The core study aims to provide the following features:
FHIR US Core V4 Profile data - For resources that are supported by Cumulus, we attempt to extract all required/extensible fields from a FHIR dataset, if presentFlattened FHIR resources - The core study provided flattened tables from nested FHIR resources, making queries easier to construct without having to worry about the nuances of conditional unnesting against potentially missing dataSummary Exports - The core study will provide some basic count data across the entire cohort that you’ve processed via ETL, which can be useful as a verification step for validating the integrity of the data you’re extracting from your EHR system If you are authoring a study, and are focused only on clinical analysis (i.e. you aren’t working on data quality/data governance issues), we strongly recommend you use the core study as the starting point for your own work. See Creating Studies for more information.
Unless otherwise noted, column names correspond to a FHIR path relative to the resource table in question, with resources delineated by underscores. So, ‘category_code’ in the Condition table would correspond to the code element inside of the category element of the Condition resource.
Common exceptions to this rule:
cnt is a Cumulus specific notation for a column that contains counts of resources.age_at_visit is calculated from a Patient’s birthDate and the period.start.day of an Encounterpostalcode_3 is calculated from a Patient’s address.postalCodeThe Encounter resource includes several elements from the referenced Patient (gender, postalcode_3, and the US Core race and ethnicity extensions) that are commonly used in informatics analysis Fields that contain date values are presented by different rounding methods (day, week, month, year) for convenience for various binning strategies We construct *_ref fields from a resource’s base id field (i.e creating a Patient/123456 patient_ref field from an id of 123456), to make it easier to join data with reference fields in other resources. The core tables include all FHIR required/must support fields noted in the [FHIR resource profiles(http://hl7.org/fhir/us/core/STU4/artifacts.html#structures-resource-profiles). Additionally, there are fields that are useful to informatics analysis that are commonly available from EHRs, but are not guaranteed to be populated, so consult with your research partners if you are authoring a study using some of these data elements.
If not all the resources for a given encounter are loaded into the database yet, that encounter is considered “incomplete” and may be left out of the core tables.
You can see which encounters were ignored as incomplete by examining the core__incomplete_encounters table which holds the ID of all incomplete encounters.
Usually, you can resolve this by running the ETL process again for the encounters, making sure to include all associated resources.
The core study includes several fields that are considered optional by US Core. Such fields are not even marked as “Must Support” in US Core and are defined in the base FHIR spec only.
These are included due to their general utility in clinical informatics studies. In practice, we have found that this data is usually present in FHIR exports from EHR systems, but note that it is not guaranteed that a study relying on these fields will work across multiple institutions without some additional work.
Per resource, the optional fields are as follows:
AllergyIntolerance type category criticality encounter recordedDate reaction.substance reaction.severity Condition DocumentReference Encounter Observation - laboratory Observation - vital signs encounter valueCodeableConcept interpretation The core__observation table is currently deprecated, and will be removed in a future version. When possible, use one of the targeted profile tables (labs, vital signs) instead.
