conceptql 0.2.0 → 0.4.0

data/config/provenance.yml

@@ -0,0 +1,489 @@
+---
+:carrier_claim:
+  - 45756835
+  - 45756836
+  - 45756837
+  - 45756838
+  - 45756839
+  - 45756840
+  - 45756841
+  - 45756842
+  - 45756843
+  - 45756844
+  - 45756845
+  - 45756846
+  - 45756847
+  - 45756848
+  - 45756849
+  - 45756850
+  - 45756851
+  - 45756852
+  - 45756853
+  - 45756854
+  - 45756855
+  - 45756900
+  - 45756901
+  - 45756902
+  - 45756903
+  - 45756904
+  - 45756905
+  - 45756906
+  - 45756907
+  - 45756908
+  - 45756909
+  - 45756910
+  - 45756911
+  - 45756912
+  - 100000062
+  - 100011039
+  - 100011036
+:carrier_claim_detail:
+  - 45756843
+  - 45756844
+  - 45756845
+  - 45756846
+  - 45756847
+  - 45756848
+  - 45756849
+  - 45756850
+  - 45756851
+  - 45756852
+  - 45756853
+  - 45756854
+  - 45756855
+  - 45756900
+  - 45756901
+  - 45756902
+  - 45756903
+  - 45756904
+  - 45756905
+  - 45756906
+  - 45756907
+  - 45756908
+  - 45756909
+  - 45756910
+  - 45756911
+  - 45756912
+  - 100000062
+  - 100011039
+  - 100011036
+:carrier_claim_header:
+  - 45756835
+  - 45756836
+  - 45756837
+  - 45756838
+  - 45756839
+  - 45756840
+  - 45756841
+  - 45756842
+  - 100000062
+  - 100011039
+  - 100011036
+:carrier_claim_primary_or_first:
+  - 45756835
+  - 45756843
+  - 45756900
+:claim:
+  - 45756835
+  - 45756836
+  - 45756837
+  - 45756838
+  - 45756839
+  - 45756840
+  - 45756841
+  - 45756842
+  - 45756843
+  - 45756844
+  - 45756845
+  - 45756846
+  - 45756847
+  - 45756848
+  - 45756849
+  - 45756850
+  - 45756851
+  - 45756852
+  - 45756853
+  - 45756854
+  - 45756855
+  - 38003566
+  - 38003567
+  - 38003568
+  - 44818705
+  - 45756900
+  - 45756901
+  - 45756902
+  - 45756903
+  - 45756904
+  - 45756905
+  - 45756906
+  - 45756907
+  - 45756908
+  - 45756909
+  - 45756910
+  - 45756911
+  - 45756912
+  - 44818517
+  - 100000062
+  - 100011039
+  - 100011036
+:inpatient:
+  - 38000183
+  - 38000184
+  - 38000185
+  - 38000186
+  - 38000187
+  - 38000188
+  - 38000189
+  - 38000190
+  - 38000191
+  - 38000192
+  - 38000193
+  - 38000194
+  - 38000195
+  - 38000196
+  - 38000197
+  - 38000198
+  - 38000199
+  - 38000200
+  - 38000201
+  - 38000202
+  - 38000203
+  - 38000204
+  - 38000205
+  - 38000206
+  - 38000207
+  - 38000208
+  - 38000209
+  - 38000210
+  - 38000211
+  - 38000212
+  - 38000213
+  - 38000214
+  - 44818709
+  - 44818710
+  - 44818711
+  - 44818712
+  - 44818713
+  - 38000248
+  - 38000249
+  - 38000250
+  - 38000251
+  - 38000252
+  - 38000253
+  - 38000254
+  - 38000255
+  - 38000256
+  - 38000257
+  - 38000258
+  - 38000259
+  - 38000260
+  - 38000261
+  - 38000262
+  - 38000263
+  - 38000264
+  - 38000265
+  - 38000180
+  - 44814639
+  - 100000060
+  - 100011032
+  - 100011033
+:inpatient_detail:
+  - 38000183
+  - 38000184
+  - 38000185
+  - 38000186
+  - 38000187
+  - 38000188
+  - 38000189
+  - 38000190
+  - 38000191
+  - 38000192
+  - 38000193
+  - 38000194
+  - 38000195
+  - 38000196
+  - 38000197
+  - 38000198
+  - 44818709
+  - 44818710
+  - 44818711
+  - 44818712
+  - 44818713
+  - 38000248
+  - 38000249
+  - 100000060
+  - 100011032
+  - 100011033
+:inpatient_header:
+  - 38000199
+  - 38000200
+  - 38000201
+  - 38000202
+  - 38000203
+  - 38000204
+  - 38000205
+  - 38000206
+  - 38000207
+  - 38000208
+  - 38000209
+  - 38000210
+  - 38000211
+  - 38000212
+  - 38000213
+  - 38000214
+  - 38000250
+  - 38000251
+  - 38000252
+  - 38000253
+  - 38000254
+  - 38000255
+  - 38000256
+  - 38000257
+  - 38000258
+  - 38000259
