, some limitation
+        meaning: HP:0012826
+        annotations:
+          grade: '2'
+          impact: some daily activity limitation
+      SEVERE:
+        title: Severe symptoms, significant limitation
+        meaning: HP:0012828
+        annotations:
+          grade: '3'
+          impact: significant daily activity limitation
+      LIFE_THREATENING:
+        title: Life-threatening symptoms
+        aliases:
+        - Profound
+        annotations:
+          grade: '4'
+          impact: urgent intervention required
+  AllergyTypeEnum:
+    title: Types of allergic reactions
+    permissible_values:
+      DRUG:
+        title: Drug allergy
+        aliases:
+        - Hypersensitivity
+        meaning: NCIT:C3114
+        annotations:
+          examples: penicillin, sulfa drugs
+      FOOD:
+        title: Food allergy
+        annotations:
+          common: nuts, shellfish, eggs, milk
+      ENVIRONMENTAL:
+        title: Environmental allergy
+        annotations:
+          examples: pollen, dust, mold
+      CONTACT:
+        title: Contact dermatitis
+        annotations:
+          examples: latex, nickel, poison ivy
+      INSECT:
+        title: Insect sting allergy
+        annotations:
+          examples: bee, wasp, hornet
+      ANAPHYLAXIS:
+        title: Severe systemic reaction
+        annotations:
+          severity: life-threatening
+  VaccineTypeEnum:
+    title: Types of vaccines
+    permissible_values:
+      LIVE_ATTENUATED:
+        title: Weakened live pathogen
+        annotations:
+          examples: MMR, varicella, yellow fever
+      INACTIVATED:
+        title: Killed pathogen
+        annotations:
+          examples: flu shot, hepatitis A, rabies
+      SUBUNIT:
+        title: Pathogen pieces
+        annotations:
+          examples: hepatitis B, HPV, pertussis
+      TOXOID:
+        title: Inactivated toxin
+        annotations:
+          examples: diphtheria, tetanus
+      MRNA:
+        title: mRNA vaccine
+        annotations:
+          examples: COVID-19 (Pfizer, Moderna)
+      VIRAL_VECTOR:
+        title: Modified virus carrier
+        annotations:
+          examples: COVID-19 (J&J, AstraZeneca)
+  BMIClassificationEnum:
+    title: Body Mass Index classifications
+    permissible_values:
+      UNDERWEIGHT:
+        title: BMI less than 18.5
+        annotations:
+          bmi_range: <18.5
+      NORMAL_WEIGHT:
+        title: BMI 18.5-24.9
+        annotations:
+          bmi_range: 18.5-24.9
+      OVERWEIGHT:
+        title: BMI 25.0-29.9
+        annotations:
+          bmi_range: 25.0-29.9
+      OBESE_CLASS_I:
+        title: BMI 30.0-34.9
+        annotations:
+          bmi_range: 30.0-34.9
+      OBESE_CLASS_II:
+        title: BMI 35.0-39.9
+        annotations:
+          bmi_range: 35.0-39.9
+      OBESE_CLASS_III:
+        title: BMI 40.0 or greater
+        annotations:
+          bmi_range: ≥40.0
+          aliases: morbid obesity