conceptql 0.2.0 → 0.3.0
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- checksums.yaml +4 -4
- data/.gitignore +2 -0
- data/CHANGELOG.md +32 -104
- data/Gemfile +2 -0
- data/README.md +43 -21
- data/Rakefile +34 -0
- data/conceptql.gemspec +3 -4
- data/config/provenance.yml +454 -0
- data/doc/converter.rb +33 -0
- data/doc/metadata.md +89 -0
- data/doc/spec.md +1775 -861
- data/doc/spec.md.cql +1930 -0
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- data/doc/spec/ff7d5b5573d09bd7c4cdd3aeda124d18bf82ec46673a62881b399a75d69f3f53.png +0 -0
- data/lib/conceptql.rb +21 -1
- data/lib/conceptql/annotate_grapher.rb +127 -0
- data/lib/conceptql/behaviors/drugish.rb +12 -0
- data/lib/conceptql/behaviors/labish.rb +13 -0
- data/lib/conceptql/behaviors/metadatable.rb +156 -71
- data/lib/conceptql/behaviors/provenanceable.rb +30 -0
- data/lib/conceptql/cli.rb +81 -37
- data/lib/conceptql/database.rb +42 -0
- data/lib/conceptql/date_adjuster.rb +22 -4
- data/lib/conceptql/fake_annotater.rb +129 -0
- data/lib/conceptql/knitter.rb +221 -0
- data/lib/conceptql/nodifier.rb +34 -23
- data/lib/conceptql/operators/after.rb +20 -3
- data/lib/conceptql/operators/any_overlap.rb +3 -1
- data/lib/conceptql/operators/before.rb +19 -3
- data/lib/conceptql/operators/binary_operator_operator.rb +24 -20
- data/lib/conceptql/operators/casting_operator.rb +39 -31
- data/lib/conceptql/operators/co_reported.rb +42 -0
- data/lib/conceptql/operators/complement.rb +21 -16
- data/lib/conceptql/operators/concurrent_within.rb +57 -0
- data/lib/conceptql/operators/condition_occurrence_source_vocabulary_operator.rb +34 -0
- data/lib/conceptql/operators/condition_occurrence_source_vocabulary_operator_union.rb +28 -0
- data/lib/conceptql/operators/condition_type.rb +12 -4
- data/lib/conceptql/operators/contains.rb +6 -2
- data/lib/conceptql/operators/count.rb +10 -2
- data/lib/conceptql/operators/cpt.rb +5 -2
- data/lib/conceptql/operators/cpt_or_hcpcs.rb +27 -0
- data/lib/conceptql/operators/date_range.rb +20 -8
- data/lib/conceptql/operators/death.rb +4 -2
- data/lib/conceptql/operators/drg.rb +42 -0
- data/lib/conceptql/operators/drug_type_concept.rb +11 -2
- data/lib/conceptql/operators/during.rb +4 -2
- data/lib/conceptql/operators/equal.rb +4 -1
- data/lib/conceptql/operators/except.rb +16 -4
- data/lib/conceptql/operators/filter.rb +6 -3
- data/lib/conceptql/operators/first.rb +3 -1
- data/lib/conceptql/operators/from.rb +32 -5
- data/lib/conceptql/operators/from_seer_visits.rb +11 -5
- data/lib/conceptql/operators/gender.rb +9 -2
- data/lib/conceptql/operators/hcpcs.rb +5 -2
- data/lib/conceptql/operators/icd10.rb +6 -15
- data/lib/conceptql/operators/icd10_pcs.rb +28 -0
- data/lib/conceptql/operators/icd9.rb +6 -15
- data/lib/conceptql/operators/icd9_procedure.rb +5 -2
- data/lib/conceptql/operators/intersect.rb +15 -10
- data/lib/conceptql/operators/invalid.rb +36 -0
- data/lib/conceptql/operators/last.rb +3 -1
- data/lib/conceptql/operators/loinc.rb +5 -2
- data/lib/conceptql/operators/medcode.rb +5 -16
- data/lib/conceptql/operators/medcode_procedure.rb +3 -2
- data/lib/conceptql/operators/ndc.rb +5 -2
- data/lib/conceptql/operators/numeric.rb +30 -11
- data/lib/conceptql/operators/observation_by_enttype.rb +5 -2
- data/lib/conceptql/operators/observation_period.rb +6 -4
- data/lib/conceptql/operators/occurrence.rb +47 -11
- data/lib/conceptql/operators/one_in_two_out.rb +96 -33
- data/lib/conceptql/operators/operator.rb +628 -95
- data/lib/conceptql/operators/overlapped_by.rb +8 -5
- data/lib/conceptql/operators/overlaps.rb +7 -5
- data/lib/conceptql/operators/pass_thru.rb +12 -2
- data/lib/conceptql/operators/person.rb +7 -5
- data/lib/conceptql/operators/person_filter.rb +5 -1
- data/lib/conceptql/operators/place_of_service_code.rb +12 -5
- data/lib/conceptql/operators/place_of_service_filter.rb +47 -0
- data/lib/conceptql/operators/procedure_occurrence.rb +4 -2
- data/lib/conceptql/operators/prodcode.rb +5 -2
- data/lib/conceptql/operators/provenance.rb +66 -0
- data/lib/conceptql/operators/provider_filter.rb +36 -0
- data/lib/conceptql/operators/race.rb +11 -4
- data/lib/conceptql/operators/read.rb +149 -0
- data/lib/conceptql/operators/recall.rb +42 -7
- data/lib/conceptql/operators/revenue_code.rb +40 -0
- data/lib/conceptql/operators/rxnorm.rb +5 -1
- data/lib/conceptql/operators/snomed.rb +3 -2
- data/lib/conceptql/operators/source_vocabulary_operator.rb +44 -14
- data/lib/conceptql/operators/standard_vocabulary_operator.rb +36 -15
- data/lib/conceptql/operators/started_by.rb +2 -1
- data/lib/conceptql/operators/sum.rb +7 -1
- data/lib/conceptql/operators/temporal_operator.rb +75 -9
- data/lib/conceptql/operators/time_window.rb +13 -23
- data/lib/conceptql/operators/to_seer_visits.rb +6 -1
- data/lib/conceptql/operators/trim_date_end.rb +20 -12
- data/lib/conceptql/operators/trim_date_start.rb +22 -12
- data/lib/conceptql/operators/union.rb +39 -2
- data/lib/conceptql/operators/visit_occurrence.rb +5 -3
- data/lib/conceptql/operators/vocabulary_operator.rb +45 -0
- data/lib/conceptql/query.rb +68 -22
- data/lib/conceptql/query_modifiers/drug_query_modifier.rb +45 -0
- data/lib/conceptql/query_modifiers/pos_query_modifier.rb +31 -0
- data/lib/conceptql/query_modifiers/query_modifier.rb +16 -0
- data/lib/conceptql/scope.rb +169 -31
- data/lib/conceptql/sql_formatter.rb +22 -0
- data/lib/conceptql/version.rb +1 -1
- data/test/all.rb +3 -0
- data/test/all_operations_test.rb +45 -0