+  - 38000260
+  - 38000261
+  - 38000262
+  - 38000263
+  - 38000264
+  - 38000265
+  - 100000060
+  - 100011032
+  - 100011033
+:inpatient_primary:
+  - 38000183
+  - 38000199
+  - 38000248
+  - 38000250
+  - 100000060
+  - 100011032
+  - 100011033
+:inpatient_primary_or_first:
+  - 38000183
+  - 38000184
+  - 38000199
+  - 38000200
+  - 38000248
+  - 38000249
+  - 38000250
+  - 38000251
+  - 100000060
+  - 100011032
+  - 100011033
+:outpatient:
+  - 38000215
+  - 38000216
+  - 38000217
+  - 38000218
+  - 38000219
+  - 38000220
+  - 38000221
+  - 38000222
+  - 38000223
+  - 38000224
+  - 38000225
+  - 38000226
+  - 38000227
+  - 38000228
+  - 38000229
+  - 38000230
+  - 38000231
+  - 38000232
+  - 38000233
+  - 38000234
+  - 38000235
+  - 38000236
+  - 38000237
+  - 38000238
+  - 38000239
+  - 38000240
+  - 38000241
+  - 38000242
+  - 38000243
+  - 38000244
+  - 38000266
+  - 38000267
+  - 38000268
+  - 38000269
+  - 38000270
+  - 38000271
+  - 38000272
+  - 38000273
+  - 38000274
+  - 45756856
+  - 45756857
+  - 45756858
+  - 45756859
+  - 45756860
+  - 45756861
+  - 45756862
+  - 45756863
+  - 45756864
+  - 45756865
+  - 45756866
+  - 45756867
+  - 45756868
+  - 45756869
+  - 45756870
+  - 45756871
+  - 45756872
+  - 45756873
+  - 45756874
+  - 45756875
+  - 45756876
+  - 45756877
+  - 45756878
+  - 45756879
+  - 45756880
+  - 45756881
+  - 45756882
+  - 45756883
+  - 45756884
+  - 45756885
+  - 45756886
+  - 45756887
+  - 45756888
+  - 45756889
+  - 45756890
+  - 45756891
+  - 45756892
+  - 45756893
+  - 45756894
+  - 45756895
+  - 45756896
+  - 45756897
+  - 45756898
+  - 45756899
+  - 44814640
+  - 100000061
+  - 100011031
+  - 100011034
+  - 100011035
+:outpatient_detail:
+  - 38000215
+  - 38000216
+  - 38000217
+  - 38000218
+  - 38000219
+  - 38000220
+  - 38000221
+  - 38000222
+  - 38000223
+  - 38000224
+  - 38000225
+  - 38000226
+  - 38000227
+  - 38000228
+  - 38000229
+  - 38000266
+  - 38000267
+  - 45756856
+  - 45756857
+  - 45756858
+  - 45756859
+  - 45756860
+  - 45756861
+  - 45756862
+  - 45756863
+  - 45756864
+  - 45756865
+  - 45756866
+  - 45756867
+  - 45756868
+  - 45756869
+  - 45756870
+  - 45756871
+  - 45756872
+  - 45756873
+  - 45756874
+  - 45756875
+  - 45756876
+  - 45756877
+  - 45756878
+  - 45756879
+  - 45756880
+  - 45756881
+  - 45756882
+  - 45756883
+  - 45756884
+  - 45756885
+  - 45756886
+  - 45756887
+  - 45756888
+  - 45756889
+  - 45756890
+  - 45756891
+  - 45756892
+  - 45756893
+  - 45756894
+  - 45756895
+  - 45756896
+  - 45756897
+  - 45756898
+  - 45756899
+  - 100000061
+  - 100011031
+  - 100011034
+  - 100011035
+:outpatient_header:
+  - 38000230
+  - 38000231
+  - 38000232
+  - 38000233
+  - 38000234
+  - 38000235
+  - 38000236
+  - 38000237
+  - 38000238
+  - 38000239
+  - 38000240
+  - 38000241
+  - 38000242
+  - 38000243
+  - 38000244
+  - 38000268
+  - 38000269
+  - 38000270
+  - 38000271
+  - 38000272
+  - 38000273
+  - 38000274
+  - 100000061
+  - 100011031
+  - 100011034
+  - 100011035
+:outpatient_primary:
+  - 38000266
+  - 38000268
+:outpatient_primary_or_first:
+  - 38000215
+  - 38000230
+  - 38000266
+  - 38000267
+  - 38000268
+  - 38000269
+:primary:
+  - 38000183
+  - 38000199
+  - 38000248
+  - 38000250
+  - 38000266
+  - 38000268
+:primary_or_first:
+  - 38000183
+  - 38000184
+  - 38000199
+  - 38000200
+  - 38000215
+  - 38000230
+  - 45756835
+  - 45756843
+  - 38000248
+  - 38000249
+  - 38000250
+  - 38000251
+  - 38000266
+  - 38000267
+  - 38000268
+  - 38000269
+  - 45756900

