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Update LinkML and regenerate model #156

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4 changes: 2 additions & 2 deletions Pipfile.lock

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18,034 changes: 62 additions & 17,972 deletions crdch_model/crdch_model.py

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2 changes: 1 addition & 1 deletion crdch_model/csv/crdch_model.csv
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
id,mappings,description
AlcoholExposureObservation,,"A structured object that describes a single data item about an individual's exposure to alcohol, as generated through a point-in-time observation, measurement, or interpretation."
BiologicProduct,,"A living organism, or a metabolically active biological system such as a cell culture, tissue culture, or organoid that is maintained or propagated in vitro."
BodySite,,"A site in the body of an organism, typically described in terms of an anatomical location and optional qualifiers (e.g. left/right, upper/lower). But body sites as defined here may include 'non-anatomic' sites, such as the location of an implanted medical device."
BodySite,,"A site in the body of an organism, typically described in terms of an anatomical concept and optional qualifiers (e.g. left/right, upper/lower). But body sites as defined here may include non-canonical sites, such as an implanted medical device."
CancerGradeObservation,,A data structure with key (observation_type) and value (value_codeable_concept) attributes that represents a single cancer grade observation
CancerGradeObservationSet,,"A structured object to hold related data items about the grade of cancer (e.g. overall, primary gleason, secondary gleason, etc.)."
CancerStageObservation,,"A data structure with key (observation_type) and value (value_codeable_concept) attributes that represents a single cancer staging observation, such as the Clinical Metastasis (M) component of a clinical TNM staging."
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2 changes: 1 addition & 1 deletion crdch_model/graphql/crdch_model.graphql
Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,6 @@ type CancerStageObservation
focus: Entity
subject: Subject
performedBy: Organization
valueEntity: Entity
valueCodeableConcept: CodeableConcept!
}

Expand Down Expand Up @@ -495,6 +494,7 @@ type Treatment
treatmentIntent: CodeableConcept
treatmentEffect: CodeableConcept
treatmentOutcome: CodeableConcept
treatmentDose: Quantity
}


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