Merge pull request #53 from CODEX-CELIDA/chore/update-cpg

chore: update cpg-on-ebm-on-fhir

docs/36a_PEEP.md

@@ -45,7 +45,7 @@ Population
 |  |  | Inclusion  / Exclusion  | Name | Type | definition.type | definition.value |
 | PopulationVentilatedCOVID19patientsWithARDS-fio2-[0.0, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9] | Ventilated Patients suffering from COVID-19 induced ARDS |  | COVID-19 | Condition | SCT [404684003 "Clinical finding (finding)](https://browser.ihtsdotools.org/?perspective=full&conceptId1=404684003&edition=MAIN/2022-04-30&release=&languages=en)" | $sct#840539006 "Disease caused by severe acute respiratory syndrome coronavirus 2 (disorder)" |
 |  | ventilated | Procedure | SCT [71388002 "Procedure (procedure)](https://browser.ihtsdotools.org/?perspective=full&conceptId1=71388002&edition=MAIN/2022-05-31&release=&languages=en)" | $sct#40617009 "Artificial ventilation (regime/therapy)" |
-|  | FiO2 | ventilationObservableLOINC | $loinc#3150-0 "Inhaled oxygen concentration"* as used in [GECCO FiO2](https://simplifier.net/guide/GermanCoronaConsensusDataSet-ImplementationGuide-1.0.5/Home/GECCOCore/Vitalsigns/FiO2.guide.md?version=current)
+|  | FiO2 | observation | $loinc#3150-0 "Inhaled oxygen concentration"* as used in [GECCO FiO2](https://simplifier.net/guide/GermanCoronaConsensusDataSet-ImplementationGuide-1.0.5/Home/GECCOCore/Vitalsigns/FiO2.guide.md?version=current)
 * Alternative (as decimal, without % unit): [71835-3 Oxygen/Gas total [Pure volume fraction] Inhaled gas](https://loinc.org/71835-3/)
  | FiO2 [0.0, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9] |
 

input/fsh/covid19-inpatient-therapy/17-therapeutic-anticoagulation/recommendation_17_population.fsh

@@ -31,10 +31,10 @@ Description: "Population for recommendation 17 from guideline from https://www.a
     * valueCodeableConcept = $sct#840539006 "Disease caused by Severe acute respiratory syndrome coronavirus 2 (disorder)"
 * characteristic[condition][=].exclude = false
 // include patients with d-dimer >= 2 mg/l
-* characteristic[laboratory][+]
+* characteristic[observation][+]
   * linkId = "ddimer-range"
   * definitionByTypeAndValue
     * type = $loinc#48066-5 "Fibrin D-dimer DDU [Mass/volume] in Platelet poor plasma"
     * valueRange
       * low = 2 'mg/L'
-* characteristic[laboratory][=].exclude = false
+* characteristic[observation][=].exclude = false

input/fsh/covid19-inpatient-therapy/36a-peep/recommendation_36a_population.fsh

@@ -25,13 +25,13 @@ Description: "Ventilated COVID-19 patients, inspiratory oxygen fraction currentl
       * valueCodeableConcept = $sct#40617009 "Artificial ventilation (regime/therapy)"
   * characteristic[procedure][=].exclude = false
 
-  * characteristic[ventilationObservableLOINC][+]
+  * characteristic[observation][+]
     * definitionByTypeAndValue
       * type = $loinc#3150-0 "Inhaled oxygen concentration"
       * valueRange
         * low = 0 '%' "%"
         * high = 39.9999999999999 '%' "%"
-  * characteristic[ventilationObservableLOINC][=].exclude = false
+  * characteristic[observation][=].exclude = false
 * characteristic[=].exclude = false
 
 Instance: PopulationVentilatedCOVID19patients-fio2-point4
@@ -59,7 +59,7 @@ Description: "Ventilated COVID-19 patients, inspiratory oxygen fraction currentl
       * valueCodeableConcept = $sct#40617009 "Artificial ventilation (regime/therapy)"
   * characteristic[procedure][=].exclude = false
 
-  * characteristic[ventilationObservableLOINC][+]
+  * characteristic[observation][+]
     * definitionByTypeAndValue
       * type = $loinc#3150-0 "Inhaled oxygen concentration"
       * valueRange
@@ -92,7 +92,7 @@ Description: "Ventilated COVID-19 patients, inspiratory oxygen fraction currentl
       * valueCodeableConcept = $sct#40617009 "Artificial ventilation (regime/therapy)"
   * characteristic[procedure][=].exclude = false
 