data/config/race.yml

@@ -0,0 +1,50 @@
+8657:
+  - 38003572
+  - 38003573
+8515:
+  - 38003574
+  - 38003575
+  - 38003576
+  - 38003577
+  - 38003578
+  - 38003579
+  - 38003580
+  - 38003581
+  - 38003582
+  - 38003583
+  - 38003584
+  - 38003585
+  - 38003586
+  - 38003587
+  - 38003588
+  - 38003589
+  - 38003590
+  - 38003591
+  - 38003592
+  - 38003593
+  - 38003594
+  - 38003595
+  - 38003596
+  - 38003597
+8516:
+  - 38003598
+  - 38003599
+  - 38003600
+  - 38003601
+  - 38003602
+  - 38003603
+  - 38003604
+  - 38003605
+  - 38003606
+  - 38003607
+  - 38003608
+  - 38003609
+8557:
+  - 38003610
+  - 38003611
+  - 38003612
+  - 38003613
+8527:
+  - 38003614
+  - 38003615
+  - 38003616

data/config/vocabularies.csv

@@ -0,0 +1,87 @@
+id,omopv4_vocabulary_id,vocabulary_full_name,vocabulary_short_name,domain,hidden,format_regexp,aliases,requires_lexicon
+ADMSRCE,1000000,ADMSRCE,,,,,,
+ADMTYPE,1000001,ADMTYPE,,,,,,
+ATC,21,WHO Anatomic Therapeutic Chemical Classification,WHO ATC,drug_exposure,,"^[ABCDGHJLMNPRSVabcdghjlmnprsv](\d{2}([A-Za-z]{1,2}(\d{2})?)?)?$",,
+BETOS,1000002,BETOS,,,,,,
+Clinical Code Type,1000004,Clinical Code Type,,,,,,
+Concept Class,68,OMOP Concept Class,,,Y,,,
+Condition Type,37,OMOP Condition Occurrence Type,,condition_occurrence,Y,,,
+CPT4,4,Current Procedural Terminology version 4 (AMA),CPT,procedure_occurrence,,"^\w\d{3}\w$",cpt,
+CPT4_HCPCS,,CPT4 and HCPCS merged (OI supplemental),CPT4/HCPCS,procedure_occurrence,,"^\w\d{3}\w$",,Y
+CS_Schema,1000003,CS_Schema,,,,,,
+Currency,65,International Currency Symbol (ISO 4217),,,Y,,,
+Death Type,45,OMOP Death Type,,death,Y,,,
+Device Type,63,OMOP Device Type,,observation,Y,,,
+Domain,59,OMOP Domain,,,Y,,,
+DRG,40,Diagnosis-related group (CMS),DRG,procedure_occurrence,,"^\d{3}$",,
+DrugTextString,26400,Drug Text String,Drug Text String,drug_exposure,,,,
+Drug Type,36,OMOP Drug Exposure Type,,drug_exposure,Y,,,
+DURATION_UNIT,1000005,DURATION_UNIT,,,,,,
+Ethnicity,44,OMOP Ethnicity,,person,Y,,,
+Gemscript,56,,Gemscript,drug_exposure,,"^\d{8}$",,
+Gender,12,OMOP Gender,,person,Y,,,
+HCFASPEC,1000006,HCFASPEC,,,,,,
+HCFATYPE,1000007,HCFATYPE,,,,,,
+HCPCS,5,Healthcare Common Procedure Coding System (CMS),HCPCS,procedure_occurrence,,"^[A-Za-z]\d{4}$",,
+ICD03_Morphology,1000008,ICD03_Morphology,,,,"^\d{4}/\d$",,
+ICD03_Topography,1000009,ICD03_Topography,,,,"^[A-Za-z]\d{2}(\.\d{1,2})?$",,
+ICD10,34,"International Classification of Diseases, Tenth Revision (WHO)",ICD-10 WHO,condition_occurrence,,"^([A-Za-z][0-9][0-9A-Za-z](\.\w{1,4})?|[A-Za-z][0-9][0-9A-Za-z]-[A-Za-z][0-9][0-9A-Za-z]|(?:I|II|III|IV|V|VI|VII|VIII|IX|X|XI|XII|XIII|XIV|XV|XVI|XVII|XVIII|XIX|XX|XXI|XXII))$",,
+ICD10PCS,35,"ICD-10 Procedure Coding System (CMS)",ICD-10 PCS,procedure_occurrence,,"^[0-9BCDFGHX][0-9A-HJ-NP-Z]{6}$",icd10_pcs,
+ICD10CM,70,"International Classification of Diseases, Tenth Revision, Clinical Modification (NCHS)",ICD-10 CM,condition_occurrence,,"^(?:QA[0-9]|[A-Za-z][0-9][0-9ABab])(\.[0-9A-Za-z]{1,4})?$",,
+ICD9CM,2,"International Classification of Diseases, Ninth Revision, Clinical Modification, Volume 1 and 2 (NCHS)",ICD-9 CM,condition_occurrence,,"^(V\d{2}(\.\d{1,2})?|\d{3}(\.\d{1,2})?|E\d{3}(\.\d)?)$",icd9,
