Flat File Laboratory Result Processing Guidance - Arizona ...
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Flat File Laboratory Result Processing Guidance
This document outlines the requirements for clinical laboratories to send a flat-file of Coronavirus 2019 (COVID-19)
results to the Arizona Department of Health Services (ADHS). This process is currently available for COVID-19
results but if you’d like to send other diseases please reach out to the Electronic Laboratory Reporting (ELR) team
(elr@azdhs.gov) to discuss. Facilities using this flat file process will fulfill mandated COVID-19 reporting
requirements once in production.
While onboarding with this method of reporting, facilities are expected to report results by an alternative
method such as by faxing or securely emailing results. Only after approval from ADHS can the facility stop
reporting by other methods.
Onboarding Process
1. Notify ADHS that your facility is interested in this process by sending an email to the ADHS Electronic
Laboratory Reporting Program (elr@azdhs.gov).
a. In the email, include the name and contact information for the primary facility contact(s).
2. Sign and return the ADHS user agreements to create an ADHS SFTP Account.
a. One service account will be created for your facility and credentials will be sent to the facility point
of contact.
3. Create an initial file with real patient data according to the specifications in Appendix 1.
4. Select your file, drag and drop the initial file in the TEST\IN SFTP folder for your facility and notify
elr@azdhs.gov when the file has been submitted.
a. ADHS will process the file through the ADHS test environment and the ADHS Electronic
Laboratory Reporting Program will follow up with any data quality concerns.
b. Patient records in the test file must not exceed 500 rows.
5. Additional files may need to be submitted to the TEST\IN SFTP folder to ensure that any necessary
corrections were implemented.
6. Once the ADHS Electronic Laboratory Reporting Program ensures that the file can process without errors,
ADHS will notify the facility that they are ready to submit data to the ADHS production environment.
a. After this notification, the facility may start submitting daily files into their PROD\IN SFTP folder
and notification to ADHS is no longer required.
b. Patient records in the production file must not exceed 10,000 rows.
7. ADHS will monitor the production file submissions to ensure successful processing and may reach out to
facilities if issues are identified. Facilities are expected to respond back within 24 hours.
8. After your facility is in production a historical file must be created by result date oldest to newest.Appendix 1 - File Specifications
Acceptable file formats:
1. Comma Separated Values (.csv)
2. Microsoft Excel Spreadsheet (.xlsx)
a. Tab name must remain “Sheet1” for the Microsoft Excel format
b. There should be no more than 1 worksheet in the Microsoft Excel format
All cells must use the “General” format (including all dates). Do not add extra formatting, such as text wrapping.
Do not include commas in data fields if possible. (Prohibited characters in all cells includes: ^ / \ & | ~).
Do not change file formats during the onboarding process.
Submitted files should NOT have blank rows in between data rows or will cause the file to fail to process.
Column headers should be the 1st row in the .csv or .xlsx file.
ALL COLUMNS MUST BE INCLUDED IN THE SUBMITTED FILE.
The table below describes the data elements expected for sending laboratory reports. In the table:
● The first column, (seq), refers to the field order
● The second column, (use), describes whether the field is required (R) or required but may be empty (RE)
● The third column, (column header), describes the name of the field
● The fourth column, (max char), is maximum allowable number of characters allowed for each data element
● The fifth column provides example data submitted in the required format.
● The last column, (guidance), provides instructions on how to populate that field
After submitting to production, any additions/changes to the sequences in yellow need to be coordinated in advance
with ADHS.
Seq Use Column Header Max Example Data Guidance
Char
1 R Sending_Application 50 StarLims Application generating result. Name of the
laboratory information management system
(LIMS) or (POC) device.
2 RE Sending_Application_ID 50 2.16.840.1.1138 Sending Application Identifier (OID)
3 R Lab_Name 50 Central Lab Public Name of Lab- No Acronyms
4 R Lab_CLIA 15 12D1234567 CLIA or waiver numerical Identifier
5 R Lab_Address 120 1 Main St. Physical Street Address of Lab
6 R Lab_City 50 Yuma Full Name of City where Lab is located
7 R Lab_State 2 AZ U.S States or Territory coded value (Appendix 2)
8 R Lab_Zip 10 85364 Lab 5-digit ZIPcode or 10-digit ZIP+4 code
9 R Lab_Phone 10 6023643676 No formatting, parentheses or dashes
10 RE Patient_ID 50 18827 Unique to each patient. If blank, copy specimen
ID to this field. Please do NOT send SSN
11 R Patient_First_Name 50 Test Patient First Name
Date Last Updated: 1/15/2021 2 of 5Seq Use Column Header Max Example Data Guidance
Char
12 R Patient_Last_Name 50 Patient Patient Last Name
13 R Patient_Date_of_Birth 8 19000101 No special characters. Format: YYYYMMDD
14 R Patient_Sex 1 M Coded value from Appendix 5
15 RE Race 1 W Coded value from Appendix 6
16 RE Ethnicity 2 NH Coded value from Appendix 7
17 RE Patient_Street_Address 50 100 1st St. Patient Street Address
18 RE Patient_City 50 Yuma Patient City
19 RE Patient_State 2 AZ Patient State or Territory See Appendix 2, 3 and 4
20 RE Patient_Zip 10 85364 5 digit ZIP code or 10-digit ZIP+4
21 RE Patient_County 15 Yuma County Text value or FIPS Code (Appendix 8)
22 RE Patient_Phone_Number 10 6023643676 No formatting, parentheses or dashes
23 R Ordering_Facility 100 Yuma Clinic Name of Ordering Facility
24 RE Ordering_Facility_Address 75 21 Central Ave. Address of Ordering Facility
25 RE Ordering_Facility_City 50 Yuma City of Ordering Facility
26 RE Ordering_Facility_State 2 AZ U.S States or territory identifier (Appendix 2)
27 RE Ordering_Facility_Zip 10 85364 5-digit ZIPcode or ZIP+4
28 RE Provider_First_Name 50 Tom First Name of Ordering Provider
29 RE Provider_Last_Name 50 Smith Last Name of Ordering Provider
30 RE Provider_Phone_Number 10 6023643676 No formatting, parentheses or dashes
31 R Specimen_ID 50 157784 Unique per observation
32 R Collection_Date 8 20201010 No special characters: Format: YYYYMMDD
33 R Specimen_Type 50 Nasal Swab Specimen Type (text)
34 RE Specimen_Site 50 Nose Site on body from where specimen taken (text)
35 R Test_Code 15 94500-6 LOINC code for test performed. If a local code or
no code, contact ADHS for mapping guidance.