- data/test/code_list_test.rb +23 -0
- 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 +34044 -0
- data/test/data/omopv4/death.csv +1 -0
- 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 +2 -0
- data/test/data/omopv4/location.csv +0 -0
- data/test/data/omopv4/observation.csv +2 -0
- data/test/data/omopv4/observation_period.csv +1 -0
- data/test/data/omopv4/organization.csv +0 -0
- data/test/data/omopv4/payer_plan_period.csv +0 -0
- data/test/data/omopv4/person.csv +250 -0
- data/test/data/omopv4/procedure_cost.csv +0 -0
- data/test/data/omopv4/procedure_occurrence.csv +35099 -0
- data/test/data/omopv4/provider.csv +0 -0
- data/test/data/omopv4/visit_occurrence.csv +14931 -0
- data/test/data/omopv4_plus/care_site.csv +0 -0
- data/test/data/omopv4_plus/cohort.csv +0 -0
- data/test/data/omopv4_plus/concept.csv +352 -0
- data/test/data/omopv4_plus/condition_era.csv +0 -0
- data/test/data/omopv4_plus/condition_occurrence.csv +46673 -0
- data/test/data/omopv4_plus/death.csv +9 -0
- data/test/data/omopv4_plus/drug_cost.csv +13921 -0
- data/test/data/omopv4_plus/drug_era.csv +0 -0
- data/test/data/omopv4_plus/drug_exposure.csv +13921 -0
- data/test/data/omopv4_plus/headers/care_site.csv +1 -0
- data/test/data/omopv4_plus/headers/cohort.csv +1 -0
- data/test/data/omopv4_plus/headers/concept.csv +1 -0
- data/test/data/omopv4_plus/headers/condition_era.csv +1 -0
- data/test/data/omopv4_plus/headers/condition_occurrence.csv +1 -0
- data/test/data/omopv4_plus/headers/death.csv +1 -0
- data/test/data/omopv4_plus/headers/drug_cost.csv +1 -0
- data/test/data/omopv4_plus/headers/drug_era.csv +1 -0
- data/test/data/omopv4_plus/headers/drug_exposure.csv +1 -0
- data/test/data/omopv4_plus/headers/location.csv +1 -0
- data/test/data/omopv4_plus/headers/observation.csv +1 -0
- data/test/data/omopv4_plus/headers/observation_period.csv +1 -0
- data/test/data/omopv4_plus/headers/organization.csv +1 -0
- data/test/data/omopv4_plus/headers/payer_plan_period.csv +1 -0
- data/test/data/omopv4_plus/headers/person.csv +1 -0
- data/test/data/omopv4_plus/headers/procedure_cost.csv +1 -0
- data/test/data/omopv4_plus/headers/procedure_occurrence.csv +1 -0
- data/test/data/omopv4_plus/headers/provider.csv +1 -0
- data/test/data/omopv4_plus/headers/source_to_concept_map.csv +1 -0
- data/test/data/omopv4_plus/headers/visit_occurrence.csv +1 -0
- data/test/data/omopv4_plus/headers/vocabulary.csv +1 -0
- data/test/data/omopv4_plus/location.csv +0 -0
- data/test/data/omopv4_plus/observation.csv +0 -0
- data/test/data/omopv4_plus/observation_period.csv +147 -0
- data/test/data/omopv4_plus/organization.csv +736 -0
- data/test/data/omopv4_plus/payer_plan_period.csv +808 -0
- data/test/data/omopv4_plus/person.csv +250 -0
- data/test/data/omopv4_plus/procedure_cost.csv +20123 -0
- data/test/data/omopv4_plus/procedure_occurrence.csv +27273 -0
- data/test/data/omopv4_plus/provider.csv +10193 -0
- data/test/data/omopv4_plus/source_to_concept_map.csv +285 -0
- data/test/data/omopv4_plus/visit_occurrence.csv +45125 -0
- data/test/data/omopv4_plus/vocabulary.csv +60 -0
- data/test/db.rb +15 -0
- data/test/db_setup.rb +408 -0
- data/test/db_teardown.rb +33 -0
- data/test/fake_annotater_test.rb +31 -0
- data/test/helper.rb +129 -0
- data/test/knitter/conceptql.md.cql +39 -0
- data/test/knitter/conceptql.md.expect +43 -0
- data/test/knitter/empty.md.cql +0 -0
- data/test/knitter/except.md.cql +13 -0
- data/test/knitter/except.md.expect +14 -0
- data/test/knitter/fake.md.cql +10 -0
- data/test/knitter/fake.md.expect +13 -0
- data/test/knitter/many.md.cql +7 -0
- data/test/knitter/many.md.expect +14 -0
- data/test/knitter/no_conceptql.md.cql +36 -0
- data/test/knitter/title.md.cql +12 -0
- data/test/knitter/title.md.expect +15 -0
- data/test/knitter/union.md.cql +11 -0
- data/test/knitter/union.md.expect +14 -0
- data/test/knitter_test.rb +69 -0
- data/test/query_test.rb +36 -0
- data/test/results/omopv4/after/anno_1 +25 -0
- data/test/results/omopv4/after/anno_2 +48 -0
- data/test/results/omopv4/after/anno_3 +34 -0
- data/test/results/omopv4/after/anno_4 +60 -0
- data/test/results/omopv4/after/anno_5 +68 -0
- data/test/results/omopv4/after/anno_6 +60 -0
- data/test/results/omopv4/after/crit_at_least +7 -0
- data/test/results/omopv4/after/crit_basic +32 -0
- data/test/results/omopv4/after/crit_occurrences +12 -0
- data/test/results/omopv4/after/crit_within +6 -0
- data/test/results/omopv4/any_overlap/crit_basic1 +15 -0
- data/test/results/omopv4/any_overlap/crit_basic2 +15 -0
- data/test/results/omopv4/any_overlap/crit_occurrences1 +2 -0
- data/test/results/omopv4/any_overlap/crit_occurrences2 +15 -0
- data/test/results/omopv4/any_overlap/crit_within +8 -0
- data/test/results/omopv4/before/crit_at_least +6 -0
- data/test/results/omopv4/before/crit_basic1 +48 -0
- data/test/results/omopv4/before/crit_basic2 +7 -0
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- data/test/results/omopv4/before/crit_within +18 -0
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- data/test/statements/complex/anno_1 +29 -0
- data/test/statements/complex/crit_1 +278 -0
- data/test/statements/complex/crit_2 +43 -0
- data/test/statements/complex/crit_3 +54 -0
- data/test/statements/complex/crit_4 +17 -0
- data/test/statements/complex/crit_5 +17 -0
- data/test/statements/complex/crit_6 +20 -0
- data/test/statements/complex/crit_7 +14 -0
- data/test/statements/complex/crit_out_of_order_ctes +39 -0
- data/test/statements/complex/scanno_1 +1508 -0