Column Type Description cnt bigint category varchar recordeddate_month varchar code_display varchar reaction_manifestation_display varchar
Column Type Description cnt bigint count category_code varchar Encounter Code (Healthcare Setting) recordeddate_month varchar Month condition recorded code_display varchar Condition code
Column Type Description cnt bigint Count type_display varchar Type of Document (display) author_month varchar Month document was authored class_display varchar Encounter Code (Healthcare Setting)
Column Type Description cnt bigint Count class_display varchar Encounter Code (Healthcare Setting) type_display varchar Encounter Type servicetype_display varchar Encounter Service priority_display varchar Encounter Priority
Column Type Description cnt bigint Count class_display varchar Encounter Code (Healthcare Setting) type_display varchar Encounter Type servicetype_display varchar Encounter Service priority_display varchar Encounter Priority period_start_month varchar Month encounter recorded
Column Type Description cnt bigint Count period_start_month varchar Month encounter recorded class_display varchar Encounter Code (Healthcare Setting age_at_visit varchar Patient Age at Encounter gender varchar Biological sex at birth race_display varchar Patient reported race ethnicity_display varchar Patient reported ethnicity
Column Type Description cnt bigint Count class_display varchar Encounter Code (Healthcare Setting) priority_display varchar Encounter Priority period_start_month varchar Month encounter recorded
Column Type Description cnt bigint Count class_display varchar Encounter Code (Healthcare Setting) servicetype_display varchar Encounter Service period_start_month varchar Month encounter recorded
Column Type Description cnt bigint class_display varchar type_display varchar period_start_month varchar
Column Type Description cnt bigint Count status varchar Perscribing event state intent varchar Medication order kind authoredon_month varchar Month medication request issued medication_display varchar Medication Name
Column Type Description cnt bigint Count effectivedatetime_month varchar Month of lab result observation_code varchar Lab result coding valuecodeableconcept_display varchar Lab result display text class_display varchar Encounter Code (Healthcare Setting)
Column Type Description cnt bigint Count gender varchar Biological sex at birth race_display varchar Patient reported race ethnicity_display varchar Patient reported ethnicity
Column Type Description id varchar allergyintolerance_ref varchar clinicalstatus_code varchar verificationstatus_code varchar type varchar category varchar criticality varchar code_code varchar code_system varchar code_display varchar patient_ref varchar encounter_ref varchar recordeddate date recordeddate_week date recordeddate_month date recordeddate_year date reaction_row bigint reaction_substance_code varchar reaction_substance_system varchar reaction_substance_display varchar reaction_manifestation_code varchar reaction_manifestation_system varchar reaction_manifestation_display varchar reaction_severity varchar
Column Type Description id varchar category_code varchar category_system varchar category_display varchar code varchar system varchar code_display varchar subject_ref varchar encounter_ref varchar condition_ref varchar recordeddate date recordeddate_week date recordeddate_month date recordeddate_year date clinicalstatus_code varchar verificationstatus_code varchar
Column Type Description id varchar code varchar system varchar display varchar userselected boolean
Column Type Description id varchar code varchar system varchar display varchar userselected boolean
Column Type Description id varchar row bigint code varchar system varchar display varchar userselected boolean
Column Type Description id varchar code varchar system varchar display varchar userselected boolean
Column Type Description id varchar code varchar system varchar display varchar userselected boolean
Column Type Description id varchar status varchar type_code varchar type_system varchar type_display varchar category_code varchar docstatus varchar date date author_day date author_week date author_month date author_year date format_code varchar subject_ref varchar encounter_ref varchar documentreference_ref varchar
Column Type Description id varchar row bigint code varchar system varchar display varchar userselected boolean
Column Type Description id varchar code varchar system varchar display varchar
Column Type Description id varchar code varchar system varchar display varchar userselected boolean
Column Type Description from_system varchar(3) from_code varchar(14) analyte varchar(28) code_system varchar(16) code varchar(7) display varchar(33)
Column Type Description id varchar status varchar class_code varchar(6) class_display varchar(21) type_code varchar type_system varchar type_display varchar servicetype_code varchar servicetype_system varchar servicetype_display varchar priority_code varchar priority_system varchar priority_display varchar reasoncode_code varchar reasoncode_system varchar reasoncode_display varchar dischargedisposition_code varchar dischargedisposition_system varchar dischargedisposition_display varchar age_at_visit bigint gender varchar race_display varchar ethnicity_display varchar postalcode_3 varchar period_start_day date period_end_day date period_start_week date period_start_month date period_start_year date subject_ref varchar encounter_ref varchar
Column Type Description id varchar row bigint code varchar system varchar display varchar userselected boolean