+ICD9Proc,3,"International Classification of Diseases, Ninth Revision, Clinical Modification, Volume 3 (NCHS)",ICD-9 Proc,procedure_occurrence,,"^\d{2}(\.\d{1,2})?$",icd9_procedure,
+LOINC,6,Logical Observation Identifiers Names and Codes (Regenstrief Institute),,observation,,"^\w{3,7}-\w$",,
+GDM_CEN_TRACT_MEAS,0,Census Tract Measures from SEER,,observation,,,,
+SEER_YOST_ACS_06_10,0,SEER's Yost Index calculated from ACS 2006-2010,,observation,,,,
+SEER_YOST_ACS_10_14,0,SEER's Yost Index calculated from ACS 2010-2014,,observation,,,,
+SEER_YOST_ACS_13_17,0,SEER's Yost Index calculated from ACS 2013-2017,,observation,,,,
+MARCLA_OBS_TYPE,0,Market Clarity Observation Type,,observation,,,,
+Meas Type,64,OMOP Measurement Type,,observation,Y,,,
+NDC,9,National Drug Code (FDA and manufacturers),,drug_exposure,,"^(\d{5}\w{4}|\d{5}\w{6})$",,
+Note Type,58,OMOP Note Type,,,Y,,,
+NUCC,47,National Uniform Claim Committee Health Care Provider Taxonomy Code Set (NUCC),,,Y,,,
+Observation Type,39,OMOP Observation Type,,observation,Y,,,
+Obs Period Type,61,OMOP Observation Period Type,,observation_period,Y,,,
+OI_FILE_TYPE,1000010,OI_FILE_TYPE,,,,,,
+OI_INFORMATION_TYPE,1000011,OI_INFORMATION_TYPE,,,,,,
+OI_PROV,1000012,OI_PROV,,,,,,
+Place of Service,14,Place of Service Codes for Professional Claims (CMS),,visit_occurrence,Y,,,
+PLCSRVC,1000013,PLCSRVC,,,,,,
+Procedure Type,38,OMOP Procedure Occurrence Type,,procedure_occurrence,Y,,,
+PROVIDER_FACILITY_TYPE,1000014,PROVIDER_FACILITY_TYPE,,,,,,
+Race,13,Race and Ethnicity Code Set (USBC),,person,Y,,,
+Relationship,66,OMOP Relationship,,,Y,,,
+Revenue Code,43,UB04/CMS1450 Revenue Codes (CMS),Revenue Code,procedure_occurrence,,,revenue_code,
+RxNorm,8,RxNorm (NLM),,drug_exposure,,"^\d{2,8}$",,
+SEER_ADJAJC6M,1000015,SEER_ADJAJC6M,,,,,,
+SEER_ADJAJC6N,1000016,SEER_ADJAJC6N,,,,,,
+SEER_ADJAJC6T,1000017,SEER_ADJAJC6T,,,,,,
+SEER_BEH,1000018,SEER_BEH,,,,,,
+SEER_CENSUS_POV_IND,1000019,SEER_CENSUS_POV_IND,,,,,,
+SEER_DAJCC7,1000020,SEER_DAJCC7,,,,,,
+SEER_DAJCCSTG,1000021,SEER_DAJCCSTG,,,,,,
+SEER_DXCONF,1000022,SEER_DXCONF,,,,,,
+SEER_GRADE,1000023,SEER_GRADE,,,,,,
+SEER_LAT,1000024,SEER_LAT,,,,,,
+SEER_MARST,1000025,SEER_MARST,,,,,,
+SEER_MSEX,1000026,SEER_MSEX,,,,,,
+SEER_NHIADE,1000027,SEER_NHIADE,,,,,,
+SEER_NOSRG,1000028,SEER_NOSRG,,,,,,
+SEER_RAD,1000029,SEER_RAD,,,,,,
+SEER_RADSURG,1000030,SEER_RADSURG,,,,,,
+SEER_SEQ,1000031,SEER_SEQ,,,,,,
+SEER_SITERWHO,1000032,SEER_SITERWHO,,,,,,
+SEER_SRACE,1000033,SEER_SRACE,,,,,,
+SEER_SRC,1000034,SEER_SRC,,,,,,
+SEER_SXPRIF,1000035,SEER_SXPRIF,,,,,,
+SEER_SXSITF,1000036,SEER_SXSITF,,,,,,
+SEER_TYPEFU,1000037,SEER_TYPEFU,,,,,,
+SEER_URBRUR,1000038,SEER_URBRUR,,,,,,
+SNOMED,1,SNOMED-CT,SNOMED-CT,condition_occurrence,,"^\d{6,18}$",,
+Specialty,48,Medicare provider/supplier specialty codes (CMS),,provider,Y,,,
+STUS_CD,1000039,STUS_CD,,,,,,
+TYPESRVC,1000040,TYPESRVC,,,,,,
+UCUM,11,Unified Code for Units of Measure (Regenstrief Institute),,,Y,,,
+Visit,24,OMOP Visit,,visit_occurrence,Y,,,
+Visit Type,62,OMOP Visit Type,,visit_occurrence,Y,,,
+Vocabulary,67,OMOP Vocabulary,,,Y,,,

