conceptql 0.3.0 → 0.4.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (1208) hide show
  1. checksums.yaml +5 -5
  2. data/CHANGELOG.md +228 -27
  3. data/LICENSE +21 -0
  4. data/README.md +28 -98
  5. data/bin/conceptql +2 -1
  6. data/bin/conceptql_utils +6 -0
  7. data/config/multiple_vocabularies.csv +4 -0
  8. data/config/provenance.yml +471 -436
  9. data/config/race.yml +50 -0
  10. data/config/vocabularies.csv +87 -0
  11. data/lib/conceptql/behaviors/code_lister.rb +23 -0
  12. data/lib/conceptql/behaviors/drugish.rb +13 -8
  13. data/lib/conceptql/behaviors/labish.rb +15 -9
  14. data/lib/conceptql/behaviors/metadatable.rb +102 -34
  15. data/lib/conceptql/behaviors/provenanceable.rb +15 -19
  16. data/lib/conceptql/behaviors/single_event.rb +11 -0
  17. data/lib/conceptql/behaviors/timeless.rb +11 -0
  18. data/lib/conceptql/behaviors/utilizable.rb +206 -0
  19. data/lib/conceptql/behaviors/windowable.rb +27 -0
  20. data/lib/conceptql/cli.rb +99 -134
  21. data/lib/conceptql/columnizer.rb +75 -0
  22. data/lib/conceptql/data_model/base.rb +462 -0
  23. data/lib/conceptql/data_model/gdm.rb +155 -0
  24. data/lib/conceptql/data_model/gdm_wide.rb +42 -0
  25. data/lib/conceptql/data_model/omopv4_plus.rb +12 -0
  26. data/lib/conceptql/data_model.rb +30 -0
  27. data/lib/conceptql/database.rb +195 -23
  28. data/lib/conceptql/date_adjuster.rb +57 -27
  29. data/lib/conceptql/diagram.rb +243 -0
  30. data/lib/conceptql/lexicon/lexicon_gdm.rb +47 -0
  31. data/lib/conceptql/lexicon/lexicon_no_db.rb +49 -0
  32. data/lib/conceptql/lexicon/lexicon_ohdsi.rb +63 -0
  33. data/lib/conceptql/lexicon/lexicon_strategy.rb +116 -0
  34. data/lib/conceptql/lexicon.rb +111 -0
  35. data/lib/conceptql/nodifier.rb +45 -15
  36. data/lib/conceptql/operators/after.rb +24 -21
  37. data/lib/conceptql/operators/any_overlap.rb +6 -6
  38. data/lib/conceptql/operators/before.rb +24 -16
  39. data/lib/conceptql/operators/binary_operator_operator.rb +52 -13
  40. data/lib/conceptql/operators/casting_operator.rb +24 -17
  41. data/lib/conceptql/operators/co_reported.rb +78 -9
  42. data/lib/conceptql/operators/concurrent_within.rb +29 -17
  43. data/lib/conceptql/operators/contains.rb +9 -9
  44. data/lib/conceptql/operators/count.rb +9 -9
  45. data/lib/conceptql/operators/date_range.rb +40 -18
  46. data/lib/conceptql/operators/death.rb +10 -2
  47. data/lib/conceptql/operators/dedup.rb +31 -0
  48. data/lib/conceptql/operators/during.rb +5 -12
  49. data/lib/conceptql/operators/episode.rb +146 -0
  50. data/lib/conceptql/operators/equal.rb +6 -3
  51. data/lib/conceptql/operators/ethnicity.rb +49 -0
  52. data/lib/conceptql/operators/except.rb +15 -20
  53. data/lib/conceptql/operators/filter.rb +20 -8
  54. data/lib/conceptql/operators/first.rb +14 -3
  55. data/lib/conceptql/operators/from.rb +33 -12
  56. data/lib/conceptql/operators/gender.rb +27 -11
  57. data/lib/conceptql/operators/hospice.rb +19 -0
  58. data/lib/conceptql/operators/hospitalization.rb +19 -0
  59. data/lib/conceptql/operators/information_periods.rb +36 -0
  60. data/lib/conceptql/operators/invalid.rb +4 -5
  61. data/lib/conceptql/operators/last.rb +14 -3
  62. data/lib/conceptql/operators/match.rb +91 -0
  63. data/lib/conceptql/operators/multiple_vocabularies.rb +172 -0
  64. data/lib/conceptql/operators/numeric.rb +52 -29
  65. data/lib/conceptql/operators/numeric_filter.rb +68 -0
  66. data/lib/conceptql/operators/occurrence.rb +133 -48
  67. data/lib/conceptql/operators/one_in_two_out.rb +198 -62
  68. data/lib/conceptql/operators/operator.rb +321 -408
  69. data/lib/conceptql/operators/pass_thru.rb +9 -5
  70. data/lib/conceptql/operators/person.rb +12 -2
  71. data/lib/conceptql/operators/person_filter.rb +5 -3
  72. data/lib/conceptql/operators/place_of_service_filter.rb +11 -15
  73. data/lib/conceptql/operators/provenance.rb +25 -36
  74. data/lib/conceptql/operators/provider_filter.rb +40 -14
  75. data/lib/conceptql/operators/race.rb +48 -7
  76. data/lib/conceptql/operators/read.rb +77 -58
  77. data/lib/conceptql/operators/recall.rb +20 -20
  78. data/lib/conceptql/operators/snf.rb +19 -0
  79. data/lib/conceptql/operators/sum.rb +23 -12
  80. data/lib/conceptql/operators/temporal_operator.rb +80 -54
  81. data/lib/conceptql/operators/time_window.rb +13 -15
  82. data/lib/conceptql/operators/trim_date.rb +71 -0
  83. data/lib/conceptql/operators/trim_date_end.rb +20 -40
  84. data/lib/conceptql/operators/trim_date_start.rb +20 -43
  85. data/lib/conceptql/operators/union.rb +59 -35
  86. data/lib/conceptql/operators/vocabulary.rb +151 -0
  87. data/lib/conceptql/paths.rb +41 -0
  88. data/lib/conceptql/query.rb +168 -46
  89. data/lib/conceptql/query_modifiers/gdm/admission_date_query_modifier.rb +46 -0
  90. data/lib/conceptql/query_modifiers/gdm/drug_query_modifier.rb +54 -0
  91. data/lib/conceptql/query_modifiers/gdm/lab_query_modifier.rb +57 -0
  92. data/lib/conceptql/query_modifiers/gdm/pos_query_modifier.rb +46 -0
  93. data/lib/conceptql/query_modifiers/gdm/provenance_query_modifier.rb +45 -0
