CSV Submitter Resources
NEDSS COVID-19 Laboratory Submitter Resources
This page is intended to serve as a resource page for CSV submitter facilities conducting in-house or on-site SARS-CoV-2 (COVID-19) testing who have already registered to report to NEDSS. Here you will find supplemental information to assist with the registration, testing, and onboarding.
If your facility has not yet registered, complete the CSV Lab Submitter Registration Form.
Lab Webinar Training
Updated COVID-19 Lab Reporting Requirements covering New 56 Column Template including Ask on Order Entry (AOE) Questions
DSHS Public Health Informatics Data recently held a webinar training update for facilities submitting lab data via CSV formatted template to DSHS. A link to access the video recording of that training is available below along with a copy of the presentation slides.
DSHS PHID video training resources are available.
The content of these videos is outlined below.
| Training added Date | Description | Link Specific Topic Covered |
|---|---|---|
| June 2021 | Introduction to COVID-19 Lab Reporting via CSV |
|
| Feb 2021 | Correcting CSV Validation Errors | |
| Dec 2020 | Webinar Training on Updated 56 Column AOE Template | |
| Apr 2022 | Transcripts to DSHS PHID Video Training Resources |
Related Handouts:
- PowerPoint Presentation of Training (PDF)
- 56 Column CSV Clean Template (view template section below)
- 56 Column CSV Data Dictionary (view template section below)
Note for Facilities Assigned to Persivia:
If your facility is currently assigned to Persivia, please continue to name your filename with the same file naming convention you have been using.
What is NEDSS and what is its significance to the COVID-19 response?
The Texas National Electronic Disease Surveillance System (NEDSS) is the primary system utilized by public health epidemiologists and surveillance staff across Texas to monitor and respond to most notifiable infectious disease conditions. Since 2004, NEDSS has played a critical role in preventing the further transmission of infectious diseases in Texas. It serves as the primary system for processing and distributing electronic laboratory reports (ELRs) which trigger public health investigations of notifiable disease conditions. Public health epidemiologists and surveillance staff routinely conduct disease investigations based on ELRs assigned to their area through NEDSS. The purpose of disease investigations is to identify cases, assess their close contacts, apply mitigation efforts, and reduce the further spread of the disease. Public health staff capture the results of those investigations in NEDSS and utilize the data to identify and monitor disease trends in their communities. The data captured through investigations also helps to identify vulnerable populations, pockets of need, and changes in disease epidemiology.
NEDSS data is utilized to feed the DSHS dashboards available to the public. This data helps public health leadership to effectively monitor and respond to the ongoing pandemic situation.
What are the two options for COVID-19 electronic lab reporting to NEDSS?
There are two options for reporting COVID-19 ELRs to NEDSS:
- Health Level 7 International (HL7) standardized message format, or
- Texas alternative comma separated value (.CSV) standardized message format compliant with rules outlined in DSHS COVID-19 data dictionary.
Facilities reporting via the Texas CSV-approved template can utilize the resources listed here to assist in the registration, testing, and onboarding process. Submitters should follow all instructions as received from DSHS after registration and may use the information presented here as supplementary information.
COVID-19 Reporting Guidelines for Submission by CSV Template
This guide was designed to assist facilities with the registration, testing/validation, and onboarding process for reporting COVID-19 labs to DSHS. This guide is specifically developed for facilities that submit their results via the DSHS-approved comma-separated value (CSV) template. Facilities that are unable to submit via HL7 standard should submit via the CSV template.
Download the entire guide:
For quick access to shortened instructions from the guide, please see the links provided below:
- Frequently Asked Questions (FAQs) – CSV Registration, Testing, and Onboarding (PDF)
- Steps to Identify Correct LOINC Code (PDF)
- Tips to Getting Started with Reporting via CSV (PDF)
COVID-19 Reporting CSV Template and Data Dictionary (Updated 12/11/20)
The templates listed below are issued to facilities after completing registration. Facilities that have not registered yet may review the templates listed below to understand data submission formatting and data requirements. However, facilities that have not had their registration confirmed by DSHS are NOT authorized to submit these templates until approved to do so.
- 56_COLUMN_AOE_CLEAN_TEMPLATE.xls
This is the file format with the column headers for the 56 columns/variables of lab data required to be submitted to DSHS.
Submitters must adhere to the exact column order. Do not include additional columns and do not omit columns—these scenarios may cause the entire file to be rejected. - 56_Column_AOE_Data_Dictionary.xlsx
This data dictionary provides details on requirements for each of the required 56 columns/variables. It’s important to note the field listing permitted response options and the required formatting for each variable. If a submitted file does not conform to the data dictionary, the file may be rejected.
Contact Info
Registered facilities who need assistance or have other questions may email COVID-19ELR@dshs.texas.gov.
Useful Links
U.S. Health and Human Services
Centers for Disease Control and Prevention
Texas Department of State Health Services
- Texas COVID-19 Lab Reporting Registration – Starting point for the Texas COVID-19 lab reporting registration process
Federal Drug Administration
- COVID-19 In Vitro Diagnostics EUAs – Performing Facilities should ensure that the test being utilized is a FDA authorized test for COVID-19
- FAQs for Labs
Logical Observation Identifiers Names and Codes (LOINC)
- CDC LOINC In Vitro Diagnostic (LIVD) Test Code Mapping for SARS-CoV-2 Tests – CDC page provides LOINC and SNOMED mappings for SARS-CoV-2 diagnostic tests
- LOINC.org – Guidance from LOINC organization on SARS-CoV-2 and COVID-19 related LOINC terms
U.S. National Library of Medicine
AccessGUDID – The Global Unique Device Identification Database (GUDID) will help you determine the Device ID of the test being performed
Acronyms
- CDC (Centers for Disease Control and Prevention)
- CMS (Centers for Medicare & Medicaid Services)
- CSV (Comma Separated Value)
- ELR (Electronic Laboratory Reporting)
- HIPAA (Health Insurance Portability and Accountability Act)
- HIT (Health Information Technology)
- HL7 (Health Level 7)
- ICD-10 (International Classification of Diseases, 10th Revision)
- LIMS (Laboratory Information Management System)
- LIS (Laboratory Information System)
- LOINC (Logical Observation Identifiers Names and Codes)
- NBS (NEDSS Base System)
- NEDSS (National Electronic Disease Surveillance System)
- PHI (Private Health Information)
- sFTP (Secure File Transfer Protocol)