- data/test/statements/concurrent_within/crit_icd9 +11 -0
- data/test/statements/concurrent_within/crit_icd9_and_place_of_service +15 -0
- data/test/statements/concurrent_within/crit_negative_start +15 -0
- data/test/statements/condition_type/anno_icd9 +7 -0
- data/test/statements/condition_type/count_condition_era +4 -0
- data/test/statements/condition_type/count_condition_era_30_day_window +4 -0
- data/test/statements/condition_type/count_ehr_problem_list +4 -0
- data/test/statements/condition_type/count_era_0 +4 -0
- data/test/statements/condition_type/count_inpatient +4 -0
- data/test/statements/condition_type/count_inpatient_detail +4 -0
- data/test/statements/condition_type/count_inpatient_header +4 -0
- data/test/statements/condition_type/count_inpatient_header_2 +4 -0
- data/test/statements/condition_type/count_inpatient_header_3 +4 -0
- data/test/statements/condition_type/count_inpatient_header_4 +4 -0
- data/test/statements/condition_type/count_inpatient_header_5 +4 -0
- data/test/statements/condition_type/count_inpatient_outpatient_detail +5 -0
- data/test/statements/condition_type/count_inpatient_primary +4 -0
- data/test/statements/condition_type/count_inpatient_primary_or_first +4 -0
- data/test/statements/condition_type/count_outpatient +4 -0
- data/test/statements/condition_type/count_outpatient_detail +4 -0
- data/test/statements/condition_type/count_outpatient_header +4 -0
- data/test/statements/condition_type/count_outpatient_primary +4 -0
- data/test/statements/condition_type/count_primary +4 -0
- data/test/statements/contains/crit_1 +16 -0
- data/test/statements/contains/crit_2 +16 -0
- data/test/statements/contains/crit_3 +16 -0
- data/test/statements/count/anno_multiple_upstreams +11 -0
- data/test/statements/count/anno_no_upstream1 +3 -0
- data/test/statements/count/anno_no_upstream2 +4 -0
- data/test/statements/count/crit_icd9_ndc +15 -0
- data/test/statements/count/crit_ndc +11 -0
- data/test/statements/count/crit_person +7 -0
- data/test/statements/cpt/anno_icd9_upstream +7 -0
- data/test/statements/cpt/anno_invalid_code +5 -0
- data/test/statements/cpt/count_1 +4 -0
- data/test/statements/cpt/crit_1 +4 -0
- data/test/statements/cpt/scanno_1 +4 -0
- data/test/statements/cpt_or_hcpcs/anno_bad_format +7 -0
- data/test/statements/cpt_or_hcpcs/count_1 +5 -0
- data/test/statements/cpt_or_hcpcs/crit_1 +5 -0
- data/test/statements/date_range/anno_1 +7 -0
- data/test/statements/date_range/anno_extra_argument +8 -0
- data/test/statements/date_range/anno_invalid_argument +7 -0
- data/test/statements/date_range/anno_missing_argument1 +6 -0
- data/test/statements/date_range/anno_missing_argument2 +6 -0
- data/test/statements/date_range/anno_no_upstreams +11 -0
- data/test/statements/date_range/count_1 +7 -0
- data/test/statements/date_range/count_2 +7 -0
- data/test/statements/death/anno_multiple_upstreams +10 -0
- data/test/statements/death/anno_no_upstreams +4 -0
- data/test/statements/death/crit_basic +3 -0
- data/test/statements/death/crit_person +7 -0
- data/test/statements/drug_type_concept/anno_has_upstreams +8 -0
- data/test/statements/drug_type_concept/anno_no_arguments +3 -0
- data/test/statements/drug_type_concept/crit_basic1 +4 -0
- data/test/statements/drug_type_concept/crit_basic2 +4 -0
- data/test/statements/during/crit_1 +16 -0
- data/test/statements/during/crit_2 +16 -0
- data/test/statements/equal/crit_1 +17 -0
- data/test/statements/equal/crit_2 +21 -0
- data/test/statements/except/anno_1 +13 -0
- data/test/statements/except/anno_2 +14 -0
- data/test/statements/except/count_complex +31 -0
- data/test/statements/except/crit_412_cpt +13 -0
- data/test/statements/except/crit_412_inpatient +13 -0
- data/test/statements/filter/crit_1 +15 -0
- data/test/statements/first/anno_argument +4 -0
- data/test/statements/first/anno_no_upstream +3 -0
- data/test/statements/first/crit_cpt +7 -0
- data/test/statements/first/crit_icd9 +7 -0
- data/test/statements/first/crit_union +14 -0
- data/test/statements/from/anno_has_upstreams +7 -0
- data/test/statements/from/anno_multiple_arguments +5 -0
- data/test/statements/from_seer_visits/anno_multiple_upstreams +17 -0
- data/test/statements/from_seer_visits/anno_no_upstream +3 -0
- data/test/statements/from_seer_visits/crit_1 +10 -0
- data/test/statements/from_seer_visits/crit_2 +11 -0
- data/test/statements/from_seer_visits/crit_3 +11 -0
- data/test/statements/from_seer_visits/crit_4 +12 -0
- data/test/statements/gender/anno_has_upstreams +7 -0
- data/test/statements/gender/crit_male +4 -0
- data/test/statements/hcpcs/anno_bad_format +6 -0
- data/test/statements/hcpcs/crit_A0382 +4 -0
- data/test/statements/icd10/anno_bad_format +5 -0
- data/test/statements/icd10/anno_has_upstreams +7 -0
- data/test/statements/icd10/crit_1 +4 -0
- data/test/statements/icd10pcs/anno_bad_format +6 -0
- data/test/statements/icd10pcs/anno_has_upstreams +7 -0
- data/test/statements/icd10pcs/crit_1 +4 -0
- data/test/statements/icd9/anno_empty_label +7 -0
- data/test/statements/icd9/anno_invalid_code +4 -0
- data/test/statements/icd9/anno_valid_code +4 -0
- data/test/statements/icd9/crit_1 +4 -0
- data/test/statements/icd9_procedure/crit_1 +4 -0
- data/test/statements/intersect/anno_412_inpatient +11 -0
- data/test/statements/intersect/anno_has_arguments +4 -0
- data/test/statements/intersect/anno_no_upstream +3 -0
- data/test/statements/intersect/crit_412_inpatient +11 -0
- data/test/statements/intersect/crit_412_male +11 -0