  94. data/lib/conceptql/query_modifiers/gdm/provider_query_modifier.rb +53 -0
  95. data/lib/conceptql/query_modifiers/gdm_wide/admission_date_query_modifier.rb +42 -0
  96. data/lib/conceptql/query_modifiers/gdm_wide/drug_query_modifier.rb +52 -0
  97. data/lib/conceptql/query_modifiers/gdm_wide/lab_query_modifier.rb +55 -0
  98. data/lib/conceptql/query_modifiers/gdm_wide/pos_query_modifier.rb +37 -0
  99. data/lib/conceptql/query_modifiers/gdm_wide/provenance_query_modifier.rb +38 -0
  100. data/lib/conceptql/query_modifiers/omopv4_plus/admission_date_query_modifier.rb +45 -0
  101. data/lib/conceptql/query_modifiers/omopv4_plus/drug_query_modifier.rb +80 -0
  102. data/lib/conceptql/query_modifiers/omopv4_plus/pos_query_modifier.rb +47 -0
  103. data/lib/conceptql/query_modifiers/omopv4_plus/provenance_query_modifier.rb +45 -0
  104. data/lib/conceptql/query_modifiers/omopv4_plus/provider_query_modifier.rb +26 -0
  105. data/lib/conceptql/query_modifiers/query_modifier.rb +6 -2
  106. data/lib/conceptql/rdbms/duckdb.rb +21 -0
  107. data/lib/conceptql/rdbms/generic.rb +116 -0
  108. data/lib/conceptql/rdbms/postgres.rb +47 -0
  109. data/lib/conceptql/rdbms/spark.rb +18 -0
  110. data/lib/conceptql/rdbms.rb +22 -0
  111. data/lib/conceptql/scope.rb +353 -41
  112. data/lib/conceptql/utils.rb +70 -0
  113. data/lib/conceptql/utils_cli.rb +17 -0
  114. data/lib/conceptql/version.rb +3 -1
  115. data/lib/conceptql/visitors/metadata_extractor.rb +54 -0
  116. data/lib/conceptql/vocabularies/behaviors/costish.rb +24 -0
  117. data/lib/conceptql/vocabularies/behaviors/gdmish.rb +19 -0
  118. data/lib/conceptql/vocabularies/behaviors/omopish.rb +32 -0
  119. data/lib/conceptql/vocabularies/dynamic_vocabularies.rb +63 -0
  120. data/lib/conceptql/vocabularies/entry.rb +138 -0
  121. data/lib/conceptql/vocabularies/vocabulary_class_factory.rb +85 -0
  122. data/lib/conceptql/window/base.rb +26 -0
  123. data/lib/conceptql/window/date_range.rb +25 -0
  124. data/lib/conceptql/window/table.rb +116 -0
  125. data/lib/conceptql/window.rb +72 -0
  126. data/lib/conceptql.rb +53 -10
  127. data/lib/sequel/extensions/pg_ctas_explain.rb +22 -0
  128. data/lib/sequel/extensions/pg_vacuum_table.rb +23 -0
  129. data/schemas/gdm.yml +882 -0
  130. data/schemas/gdm_wide.yml +757 -0
  131. data/schemas/ohdsi_vocabs.yml +143 -0
  132. data/schemas/omopv4_plus.yml +729 -0
  133. data/schemas/omopv4_plus_more_ignorables.tsv +13 -0
  134. metadata +271 -2065
  135. data/.gitignore +0 -25
  136. data/Gemfile +0 -6
  137. data/Guardfile +0 -56
  138. data/LICENSE.txt +0 -22
  139. data/Rakefile +0 -35
  140. data/conceptql.gemspec +0 -31
  141. data/doc/ConceptQL Specification (alpha).pdf +0 -0
  142. data/doc/converter.rb +0 -33
  143. data/doc/diagram_0.png +0 -0
  144. data/doc/implementation_notes.md +0 -39
  145. data/doc/metadata.md +0 -89
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  211. data/doc/spec.md +0 -2258
  212. data/doc/spec.md.cql +0 -1930
  213. data/lib/conceptql/annotate_grapher.rb +0 -127
  214. data/lib/conceptql/fake_annotater.rb +0 -129
  215. data/lib/conceptql/knitter.rb +0 -221
  216. data/lib/conceptql/logger.rb +0 -10
  217. data/lib/conceptql/operators/complement.rb +0 -43
  218. data/lib/conceptql/operators/condition_occurrence_source_vocabulary_operator.rb +0 -34
  219. data/lib/conceptql/operators/condition_occurrence_source_vocabulary_operator_union.rb +0 -28
  220. data/lib/conceptql/operators/condition_type.rb +0 -79
  221. data/lib/conceptql/operators/cpt.rb +0 -28
  222. data/lib/conceptql/operators/cpt_or_hcpcs.rb +0 -27
  223. data/lib/conceptql/operators/drg.rb +0 -42
  224. data/lib/conceptql/operators/drug_type_concept.rb +0 -30
  225. data/lib/conceptql/operators/from_seer_visits.rb +0 -29
  226. data/lib/conceptql/operators/hcpcs.rb +0 -28
  227. data/lib/conceptql/operators/icd10.rb +0 -19
  228. data/lib/conceptql/operators/icd10_pcs.rb +0 -28
  229. data/lib/conceptql/operators/icd9.rb +0 -19
  230. data/lib/conceptql/operators/icd9_procedure.rb +0 -28
  231. data/lib/conceptql/operators/intersect.rb +0 -39
  232. data/lib/conceptql/operators/loinc.rb +0 -28
  233. data/lib/conceptql/operators/medcode.rb +0 -17
  234. data/lib/conceptql/operators/medcode_procedure.rb +0 -28
  235. data/lib/conceptql/operators/ndc.rb +0 -32
  236. data/lib/conceptql/operators/observation_by_enttype.rb +0 -32
  237. data/lib/conceptql/operators/observation_period.rb +0 -32
  238. data/lib/conceptql/operators/overlapped_by.rb +0 -26
  239. data/lib/conceptql/operators/overlaps.rb +0 -21
  240. data/lib/conceptql/operators/place_of_service_code.rb +0 -31
  241. data/lib/conceptql/operators/procedure_occurrence.rb +0 -27
  242. data/lib/conceptql/operators/prodcode.rb +0 -32
  243. data/lib/conceptql/operators/revenue_code.rb +0 -40
  244. data/lib/conceptql/operators/rxnorm.rb +0 -28
  245. data/lib/conceptql/operators/snomed.rb +0 -25
  246. data/lib/conceptql/operators/source_vocabulary_operator.rb +0 -88
