Professional Documents
Culture Documents
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LICENSE
2011 Foundation for the National Institutes of Health (FNIH).
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this document except in
compliance with the License. You may obtain a copy of the License at http://omop.fnih.org/publiclicense.
Unless required by applicable law or agreed to in writing, documentation and software distributed under
the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND,
either express or implied. Any redistributions of this work or any derivative work or modification based on
this work should be accompanied by the following source attribution: "This work is based on work by the
Observational Medical Outcomes Partnership (OMOP) and used under license from the FNIH at
http://omop.fnih.org/publiclicense.
Any scientific publication that is based on this work should include a reference to
http://omop.fnih.org.
This document was created specifically for the Scalable Architecture for Federated Translational Inquiries
Network (SAFTINet) project, in collaboration with OMOP. It reflects changes to the OMOP CDMv2 to
create OMOP CDMv3 which were done in collaboration with FNIH OMOP and the SCANNER (Scalable
National Network for Effectiveness Research) project (http://scanner.ucsd.edu/)
SAFTINet is supported by grant number R01HS019908 from the Agency for Healthcare Research and Quality.
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TABLE OF CONTENTS
1.0 Introduction
3.0 Assumptions
12
13
14
15
17
18
21
25
27
30
33
35
38
39
46
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Organization
Title
Patrick Hosokawa
Michael Kahn
Elias Brandt
Lisa Schilling
COHO
Statistician/Analyst
Reviewers
Name
Role
Title
Christian Reich
OMOP
Project Manager
Date Reviewed
Patrick Ryan
OMOP
Co-investigator
Document References
Document Title
Type of Reference
Document Location
Business Rules
Detailed Technical
Information
Detailed Technical
Information
Page 4
Change Record
Date
Author
Version
Change Reference
02-Nov-2009
1.0
04-Oct-2011
2.0
20-Dec-2011
Patrick Hosokawa
2.1
17-Mar-2012
Patrick Hosokawa
2.2
06-Aug-2012
Patrick Hosokawa
4.0
03-Mar-2013
Patrick Hosokawa
4.1
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1.0 Introduction
This document reflects the requirements, assumptions, business rules and transformations for the
implementation of OMOP CDM V3, as recommended for SAFTINet.
The purpose of this document is two-fold:
1. Describe ETL mapping of data from SAFTINet partners into Common Data Model.
2. Serve as a blueprint for equivalent ETL mapping processes for other data sources into CDM.
In each section, the tables and their mapping are individually reviewed along with any source specific
rules and exceptions.
The intended audiences for this document are the SAFTINet team and partner ETL technical personnel.
Sections of the document are targeted specifically towards each audience with appropriate focus and
level of detail.
Page 6
DEFINITION
A query or query response performed across the grid network as
described in the following use cases
The Care Site table refers to the lower level of the provider
care hierarchy. Individual provider care locations will be
stored in this table.
Cohort
Concept
Condition
Condition Occurrence (entity)
Current Procedural
Terminology (CPT), 4th edition
Data Mapping
Demographics
Domain
Page 7
as a string data type, and allowed to have one of two known code
values: "M" for male, "F" for female -- and NULL for records
where gender is unknown or not applicable (or arguably "U" for
unknown as a sentinel value). The data domain for the gender
column is: "M", "F".
Drug
Page 8
Grid-enabled network
Grid Node
Grid Portal
International Classification of
Disease, 9th Revision, Clinical
Modifications (ICD9-CM)
Investigator
Page 9
Observational Medical
Outcomes Partnership (OMOP)
Organization (entity)
Person (entity)
Provider (entity)
Query
ROSITA
Page 10
RxNorm
Subject
Systematized Nomenclature of
Medicine - Clinical Terms
(SNOMED-CT)
Terminology
Virtual organization (aka
Partner)
Vocabulary
Page 11
3.0 Assumptions
The design follows the agreed upon general project assumptions:
Electronic Medical Data: EMR is a subset of EHR. This document will reference EHR moving forward
even if specific data source might internally use Electronic Medical Record (EMR) definition.
Financial Information: The CDM model makes use of financial information such as Fees, Payments,
Deductibles, Copayment, etc. from payer source data, such as Medicaid
Plan Detail Information: The model potentially makes use of fields related to Plan or Coverage details
such as Benefit Plan, Plan Indicator, etc. of the administrative information in the claims data. The model
makes use of medical coverage period and eligibility for prescription drugs.