- data/test/statements/intersect/crit_complex +19 -0
- data/test/statements/invalid/anno_bad_op +13 -0
- data/test/statements/invalid/scanno_1 +7 -0
- data/test/statements/last/crit_icd9 +7 -0
- data/test/statements/loinc/crit_basic +4 -0
- data/test/statements/ndc/crit_basic +4 -0
- data/test/statements/ndc/results_1 +4 -0
- data/test/statements/numeric/anno_multiple_upstreams +11 -0
- data/test/statements/numeric/num_values_1 +4 -0
- data/test/statements/numeric/num_values_2 +8 -0
- data/test/statements/numeric/num_values_3 +8 -0
- data/test/statements/observation_period/anno_has_arguments +8 -0
- data/test/statements/observation_period/anno_multiple_upstreams +11 -0
- data/test/statements/observation_period/count_all_periods +4 -0
- data/test/statements/observation_period/crit_female +7 -0
- data/test/statements/observation_period/crit_icd9 +7 -0
- data/test/statements/observation_period/crit_male +7 -0
- data/test/statements/occurrence/anno_no_upstream +3 -0
- data/test/statements/occurrence/count_412_410 +17 -0
- data/test/statements/occurrence/crit_1 +8 -0
- data/test/statements/occurrence/crit_2 +11 -0
- data/test/statements/occurrence/crit_3 +11 -0
- data/test/statements/one_in_two_out/anno_has_arguments +8 -0
- data/test/statements/one_in_two_out/anno_multiple_upstreams +15 -0
- data/test/statements/one_in_two_out/anno_no_upstream +7 -0
- data/test/statements/one_in_two_out/count_1 +10 -0
- data/test/statements/one_in_two_out/count_same_as_1 +11 -0
- data/test/statements/one_in_two_out/crit_hcpcs +10 -0
- data/test/statements/one_in_two_out/crit_icd9 +11 -0
- data/test/statements/one_in_two_out/results_1 +9 -0
- data/test/statements/one_in_two_out/results_2 +9 -0
- data/test/statements/overlapped_by/crit_1 +16 -0
- data/test/statements/overlapped_by/crit_2 +16 -0
- data/test/statements/overlapped_by/crit_3 +16 -0
- data/test/statements/overlapped_by/crit_4 +16 -0
- data/test/statements/overlaps/crit_1 +16 -0
- data/test/statements/overlaps/crit_2 +16 -0
- data/test/statements/overlaps/crit_3 +16 -0
- data/test/statements/overlaps/crit_4 +16 -0
- data/test/statements/person/anno_has_arguments +4 -0
- data/test/statements/person/anno_multiple_upstreams +11 -0
- data/test/statements/person/count_2 +3 -0
- data/test/statements/person/crit_1 +7 -0
- data/test/statements/person_filter/count_1 +20 -0
- data/test/statements/person_filter/crit_1 +20 -0
- data/test/statements/person_filter/crit_2 +13 -0
- data/test/statements/person_filter/crit_3 +13 -0
- data/test/statements/person_filter/crit_4 +13 -0
- data/test/statements/place_of_service_code/anno_has_upstreams +8 -0
- data/test/statements/place_of_service_code/anno_no_arguments +3 -0
- data/test/statements/place_of_service_code/crit_basic +4 -0
- data/test/statements/place_of_service_filter/anno_1 +8 -0
- data/test/statements/procedure_occurrence/anno_has_arguments +8 -0
- data/test/statements/procedure_occurrence/anno_multiple_upstreams +11 -0
- data/test/statements/procedure_occurrence/count_gender +7 -0
- data/test/statements/procedure_occurrence/count_icd9 +7 -0
- data/test/statements/procedure_occurrence/count_started_by +19 -0
- data/test/statements/provenance/anno_1 +8 -0
- data/test/statements/provenance/anno_bad_keyword +10 -0
- data/test/statements/provenance/count_1 +8 -0
- data/test/statements/provenance/count_2 +8 -0
- data/test/statements/provider_filter/anno_1 +10 -0
- data/test/statements/race/anno_1 +8 -0
- data/test/statements/race/anno_2 +3 -0
- data/test/statements/race/crit_1 +4 -0
- data/test/statements/read/anno_1 +4 -0
- data/test/statements/read/crit_1 +8 -0
- data/test/statements/recall/anno_1 +16 -0
- data/test/statements/recall/anno_2 +18 -0
- data/test/statements/recall/anno_3 +4 -0
- data/test/statements/recall/anno_4 +3 -0
- data/test/statements/recall/anno_5 +5 -0
- data/test/statements/recall/anno_6 +107 -0
- data/test/statements/recall/crit_1 +17 -0
- data/test/statements/recall/crit_2 +14 -0
- data/test/statements/recall/crit_3 +16 -0
- data/test/statements/recall/crit_cte_1 +17 -0
- data/test/statements/recall/crit_cte_2 +17 -0
- data/test/statements/recall/crit_nested_perm_0 +28 -0
- data/test/statements/revenue_code/crit_1 +4 -0
- data/test/statements/revenue_code/crit_basic +4 -0
- data/test/statements/revenue_code/domains_1 +4 -0
- data/test/statements/revenue_code/domains_drg100 +4 -0
- data/test/statements/rxnorm/crit_1 +4 -0
- data/test/statements/snomed/crit_1 +4 -0
- data/test/statements/started_by/crit_1 +16 -0
- data/test/statements/started_by/crit_2 +16 -0
- data/test/statements/started_by/crit_3 +16 -0
- data/test/statements/sum/anno_1 +3 -0
- data/test/statements/sum/anno_2 +8 -0
- data/test/statements/sum/num_1 +11 -0
- data/test/statements/sum/num_2 +15 -0
- data/test/statements/sum/num_3 +7 -0
- data/test/statements/time_window/anno_1 +7 -0
- data/test/statements/time_window/anno_2 +11 -0
- data/test/statements/time_window/anno_3 +11 -0
- data/test/statements/time_window/anno_4 +12 -0
- data/test/statements/time_window/anno_5 +15 -0
- data/test/statements/time_window/crit_1 +11 -0
- data/test/statements/time_window/crit_2 +11 -0
- data/test/statements/time_window/crit_3 +11 -0
- data/test/statements/time_window/crit_4 +11 -0
- data/test/statements/trim_date_end/crit_1 +16 -0
- data/test/statements/trim_date_end/crit_2 +16 -0
- data/test/statements/trim_date_end/crit_3 +16 -0
- data/test/statements/trim_date_end/crit_at_least +17 -0