  247. data/lib/conceptql/operators/standard_vocabulary_operator.rb +0 -66
  248. data/lib/conceptql/operators/started_by.rb +0 -23
  249. data/lib/conceptql/operators/to_seer_visits.rb +0 -29
  250. data/lib/conceptql/operators/visit_occurrence.rb +0 -32
  251. data/lib/conceptql/operators/vocabulary_operator.rb +0 -45
  252. data/lib/conceptql/query_modifiers/drug_query_modifier.rb +0 -45
  253. data/lib/conceptql/query_modifiers/pos_query_modifier.rb +0 -31
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  772. data/test/results/omopv4_plus/from_seer_visits/crit_4 +0 -2
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  818. data/test/results/omopv4_plus/one_in_two_out/count_1 +0 -3
  819. data/test/results/omopv4_plus/one_in_two_out/count_same_as_1 +0 -3
  820. data/test/results/omopv4_plus/one_in_two_out/crit_hcpcs +0 -2
  821. data/test/results/omopv4_plus/one_in_two_out/crit_icd9 +0 -19
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  1132. data/test/statements/provenance/anno_1 +0 -8
  1133. data/test/statements/provenance/anno_bad_keyword +0 -10
  1134. data/test/statements/provenance/count_1 +0 -8
  1135. data/test/statements/provenance/count_2 +0 -8
  1136. data/test/statements/provider_filter/anno_1 +0 -10
  1137. data/test/statements/race/anno_1 +0 -8
  1138. data/test/statements/race/anno_2 +0 -3
  1139. data/test/statements/race/crit_1 +0 -4
  1140. data/test/statements/read/anno_1 +0 -4
  1141. data/test/statements/read/crit_1 +0 -8
  1142. data/test/statements/recall/anno_1 +0 -16
  1143. data/test/statements/recall/anno_2 +0 -18
  1144. data/test/statements/recall/anno_3 +0 -4
  1145. data/test/statements/recall/anno_4 +0 -3
  1146. data/test/statements/recall/anno_5 +0 -5
  1147. data/test/statements/recall/anno_6 +0 -107
  1148. data/test/statements/recall/crit_1 +0 -17
  1149. data/test/statements/recall/crit_2 +0 -14
  1150. data/test/statements/recall/crit_3 +0 -16
  1151. data/test/statements/recall/crit_cte_1 +0 -17
  1152. data/test/statements/recall/crit_cte_2 +0 -17
  1153. data/test/statements/recall/crit_nested_perm_0 +0 -28
  1154. data/test/statements/revenue_code/crit_1 +0 -4
  1155. data/test/statements/revenue_code/crit_basic +0 -4
  1156. data/test/statements/revenue_code/domains_1 +0 -4
  1157. data/test/statements/revenue_code/domains_drg100 +0 -4
  1158. data/test/statements/rxnorm/crit_1 +0 -4
  1159. data/test/statements/snomed/crit_1 +0 -4
  1160. data/test/statements/started_by/crit_1 +0 -16
  1161. data/test/statements/started_by/crit_2 +0 -16
  1162. data/test/statements/started_by/crit_3 +0 -16
  1163. data/test/statements/sum/anno_1 +0 -3
  1164. data/test/statements/sum/anno_2 +0 -8
  1165. data/test/statements/sum/num_1 +0 -11
  1166. data/test/statements/sum/num_2 +0 -15
  1167. data/test/statements/sum/num_3 +0 -7
  1168. data/test/statements/time_window/anno_1 +0 -7
  1169. data/test/statements/time_window/anno_2 +0 -11
  1170. data/test/statements/time_window/anno_3 +0 -11
  1171. data/test/statements/time_window/anno_4 +0 -12
  1172. data/test/statements/time_window/anno_5 +0 -15
  1173. data/test/statements/time_window/crit_1 +0 -11
  1174. data/test/statements/time_window/crit_2 +0 -11
  1175. data/test/statements/time_window/crit_3 +0 -11
  1176. data/test/statements/time_window/crit_4 +0 -11
  1177. data/test/statements/trim_date_end/crit_1 +0 -16
  1178. data/test/statements/trim_date_end/crit_2 +0 -16
  1179. data/test/statements/trim_date_end/crit_3 +0 -16
  1180. data/test/statements/trim_date_end/crit_at_least +0 -17
  1181. data/test/statements/trim_date_end/crit_occurrences_1 +0 -17
  1182. data/test/statements/trim_date_end/crit_occurrences_2 +0 -17
  1183. data/test/statements/trim_date_end/crit_within +0 -17
  1184. data/test/statements/trim_date_start/crit_1 +0 -16
  1185. data/test/statements/trim_date_start/crit_2 +0 -16
  1186. data/test/statements/trim_date_start/crit_3 +0 -16
  1187. data/test/statements/trim_date_start/crit_at_least +0 -17
  1188. data/test/statements/trim_date_start/crit_occurrences_1 +0 -17
  1189. data/test/statements/trim_date_start/crit_occurrences_2 +0 -17
  1190. data/test/statements/trim_date_start/crit_within +0 -17
  1191. data/test/statements/union/anno_1 +0 -11
  1192. data/test/statements/union/anno_2 +0 -18
  1193. data/test/statements/union/anno_3 +0 -3
  1194. data/test/statements/union/anno_4 +0 -4
  1195. data/test/statements/union/anno_5 +0 -7
  1196. data/test/statements/union/anno_6 +0 -10
  1197. data/test/statements/union/count_1 +0 -11
  1198. data/test/statements/union/count_2 +0 -11
  1199. data/test/statements/union/count_3 +0 -15
  1200. data/test/statements/union/count_4 +0 -18
  1201. data/test/statements/union/count_5 +0 -18
  1202. data/test/statements/union/scanno_1 +0 -3
  1203. data/test/statements/union/scanno_2 +0 -18
  1204. data/test/statements/visit_occurrence/anno_1 +0 -11
  1205. data/test/statements/visit_occurrence/anno_2 +0 -8
  1206. data/test/statements/visit_occurrence/crit_1 +0 -7