Cleansing and Validation: The selected data fields will be handled (whether loaded directly or as part of a
transformation) with a validation plan which is to be determined later.
Data Privacy: ETL from EHR/CDW will contain clear text direct patient identifiers and dates. ROSITA will
encrypt all clear text direct patient identifiers. A random identifier (called a GUID) that is unrelated to
any patient identifier will be associated with each patient record. Birth dates and dates of service will
remain unchanged. Zip codes will also be forward to the grid node unchanged and as second variable to
only include the 3-digit zip (the leftward 3 digits). The resulting data exported to the grid node will
therefore be a limited data set containing encrypted direct identifiers with unchanged dates and both 5digit and 3-digit zip codes. The grid node will have no access to any clear text direct patient identifiers
from the EHR/CDW.
Under the assumption that payer data will be provided with clear text direct identifiers, ROSITA will
perform record linkage to link the clinical record with the financial record using clear text identifiers. If a
match is made, the same GUID assigned to the clinical data will be assigned to the financial data.
Otherwise, a new GUID will be generated that is unrelated to any patient identifier. Dates will remain
unchanged. The resulting data exported to the grid node will be consistent with a Limited Data Set
containing encrypted direct identifiers, unchanged dates, a 5- and 3-digit zip code, and a GUID random
identifier. The grid node will have no access to any clear text direct patient identifiers from payer (e.g.
Medicaid) data.
Concept Identifiers: Data are represented through standard concept identifiers using a standardized
terminology. During ETL, source data representations (raw data codes) will be translated to standard
concept identifiers through a mapping process. If no standard concept identifier is available, the concept
identifier field will contain 0 as a value.
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Page 13
Changed Field
Change
x_visit_occurrence_source_identifier Changed from
visit_occurrence_source_identifier, new
x_ prefix is so the field can pass through
to the grid
Drug_Exposure
x_visit_occurrence_source_identifier Changed from
visit_occurrence_source_identifier, new
x_ prefix is so the field can pass through
to the grid
Condition_Occurrence x_visit_occurrence_source_identifier Changed from
visit_occurrence_source_value, new x_
prefix is so the field can pass through to
the grid
Procedure_Occurrence x_visit_occurrence_source_identifier Changed from
visit_occurrence_source_value, new x_
prefix is so the field can pass through to
the grid
Observation
x_visit_occurrence_source_identifier Changed from
visit_occurrence_source_value, new x_
prefix is so the field can pass through to
the grid
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X_data_source_type
Data Type /
Required
String(50) /
Required
place_of_service_source
_value
String(20) /
Required
String (50) /
Required
organization_address_1
organization_address_2
organization_city
organization_state
organization_zip
organization_county
String (50)
String (50)
String (50)
String (2)
String (9)
String (20)
Source Field
Applied Rule
Comment
Local reference value for organization, used to
create the organization_id field on the grid
facing record. This value will also be used in
other records to refer to the organization.
Data Source Identifier (EHR / CDW / Medicaid)
The type of organization. If the organization
type is not defined in the source data refer to
the place_of_service_type section of the
Concept ID Table. Used to create
place_of_service_concept _id.
First line of the address
Second line of the address
City portion of the address
State portion of the address
Zip code of the address
County portion of the address
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ETL View
UC Internal Medicine
EHR
Academic Practice
13199 E Montview Blvd
Suite 300, Mail Stop F443
Aurora
CO
80045
Arapahoe
1.
2.
3.
Grid View
Organization Table - Grid
organization_id
organization_source_value
x_data_source_type
place_of_service_concept_id
place_of_service_source_value
location_id
x_gride_node_id
22770494
UC Internal Medicine
EHR
3389
Academic Practice
39458
1
39458
UC Internal Medicine
EHR
13199 E Montview Blvd
Suite 300, Mail Stop F443
Aurora
CO
80045
800
Arapahoe
Organization
1
Green Brought forward from ETL / Yellow Generated from ETL field / Red
Generated locally or from multiple ETL fields
The organization_source_value field will be compared to the current set of locations. If the value does not already occur in the table (new location) a row will
be added to the table and a new ID (location_id) will be generated. Either a newly generated value or a pre-existing value (if the record is found) of the
location table Primary Key will be placed into location_id.