- data/test/statements/trim_date_end/crit_occurrences_1 +17 -0
- data/test/statements/trim_date_end/crit_occurrences_2 +17 -0
- data/test/statements/trim_date_end/crit_within +17 -0
- data/test/statements/trim_date_start/crit_1 +16 -0
- data/test/statements/trim_date_start/crit_2 +16 -0
- data/test/statements/trim_date_start/crit_3 +16 -0
- data/test/statements/trim_date_start/crit_at_least +17 -0
- data/test/statements/trim_date_start/crit_occurrences_1 +17 -0
- data/test/statements/trim_date_start/crit_occurrences_2 +17 -0
- data/test/statements/trim_date_start/crit_within +17 -0
- data/test/statements/union/anno_1 +11 -0
- data/test/statements/union/anno_2 +18 -0
- data/test/statements/union/anno_3 +3 -0
- data/test/statements/union/anno_4 +4 -0
- data/test/statements/union/anno_5 +7 -0
- data/test/statements/union/anno_6 +10 -0
- data/test/statements/union/count_1 +11 -0
- data/test/statements/union/count_2 +11 -0
- data/test/statements/union/count_3 +15 -0
- data/test/statements/union/count_4 +18 -0
- data/test/statements/union/count_5 +18 -0
- data/test/statements/union/scanno_1 +3 -0
- data/test/statements/union/scanno_2 +18 -0
- data/test/statements/visit_occurrence/anno_1 +11 -0
- data/test/statements/visit_occurrence/anno_2 +8 -0
- data/test/statements/visit_occurrence/crit_1 +7 -0
- data/test/statements/visit_occurrence/crit_2 +7 -0
- data/test/statements/visit_occurrence/crit_3 +3 -0
- metadata +2016 -150
- data/lib/conceptql/behaviors/debuggable.rb +0 -70
- data/lib/conceptql/behaviors/dottable.rb +0 -103
- data/lib/conceptql/behaviors/preppable.rb +0 -20
- data/lib/conceptql/converter.rb +0 -65
- data/lib/conceptql/debugger.rb +0 -48
- data/lib/conceptql/fake_grapher.rb +0 -20
- data/lib/conceptql/graph.rb +0 -52
- data/lib/conceptql/graph_nodifier.rb +0 -203
- data/lib/conceptql/operators/concept.rb +0 -70
- data/lib/conceptql/operators/snomed_condition.rb +0 -26
- data/lib/conceptql/operators/visit.rb +0 -15
- data/lib/conceptql/tree.rb +0 -53
- data/lib/conceptql/utils/temp_table.rb +0 -72
- data/spec/conceptql/behaviors/dottable_spec.rb +0 -99
- data/spec/conceptql/converter_spec.rb +0 -51
- data/spec/conceptql/date_adjuster_spec.rb +0 -68
- data/spec/conceptql/operators/after_spec.rb +0 -16
- data/spec/conceptql/operators/before_spec.rb +0 -16
- data/spec/conceptql/operators/casting_operator_spec.rb +0 -68
- data/spec/conceptql/operators/complement_spec.rb +0 -15
- data/spec/conceptql/operators/concept_spec.rb +0 -40
- data/spec/conceptql/operators/condition_type_spec.rb +0 -128
- data/spec/conceptql/operators/contains_spec.rb +0 -19
- data/spec/conceptql/operators/cpt_spec.rb +0 -29
- data/spec/conceptql/operators/date_range_spec.rb +0 -33
- data/spec/conceptql/operators/death_spec.rb +0 -10
- data/spec/conceptql/operators/during_spec.rb +0 -30
- data/spec/conceptql/operators/except_spec.rb +0 -15
- data/spec/conceptql/operators/first_spec.rb +0 -35
- data/spec/conceptql/operators/from_spec.rb +0 -13
- data/spec/conceptql/operators/gender_spec.rb +0 -27
- data/spec/conceptql/operators/hcpcs_spec.rb +0 -29
- data/spec/conceptql/operators/icd10_spec.rb +0 -34
- data/spec/conceptql/operators/icd9_procedure_spec.rb +0 -29
- data/spec/conceptql/operators/icd9_spec.rb +0 -34
- data/spec/conceptql/operators/intersect_spec.rb +0 -28
- data/spec/conceptql/operators/last_spec.rb +0 -36
- data/spec/conceptql/operators/loinc_spec.rb +0 -29
- data/spec/conceptql/operators/medcode_procedure_spec.rb +0 -34
- data/spec/conceptql/operators/medcode_spec.rb +0 -34
- data/spec/conceptql/operators/observation_period_spec.rb +0 -10
- data/spec/conceptql/operators/occurrence_spec.rb +0 -87
- data/spec/conceptql/operators/overlapped_by_spec.rb +0 -32
- data/spec/conceptql/operators/overlaps_spec.rb +0 -21
- data/spec/conceptql/operators/person_filter_spec.rb +0 -15
- data/spec/conceptql/operators/person_spec.rb +0 -10
- data/spec/conceptql/operators/place_of_service_code_spec.rb +0 -24
- data/spec/conceptql/operators/procedure_occurrence_spec.rb +0 -10
- data/spec/conceptql/operators/prodcode_spec.rb +0 -35
- data/spec/conceptql/operators/query_double.rb +0 -20
- data/spec/conceptql/operators/query_double_spec.rb +0 -7
- data/spec/conceptql/operators/race_spec.rb +0 -21
- data/spec/conceptql/operators/rxnorm_spec.rb +0 -29
- data/spec/conceptql/operators/snomed_spec.rb +0 -29
- data/spec/conceptql/operators/source_vocabulary_operator_spec.rb +0 -35
- data/spec/conceptql/operators/standard_vocabulary_operator_spec.rb +0 -35
- data/spec/conceptql/operators/started_by_spec.rb +0 -22
- data/spec/conceptql/operators/temporal_operator_spec.rb +0 -51
- data/spec/conceptql/operators/time_window_spec.rb +0 -77
- data/spec/conceptql/operators/union_spec.rb +0 -21
- data/spec/conceptql/operators/visit_occurrence_spec.rb +0 -10
- data/spec/conceptql/query_spec.rb +0 -22
- data/spec/conceptql/tree_spec.rb +0 -50
- data/spec/doubles/stream_for_casting_double.rb +0 -9
- data/spec/doubles/stream_for_occurrence_double.rb +0 -25
- data/spec/doubles/stream_for_temporal_double.rb +0 -6
- data/spec/spec_helper.rb +0 -102
data/test/db_teardown.rb
ADDED
@@ -0,0 +1,33 @@
|
|
1
|
+
require_relative 'db'
|
2
|
+
|
3
|
+
if DB.opts[:database] && DB.opts[:database] !~ /test/
|
4
|
+
$stderr.puts <<END
|
5
|
+
The test database name doesn't include the substring "test".
|
6
|
+
Exiting now to avoid potential modification of non-test database.
|
7
|
+
Please rename your test database to include the substring "test".