data/lib/conceptql/behaviors/code_lister.rb

@@ -0,0 +1,23 @@
+# frozen_string_literal: true
+
+module ConceptQL
+  module Behaviors
+    module CodeLister
+      ConceptCode = Struct.new(:vocabulary, :code, :description) do
+        def to_s
+          if description
+            "#{vocabulary} #{code}: #{description}"
+          else
+            "#{vocabulary} #{code}"
+          end
+        end
+      end
+
+      def code_list(db)
+        describe_codes(db, arguments).map do |code, desc|
+          ConceptCode.new(preferred_name, code, desc)
+        end
+      end
+    end
+  end
+end

data/lib/conceptql/behaviors/drugish.rb

@@ -0,0 +1,17 @@
+# frozen_string_literal: true
+
+module ConceptQL
+  module Behaviors
+    module Drugish
+      def self.included(base)
+        base.define_method(:column_family) { "drug" }
+        base.require_column(:drug_name)
+        base.require_column(:drug_amount)
+        base.require_column(:drug_amount_units)
+        base.require_column(:drug_quantity)
+        base.require_column(:drug_strength_source_value)
+        base.require_column(:drug_days_supply)
+      end
+    end
+  end
+end

data/lib/conceptql/behaviors/labish.rb

@@ -0,0 +1,19 @@
+# frozen_string_literal: true
+
+module ConceptQL
+  module Behaviors
+    module Labish
+      def self.included(base)
+        base.define_method(:column_family) { "lab" }
+        base.require_column :value_as_number
+        base.require_column :value_as_string
+        base.require_column :value_as_concept_id
+        base.require_column :value_as_concept
+        base.require_column :unit_concept_id
+        base.require_column :unit_concept
+        base.require_column :range_low
+        base.require_column :range_high
+      end
+    end
+  end
+end