Class: ConceptQL::Operators::SourceVocabularyOperator

Inherits:
Operator
  • Object
show all
Defined in:
lib/conceptql/operators/source_vocabulary_operator.rb

Overview

A SourceVocabularyOperator is a superclass for a operator that represents a criterion whose column stores information associated with a source vocabulary.

If that seems confusing, then think of ICD-9 or NDC criteria. That type of criterion takes a set of values that are mapped via the source_to_concept_map table into a standard vocabulary.

This kind of criterion can have some interesting issues when we are searching for rows that match. Let’s take ICD-9 286.53 for example. That code maps to concept_id 0, so if we try to pull all conditions that match just the concept_id of 0 we’ll pull all condtions that have no match in the SNOMED standard vocabulary. That’s not what we want! So we need to search the condition_source_value field for matches on this code instead.

But there’s another, more complicated problem. Say we’re looking for ICD-9 289.81. OMOP maps this to concept_id 432585. OMOP also maps 20 other conditions, 6 of which are other ICD-9 codes, to this same concept_id. So if we look for ICD-9s that have a non-zero condition_condept_id, we might pull up conditions that match on concept_id, but aren’t the same exact code as the one we’re looking for.

My coworker came up with a nice, gneralized query that checks for matching concept_ids and matching source_code values. This class encapsulates that query.

Subclasses must provide the following methods:

  • table

    • The CDM table name where the criterion will fetch its rows

    • e.g. for ICD-9, this would be condition_occurrence

  • concept_column

    • Name of the column in the table that stores a concept_id related to the criterion

    • e.g. for ICD-9, this would be condition_concept_id

  • source_column

    • Name of the column in the table that stores the “raw” value related to the criterion

    • e.g. for ICD-9, this would be condition_source_value

  • vocabulary_id

    • The vocabulary ID of the source vocabulary for the criterion

    • e.g. for ICD-9, a value of 2 (for ICD-9-CM)

Constant Summary

Constants inherited from Operator

Operator::COLUMNS

Instance Attribute Summary

Attributes inherited from Operator

#arguments, #options, #upstreams, #values

Instance Method Summary collapse

Methods inherited from Operator

#columns, #evaluate, #initialize, #label, #select_it, #set_values, #sql, #stream, #types

Methods included from Metadatable

#allows_many_upstreams, #allows_one_upstream, #argument, #category, #desc, #humanized_class_name, #inherited, #just_class_name, #option, #predominant_types, #preferred_name, #reset_categories, #to_metadata, #types

Constructor Details

This class inherits a constructor from ConceptQL::Operators::Operator

Instance Method Details

#query(db) ⇒ Object 



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# File 'lib/conceptql/operators/source_vocabulary_operator.rb', line 32

def query(db)
  db.from(table_name)
    .join(:vocabulary__source_to_concept_map___scm, scm__target_concept_id: table_concept_column)
    .where(Sequel.expr(scm__source_code: values, scm__source_vocabulary_id: vocabulary_id).&(Sequel.expr(scm__source_code: table_source_column)))
end

#type ⇒ Object 



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# File 'lib/conceptql/operators/source_vocabulary_operator.rb', line 38

def type
  table
end