|
8
|
+
END
|
9
|
+
exit 1
|
10
|
+
end
|
11
|
+
|
12
|
+
tables = [
|
13
|
+
:care_site,
|
14
|
+
:cohort,
|
15
|
+
:location,
|
16
|
+
:provider,
|
17
|
+
:organization,
|
18
|
+
:person,
|
19
|
+
:condition_era,
|
20
|
+
:condition_occurrence,
|
21
|
+
:death,
|
22
|
+
:drug_era,
|
23
|
+
:drug_exposure,
|
24
|
+
:observation,
|
25
|
+
:observation_period,
|
26
|
+
:payer_plan_period,
|
27
|
+
:procedure_occurrence,
|
28
|
+
:visit_occurrence,
|
29
|
+
:drug_cost,
|
30
|
+
:procedure_cost
|
31
|
+
]
|
32
|
+
|
33
|
+
DB.drop_table?(*tables.reverse)
|
@@ -0,0 +1,31 @@
|
|
1
|
+
require_relative 'helper'
|
2
|
+
require 'conceptql/fake_annotater'
|
3
|
+
|
4
|
+
describe ConceptQL::FakeAnnotater do
|
5
|
+
it "should work correctly for operators with single values" do
|
6
|
+
ConceptQL::FakeAnnotater.new([:icd9, '412']).annotate.must_equal [:icd9, "412", {:annotation=>{:counts=>{:condition_occurrence=>{}}}}]
|
7
|
+
end
|
8
|
+
|
9
|
+
it "should work correctly for operators with multiple values" do
|
10
|
+
ConceptQL::FakeAnnotater.new([:icd9, '411', '412']).annotate.must_equal [:icd9, "411", "412", {:annotation=>{:counts=>{:condition_occurrence=>{}}}}]
|
11
|
+
end
|
12
|
+
|
13
|
+
it "should work correctly for operators with hash arguments" do
|
14
|
+
ConceptQL::FakeAnnotater.new(
|
15
|
+
[:any_overlap,
|
16
|
+
{:left=>[:icd9, "412"],
|
17
|
+
:right=>[:date_range, {:start=>"2010-01-01", :end=>"2010-12-31"}]}]
|
18
|
+
).annotate.must_equal([:any_overlap,
|
19
|
+
{:left=>[:icd9, "412", {:annotation=>{:counts=>{:condition_occurrence=>{}}}}],
|
20
|
+
:right=>[:date_range, {:start=>"2010-01-01", :end=>"2010-12-31", :annotation=>{:counts=>{:date=>{}}}}], :annotation=>{:counts=>{:condition_occurrence=>{}}}}
|
21
|
+
])
|
22
|
+
end
|
23
|
+
|
24
|
+
it "should work correctly for operators with upsreams" do
|
25
|
+
ConceptQL::FakeAnnotater.new([:union, [:icd9, "412"], [:cpt, "99214"]]).annotate.must_equal([:union,
|
26
|
+
[:icd9, "412", {:annotation=>{:counts=>{:condition_occurrence=>{}}}}],
|
27
|
+
[:cpt, "99214", {:annotation=>{:counts=>{:procedure_occurrence=>{}}}}],
|
28
|
+
{:annotation=>{:counts=>{:condition_occurrence=>{}, :procedure_occurrence=>{}}}}
|
29
|
+
])
|
30
|
+
end
|
31
|
+
end
|
data/test/helper.rb
ADDED
@@ -0,0 +1,129 @@
|
|
1
|
+
ENV['DATA_MODEL'] ||= 'omopv4_plus'
|
2
|
+
|
3
|
+
require_relative 'db'
|
4
|
+
|
5
|
+
if ENV['COVERAGE']
|
6
|
+
require 'coverage'
|
7
|
+
require 'simplecov'
|
8
|
+
|
9
|
+
ENV.delete('COVERAGE')
|
10
|
+
SimpleCov.instance_exec do
|
11
|
+
start do
|
12
|
+
add_filter "/test/"
|
13
|
+
add_group('Missing'){|src| src.covered_percent < 100}
|
14
|
+
add_group('Covered'){|src| src.covered_percent == 100}
|
15
|
+
yield self if block_given?
|
16
|
+
end
|
17
|
+
end
|
18
|
+
end
|
19
|
+
|
20
|
+
$: << "lib"
|
21
|
+
require 'conceptql'
|
22
|
+
require 'minitest/spec'
|
23
|
+
require 'minitest/autorun'
|
24
|
+
|
25
|
+
require 'logger'
|
26
|
+
require 'pp'
|
27
|
+
require 'fileutils'
|
28
|
+
|
29
|
+
CDB = ConceptQL::Database.new(DB, :data_model=>ENV['DATA_MODEL'].to_sym)
|
30
|
+
DB.extension :error_sql
|
31
|
+
|
32
|
+
#ENV["OVERWRITE_CONCEPTQL_TEST_RESULTS"] = '1'
|
33
|
+
|
34
|
+
class Minitest::Spec
|
35
|
+
def annotate(test_name, statement=nil)
|
36
|
+
load_check(test_name, statement){|statement| query(statement).annotate}
|
37
|
+
end
|
38
|
+
|
39
|
+
def scope_annotate(test_name, statement=nil)
|
40
|
+
load_check(test_name, statement){|statement| query(statement).scope_annotate}
|
41
|
+
end
|
42
|
+
|
43
|
+
def domains(test_name, statement=nil)
|
44
|
+
load_check(test_name, statement){|statement| query(statement).domains}
|
45
|
+
end
|
46
|
+
|
47
|
+
def results(test_name, statement=nil)
|
48
|
+
load_check(test_name, statement){|stmt| query(stmt).all}
|
49
|
+
end
|
50
|
+
|
51
|
+
def query(statement)
|
52
|
+
CDB.query(statement)
|
53
|
+
end
|
54
|
+
|
55
|
+
def dataset(statement)
|
56
|
+
statement = query(statement) unless statement.is_a?(ConceptQL::Query)
|
57
|
+
statement.query
|
58
|
+
end
|
59
|
+
|
60
|
+
def criteria_ids(test_name, statement=nil)
|
61
|
+
load_check(test_name, statement){|statement| hash_groups(statement, :criterion_domain, :criterion_id)}
