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id: http://w3id.org/ontogpt/condition
name: condition
title: condition FHIR Template
description: >-
  A FHIR-compliant template for conditions mentioned in a clinical note
license: https://creativecommons.org/publicdomain/zero/1.0/
prefixes:
  linkml: https://w3id.org/linkml/
  condition: http://w3id.org/ontogpt/condition/
  SNOMEDCT: http://purl.bioontology.org/ontology/SNOMEDCT


default_prefix: UNKNOWN

imports:
  - linkml:types
  - core

classes:
  ConditionSet:
    tree_root: true
    attributes:
      conditions:
        range: Condition
        multivalued: true
        inlined_as_list: true

  Condition:
    #is_a: NamedEntity
    attributes:
      label:
        description: The concise name of the condition, problem, or diagnosis.
      clinical_status:
        description: The clinical status of the condition.
        range: ConditionClinicalStatus
        ifabsent: string("unknown")  
      severity:
        description: Subjective severity of condition.
        range: ConditionDiagnosisSeverity
        ifabsent: string("unknown")
      code:
        description: The condition, problem, or diagnosis found in this note.
        range: ConditionProblemDiagnosis
        ifabsent: string("unknown")

  ConditionProblemDiagnosis:
    is_a: NamedEntity
    id_prefixes:
      - SNOMEDCT
    annotations:
      annotators: bioportal:SNOMEDCT
#    slot_usage:
#      id:
#        values_from: 
#          - ConditionProblemDiagnosisIdentifier



enums:
  ConditionClinicalStatus:
    permissible_values:
      active:
        description: The subject is currently experiencing the condition or situation, there is evidence of the condition or situation, or considered to be a significant risk.
      recurrence:
        description: The subject is experiencing a reoccurence or repeating of a previously resolved condition or situation, e.g. urinary tract infection, food insecurity.
      relapse:
        description: The subject is experiencing a return of a condition or situation after a period of improvement or remission, e.g. relapse of cancer, alcoholism.
      inactive:
        description: The subject is no longer experiencing the condition or situation and there is no longer evidence or appreciable risk of the condition or situation.
      remission:
        description: The subject is not presently experiencing the condition or situation, but there is a risk of the condition or situation returning.
      resolved:
        description: The subject is not presently experiencing the condition or situation and there is a negligible perceived risk of the condition or situation returning.
      unknown:
        description: The authoring/source system does not know which of the status values currently applies for this condition.
  
  ConditionDiagnosisSeverity:
    permissible_values:
      severe:
        meaning: SNOMEDCT:24484000
      moderate:
        meaning: SNOMEDCT:6736007
      mild:
        meaning: SNOMEDCT:255604002

  ConditionProblemDiagnosisIdentifier:
    reachable_from:
      source_ontology: bioportal:SNOMEDCT
      source_nodes:
        - SNOMEDCT:404684003 ## clinical finding

extracted_object:
  conditions:
    - label: Left malignant pleural effusion
      clinical_status: unknown
      severity: severe
      code: SNOMEDCT:7771000
    - label: Respiratory Failure
      clinical_status: unknown
      code: SNOMEDCT:409622000
    - label: Postobstructive Pneumonia
      clinical_status: unknown
      code: SNOMEDCT:371072008
    - label: Gastrointestinal bleed
      clinical_status: unknown
      code: AUTO:Gastrointestinal%20bleed
    - label: Thrombocytopenia
      clinical_status: unknown
      code: SNOMEDCT:302215000
    - label: Acute Renal Failure
      clinical_status: unknown
      code: AUTO:Acute%20Renal%20Failure
    - label: Hyponatremia
      clinical_status: unknown
      code: SNOMEDCT:89627008
    - label: Non-small cell lung CA
      clinical_status: active
      code: SNOMEDCT:264885008
    - label: Leukemoid Reaction
      clinical_status: unknown
      code: SNOMEDCT:56478004
    - label: Elevated Liver Function Tests
      clinical_status: unknown
      code: SNOMEDCT:75540009
named_entities:
  - id: SNOMEDCT:7771000
    label: Left malignant pleural effusion
  - id: SNOMEDCT:409622000
    label: Respiratory failure secondary to above
  - id: SNOMEDCT:371072008
    label: Likely postobstructive pneumonia
  - id: AUTO:Gastrointestinal%20bleed
    label: Gastrointestinal bleed
  - id: SNOMEDCT:302215000
    label: Thrombocytopenia
  - id: AUTO:Acute%20Renal%20Failure
    label: Acute Renal Failure
  - id: SNOMEDCT:89627008
    label: Hyponatremia
  - id: SNOMEDCT:264885008
    label: Non-small cell lung CA, possible metastases to the bones
  - id: SNOMEDCT:56478004
    label: Leukemoid reaction, likely secondary to malignancy
  - id: SNOMEDCT:75540009
    label: Elevated liver function tests