x_zip_deidentified will be generated from organization_zip. This field was created specifically for person locations to support the creation of Safe Harbor
Limited Data Sets.
x_location_type will be derived from the XML record type (Organization in this case)
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Data Type
String (50) /
Required
x_data_source_type
String(20) /
Required
String (50) /
Required
organization_source
_value
place_of_service_source
_value
String (50)
x_care_site_name
care_site_address_1
care_site_address_2
care_site_city
care_site_state
care_site_zip
care_site_county
String(50)
String (50)
String (50)
String (50)
String (2)
String (9)
String (20)
Source Field
Applied Rule
Comment
Local reference value for care site, used to create
the care_site_id field on the grid facing record. This
value will also be used in other records to refer to
the care site.
Data Source Identifier (EHR / CDW / Medicaid)
Local reference value for organization. This value
will be matched against the organization table to
obtain the corresponding organization_id.
The type of care site. If the care site type is not
defined in the source data refer to the
place_of_service_type section of the Concept ID
Table. Used to create place_of_service_concept _id.
Name of the clinic (care site)
First line of the address
Second line of the address
City portion of the address
State portion of the address
Zip code of the address
County portion of the address
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ETL View
UC Internal Medicine
EHR
University of Colorado
Internal Medicine
Eastside Clinic
13199 E Montview Blvd
Suite 300, Mail Stop F443
Aurora
CO
80045
Arapahoe
1.
2.
3.
Grid View
Care Site Table - Grid
care_site_id
care_site_source_value
x_data_source_type
location_id
organization_id
place_of_service_concept_id
place_of_service_source_value
x_care_site_name
x_grid_node_id
22770494
UC Internal Medicine
EHR
49382
382392
39458
Internal Medicine
Eastside Clinic
1
49382
UPI Building
EHR
13199 E Montview Blvd
Suite 300, Mail Stop F443
Aurora
CO
80045
800
Arapahoe
Care Site
1
Green Brought forward from ETL / Yellow Generated from ETL field / Red
Generated locally or from multiple ETL fields
The care_site_source_value field will be compared to the current set of locations. If the value does not already occur in the table (new location) a row will
be added to the table and a new ID (location_id) will be generated. Either a newly generated value or a pre-existing value (if the record is found) of the
location table Primary Key will be placed into location_id.
x _zip_deidentified will be generated from care_site_zip. This field was created specifically for person locations to support the creation of Safe Harbor
Limited Data Sets
x_location_type will be derived from the XML record type (Care Site in this case)
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Data Type
String (50) /
Required
x_data_source_type
npi
dea
specialty_source_value
String(20) /
Required
String (50)
String (50)
String (50)
x_provider_first
x_provider_middle
x_provider_last
care_site_source_value
String (75)
String (75)
String (75)
String (50)
x_organization_source
_value
String (50) /
Required
Source Field
Applied Rule
Comment
Local reference value for provider, used to create
the provider_id field on the grid facing record. This
value will also be used in other records to refer to
the provider.
Data Source Identifier (EHR / CDW / Medicaid)
Provider NPI
Provider DEA Number
Provider type as recorded at the source (e.g.
Physican, NP, MA, etc). If the provider type is not
defined in the source data refer to the Health Care
Provider Specialty section of the Concept ID Table.
Used to create specialty_concept_id
Provider First Name
Provider Middle Name (or initial)
Provider Last Name
Local reference value for Care Site. This value will
be matched against the Care Site table to obtain the
corresponding care_site_id.
Local reference value for Organization. This value
will be matched against the Care Site table to obtain
the corresponding organization_id.
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ETL View
Provider Table - XML
provider_source_value
x_data_source_type
npi
dea
specialty_source_value
x_provider_first
x_provider_middle
x_provider_last
care_site_source_value
x_organization_source_value
349302
EHR
34930302
49492
General Practitioner
Marcus
W
Welby
UC Internal Medicine
University of Colorado
Grid View
Provider Table - Grid
provider_id
provider_source_value
x_data_source_type
npi
dea
specialty_source_value
specialty_concept_id
x_provider_first
x_provider_middle
x_provider_last
care_site_id
x_organization_id
x_grid_node_id
2399450
349302
EHR
34930302
49492
General Practitioner
20302
Marcus
W
Welby
22770494
3939
1
Green Brought forward from ETL / Yellow Generated from ETL field / Red
Generated locally or from multiple ETL fields / Blue Item under discussion
Page 20
x_data_source_type
medicaid_id_number
ssn
last
middle
first
address_1
address_2
city
state
zip
county
year_of_birth
Source Field
String (20) /
Required
String (50)
String (50)
String (75)
String (75)
String (75)
String (50)
String (50)
String (50)
String (2)
String (9)
String (20)
Applied Rule
Comment
Person unique identifier at the source (MRN). Used
to create the person_id field on the grid facing
record. This value will also be used in other records
to refer to the person.
Data Source Identifier (EHR / CDW / Medicaid)
Medicaid ID Number
Social Security Number
Last Name
Middle Name or Initial
First Name
The first line of the person's actual address.
The first line of the person's actual address.
The city portion of the person's actual address.
The state portion of the person's actual address.
Zip code of the person's actual address.
The county portion of the persons address as
recorded at source.
Year of birth
month_of_birth
day_of_birth
gender_source_value
Number(4) /
Required
Number (2)
Number (2)
String (50)
race_source_value
String (50)
ethnicity_source_value
String (50)
Month of birth
Day of birth
Local reference value for gender of the person.
Used to create gender_concept_id
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provider_source_value
String (50)
care_site_source_value
String (50)
x_organization_source
_value
String (50) /
Required
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ETL View
X_Demographic Table - XML
person_source_value
x_data_source_type
medicaid_id_number
ssn
last
middle
first
address_1
address_2
city
state
zip
county
year_of_birth
month_of_birth
day_of_birth
gender_source_value
race_source_value
ethnicity_source_value
provider_source_value
care_site_source_value
x_organization_source_value
29201082
EHR
3903432
999-99-9999
Doe
D
John
123 Fake St
Apt 566
Aurora
CO
80045
Arapahoe
1965
2
9
Male
White
Non-Hispanic
35346346
UC Internal Medicine
University of Colorado
GRID View
Person Table - Grid
person_id
person_source_value2
location_id1
year_of_birth
month_of_birth
day_of_birth
gender_concept_id
gender_source_value
race_concept_id
race_source_value
ethnicity_concept_id
ethnicity_source_value
provider_id3
care_site_id
x_organization_id
x_grid_node_id
22770494
49382
1965
2
9
675
Male
344
White
202
Non-Hispanic
34235556
22770494
382392
1
location_id1
39458
location_source_value
x_data_source_type
EHR
4
address_1
address_24
city
Aurora
state
CO
zip
80045
x_zip_deidentified5
800
county
Arapahoe
6
x_location_type
34344
x_grid_node_id
1
Green Brought forward from ETL / Yellow Generated from ETL field / Red
Generated locally or from multiple ETL fields
Page 23
1.
2.
3.
4.
5.
6.
The location ID value is not linked to a location_source_ value in this case. When the address information is transferred to the location table, the resulting
ID value will be placed in the person record for reference
The grid version of the person table contains a blank field for person_source_value to comply with the OMOP standard. The value for
person_source_value on the ETL side will not be carried forward due to privacy concerns.
The grid facing provider_id will be derived from the ETL field provider_source_value.
When creating the location table the local values for person address will not be passed through to the grid, although they are labeled green because in
other instances, such as Organization and Care Site, they do move forward to the grid facing database
x _zip_deidentified will be generated from zip. This field was created specifically for person locations to support the creation of Safe Harbor
Limited Data Sets
x_location_type will be derived from the XML record type (Person in this case)
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Data Type
String (50) /
Required
x_data_source_type
String (20) /
Required
String (50) /
Required
person_source_value
visit_start_date
visit_end_date
place_of_service
_source_value
Source Field
DATE/
Required
DATE /
Required
String (50)
x_provider_source_value
String (50)
care_site_source_value
String (50)
Applied Rule
Comment
Local reference value for visit, used to create the
visit_occurrence_id field on the grid facing record.
Data Source Identifier (EHR / CDW / Medicaid)
Person unique identifier at the source (MRN). This
value will be matched against the Person table to
obtain the corresponding person_id.
The date on which the Visit started
The date on which the Visit ended
Visit type (office visit, med refill, face-to-face,
telephone, med refill etc). If the visit site type is
not defined in the source data refer to the
Visit_Type section of the Concept ID Table. Used to
create place_of_service_concept_id
Local reference value for the provider conducting
the visit. This value will be matched against the
Provider table to obtain the corresponding
provider_id.
Local reference value for the Care Site of the visit.
This value will be matched against the Care Site
table to obtain the corresponding care_site_id.
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ETL View
Visit Occurrence Table - XML
x_visit_occurrence_source
_identifier
x_data_source_type
person_source_value
visit_start_date
visit_end_date
place_of_service_source_value
x_provider_source_value
care_site_source_value
349302
EHR
2302202
5/23/2011
5/25/2011
Physical
20302340
UC Internal Medicine
Grid View
Visit Occurrence Table - Grid
visit_occurrence_id
x_data_source_type
person_id
visit_start_date
visit_end_date
place_of_service_concept_id
place_of_service_source_value
x_provider_id
care_site_id
x_grid_node_id
3203402
EHR
30205202
5/23/2011
5/25/2011
302023003
Physical
04594020
202033
1
Green Brought forward from ETL / Yellow Generated from ETL field / Red
Generated locally or from multiple ETL fields
Page 26
Data Type
String (50) /
Required
x_data_source_type
String (20) /
Required
String (50) /
Required
person_source_value
drug_source_value
String (50)
drug_source_value
_vocabulary
drug_exposure_start
_date
String (50) /
Required
Date /
Required
drug_exposure_end_date
Date
drug_type_source_value
String (50) /
Required
stop_reason
String (20)
refills
Number(4)
Source Field
Applied Rule
Comment
Unique Transaction Identifier - Could be an Rx Order
ID, used to create the drug_exposure_id field on the
grid facing record.
Data Source Identifier (EHR / CDW / Medicaid)
Person unique identifier at the source (MRN). This
value will be matched against the Person table to
obtain the corresponding person_id.
Local reference value for drug identifier. The types
of identifiers allowed include National Drug Codes
(NDCs), Generic Product Identifier (GPI) codes. Used
to create the drug_concept_id field on the grid
facing record.
Vocabulary from which the source values are
derived (used for 2-field match to concept ID)
This is the Start Date for the current instance of drug
utilization. Valid indicators include a start date of a
prescription, the date a prescription was filled, or
the date on which a drug administration procedure
was recorded.
This is the End Date for the current instance of drug
utilization. It is not available from all sources
Type of drug exposure (prescription, med history,
fulfillment) as recorded in source data. If the drug
type is not defined in the source data refer to the
Drug Exposure Type section of the Concept ID Table.
Used to create drug_type_concept_id
The reason the medication was stopped, where
available. Reasons include Regimen completed,
Changed, Removed, etc.
The number of refills for the prescription
Page 27
quantity
Number (8,2)
days_supply
Number (4)
x_drug_name
String (255) /
Required
String (50)
String (500)
String (50) /
Required
x_drug_strength
sig
provider_source_value
x_visit_occurrence_
source_identifier
String (50)
relevant_condition
_source_value
String (50)
Page 28
ETL View
Drug Exposure Table - ETL
drug_exposure_source_identifier
x_data_source_type
person_source_value
drug_source_value
drug_source_value_vocabulary
drug_exposure_start_date
drug_exposure_end_date
drug_type_source_value
stop_reason
Refills
quantity
days_Supply
x_drug_name
x_drug_strength
sig
provider_source_value
x_visit_occurrence_source
_identifier
relevant_condition_source_value
30003400
EHR
2302202
4594930302
NDC
4/19/2011
5/19/2011
Prescription
Regimen Completed
1
60
30
Amoxicillin
500
239292
3499202
393821
Grid View
Drug Exposure Table - Grid
drug_exposure_id
x_data_source_type
person_id
drug_concept_id
drug_source_value
drug_exposure_start_date
drug_exposure_end_date
drug_type_concept_id
stop_reason
refills
quantity
days_Supply
x_drug_name
x_drug_strength
sig
prescribing_provider_id
visit_occurrence_id
relevant_condition_concept_id
x_grid_node_id
9947839
EHR
30205202
499506
4594930302
4/19/2011
5/19/2011
983921
Regimen Completed
1
60
30
Amoxicillin
500
3935050
040200
059439333
1
Green Brought forward from ETL / Yellow Generated from ETL field / Red
Generated locally or from multiple ETL fields
Page 29
Data Type
String (50) /
Required
x_data_source_type
String (20) /
Required
String (50) /
Required
person_source_value
condition_source_value
condition_source_value
_vocabulary
x_condition_source_desc
condition_start_date
x_condition_update_date
condition_end_date
Source Field
String (50) /
Required
String(50) /
Applied Rule
Comment
Source Condition Primary Key; could be a unique
record identifier. Used to create the
condition_occurrence_id field on the grid facing
record.
Data Source Identifier (EHR / CDW / Medicaid)
Person unique identifier at the source (MRN). This
value will be matched against the Person table to
obtain the corresponding person_id.
Local diagnosis code (e.g. ICD-9, SNOMED etc).
Used to create condition_concept_id
Type of code (e.g. ICD-9) used for condition.
Required
String (50)
Date / Required
Date
Date
condition_type_source
_value
String (50) /
Required
stop_reason
String (20)
associated_provider
_source_value
String (50)
Page 30
x_visit_occurrence
_source_identifier
String (50)
Page 31
ETL View
Condition Occurrence Table - ETL
condition_occurrence_source_identifier
x_data_source_type
person_source_value
condition_source_value
condition_source_value_vocabulary
x_condition_source_desc
condition_start_date
x_condition_update_date
condition_end_date
condition_type_source_value
stop_reason
associated_provider_source_value
x_visit_occurrence_source_identifier
Grid View
30003400
EHR
393030
162.9
ICD9
Malignant Neop
4/19/2011
10/19/2011
Chief Complaint
392904
403030
8349393
EHR
94849303
884934
162.9
Malignant Neop
4/19/2011
10/19/2011
499404
39304
90493023
1
Green Brought forward from ETL / Yellow Generated from ETL field / Red
Generated locally or from multiple ETL fields
Page 32
Data Type
String (50)
/Required
x_data_source_type
String (20) /
Required
String (50) /
Required
person_source_value
procedure_source_value
String (50) /
Required
procedure_source_value
_vocabulary
procedure_date
String(50) /
Required
DATE / Required
procedure_type_source
_value
String (50)
provider_record_source
_value
String (50)
x_visit_occurrence
_source_identifier
String (50)
relevant_condition
_source_value
String (50)
Source Field
Applied Rule
Comment
Source Procedure Primary Key. Used to create the
procedure_occurrence_id field on the grid facing
record.
Data Source Identifier (EHR / CDW / Medicaid)
Person unique identifier at the source (MRN). This
value will be matched against the Person table to
obtain the corresponding person_id.
The Procedure Code as captured from the source
data. Values include CPT-4, ICD-9-CM (Procedure),
HCPCS, and other procedure codes. Used to create
procedure_concept_id.
Type of code (e.g. CPT) used for condition.
The date on which the procedure began (or was
performed)
The procedure type as stored in source. If the
procedure type is not defined in the source data
refer to the Procedure Occurrence section of the
Concept ID Table. Used to create
procedure_type_concept_id.
Local Reference value for Provider. This value will be
matched against the Provider table to obtain the
corresponding provider_id.
Local Reference value for visit. This value will be
matched against the Visit Occurrence table to obtain
the corresponding visit_occurrence_id.
First Associated Diagnosis Code. Used to create
relevant_condition_concept_id.
Page 33
ETL View
Procedure Occurrence Table - ETL
procedure_occurrence_source_identifier
x_data_source_type
person_source_value
procedure_source_value
procedure_source_value_vocabulary
procedure_date
procedure_type_source_value
provider_record_source_value
x_visit_occurrence_source_identifier
relevant_condition_source_value
Grid View
9848493
EHR
594928
49750
CPT
4/19/2011
Inpatient header
23902023
2302320
20230
393948230
EHR
3493030
39949023
49750
4/19/2011
884934
34040222
20923042
23032009
1
Green Brought forward from ETL / Yellow Generated from ETL field / Red
Generated locally or from multiple ETL fields
Page 34
Data Type
String (50) /
Required
x_data_source_type
String (20) /
Required
String (50) /
Required
person_source_value
observation_source
_value
observation_source
_value_vocabulary
observation_date
observation_time
value_as_number
String (50) /
Required
String(50) /
Required
Date / Required
Time
NUMBER(14,3)
value_as_string
String (60)
unit_source_value
String (50)
range_low
NUMBER(14,3)
Source Field
Applied Rule
Comment
Source Primary Key for Observation Record. Used to
create the obs_occurrence_id field on the grid facing
record.
Data Source Identifier (EHR / CDW / Medicaid)
Person unique identifier at the source (MRN). This
value will be matched against the Person table to
obtain the corresponding person_id.
The Observation Code as it appears in the source
data. Used to create obs_concept_id
Vocabulary used for the observation
The date of the Observation
The time of the observation
The observation result stored as a numeric value.
This is applicable to observations where the result is
expressed as a numeric value.
The observation result stored as character string. It
is applicable to the observations where the result is
expressed as a character string. Used to create
obs_value_as_concept_id.
Unit of measure for Observation result when
measured as a numeric value. Used to create
unit_concept_id
The lower limit of the numeric range of the
Observation value. It is not applicable if the
observation results are non-numeric or categorical,
and must be in the same units of measure as the
observation value
Page 35
range_high
NUMBER(14,3)
observation_type_source
_value
String (50) /
Required
associated_provider
_source_value
String (50)
x_visit_occurrence_
source_identifier
String (50)
relevant_condition
_source_value
x_obs_comment
String (50)
String (500)
Page 36
ETL View
Observation Table - ETL
observation_source_identifier
x_data_source_type
person_source_value
observation_source_value
observation_source_value_vocabulary
observation_date
observation_time
value_as_number
value_as_string
unit_source_value
range_low
range_high
observation_type_source_value
asociated_provider_source_value
x_visit_occurrence_source_identifier
relevant_condition_source_value
x_obs_comment
40230320
EHR
20202302
BP_Systolic
University Lab
7/12/2011
4:53:00 PM
148
mmHg
50
200
Lab Value
930392
2020200
401.2
Grid View
Observation Table - Grid
observation_id
x_data_source_type
person_id
observation_concept_id
observation_source_value
observation_date
observation_time
value_as_number
value_as_string
value_as_concept_id
unit_concept_id
unit_source_value
range_low
range_high
observation_type_concept_id
associated_provider_id
visit_occurrence_id
relevant_condition_concept_id
x_obs_comment
x_grid_node_id
23902323
EHR
3903030
102190
8393929
7/12/2011
4:53:00 PM
148
020333
mmHg
50
200
2032002
939393
2002303
302023
1
Green Brought forward from ETL / Yellow Generated from ETL field / Red
Generated locally or from multiple ETL fields
Page 37
Recordset should consist of all information (including inpatient and outpatient visits) about any patients
with activity (outpatient visits) at a participating primary care site within the past 5 years (back to
1/1/2007 for initial SAFTINet load)
For any patient seen within the past 5 years we request data retrospectively as described below.
Page 38
Organization
Care Site
Provider
Person
One record per grouping of care sites operating under a single health care hierarchy
Include a record for any location where care is provided (examples include clinics, mobile
units and "home-health care"). Multiple separate care-sites in a single building could be
grouped together, or not depending on partner's preference
Include a record for every provider who appears in the "provider" table OR the subset of
the table that can be linked to a claim, a visit, or a prescription, whatever is easiest. If
filtering, include all providers who have been active since 1/1/2007 even if not currently
active.
Include a record for each person who has had some sort of contact with the participating
clinics since 1/1/2007 (regardless of current activity status). This set of persons can be
used to filter the rest of the clinical data - only pull data related to this set of patients.
Page 39
For the following four tables, we wish to collect the specified record types. Please check the Collected? column for
any record types that will be included in the source data file. Also, please list the local source value for that type.
Example: If the local tag for Systolic BP that will go into the observation_source_value field is SBP, put that in the
local name column where systolic BP is listed.
Record Type
Drug
Exposure
Condition
Occurrence
Observation
Minimum
Date
Result Type
Collected?
Local Name
Prescription
Medication List
Administered Drugs
Fulfillment
Include a record for each entry on the problem list as well as a record for each encounter level diagnosis code.
Generally, these will be ICD-9 codes.
Problem list
Visit-level diagnosis codes
ICD-9 codes from claims record
Data that do not fit in another table belong here. Observation table contains data from the following categories: lab
observations (i.e. test results), general clinical findings, signs, and symptoms, along with other domains listed below.
Vital Signs
Height
1/1/2007
Height Percentile (for children)
1/1/2007
Weight
1/1/2007
Weight Percentile (for children) 1/1/2007
Pulse oximetry
1/1/2007
Pulse
1/1/2007
Blood Pressure - Systolic
Blood Pressure - Diastolic
Social History
Smoking Status
(Current/Past/Former/Second
Hand Exposure)
Drinking Status
1/1/2007
1/1/2007
All Records /
No Date Limit
All Records /
No Date Limit
Past Medical History (To be defined)
SAFTINet ETL Specifications Document
Page 40
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
Page 41
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
Yes/No
Yes/No
Yes/No
Yes/No
Page 42
MAS 1e
MAS 1f
MAS 1f Text
MAS 1g
MAS 1g Text
MAS 2
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
MAS Q1
MAS Q2
MAS Q2a
1/1/2007
1/1/2007
1/1/2007
Yes/No
Yes/No
Text
Yes/No
Text
Categorical or
Numeric
Yes/No
Categorical
Yes/No
MAS Q2b
Asthma Control Test
ACT Total Score
ACT Category1
ACT-1
ACT-2
ACT-3
ACT-4
ACT-5
Childhood Asthma Control Test
C-ACT Total Score
C-ACT Category1
C-ACT-1
C-ACT-2
C-ACT-3
C-ACT-4
C-ACT-5
C-ACT-6
C-ACT-7
PHQ-2 Q1 score
PHQ-2 Q2 score
PHQ-2 total score
PHQ-9 FuncQ score
PHQ-9 Q1 score
PHQ-9 Q2 score
PHQ-9 Q3 score
PHQ-9 Q4 score
PHQ-9 Q5 score
PHQ-9 Q6 score
1/1/2007
Yes/No
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
Page 43
PHQ-9 Q7 score
PHQ-9 Q8 score
PHQ-9 Q9 score
PHQ-9 Total score
Demographic Information
Highest Education Level
Achieved
Language Preference
Procedure
Occurrence
1/1/2007
1/1/2007
1/1/2007
1/1/2007
All Records /
No Date Limit
All Records /
No Date Limit
Imputed Race / Ethnicity
All Records /
No Date Limit
Person % Fed Poverty level
1/1/2007
Person family size
1/1/2007
Family income
1/1/2007
Person relationship status
1/1/2007
Person Practice Status (active or Most Recent
moved or gone elsewhere)
/ No Date
Limit
Include a record for each procedure performed on a patient (CPT-4, ICD-9-CM (Procedures), and HCPCS codes). If you
want to filter the procedure table, at least include the following procedures
Procedures
Bone mineral density (DEXA
scan)
Colonoscopy
Diabetic Eye Exam
Diabetic Foot Exam
Double contrast barium enema
Mammogram
Pap Smear
Pulmonary Function Test
Spirometry
Mechanical Ventilation
Continuous nebulized therapy
Endotracheal intubation
Critical Care
Fecal occult blood test
Immunizations
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
1/1/2007
Page 44
Pneumovax
Other Immunizations
Education
Education Nutrition
Education Weight loss
management
1/1/2007
1/1/2007
1/1/2007
Page 45
UC Internal Medicine
EHR
Academic Practice
13199 E Montview Blvd
Suite 300, Mail Stop F443
Aurora
CO
80045
Arapahoe
Should be represented as follows in the file (the actual text should be all on one line):
UC Internal Medicine|EHR|Academic Practice|13199 E Montview Blvd|Suite 300, Mail Stop
F443|Auora|CO|80045|Arapahoe
Files should contain one record per row. No header row is needed, the first row should be actual
data
Quotation marks occurring within column values should be escaped so the processor can locate
them. This should be done with the \ character the end result should look like \
Page 46
Backslash marks occurring within column values should also be escaped with a second backslash
the end result should look like \\
Page 47