36 R Test_Name 200 SARS COV2 PCR Text name for the test performed in LIMS
37 R Result 50 Not Detected Result (Text/Numeric/Titer)
38 R Result_Date 8 20201011 No special characters: Format: YYYYMMDD
39 RE Notes 500 Additional comments
Date Last Updated: 1/15/2021 3 of 5Appendix 2: U.S States or Territory Coded Values (2 letter state/territory codes)
Coded values should be used for: Lab_State, Patient_State (when Patient Country = U.S.),
Ordering_Facility_State
Code State/Territory Code State/Territory Code State/Territory Code State/Territory
AK Alaska IA Iowa MS Mississippi PW Palau
AL Alabama ID Idaho MT Montana RI Rhode Island
AR Arkansas IL Illinois NC North Carolina SC South Carolina
American
AS Samoa IN Indiana ND North Dakota SD South Dakota
AZ Arizona KS Kansas NE Nebraska TN Tennessee
CA California KY Kentucky NH New Hampshire TX Texas
CO Colorado LA Louisiana NJ New Jersey UM U.S. Minor Outlying Islands
CT Connecticut MA Massachusetts NM New Mexico UT Utah
District of
DC Columbia MD Maryland NV Nevada VA Virginia
DE Delaware ME Maine NY New York VI U.S. Virgin Islands
FL Florida MH Marshall Islands OH Ohio VT Vermont
FM Micronesia MI Michigan OK Oklahoma WA Washington
GA Georgia MN Minnesota OR Oregon WI Wisconsin
GU Guam MO Missouri PA Pennsylvania WV West Virginia
Northern Mariana
HI Hawaii MP Islands PR Puerto Rico WY Wyoming
Appendix 3: Mexico States Coded Values
Coded values should be used for the column header: Lab_State, Patient_State (when Patient Country =
Mexico), & Ordering_Facility_State
Coded Values Mexican State Coded Values Mexican State Coded Value Mexican State
AG Aguascalientes GR Guerrero QR Quintana Roo
BN Baja California HD Hidalgo SI Sinaloa
BS Baja California Sur JA Jalisco SL San Luis Potosi
CH Chihuahua MC Michoacan SO Sonora
CL Colima MR Morelos TB Tabasco
CM Campeche MX Mexico TL Tlaxcala
CP Chiapas NA Nayarit TM Tamaulipas
CU Coahuila NL Nuevo Leon VE Veracruz
DF Distrito Federal OA Oaxaca YU Yucatan
DU Durango PU Puebla ZA Zacatecas
GJ Guanajuato QE Queretaro
Date Last Updated: 1/15/2021 4 of 5Appendix 4: Canadian Provinces and Territories Coded Values
Coded values should be used for the following column header: Lab_StatePatient_State (when Patient Country =
Canada), Ordering_Facility_State
Coded Value Provinces/Territory Coded Value Province/Territory Coded Value Province/Territory
AB Alberta ON Ontario QC Quebec
BC British Columbia PE Prince Edward Island SK Saskatchewan
MB Manitoba NL Newfoundland and Labrador YT Yukon
NB New Brunswick NS Nova Scotia
NU Nunavut NT Northwest Territories
Appendix 5: Appendix 6: Coded Values for Patient_Race
Coded values for Patient_Sex If Race is unknown, please keep this field blank.
Coded Value Sex Coded Value Race
M Male N American Indian or Alaska Native
F Female A Asian or Pacific Islander
U Unknown B Black
W White
P Hawaiian or Pacific Islander
Appendix 7:
Coded values for Patient_Ethnicity O Other
If unknown, include as “U”
Coded value Ethnicity
H Hispanic
NH Non-Hispanic
U Unknown
Appendix 8: Coded values (FIPS) for Arizona Counties
Coded or specified text values can be used for the following data element: Patient_County
Code County Code County Code County Code County
04001 Apache 04009 Graham 04015 Mohave 04023 Santa Cruz
04003 Cochise 04011 Greenlee 04017 Navajo 04025 Yavapai
04005 Coconino 04012 La Paz 04019 Pima 04027 Yuma
04007 Gila 04013 Maricopa 04021 Pinal
Date Last Updated: 1/15/2021 5 of 5You can also read