|
62
|
+
end
|
63
|
+
|
64
|
+
# If no statement is passed, this function loads the statement from the specified test
|
65
|
+
# file. If a statement is passed, it is written to the file.
|
66
|
+
def load_statement(test_name, statement)
|
67
|
+
path = "test/statements/#{test_name}"
|
68
|
+
if statement
|
69
|
+
FileUtils.mkdir_p(File.dirname(path))
|
70
|
+
File.write(path, JSON.pretty_generate(statement))
|
71
|
+
statement
|
72
|
+
else
|
73
|
+
JSON.parse(File.read(path))
|
74
|
+
end
|
75
|
+
end
|
76
|
+
|
77
|
+
def check_output(test_name, results)
|
78
|
+
path = "test/results/#{ENV["DATA_MODEL"]}/#{test_name}"
|
79
|
+
|
80
|
+
if ENV["OVERWRITE_CONCEPTQL_TEST_RESULTS"]
|
81
|
+
save_results(path, results)
|
82
|
+
end
|
83
|
+
|
84
|
+
expected = begin
|
85
|
+
File.read(path)
|
86
|
+
rescue Errno::ENOENT
|
87
|
+
save_results(path, [])
|
88
|
+
"[]"
|
89
|
+
end
|
90
|
+
|
91
|
+
JSON.parse(results.to_json).must_equal(JSON.parse(expected))
|
92
|
+
results
|
93
|
+
end
|
94
|
+
|
95
|
+
def save_results(path, results)
|
96
|
+
FileUtils.mkdir_p(File.dirname(path))
|
97
|
+
File.write(path, JSON.pretty_generate(results))
|
98
|
+
end
|
99
|
+
|
100
|
+
def numeric_values(test_name, statement=nil)
|
101
|
+
load_check(test_name, statement){|statement| hash_groups(statement, :criterion_domain, :value_as_number)}
|
102
|
+
end
|
103
|
+
|
104
|
+
def criteria_counts(test_name, statement=nil)
|
105
|
+
load_check(test_name, statement){|statement| query(statement).query.from_self.group_and_count(:criterion_domain).to_hash(:criterion_domain, :count)}
|
106
|
+
end
|
107
|
+
|
108
|
+
def optimized_criteria_counts(test_name, statement=nil)
|
109
|
+
load_check(test_name, statement){|statement| query(statement).optimized.query.from_self.group_and_count(:criterion_domain).to_hash(:criterion_domain, :count)}
|
110
|
+
end
|
111
|
+
|
112
|
+
def hash_groups(statement, key, value)
|
113
|
+
dataset(statement).from_self.distinct.order(*value).to_hash_groups(key, value)
|
114
|
+
rescue
|
115
|
+
puts $!.sql if $!.respond_to?(:sql)
|
116
|
+
raise
|
117
|
+
end
|
118
|
+
|
119
|
+
def load_check(test_name, statement)
|
120
|
+
check_output(test_name, yield(load_statement(test_name, statement)))
|
121
|
+
end
|
122
|
+
|
123
|
+
def log
|
124
|
+
DB.loggers << Logger.new($stdout)
|
125
|
+
yield
|
126
|
+
ensure
|
127
|
+
DB.loggers.clear
|
128
|
+
end
|
129
|
+
end
|
@@ -0,0 +1,39 @@
|
|
1
|
+
# ConceptQL Specification
|
2
|
+
|
3
|
+
ConceptQL (pronounced concept-Q-L) is a high-level language that allows researchers to unambiguously define their research algorithms.
|
4
|
+
|
5
|
+
## Motivation for ConceptQL
|
6
|
+
|
7
|
+
Outcomes Insights intends to build a vast library of research algorithms and apply those algorithms to large databases of claims data. Early into building the library, we realized we had to overcome two major issues:
|
8
|
+
|
9
|
+
1. Methods sections of research papers commonly use natural language to specify the criteria used to build cohorts from a claims database.
|
10
|
+
- Algorithms defined in natural language are often imprecise, open to multiple interpretations, and generally difficult to reproduce.
|
11
|
+
- Researchers could benefit from a language that removes the ambiguity of natural language while increasing the reproducibility of their research algorithms.
|
12
|
+
1. Querying against claims databases is often difficult.
|
13
|
+
- Hand-coding algorithms to extract cohorts from datasets is time-consuming, error-prone, and opaque.
|
14
|
+
- Researchers could benefit from a language that allows algorithms to be defined at a high-level and then gets translated into the appropriate queries against a database.
|
15
|
+
|
16
|
+
We developed ConceptQL to address these two issues.
|
17
|
+
|
18
|
+
We are writing a tool that can read research algorithms defined in ConceptQL. The tool can create a diagram for the algorithm which makes it easy to visualize and understand. The tool can also translate the algorithm into a SQL query which runs against data structured in [OMOP's Common Data Model (CDM)](http://omop.org/CDM). The purpose of the CDM is to standardize the format and content of observational data, so standardized applications, tools and methods can be applied to them.
|
19
|
+
|
20
|
+
For instance, using ConceptQL we can take a statement that looks like this:
|
21
|
+
|
22
|
+
```JSON
|
23
|
+
|
24
|
+
["icd9", "412"]
|
25
|
+
|
26
|
+
```
|
27
|
+
|
28
|
+
And generate a diagram that looks like this:
|
29
|
+
|
30
|
+
```ConceptQL
|
31
|
+
[
|
32
|
+
"icd9",
|
33
|
+
"412"
|
34
|
+
]
|
35
|
+
```
|
36
|
+
|
37
|
+
And generate SQL that looks like this:
|
38
|
+
|
39
|
+
|
@@ -0,0 +1,43 @@
|
|
1
|
+
# ConceptQL Specification
|
2
|
+
|
3
|
+
ConceptQL (pronounced concept-Q-L) is a high-level language that allows researchers to unambiguously define their research algorithms.
|
4
|
+
|
5
|
+
## Motivation for ConceptQL
|
6
|
+
|
7
|
+
Outcomes Insights intends to build a vast library of research algorithms and apply those algorithms to large databases of claims data. Early into building the library, we realized we had to overcome two major issues:
|
8
|
+
|
9
|
+
1. Methods sections of research papers commonly use natural language to specify the criteria used to build cohorts from a claims database.
|
10
|
+
- Algorithms defined in natural language are often imprecise, open to multiple interpretations, and generally difficult to reproduce.
|
11
|
+
- Researchers could benefit from a language that removes the ambiguity of natural language while increasing the reproducibility of their research algorithms.
|
12
|
+
1. Querying against claims databases is often difficult.
|
13
|
+
- Hand-coding algorithms to extract cohorts from datasets is time-consuming, error-prone, and opaque.
|
14
|
+
- Researchers could benefit from a language that allows algorithms to be defined at a high-level and then gets translated into the appropriate queries against a database.
|
15
|
+
|
16
|
+
We developed ConceptQL to address these two issues.
|
17
|
+
|
18
|
+
We are writing a tool that can read research algorithms defined in ConceptQL. The tool can create a diagram for the algorithm which makes it easy to visualize and understand. The tool can also translate the algorithm into a SQL query which runs against data structured in [OMOP's Common Data Model (CDM)](http://omop.org/CDM). The purpose of the CDM is to standardize the format and content of observational data, so standardized applications, tools and methods can be applied to them.