  1207. data/test/statements/visit_occurrence/crit_2 +0 -7
  1208. data/test/statements/visit_occurrence/crit_3 +0 -3
@@ -0,0 +1,757 @@
1
+ ---
2
+ :patients:
3
+ :columns:
4
+ :id:
5
+ :type: :Bigint
6
+ :primary_key: true
7
+ :comment: Surrogate key for record
8
+ :null: false
9
+ :gender_concept_id:
10
+ :type: :Bigint
11
+ :comment:
12
+ FK reference to the [concepts](#concepts) table for the unique gender
13
+ of the patient
14
+ :foreign_key: concepts
15
+ :birth_date:
16
+ :type: Date
17
+ :comment: Date of birth (yyyy-mm-dd)
18
+ :race_concept_id:
19
+ :type: :Bigint
20
+ :comment:
21
+ FK reference to the [concepts](#concepts) table for the unique race
22
+ of the patient
23
+ :foreign_key: concepts
24
+ :ethnicity_concept_id:
25
+ :type: :Bigint
26
+ :comment:
27
+ FK reference to the [concepts](#concepts) table for the ethnicity
28
+ of the patient
29
+ :foreign_key: concepts
30
+ :address_id:
31
+ :type: :Bigint
32
+ :comment:
33
+ FK reference to the place of residency for the patient in the location
34
+ table, where the detailed address information is stored
35
+ :foreign_key: addresses
36
+ :practitioner_id:
37
+ :type: :Bigint
38
+ :comment:
39
+ FK reference to the primary care practitioner the patient is seeing
40
+ in the [practitioners](#practitioners) table
41
+ :foreign_key: practitioners
42
+ :patient_id_source_value:
43
+ :type: String
44
+ :comment: Originial patient identifier defined in the source data
45
+ :null: false
46
+ :practitioners:
47
+ :columns:
48
+ :id:
49
+ :type: :Bigint
50
+ :primary_key: true
51
+ :comment: Surrogate key for record
52
+ :null: false
53
+ :practitioner_name:
54
+ :type: String
55
+ :comment: Practitioner's name, if available
56
+ :primary_identifier:
57
+ :type: String
58
+ :comment: Primary practitioner identifier
59
+ :null: false
60
+ :primary_identifier_type:
61
+ :type: String
62
+ :comment:
63
+ Type of identifier specified in primary identifier field (UPIN, NPI,
64
+ etc)
65
+ :null: false
66
+ :secondary_identifier:
67
+ :type: String
68
+ :comment: Secondary practitioner identifier (Optional)
69
+ :secondary_identifier_type:
70
+ :type: String
71
+ :comment:
72
+ Type of identifier specified in secondary identifier field (UPIN,
73
+ NPI, etc)
74
+ :specialty_concept_id:
75
+ :type: :Bigint
76
+ :comment:
77
+ FK reference to an identifier in the [concepts](#concepts) table for
78
+ specialty
79
+ :foreign_key: concepts
80
+ :address_id:
81
+ :type: :Bigint
82
+ :comment:
83
+ FK reference to the address of the location where the practitioner
84
+ is practicing
85
+ :foreign_key: addresses
86
+ :birth_date:
87
+ :type: Date
88
+ :comment: Date of birth (yyyy-mm-dd)
89
+ :gender_concept_id:
90
+ :type: :Bigint
91
+ :comment:
92
+ FK reference to an identifier in the [concepts](#concepts) table for
93
+ the unique gender of the practitioner
94
+ :foreign_key: concepts
95
+ :facilities:
96
+ :columns:
97
+ :id:
98
+ :type: :Bigint
99
+ :primary_key: true
100
+ :comment: Surrogate key for record
101
+ :null: false
102
+ :facility_name:
103
+ :type: String
104
+ :comment: Facility name, if available
105
+ :primary_identifier:
106
+ :type: String
107
+ :comment: Primary facility identifier
108
+ :null: false
109
+ :primary_identifier_type:
110
+ :type: String
111
+ :comment:
112
+ Type of identifier specified in primary identifier field (UPIN, NPI,
113
+ etc)
114
+ :null: false
115
+ :secondary_identifier:
116
+ :type: String
117
+ :comment: Secondary facility identifier (Optional)
118
+ :secondary_identifier_type:
119
+ :type: String
120
+ :comment:
121
+ Type of identifier specified in secondary identifier field (UPIN,
122
+ NPI, etc)
123
+ :facility_type_concept_id:
124
+ :type: :Bigint
125
+ :comment:
126
+ FK reference to [concepts](#concepts) table representing the facility
127
+ type
128
+ :foreign_key: concepts
129
+ :specialty_concept_id:
130
+ :type: :Bigint
131
+ :comment:
132
+ A foreign key to an identifier in the [concepts](#concepts) table
133
+ for specialty
134
+ :foreign_key: concepts
135
+ :address_id:
136
+ :type: :Bigint
137
+ :comment: A foreign key to the address of the location of the facility
138
+ :foreign_key: addresses
139
+ :contexts_practitioners:
140
+ :columns:
141
+ :context_id:
142
+ :type: :Bigint
143
+ :comment: FK reference to [contexts](#contexts) table
144
+ :foreign_key: contexts
145
+ :null: false
146
+ :practitioner_id:
147
+ :type: :Bigint
148
+ :comment: FK reference to [practitioners](#practitioners) table
149
+ :foreign_key: practitioners
150
+ :null: false
151
+ :role_type_concept_id:
152
+ :type: :Bigint
153
+ :comment:
154
+ FK reference to the [concepts](#concepts) table representing roles
155
+ [practitioners](#practitioners) can play in an encounter
156
+ :foreign_key: concepts
157
+ :specialty_type_concept_id:
158
+ :type: :Bigint
159
+ :comment:
160
+ FK reference to [concepts](#concepts) table representing the practitioner's
161
+ specialty type for the services/diagnoses associated with this record
162
+ :foreign_key: concepts
163