-  * characteristic[ventilationObservableLOINC][+]
+  * characteristic[observation][+]
     * definitionByTypeAndValue
       * type = $loinc#3150-0 "Inhaled oxygen concentration"
       * valueRange
@@ -125,7 +125,7 @@ Description: "Ventilated COVID-19 patients, inspiratory oxygen fraction currentl
       * valueCodeableConcept = $sct#40617009 "Artificial ventilation (regime/therapy)"
   * characteristic[procedure][=].exclude = false
 
-  * characteristic[ventilationObservableLOINC][+]
+  * characteristic[observation][+]
     * definitionByTypeAndValue
       * type = $loinc#3150-0 "Inhaled oxygen concentration"
       * valueRange
@@ -158,7 +158,7 @@ Description: "Ventilated COVID-19 patients, inspiratory oxygen fraction currentl
       * valueCodeableConcept = $sct#40617009 "Artificial ventilation (regime/therapy)"
   * characteristic[procedure][=].exclude = false
 
-  * characteristic[ventilationObservableLOINC][+]
+  * characteristic[observation][+]
     * definitionByTypeAndValue
       * type = $loinc#3150-0 "Inhaled oxygen concentration"
       * valueRange
@@ -190,7 +190,7 @@ Description: "Ventilated COVID-19 patients, inspiratory oxygen fraction currentl
       * valueCodeableConcept = $sct#40617009 "Artificial ventilation (regime/therapy)"
   * characteristic[procedure][=].exclude = false
 
-  * characteristic[ventilationObservableLOINC][+]
+  * characteristic[observation][+]
     * definitionByTypeAndValue
       * type = $loinc#3150-0 "Inhaled oxygen concentration"
       * valueRange
@@ -223,7 +223,7 @@ Description: "Ventilated COVID-19 patients, inspiratory oxygen fraction currentl
       * valueCodeableConcept = $sct#40617009 "Artificial ventilation (regime/therapy)"
   * characteristic[procedure][=].exclude = false
 
-  * characteristic[ventilationObservableLOINC][+]
+  * characteristic[observation][+]
     * definitionByTypeAndValue
       * type = $loinc#3150-0 "Inhaled oxygen concentration"
       * valueRange
@@ -255,7 +255,7 @@ Description: "Ventilated COVID-19 patients, inspiratory oxygen fraction currentl
       * valueCodeableConcept = $sct#40617009 "Artificial ventilation (regime/therapy)"
   * characteristic[procedure][=].exclude = false
 
-  * characteristic[ventilationObservableLOINC][+]
+  * characteristic[observation][+]
     * definitionByTypeAndValue
       * type = $loinc#3150-0 "Inhaled oxygen concentration"
       * valueQuantity = 100 '%' "%"

input/fsh/covid19-inpatient-therapy/36b-proning/recommendation_36b_population.fsh

@@ -22,11 +22,11 @@ Description: "Ventilated COVID-19 patients with severe ARDS, defined by oxygenat
     * definitionByTypeAndValue
       * valueCodeableConcept = $sct#67782005 "Acute respiratory distress syndrome (disorder)"
   * characteristic[condition][=].exclude = false
-  * characteristic[laboratory][+]
+  * characteristic[observation][+]
     * linkId = "horowitz-limit"
     * definitionByTypeAndValue
       * type = $loinc#50984-4 "Horowitz index in Arterial blood"
       * valueRange
         * high = 150 'mm[Hg]' "mm[Hg]"
-  * characteristic[laboratory][=].exclude = false
+  * characteristic[observation][=].exclude = false
 * characteristic[=].exclude = false

scripts/create-intros.py

@@ -7,7 +7,8 @@
 import os
 from pathlib import Path
 
-base_path = Path(os.path.dirname(os.path.realpath(__file__)))
+#base_path = Path(os.path.dirname(os.path.realpath(__file__)))
+base_path = Path.cwd()
 output_path = base_path / 'input' / 'intro-notes'
 ig_fname = base_path / 'input' / 'data' / 'ig.yml'
 linklist_fname = base_path / 'input' / 'includes' / 'link-list-generated.md'

sushi-config.yaml

@@ -13,7 +13,7 @@ publisher:
 
 dependencies:
   de.netzwerk-universitaetsmedizin.ebm-cpg:
-    version: 0.8.0-snapshot
+    version: 1.0.0
 
 pages:
   index.md: