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.
- checksums.yaml +5 -5
- data/CHANGELOG.md +228 -27
- data/LICENSE +21 -0
- data/README.md +28 -98
- data/bin/conceptql +2 -1
- data/bin/conceptql_utils +6 -0
- data/config/multiple_vocabularies.csv +4 -0
- data/config/provenance.yml +471 -436
- data/config/race.yml +50 -0
- data/config/vocabularies.csv +87 -0
- data/lib/conceptql/behaviors/code_lister.rb +23 -0
- data/lib/conceptql/behaviors/drugish.rb +13 -8
- data/lib/conceptql/behaviors/labish.rb +15 -9
- data/lib/conceptql/behaviors/metadatable.rb +102 -34
- data/lib/conceptql/behaviors/provenanceable.rb +15 -19
- data/lib/conceptql/behaviors/single_event.rb +11 -0
- data/lib/conceptql/behaviors/timeless.rb +11 -0
- data/lib/conceptql/behaviors/utilizable.rb +206 -0
- data/lib/conceptql/behaviors/windowable.rb +27 -0
- data/lib/conceptql/cli.rb +99 -134
- data/lib/conceptql/columnizer.rb +75 -0
- data/lib/conceptql/data_model/base.rb +462 -0
- data/lib/conceptql/data_model/gdm.rb +155 -0
- data/lib/conceptql/data_model/gdm_wide.rb +42 -0
- data/lib/conceptql/data_model/omopv4_plus.rb +12 -0
- data/lib/conceptql/data_model.rb +30 -0
- data/lib/conceptql/database.rb +195 -23
- data/lib/conceptql/date_adjuster.rb +57 -27
- data/lib/conceptql/diagram.rb +243 -0
- data/lib/conceptql/lexicon/lexicon_gdm.rb +47 -0
- data/lib/conceptql/lexicon/lexicon_no_db.rb +49 -0
- data/lib/conceptql/lexicon/lexicon_ohdsi.rb +63 -0
- data/lib/conceptql/lexicon/lexicon_strategy.rb +116 -0
- data/lib/conceptql/lexicon.rb +111 -0
- data/lib/conceptql/nodifier.rb +45 -15
- data/lib/conceptql/operators/after.rb +24 -21
- data/lib/conceptql/operators/any_overlap.rb +6 -6
- data/lib/conceptql/operators/before.rb +24 -16
- data/lib/conceptql/operators/binary_operator_operator.rb +52 -13
- data/lib/conceptql/operators/casting_operator.rb +24 -17
- data/lib/conceptql/operators/co_reported.rb +78 -9
- data/lib/conceptql/operators/concurrent_within.rb +29 -17
- data/lib/conceptql/operators/contains.rb +9 -9
- data/lib/conceptql/operators/count.rb +9 -9
- data/lib/conceptql/operators/date_range.rb +40 -18
- data/lib/conceptql/operators/death.rb +10 -2
- data/lib/conceptql/operators/dedup.rb +31 -0
- data/lib/conceptql/operators/during.rb +5 -12
- data/lib/conceptql/operators/episode.rb +146 -0
- data/lib/conceptql/operators/equal.rb +6 -3
- data/lib/conceptql/operators/ethnicity.rb +49 -0
- data/lib/conceptql/operators/except.rb +15 -20
- data/lib/conceptql/operators/filter.rb +20 -8
- data/lib/conceptql/operators/first.rb +14 -3
- data/lib/conceptql/operators/from.rb +33 -12
- data/lib/conceptql/operators/gender.rb +27 -11
- data/lib/conceptql/operators/hospice.rb +19 -0
- data/lib/conceptql/operators/hospitalization.rb +19 -0
- data/lib/conceptql/operators/information_periods.rb +36 -0
- data/lib/conceptql/operators/invalid.rb +4 -5
- data/lib/conceptql/operators/last.rb +14 -3
- data/lib/conceptql/operators/match.rb +91 -0
- data/lib/conceptql/operators/multiple_vocabularies.rb +172 -0
- data/lib/conceptql/operators/numeric.rb +52 -29
- data/lib/conceptql/operators/numeric_filter.rb +68 -0
- data/lib/conceptql/operators/occurrence.rb +133 -48
- data/lib/conceptql/operators/one_in_two_out.rb +198 -62
- data/lib/conceptql/operators/operator.rb +321 -408
- data/lib/conceptql/operators/pass_thru.rb +9 -5
- data/lib/conceptql/operators/person.rb +12 -2
- data/lib/conceptql/operators/person_filter.rb +5 -3
- data/lib/conceptql/operators/place_of_service_filter.rb +11 -15
- data/lib/conceptql/operators/provenance.rb +25 -36
- data/lib/conceptql/operators/provider_filter.rb +40 -14
- data/lib/conceptql/operators/race.rb +48 -7
- data/lib/conceptql/operators/read.rb +77 -58
- data/lib/conceptql/operators/recall.rb +20 -20
- data/lib/conceptql/operators/snf.rb +19 -0
- data/lib/conceptql/operators/sum.rb +23 -12
- data/lib/conceptql/operators/temporal_operator.rb +80 -54
- data/lib/conceptql/operators/time_window.rb +13 -15
- data/lib/conceptql/operators/trim_date.rb +71 -0
- data/lib/conceptql/operators/trim_date_end.rb +20 -40
- data/lib/conceptql/operators/trim_date_start.rb +20 -43
- data/lib/conceptql/operators/union.rb +59 -35
- data/lib/conceptql/operators/vocabulary.rb +151 -0
- data/lib/conceptql/paths.rb +41 -0
- data/lib/conceptql/query.rb +168 -46
- data/lib/conceptql/query_modifiers/gdm/admission_date_query_modifier.rb +46 -0
- data/lib/conceptql/query_modifiers/gdm/drug_query_modifier.rb +54 -0
- data/lib/conceptql/query_modifiers/gdm/lab_query_modifier.rb +57 -0
- data/lib/conceptql/query_modifiers/gdm/pos_query_modifier.rb +46 -0
- data/lib/conceptql/query_modifiers/gdm/provenance_query_modifier.rb +45 -0
- data/lib/conceptql/query_modifiers/gdm/provider_query_modifier.rb +53 -0
- data/lib/conceptql/query_modifiers/gdm_wide/admission_date_query_modifier.rb +42 -0
- data/lib/conceptql/query_modifiers/gdm_wide/drug_query_modifier.rb +52 -0
- data/lib/conceptql/query_modifiers/gdm_wide/lab_query_modifier.rb +55 -0
- data/lib/conceptql/query_modifiers/gdm_wide/pos_query_modifier.rb +37 -0
- data/lib/conceptql/query_modifiers/gdm_wide/provenance_query_modifier.rb +38 -0
- data/lib/conceptql/query_modifiers/omopv4_plus/admission_date_query_modifier.rb +45 -0
- data/lib/conceptql/query_modifiers/omopv4_plus/drug_query_modifier.rb +80 -0
- data/lib/conceptql/query_modifiers/omopv4_plus/pos_query_modifier.rb +47 -0
- data/lib/conceptql/query_modifiers/omopv4_plus/provenance_query_modifier.rb +45 -0
- data/lib/conceptql/query_modifiers/omopv4_plus/provider_query_modifier.rb +26 -0
- data/lib/conceptql/query_modifiers/query_modifier.rb +6 -2
- data/lib/conceptql/rdbms/duckdb.rb +21 -0
- data/lib/conceptql/rdbms/generic.rb +116 -0
- data/lib/conceptql/rdbms/postgres.rb +47 -0
- data/lib/conceptql/rdbms/spark.rb +18 -0
- data/lib/conceptql/rdbms.rb +22 -0
- data/lib/conceptql/scope.rb +353 -41
- data/lib/conceptql/utils.rb +70 -0
- data/lib/conceptql/utils_cli.rb +17 -0
- data/lib/conceptql/version.rb +3 -1
- data/lib/conceptql/visitors/metadata_extractor.rb +54 -0
- data/lib/conceptql/vocabularies/behaviors/costish.rb +24 -0
- data/lib/conceptql/vocabularies/behaviors/gdmish.rb +19 -0
- data/lib/conceptql/vocabularies/behaviors/omopish.rb +32 -0
- data/lib/conceptql/vocabularies/dynamic_vocabularies.rb +63 -0
- data/lib/conceptql/vocabularies/entry.rb +138 -0
- data/lib/conceptql/vocabularies/vocabulary_class_factory.rb +85 -0
- data/lib/conceptql/window/base.rb +26 -0
- data/lib/conceptql/window/date_range.rb +25 -0
- data/lib/conceptql/window/table.rb +116 -0
- data/lib/conceptql/window.rb +72 -0
- data/lib/conceptql.rb +53 -10
- data/lib/sequel/extensions/pg_ctas_explain.rb +22 -0
- data/lib/sequel/extensions/pg_vacuum_table.rb +23 -0
- data/schemas/gdm.yml +882 -0
- data/schemas/gdm_wide.yml +757 -0
- data/schemas/ohdsi_vocabs.yml +143 -0
- data/schemas/omopv4_plus.yml +729 -0
- data/schemas/omopv4_plus_more_ignorables.tsv +13 -0
- metadata +271 -2065
- data/.gitignore +0 -25
- data/Gemfile +0 -6
- data/Guardfile +0 -56
- data/LICENSE.txt +0 -22
- data/Rakefile +0 -35
- data/conceptql.gemspec +0 -31
- data/doc/ConceptQL Specification (alpha).pdf +0 -0
- data/doc/converter.rb +0 -33