+ :observations:
164
+ :columns:
165
+ :id:
166
+ :type: :Bigint
167
+ :primary_key: true
168
+ :comment: Surrogate key for record
169
+ :null: false
170
+ :context_id:
171
+ :type: :Bigint
172
+ :comment: FK reference to [contexts](#contexts) table
173
+ :foreign_key: contexts
174
+ :null: false
175
+ :patient_id:
176
+ :type: :Bigint
177
+ :comment: FK reference to [patients](#patients) table
178
+ :foreign_key: patients
179
+ :null: false
180
+ :start_date:
181
+ :type: Date
182
+ :comment: Start date of record (yyyy-mm-dd)
183
+ :null: false
184
+ :end_date:
185
+ :type: Date
186
+ :comment: End date of record (yyyy-mm-dd)
187
+ :null: false
188
+ :clinical_code_concept_id:
189
+ :type: :Bigint
190
+ :comment:
191
+ FK reference to [concepts](#concepts) table for the code assigned
192
+ to the record
193
+ :foreign_key: concepts
194
+ :null: false
195
+ :quantity:
196
+ :type: :Bigint
197
+ :comment: Quantity, if available (e.g., procedures)
198
+ :seq_num:
199
+ :type: Integer
200
+ :comment:
201
+ The sequence number for the variable assigned (e.g. dx3 gets sequence
202
+ number 3)
203
+ :provenance_concept_id:
204
+ :type: :Bigint
205
+ :comment:
206
+ "Additional type information (ex: primary, admitting, problem list,
207
+ etc)"
208
+ :foreign_key: concepts
209
+ :clinical_code_source_value:
210
+ :type: String
211
+ :comment: Source code from raw data
212
+ :null: false
213
+ :clinical_code_vocabulary_id:
214
+ :type: String
215
+ :comment: FK reference to the vocabulary the clinical code comes from
216
+ :foreign_key: vocabularies
217
+ :null: false
218
+ :measurement_detail_id:
219
+ :type: :Bigint
220
+ :comment: FK reference to [measurement_details](#measurement_details) table
221
+ :foreign_key: measurement_details
222
+ :drug_exposure_detail_id:
223
+ :type: :Bigint
224
+ :comment: FK reference to [drug_exposure_details](#drug_exposure_details) table
225
+ :foreign_key: drug_exposure_details
226
+ :context_start_date:
227
+ :type: Date
228
+ :comment: Start date of record (yyyy-mm-dd)
229
+ :null: false
230
+ :context_end_date:
231
+ :type: Date
232
+ :comment: End date of record (yyyy-mm-dd)
233
+ :context_facility_id:
234
+ :type: :Bigint
235
+ :comment: FK reference to [facilities](#facilities) table
236
+ :foreign_key: facilities
237
+ :care_site_type_concept_id:
238
+ :type: :Bigint
239
+ :comment:
240
+ FK reference to [concepts](#concepts) table representing the care
241
+ site type within the facility
242
+ :foreign_key: concepts
243
+ :pos_concept_id:
244
+ :type: :Bigint
245
+ :comment:
246
+ FK reference to [concepts](#concepts) table representing the place
247
+ of service associated with this record
248
+ :foreign_key: concepts
249
+ :source_type_concept_id:
250
+ :type: :Bigint
251
+ :comment:
252
+ FK reference to [concepts](#concepts) table representing the file
253
+ name (e.g MEDPAR). If data represents a subset of a file, concatenate the
254
+ name of the file used and subset (e.g MEDPAR_SNF)
255
+ :foreign_key: concepts
256
+ :null: false
257
+ :service_specialty_type_concept_id:
258
+ :type: :Bigint
259
+ :comment:
260
+ FK reference to [concepts](#concepts) table representing the specialty
261
+ type for the services/diagnoses associated with this record
262
+ :foreign_key: concepts
263
+ :record_type_concept_id:
264
+ :type: :Bigint
265
+ :comment:
266
+ FK reference to [concepts](#concepts) table representing the type
267
+ of [contexts](#contexts) the record represents (line, claim, etc.)
268
+ :foreign_key: concepts
269
+ :null: false
270
+ :collection_start_date:
271
+ :type: Date
272
+ :comment: Start date of record (yyyy-mm-dd)
273
+ :null: false
274
+ :collection_end_date:
275
+ :type: Date
276
+ :comment: End date of record (yyyy-mm-dd)
277
+ :null: false
278
+ :duration:
279
+ :type: Float
280
+ :comment: Duration of collection. (e.g. hospitalization length of stay)
281
+ :duration_unit_concept_id:
282
+ :type: :Bigint
283
+ :comment:
284
+ FK reference to [concepts](#concepts) table representing the unit
285
+ of duration (hours, days, weeks etc.)
286
+ :collection_facility_id:
287
+ :type: :Bigint
288
+ :comment: FK reference to [facilities](#facilities) table
289
+ :foreign_key: facilities
290
+ :collection_type_concept_id:
291
+ :type: :Bigint
292
+ :comment:
293
+ FK reference to [concepts](#concepts) table representing the type
294
+ of collection this record represents
295
+ :foreign_key: concepts
296
+ :refills:
297
+ :type: Integer
298
+ :comment:
299
+ The number of refills after the initial prescription; the initial
300
+ prescription is not counted (i.e., values start with 0)
301
+ :days_supply:
302
+ :type: Integer
303
+ :comment:
304
+ The number of days of supply as recorded in the original prescription
305
+ or dispensing record
306
+ :number_per_day:
307
+ :type: Float
308
+ :comment: The number of pills taken per day
309
+ :dose_form_concept_id:
310
+ :type: :Bigint
311
+ :comment:
312
+ FK reference to [concepts](#concepts) table for the form of the drug
313
+ (capsule, injection, etc.)
314
+ :foreign_key: concepts
315
+ :dose_unit_concept_id:
316
+ :type: :Bigint
317
+ :comment:
318
+ FK reference to [concepts](#concepts) table for the units in which
319
+ the dose_value is expressed
320
+ :foreign_key: concepts
321
+ :route_concept_id:
322
+ :type: :Bigint
323
+ :comment:
324
+ FK reference to [concepts](#concepts) table for route in which drug
325
+ is given
326
+ :foreign_key: concepts
327
+ :dose_value:
328
+ :type: Float
329
+ :comment: Numeric value for the dose of the drug
330
+ :strength_source_value:
331
+ :type: String
332
+ :comment:
333
+ Drug strength as reported in the raw data. This can include both dose
334
+ value and units
335
+ :ingredient_source_value:
336
+ :type: String
337
+ :comment: Ingredient/Generic name of drug as reported in the raw data
338
+ :drug_name_source_value:
339
+ :type: String
340
+ :comment: Product/Brand name of drug as reported in the raw data
341
+ :admit_admission_date:
342
+ :type: Date
343
+ :comment: Date of admission (yyyy-mm-dd)
344
+ :null: false
345
+ :admit_discharge_date:
346
+ :type: Date
347
+ :comment: Date of discharge (yyyy-mm-dd)
348
+ :null: false
349
+ :admit_source_concept_id:
350
+ :type: :Bigint
351
+ :comment:
352
+ Database specific code indicating source of admission (e.g., ER visit,
353
+ transfer, etc.)
354
+ :discharge_location_concept_id:
355
+ :type: :Bigint
356
+ :comment:
357
+ Database specific code indicating discharge location (e.g., death,
358
+ home, transfer, long-term care, etc.)
359
+ :admission_type_concept_id:
360
+ :type: :Bigint
361
+ :comment:
362
+ FK reference to [concepts](#concepts) table representing the type
363
+ of admission the record is (Emergency, Elective, etc.)
364
+ :foreign_key: concepts
365
+ :result_as_number:
366
+ :type: Float
367
+ :comment:
368
+ The observation result stored as a number, applicable to observations
369
+ where the result is expressed as a numeric value
370
+ :result_as_string:
371
+ :type: String
372
+ :comment:
373
+ The observation result stored as a string, applicable to observations
374
+ where the result is expressed as verbatim text
375
+ :result_as_concept_id:
376
+ :type: :Bigint
377
+ :comment:
378
+ FK reference to [concepts](#concepts) table for the result associated
379
+ with the detail_concept_id (e.g., positive/negative, present/absent, low/high,
380
+ etc.)
381
+ :foreign_key: concepts
382
+ :result_modifier_concept_id:
383
+ :type: :Bigint
384
+ :comment:
385
+ FK reference to [concepts](#concepts) table for result modifier (=,
386
+ <, >, etc.)
387
+ :foreign_key: concepts
388
+ :unit_concept_id:
389
+ :type: :Bigint
390
+ :comment:
391
+ FK reference to [concepts](#concepts) table for the measurement units
392
+ (e.g., mmol/L, mg/dL, etc.)
393
+ :foreign_key: concepts
394
+ :normal_range_low:
395
+ :type: Float
396
+ :comment: Lower bound of the normal reference range assigned by the laboratory
397
+ :normal_range_high:
398
+ :type: Float
399
+ :comment: Upper bound of the normal reference range assigned by the laboratory
400
+ :normal_range_low_modifier_concept_id:
401
+ :type: :Bigint
402
+ :comment:
403
+ FK reference to [concepts](#concepts) table for result modifier (=,
404
+ <, >, etc.)
405
+ :foreign_key: concepts
406
+ :normal_range_high_modifier_concept_id:
407
+ :type: :Bigint
408
+ :comment:
409
+ FK reference to [concepts](#concepts) table for result modifier (=,
410
+ <, >, etc.)
411
+ :foreign_key: concepts
412
+ :payer_reimbursements:
413
+ :columns:
414
+ :id:
415
+ :type: :Bigint
416
+ :primary_key: true
417
+ :comment: Surrogate key for record
418
+ :context_id:
419
+ :type: :Bigint
420
+ :comment: FK reference to context table
421
+ :foreign_key: contexts
422
+ :null: false
423
+ :patient_id:
424
+ :type: :Bigint
425
+ :comment: FK to reference to [patients](#patients) table
426
+ :foreign_key: patients
427
+ :null: false
428
+ :clinical_code_id:
429
+ :type: :Bigint
430
+ :comment:
431
+ FK reference to [clinical_codes](#clinical_codes) table to be used
432
+ if a specific code is the direct cause for the reimbursement
433
+ :foreign_key: clinical_codes
434
+ :currency_concept_id:
435
+ :type: :Bigint
436
+ :comment:
437
+ FK reference to [concepts](#concepts) table for the 3-letter code
438
+ used to delineate international currencies (e.g., USD = US Dollar)
439
+ :foreign_key: concepts
440
+ :null: false
441
+ :total_charged:
442
+ :type: Float
443
+ :comment:
444
+ The total amount charged by the provider of the good/service (e.g.
445
+ hospital, physician pharmacy, dme provider) billed to a payer. This information
446
+ is usually provided in claims data.
447
+ :total_paid:
448
+ :type: Float
449
+ :comment:
450
+ "The total amount paid from all payers for the expenses of the service/device/drug.
451
+ This field is calculated using the following formula: paid_by_payer + paid_by_patient
452
+ + paid_by_primary. In claims data, this field is considered the calculated
453
+ field the payer expects the provider to get reimbursed for the service/device/drug
454
+ from the payer and from the patient, based on the payer's contractual obligations."
455
+ :paid_by_payer:
456
+ :type: Float
457
+ :comment:
458
+ "The amount paid by the Payer for the service/device/drug. In claims
459
+ data, generally there is one field representing the total payment from the
460
+ payer for the service/device/drug. However, this field could be a calculated
461
+ field if the source data provides separate payment information for the ingredient
462
+ cost and the dispensing fee. If the paid_ingredient_cost or paid_dispensing_fee
463
+ fields are populated with nonzero values, the paid_by_payer field is calculated
464
+ using the following formula: paid_ingredient_cost + paid_dispensing_fee. If
465
+ there is more than one Payer in the source data, several cost records indicate
466
+ that fact. The Payer reporting this reimbursement should be indicated under
467
+ the payer_plan_id field."
468
+ :paid_by_patient:
469
+ :type: Float
470
+ :comment:
471
+ "The total amount paid by the patient as a share of the expenses.
472
+ This field is most often used in claims data to report the contracted amount
473
+ the patient is responsible for reimbursing the provider for said service/device/drug.
474
+ This is a calculated field using the following formula: paid_patient_copay
475
+ + paid_patient_coinsurance + paid_patient_deductible. If the source data has
476
+ actual patient payments (e.g. the patient payment is not a derivative of the
477
+ payer claim and there is verification the patient paid an amount to the provider),
478
+ then the patient payment should have it's own cost record with a payer_plan_id
479
+ set to 0 to indicate the payer is actually the patient, and the actual patient
480
+ payment should be noted under the total_paid field. The paid_by_patient field
481
+ is only used for reporting a patient's responsibility reported on an insurance
482
+ claim."
483
+ :paid_patient_copay:
484
+ :type: Float
485
+ :comment:
486
+ The amount paid by the patient as a fixed contribution to the expenses.
487
+ paid_patient_copay does contribute to the paid_by_patient variable. The paid_patient_copay
488
+ field is only used for reporting a patient's copay amount reported on an insurance
489
+ claim.
490
+ :paid_patient_coinsurance:
491
+ :type: Float
492
+ :comment:
493
+ The amount paid by the patient as a joint assumption of risk. Typically,
494
+ this is a percentage of the expenses defined by the Payer Plan after the patient's
495
+ deductible is exceeded. paid_patient_coinsurance does contribute to the paid_by_patient
496
+ variable. The paid_patient_coinsurance field is only used for reporting a
497
+ patient's coinsurance amount reported on an insurance claim.
498
+ :paid_patient_deductible:
499
+ :type: Float
500
+ :comment:
501
+ The amount paid by the patient that is counted toward the deductible
502
+ defined by the Payer Plan. paid_patient_deductible does contribute to the
503
+ paid_by_patient variable. The paid_patient_deductible field is only used for
504
+ reporting a patient's deductible amount reported on an insurance claim.
505
+ :paid_by_primary:
506
+ :type: Float
507
+ :comment:
508
+ The amount paid by a primary Payer through the coordination of benefits.
509
+ paid_by_primary does contribute to the total_paid variable. The paid_by_primary
510
+ field is only used for reporting a patient's primary insurance payment amount
511
+ reported on the secondary payer insurance claim. If the source data has actual
512
+ primary insurance payments (e.g. the primary insurance payment is not a derivative
513
+ of the payer claim and there is verification another insurance company paid
514
+ an amount to the provider), then the primary insurance payment should have
515
+ it's own cost record with a payer_plan_id set to the applicable payer, and
516
+ the actual primary insurance payment should be noted under the paid_by_payer
517
+ field.
518
+ :paid_ingredient_cost:
519
+ :type: Float
520
+ :comment:
521
+ The amount paid by the Payer to a pharmacy for the drug, excluding
522
+ the amount paid for dispensing the drug. paid_ingredient_cost contributes
523
+ to the paid_by_payer field if this field is populated with a nonzero value.
524
+ :paid_dispensing_fee:
525
+ :type: Float
526
+ :comment:
527
+ The amount paid by the Payer to a pharmacy for dispensing a drug,
528
+ excluding the amount paid for the drug ingredient. paid_dispensing_fee contributes
529
+ to the paid_by_payer field if this field is populated with a nonzero value.
530
+ :information_period_id:
531
+ :type: :Bigint
532
+ :comment: FK reference to the [information_periods](#information_periods) table
533
+ :amount_allowed:
534
+ :type: Float
535
+ :comment:
536
+ "The contracted amount agreed between the payer and provider. This
537
+ information is generally available in claims data. This is similar to the
538
+ total_paid amount in that it shows what the payer expects the provider to
539
+ be reimbursed after the payer and patient pay. This differs from the total_paid
540
+ amount in that it is not a calculated field, but a field available directly
541
+ in claims data. Use case: This will capture non-covered services. Non-covered
542
+ services are indicated by an amount allowed and patient responsibility variables
543
+ (copay, coinsurance, deductible) will be equal $0 in the source data. This
544
+ means the patient is responsible for the total_charged value. The amount_allowed
545
+ field is payer specific and the payer should be indicated by the payer_plan_id
546
+ field."
547
+ :costs:
548
+ :columns:
549
+ :id:
550
+ :type: :Bigint
551
+ :primary_key: true
552
+ :comment: Surrogate key for record
553
+ :null: false
554
+ :context_id:
555
+ :type: :Bigint
556
+ :comment: FK reference to context table
557
+ :foreign_key: contexts
558
+ :null: false
559
+ :patient_id:
560
+ :type: :Bigint
561
+ :comment: FK reference to [patients](#patients) table
562
+ :foreign_key: patients
563
+ :null: false
564
+ :clinical_code_id:
565
+ :type: :Bigint
566
+ :comment:
567
+ FK reference to [clinical_codes](#clinical_codes) table to be used
568
+ if a specific code is the direct cause for the reimbursement
569
+ :foreign_key: clinical_codes
570
+ :currency_concept_id:
571
+ :type: :Bigint
572
+ :comment:
573
+ FK reference to [concepts](#concepts) table for the 3-letter code
574
+ used to delineate international currencies (e.g., USD = US Dollar)
575
+ :foreign_key: concepts
576
+ :null: false
577
+ :cost_base:
578
+ :type: String
579
+ :comment:
580
+ Defines the basis for the cost in the table (e.g., 2013 for a specific
581
+ cost-to-charge ratio, or a specific cost from an external cost
582
+ :null: false
583
+ :value:
584
+ :type: Float
585
+ :comment: Cost value
586
+ :null: false
587
+ :value_type_concept_id:
588
+ :type: :Bigint
589
+ :comment:
590
+ FK reference to [concepts](#concepts) table to concept that defines
591
+ the type of economic information in the value field (e.g., cost-to-charge
592
+ ratio, calculated cost, reported cost)
593
+ :foreign_key: concepts
594
+ :null: false
595
+ :addresses:
596
+ :columns:
597
+ :id:
598
+ :type: :Bigint
599
+ :primary_key: true
600
+ :comment: Surrogate key for record
601
+ :null: false
602
+ :address_1:
603
+ :type: String
604
+ :comment: Typically used for street address
605
+ :address_2:
606
+ :type: String
607
+ :comment:
608
+ Typically used for additional detail such as building, suite, floor,
609
+ etc.
610
+ :city:
611
+ :type: String
612
+ :comment: The city field as it appears in the source data
613
+ :state:
614
+ :type: String
615
+ :comment: The state field as it appears in the source data
616
+ :zip:
617
+ :type: String
618
+ :comment: The zip or postal code
619
+ :county:
620
+ :type: String
621
+ :comment: The county, if available
622
+ :census_tract:
623
+ :type: String
624
+ :comment: The census tract if available
625
+ :hsa:
626
+ :type: String
627
+ :comment:
628
+ The Health Service Area, if available (originally defined by the National
629
+ Center for Health Statistics)
630
+ :country:
631
+ :type: String
632
+ :comment: The country if necessary
633
+ :deaths:
634
+ :columns:
635
+ :id:
636
+ :type: :Bigint
637
+ :primary_key: true
638
+ :comment: Surrogate key for record
639
+ :null: false
640
+ :patient_id:
641
+ :type: :Bigint
642
+ :comment: FK reference to [patients](#patients) table
643
+ :foreign_key: patients
644
+ :null: false
645
+ :date:
646
+ :type: Date
647
+ :comment: Date of death (yyyy-mm-dd)
648
+ :null: false
649
+ :cause_concept_id:
650
+ :type: :Bigint
651
+ :comment:
652
+ FK reference to [concepts](#concepts) table for cause of death (typically
653
+ ICD-9 or ICD-10 code)
654
+ :foreign_key: concepts
655
+ :cause_type_concept_id:
656
+ :type: :Bigint
657
+ :comment:
658
+ FK reference to [concepts](#concepts) table for the type of cause
659
+ of death (e.g. primary, secondary, etc. )
660
+ :foreign_key: concepts
661
+ :practitioner_id:
662
+ :type: :Bigint
663
+ :comment: FK reference to [practitioners](#practitioners) table
664
+ :foreign_key: practitioners
665
+ :information_periods:
666
+ :columns:
667
+ :id:
668
+ :type: :Bigint
669
+ :primary_key: true
670
+ :comment: Surrogate key for record
671
+ :null: false
672
+ :patient_id:
673
+ :type: :Bigint
674
+ :comment: FK reference to [patients](#patients) table
675
+ :foreign_key: patients
676
+ :null: false
677
+ :start_date:
678
+ :type: Date
679
+ :comment: Start date of record (yyyy-mm-dd)
680
+ :null: false
681
+ :end_date:
682
+ :type: Date
683
+ :comment: End date of record (yyyy-mm-dd)
684
+ :null: false
685
+ :information_type_concept_id:
686
+ :type: :Bigint
687
+ :comment:
688
+ FK reference to [concepts](#concepts) table representing the information
689
+ type (e.g., insurance coverage, hospital data, up-to-standard date)
690
+ :foreign_key: concepts
691
+ :null: false
692
+ :concepts:
693
+ :columns:
694
+ :id:
695
+ :type: :Bigint
696
+ :primary_key: true
697
+ :comment: Surrogate key for record (this is the concept_id)
698
+ :null: false
699
+ :vocabulary_id:
700
+ :type: String
701
+ :comment:
702
+ FK reference to the vocabularies table for the vocabulary associated
703
+ with the concept (see OMOP or UMLS)
704
+ :foreign_key: vocabularies
705
+ :null: false
706
+ :concept_code:
707
+ :type: String
708
+ :comment:
709
+ Actual code as text string from the source vocabulary (e.g., "410.00"
710
+ for ICD-9)
711
+ :null: false
712
+ :concept_text:
713
+ :type: String
714
+ :comment: Text descriptor associated with the concept_code
715
+ :null: false
716
+ :vocabularies:
717
+ :columns:
718
+ :id:
719
+ :type: String
720
+ :primary_key: true
721
+ :comment: Short name of the vocabulary which acts as a natural key for record
722
+ :null: false
723
+ :omopv4_vocabulary_id:
724
+ :type: Integer
725
+ :comment: Old ID used in OMOPv4
726
+ :null: false
727
+ :vocabulary_name:
728
+ :type: String
729
+ :comment: Full name of the vocabulary
730
+ :null: false
731
+ :domain:
732
+ :type: String
733
+ :comment: Domain to which the majority of the vocabulary is assigned
734
+ :concepts_count:
735
+ :type: Integer
736
+ :comment:
737
+ Number of row in the [concepts](#concepts) table assigned to this
738
+ vocabulary
739
+ :is_clinical_vocabulary:
740
+ :type: TrueClass
741
+ :comment: Are concepts from this vocabulary stored in [clinical_codes](#clinical_codes)?
742
+ :mappings:
743
+ :columns:
744
+ :concept_1_id:
745
+ :type: :Bigint
746
+ :comment: FK reference to [concepts](#concepts) table for the source concept
747
+ :foreign_key: concepts
748
+ :null: false
749
+ :relationship_id:
750
+ :type: String
751
+ :comment: The type or nature of the relationship (e.g., "is_a")
752
+ :null: false
753
+ :concept_2_id:
754
+ :type: :Bigint
755
+ :comment: FK reference to [concepts](#concepts) table for the destination concept
756
+ :foreign_key: concepts
757
+ :null: false