Column Type Description id varchar row bigint code varchar system varchar display varchar userselected boolean
Column Type Description id varchar row bigint code varchar system varchar display varchar userselected boolean
Column Type Description id varchar row bigint code varchar system varchar display varchar userselected boolean
Column Type Description id varchar row bigint code varchar system varchar display varchar userselected boolean
Column Type Description code varchar(6) display varchar(21)
Column Type Description code_system varchar(6) uri varchar(37)
Column Type Description expected varchar(5) found varchar(5)
Column Type Description resource varchar(25) uri varchar(73)
Column Type Description id varchar
Column Type Description study_name varchar library_version varchar status varchar event_time timestamp(3) message varchar
Column Type Description id varchar row bigint code varchar system varchar display varchar userselected boolean
Column Type Description id varchar status varchar intent varchar category_code varchar category_system varchar category_display varchar reportedboolean boolean reported_ref varchar subject_ref varchar encounter_ref varchar authoredon date authoredon_month date medication_code varchar medication_system varchar medication_display varchar
Column Type Description id varchar row bigint code varchar system varchar display varchar userselected boolean
Column Type Description id varchar row bigint code varchar system varchar display varchar userselected boolean contained_id varchar resource_type varchar
Column Type Description id varchar code varchar system varchar display varchar userselected boolean
Column Type Description min_date date max_date date
Column Type Description data_package_version integer
Column Type Description id varchar category_code varchar category_system varchar status varchar observation_code varchar observation_system varchar interpretation_code varchar interpretation_system varchar interpretation_display varchar effectivedatetime_day date effectivedatetime_week date effectivedatetime_month date effectivedatetime_year date valuecodeableconcept_code varchar valuecodeableconcept_system varchar valuecodeableconcept_display varchar valuequantity_value double valuequantity_comparator varchar valuequantity_unit varchar valuequantity_system varchar valuequantity_code varchar valuestring varchar dataabsentreason_code varchar dataabsentreason_system varchar dataabsentreason_display varchar subject_ref varchar encounter_ref varchar observation_ref varchar
Column Type Description id varchar row bigint code varchar system varchar display varchar userselected boolean
Column Type Description id varchar row bigint code varchar system varchar display varchar userselected boolean
Column Type Description id varchar row bigint code varchar system varchar display varchar userselected boolean
Column Type Description id varchar row bigint code varchar system varchar display varchar userselected boolean
Column Type Description id varchar row bigint value double comparator varchar unit varchar system varchar code varchar
Column Type Description id varchar row bigint code varchar system varchar display varchar userselected boolean
Column Type Description id varchar code varchar system varchar display varchar userselected boolean
Column Type Description id varchar row bigint code varchar system varchar display varchar userselected boolean
Column Type Description id varchar row bigint code varchar system varchar display varchar userselected boolean
Column Type Description id varchar code varchar system varchar display varchar userselected boolean
Column Type Description id varchar observation_code varchar observation_system varchar category_code varchar category_system varchar valuecodeableconcept_code varchar valuecodeableconcept_system varchar valuecodeableconcept_display varchar effectivedatetime_day date effectivedatetime_week date effectivedatetime_month date effectivedatetime_year date status varchar subject_ref varchar encounter_ref varchar observation_ref varchar
Column Type Description id varchar observation_code varchar observation_system varchar category_code varchar category_system varchar valuecodeableconcept_code varchar valuecodeableconcept_system varchar valuecodeableconcept_display varchar valuequantity_value double valuequantity_comparator varchar valuequantity_unit varchar valuequantity_system varchar valuequantity_code varchar status varchar interpretation_code varchar interpretation_system varchar interpretation_display varchar effectivedatetime_day date effectivedatetime_week date effectivedatetime_month date effectivedatetime_year date subject_ref varchar encounter_ref varchar observation_ref varchar
Column Type Description id varchar gender varchar birthdate date postalcode_3 varchar subject_ref varchar race_display varchar ethnicity_display varchar
Column Type Description id varchar system varchar ethnicity_code varchar ethnicity_display varchar
Column Type Description id varchar system varchar race_code varchar race_display varchar
Column Type Description period_start_day date period_start_week date period_start_month date period_end_day date age_at_visit bigint author_day date author_week date author_month date author_year date gender varchar race_display varchar ethnicity_display varchar subject_ref varchar encounter_ref varchar status varchar documentreference_ref varchar diff_enc_note_days bigint enc_class_code varchar(6) enc_class_display varchar(21) doc_type_code varchar doc_type_display varchar ed_note boolean