- data/doc/diagram_0.png +0 -0
- data/doc/implementation_notes.md +0 -39
- data/doc/metadata.md +0 -89
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- data/doc/spec.md +0 -2258
- data/doc/spec.md.cql +0 -1930
- data/lib/conceptql/annotate_grapher.rb +0 -127
- data/lib/conceptql/fake_annotater.rb +0 -129
- data/lib/conceptql/knitter.rb +0 -221
- data/lib/conceptql/logger.rb +0 -10
- data/lib/conceptql/operators/complement.rb +0 -43
- data/lib/conceptql/operators/condition_occurrence_source_vocabulary_operator.rb +0 -34
- data/lib/conceptql/operators/condition_occurrence_source_vocabulary_operator_union.rb +0 -28
- data/lib/conceptql/operators/condition_type.rb +0 -79
- data/lib/conceptql/operators/cpt.rb +0 -28
- data/lib/conceptql/operators/cpt_or_hcpcs.rb +0 -27
- data/lib/conceptql/operators/drg.rb +0 -42
- data/lib/conceptql/operators/drug_type_concept.rb +0 -30
- data/lib/conceptql/operators/from_seer_visits.rb +0 -29
- data/lib/conceptql/operators/hcpcs.rb +0 -28
- data/lib/conceptql/operators/icd10.rb +0 -19
- data/lib/conceptql/operators/icd10_pcs.rb +0 -28
- data/lib/conceptql/operators/icd9.rb +0 -19
- data/lib/conceptql/operators/icd9_procedure.rb +0 -28
- data/lib/conceptql/operators/intersect.rb +0 -39
- data/lib/conceptql/operators/loinc.rb +0 -28
- data/lib/conceptql/operators/medcode.rb +0 -17
- data/lib/conceptql/operators/medcode_procedure.rb +0 -28
- data/lib/conceptql/operators/ndc.rb +0 -32
- data/lib/conceptql/operators/observation_by_enttype.rb +0 -32
- data/lib/conceptql/operators/observation_period.rb +0 -32
- data/lib/conceptql/operators/overlapped_by.rb +0 -26
- data/lib/conceptql/operators/overlaps.rb +0 -21
- data/lib/conceptql/operators/place_of_service_code.rb +0 -31
- data/lib/conceptql/operators/procedure_occurrence.rb +0 -27
- data/lib/conceptql/operators/prodcode.rb +0 -32
- data/lib/conceptql/operators/revenue_code.rb +0 -40
- data/lib/conceptql/operators/rxnorm.rb +0 -28
- data/lib/conceptql/operators/snomed.rb +0 -25
- data/lib/conceptql/operators/source_vocabulary_operator.rb +0 -88
- data/lib/conceptql/operators/standard_vocabulary_operator.rb +0 -66
- data/lib/conceptql/operators/started_by.rb +0 -23
- data/lib/conceptql/operators/to_seer_visits.rb +0 -29
- data/lib/conceptql/operators/visit_occurrence.rb +0 -32
- data/lib/conceptql/operators/vocabulary_operator.rb +0 -45
- data/lib/conceptql/query_modifiers/drug_query_modifier.rb +0 -45
- data/lib/conceptql/query_modifiers/pos_query_modifier.rb +0 -31
- data/lib/conceptql/sql_formatter.rb +0 -22
- data/test/all.rb +0 -3
- data/test/all_operations_test.rb +0 -45
- data/test/code_list_test.rb +0 -23
- data/test/data/omopv4/care_site.csv +0 -0
- data/test/data/omopv4/cohort.csv +0 -0
- data/test/data/omopv4/condition_era.csv +0 -0
- data/test/data/omopv4/condition_occurrence.csv +0 -34044
- data/test/data/omopv4/death.csv +0 -1
- data/test/data/omopv4/drug_cost.csv +0 -0
- data/test/data/omopv4/drug_era.csv +0 -0
- data/test/data/omopv4/drug_exposure.csv +0 -2
- data/test/data/omopv4/location.csv +0 -0
- data/test/data/omopv4/observation.csv +0 -2
- data/test/data/omopv4/observation_period.csv +0 -1
- data/test/data/omopv4/organization.csv +0 -0
- data/test/data/omopv4/payer_plan_period.csv +0 -0
- data/test/data/omopv4/person.csv +0 -250
- data/test/data/omopv4/procedure_cost.csv +0 -0
- data/test/data/omopv4/procedure_occurrence.csv +0 -35099
- data/test/data/omopv4/provider.csv +0 -0
- data/test/data/omopv4/visit_occurrence.csv +0 -14931
- data/test/data/omopv4_plus/care_site.csv +0 -0
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- data/test/statements/one_in_two_out/count_same_as_1 +0 -11
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@@ -0,0 +1,757 @@
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---
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:patients:
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:columns:
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:id:
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:type: :Bigint
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:primary_key: true
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:comment: Surrogate key for record
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:null: false
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:gender_concept_id:
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:type: :Bigint
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:comment:
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FK reference to the [concepts](#concepts) table for the unique gender
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of the patient
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:foreign_key: concepts
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:birth_date:
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:type: Date
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:comment: Date of birth (yyyy-mm-dd)
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:race_concept_id:
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:type: :Bigint
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:comment:
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FK reference to the [concepts](#concepts) table for the unique race
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of the patient
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:foreign_key: concepts
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:ethnicity_concept_id:
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:type: :Bigint
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:comment:
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FK reference to the [concepts](#concepts) table for the ethnicity
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of the patient
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:foreign_key: concepts
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:address_id:
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:type: :Bigint
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:comment:
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33
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+
FK reference to the place of residency for the patient in the location
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table, where the detailed address information is stored
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:foreign_key: addresses
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:practitioner_id:
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:type: :Bigint
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:comment:
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FK reference to the primary care practitioner the patient is seeing
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in the [practitioners](#practitioners) table
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:foreign_key: practitioners
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:patient_id_source_value:
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:type: String
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|
+
: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
|