|
19
|
+
|
20
|
+
For instance, using ConceptQL we can take a statement that looks like this:
|
21
|
+
|
22
|
+
```JSON
|
23
|
+
|
24
|
+
["icd9", "412"]
|
25
|
+
|
26
|
+
```
|
27
|
+
|
28
|
+
And generate a diagram that looks like this:
|
29
|
+
|
30
|
+
```JSON
|
31
|
+
|
32
|
+
["icd9","412"]
|
33
|
+
|
34
|
+
```
|
35
|
+
|
36
|
+
![](conceptql/f6b4fc31703cfb6327bbbd4614af8bb72da6d39fa3d53ada63a70157f2fad80e.png)
|
37
|
+
|
38
|
+
| person_id | criterion_id | criterion_domain | start_date | end_date | source_value |
|
39
|
+
| --------- | ------------ | ---------------- | ---------- | -------- | ------------ |
|
40
|
+
|
41
|
+
And generate SQL that looks like this:
|
42
|
+
|
43
|
+
|
File without changes
|
@@ -0,0 +1,14 @@
|
|
1
|
+
Before
|
2
|
+
|
3
|
+
```JSON
|
4
|
+
|
5
|
+
["except",{"left":["icd9","412"],"right":["condition_type","inpatient_header"]}]
|
6
|
+
|
7
|
+
```
|
8
|
+
|
9
|
+
![](except/84a61ca4ef2f20eb5dad5fa998b5183a4df982df4cdb1623cd21e4cefa445aee.png)
|
10
|
+
|
11
|
+
| person_id | criterion_id | criterion_domain | start_date | end_date | source_value |
|
12
|
+
| --------- | ------------ | ---------------- | ---------- | -------- | ------------ |
|
13
|
+
|
14
|
+
After
|
@@ -0,0 +1,13 @@
|
|
1
|
+
And generate a diagram that looks like this:
|
2
|
+
|
3
|
+
```JSON
|
4
|
+
|
5
|
+
["vsac","999"]
|
6
|
+
|
7
|
+
```
|
8
|
+
|
9
|
+
![](fake/b4c4be0eabd9bc7d878a4b8a77bbf2e172d579c9ed915729278cec58f6d4d9f0.png)
|
10
|
+
|
11
|
+
```No Results. Statement is experimental.```
|
12
|
+
|
13
|
+
And generate SQL that looks like this:
|
@@ -0,0 +1,7 @@
|
|
1
|
+
Before
|
2
|
+
|
3
|
+
```ConceptQL
|
4
|
+
["icd9","400", "401", "402", "403", "404", "405", "406", "407", "408", "409", "410", "411", "412", "413", "414", "415", "416", "417", "418", "419", "420", "421", "422", "423", "424", "425", "426", "427", "428", "429", "430", "431", "432", "433", "434", "435", "436", "437", "438", "439", "440", "441", "442", "443", "444", "445", "446", "447", "448", "449", "450", "451", "452", "453", "454", "455", "456", "457", "458", "459", "460", "461", "462", "463", "464", "465", "466", "467", "468", "469", "470", "471", "472", "473", "474", "475", "476", "477", "478", "479", "480", "481", "482", "483", "484", "485", "486", "487", "488", "489", "490", "491", "492", "493", "494", "495", "496", "497", "498", "499", "500"]
|
5
|
+
```
|
6
|
+
|
7
|
+
After
|
@@ -0,0 +1,14 @@
|
|
1
|
+
Before
|
2
|
+
|
3
|
+
```JSON
|
4
|
+
|
5
|
+
["icd9","400","401","402","403","404","405","406","407","408","409","410","411","412","413","414","415","416","417","418","419","420","421","422","423","424","425","426","427","428","429","430","431","432","433","434","435","436","437","438","439","440","441","442","443","444","445","446","447","448","449","450","451","452","453","454","455","456","457","458","459","460","461","462","463","464","465","466","467","468","469","470","471","472","473","474","475","476","477","478","479","480","481","482","483","484","485","486","487","488","489","490","491","492","493","494","495","496","497","498","499","500"]
|
6
|
+
|
7
|
+
```
|
8
|
+
|
9
|
+
![](many/8359883e5cbbe12c401f10dcae82a370e7c28c3b2d6a820dd202f5d6ba8da824.png)
|
10
|
+
|
11
|
+
| person_id | criterion_id | criterion_domain | start_date | end_date | source_value |
|
12
|
+
| --------- | ------------ | ---------------- | ---------- | -------- | ------------ |
|
13
|
+
|
14
|
+
After
|
@@ -0,0 +1,36 @@
|
|
1
|
+
# ConceptQL Specification
|
2
|
+
|
3
|
+
ConceptQL (pronounced concept-Q-L) is a high-level language that allows researchers to unambiguously define their research algorithms.
|
4
|
+
|
5
|
+
## Motivation for ConceptQL
|
6
|
+
|
7
|
+
Outcomes Insights intends to build a vast library of research algorithms and apply those algorithms to large databases of claims data. Early into building the library, we realized we had to overcome two major issues:
|
8
|
+
|
9
|
+
1. Methods sections of research papers commonly use natural language to specify the criteria used to build cohorts from a claims database.
|
10
|
+
- Algorithms defined in natural language are often imprecise, open to multiple interpretations, and generally difficult to reproduce.
|
11
|
+
- Researchers could benefit from a language that removes the ambiguity of natural language while increasing the reproducibility of their research algorithms.
|
12
|
+
1. Querying against claims databases is often difficult.
|
13
|
+
- Hand-coding algorithms to extract cohorts from datasets is time-consuming, error-prone, and opaque.
|
14
|
+
- Researchers could benefit from a language that allows algorithms to be defined at a high-level and then gets translated into the appropriate queries against a database.
|
15
|
+
|
16
|
+
We developed ConceptQL to address these two issues.
|
17
|
+
|
18
|
+
We are writing a tool that can read research algorithms defined in ConceptQL. The tool can create a diagram for the algorithm which makes it easy to visualize and understand. The tool can also translate the algorithm into a SQL query which runs against data structured in [OMOP's Common Data Model (CDM)](http://omop.org/CDM). The purpose of the CDM is to standardize the format and content of observational data, so standardized applications, tools and methods can be applied to them.
|
19
|
+
|
20
|
+
For instance, using ConceptQL we can take a statement that looks like this:
|
21
|
+
|
22
|
+
```JSON
|
23
|
+
["icd9", "412"]
|
24
|
+
```
|
25
|
+
|
26
|
+
And generate a diagram that looks like this:
|
27
|
+
|
28
|
+
```ConceptQ
|
29
|
+
[
|
30
|
+
"icd9",
|
31
|
+
"412"
|
32
|
+
]
|
33
|
+
```
|
34
|
+
|
35
|
+
And generate SQL that looks like this:
|
36
|
+
|
@@ -0,0 +1,15 @@
|
|
1
|
+
And generate a diagram that looks like this:
|
2
|
+
|
3
|
+
foo bar
|
4
|
+
|
5
|
+
```JSON
|
6
|
+
|
7
|
+
["icd9","999"]
|
8
|
+
|
9
|
+
```
|
10
|
+
|
11
|
+
![foo bar](title/2b0dbefc0c25a7c5047159f06e1027e38d7a1d5ab7c1ee701439cb13f95e7707.png)
|
12
|
+
|
13
|
+
```No Results found.```
|
14
|
+
|
15
|
+
And generate SQL that looks like this:
|