Technical Updates

Fall 2020 Enhancements for AMC

The Access & Management Center (AMC) version 1.5.3 was deployed September 9, 2020. This release includes features that will let you easily use new data sources and do routine work more efficiently. Here are the key features for the fall release:

  • Clinical Lab Data Access: Provides site administrators the ability to grant users and other site administrators access to clinical lab data.
  • Mortality Data Access: Provides site administrators the ability to grant users and other site administrators access to mortality data.
  • Master Facility Table (MFT) Onboarding Facilities in U.S Territories: Provides site administrators the ability to add facilities located in the U.S territories of Guam, Puerto Rico, U.S Virgin Islands, American Samoa, and Northern Mariana Islands.
  • MFT Reason for Inactivation: Provides site administrators the ability to enter a specific reason for inactivating a facility.

To accompany this release, an updated BioSense Platform User Manual for the Access & Management Center has been posted in the NSSP Technical Resource Center.

Questions? Please submit a ticket to the NSSP Service Deskexternal icon.

Commercial Lab Data Dictionary

The September Access & Management Center (AMC) release will include provisioning of data from six commercial laboratories. As part of this work, the NSSP team has developed a companion dictionary that will include:

  • Processing rules for Raw and Processed data by Order and Result, and
  • Processing rules for Lab Data in ESSENCE by Order, Result, and paired Order–Result testing event, or Accession ID.

The commercial laboratories participating in NSSP are anonymized as part of data processing and referred to as labs A, B, C, D, E, and F. The dictionary requirements for data elements are shown in the table below.

Commercial Laboratory Tables and Data Flow

Tab

Name Description
 

1

Lab A, C, F Lab_Raw Summary table describes data elements available in the BioSense Platform Laboratory message activity “Raw” table for commercial labs A, C, and F. Note: All facilities in this table send using HL7 format.
 

2

Lab A, C, F Lab_Order Summary table describes data elements available in the BioSense Platform Laboratory ORM (Test order message) analytic table for commercial labs A, C, and F. Note: All facilities in this table send using HL7 format.
 

3

Lab A, C, F Lab_Result Summary table describes data elements available in the BioSense Platform Laboratory ORU (Test result message) analytic table for commercial labs A, C, and F. Note: All facilities in this table send using HL7 format.

4

Lab B, D, E Lab_Raw Summary table describes data elements available in the BioSense Platform Laboratory message activity “Raw” table For labs A, B, D, and E.

5

Lab B Lab_Order Summary table describes data elements available in the BioSense Platform Laboratory ORM (Test order message) analytic table for Lab B.

6

Lab B Lab_Result Summary table describes data elements available in the BioSense Platform Laboratory ORU (Test result message) analytic table for Lab B.

7

Lab B File Layout Summary table describes the data elements included in the flat file provided from Lab B, with additional information on how fields are populated.

8

Lab D Lab_Order Summary table describes data elements available in the BioSense Platform Laboratory ORM (Test order message) analytic table for Lab D.

9

Lab D Lab_Result Summary table describes data elements available in the BioSense Platform Laboratory ORU (Test result message) analytic table for Lab D.

10

Lab D File Layout Summary table describes the data elements included in the flat file provided from Lab D, with additional information on how fields are populated.

11

Lab E Lab_Order Summary table describes data elements available in the BioSense Platform Laboratory ORM (Test order message) analytic table for Lab E.

12

Lab E Lab_Result Summary table describes data elements available in the BioSense Platform Laboratory ORU (Test result message) analytic table for Lab E.

13

Lab E File Layout Summary table describes the data elements included in the flat file provided from Lab E, with additional information on how fields are populated.

14

Lab_Error Summary table describes data elements and errors available in the BioSense Platform Lab_Error table.

15

Lab_Flat_Problem Summary table describes data elements and errors available in the BioSense Platform Lab_Flat_Problem table.

16

Lab Order Essence Summary table describes data elements and processing rules for the ESSENCE Lab Order tables.

17

Lab Result Essence Summary tables describes data elements and processing rules for the ESSENCE Lab Result tables.

18

Essence Lab By Accession ID Summary tables describes data elements and processing rules for the ESSENCE “Cache Lab By Accession ID Table base” (also known as Lab data details).

Introducing Availability of Mortality Data

Analysts, epidemiologists, and others who rely on the National Syndromic Surveillance Program (NSSP) to do their work every day will be excited to learn that NSSP–ESSENCE can now incorporate electronic mortality data. Mortality data can be combined with other health-related data for enhanced surveillance and response to public health threats and events. A noteworthy feature is the inclusion of both literal cause of death fields and ICD-10 codes. The literal cause of death fields provide the free text cause of death recorded on the death certificate at time of death. Like the “chief complaint” field within emergency department data, these fields can be queried to learn details about the health event of interest beyond final coded results. Analysts will be able to query comprehensive cause of death data—from literal fields to final ICD-10 codes—to support surveillance activities, thereby improving situational awareness and response.

To support the development of mortality data within NSSP, three public health jurisdictions* participated in a pilot to test processing, the user interface, data governance standards, and data receipt mechanisms. Pilot jurisdictions shared their mortality data with NSSP through three different methods. One jurisdiction’s data were pulled via an application programming interface (API) from a local instance of ESSENCE, mapped to an Inter Jurisdictional Exchange (IJE) format, and processed. The second jurisdiction’s data were retrieved through a secure file transfer protocol (SFTP). The third jurisdiction’s data were pulled from the National Association for Public Health Statistics and Information Systems State and Territorial Exchange of Vital Eventsexternal icon (NAPHSIS-STEVEexternal icon) mailbox to which NSSP was granted access. The pilot activities have helped the NSSP team define requirements and refine the mortality data module to enhance the user experience within ESSENCE. This new analytics and surveillance capability will allow public health professionals to translate insights about mortality into timely action.

NSSP sites interested in integrating electronic mortality data into NSSP may contact nssp@cdc.gov. The standard NSSP Data Use Agreement (DUA) and a template of the IJE file format will be shared upon request. If staff in the public health department’s vital records office are unfamiliar with NSSP DUAs, they might ask to be included in the process. Upon request, NSSP will provide additional information to share with them about the program. NSSP appreciates the interest, engagement, and contributions of public health jurisdictions across the country that help us improve our resources and service.

*The NSSP team thanks the analysts, health scientists, and epidemiologists who work in the Kansas, Oregon, and Washington state public health departments for taking time to pilot test mortality data.

MFT Enhancement Adds “Reason for Inactivation”

To further enhance the Master Facility Table (MFT) and improve long-term reporting, the NSSP team has added a “Reason for Inactivation” field. Previously, sites were asked to enter the reason a facility was being inactivated in the “Site Comments” field. With this new field, the reason will be captured separately and standardized. The following reasons for inactivation are available:

Reasons for Inactivation
  • Closed
Facility has permanently closed.
  • Merged
Facility data has been merged within another facility’s data feed.
  • 90-Day Inactive
Automated 90-day Deactivations
  • Temporary
Facility has temporarily stopped sending data but is expected to resume.
  • Voluntary
Facility has stopped sending data without certainty that data flow will resume.

When inactivating a facility, please enter the date the facility stopped sending data in the “Date Inactivated” field. This field is not the same as the “Date Deactivated” field, which provides a date stamp indicating when the facility status was changed in the MFT. Any additional information should still be recorded in the “Site Comments” field.

New Data Sources: DoD and VA

The NSSP team has been working to add data from the U.S. Department of Defense (DoD) and U.S. Department of Veterans Affairs (VA) to the BioSense Platform. Recently, more than 400 DoD facilities were successfully onboarded to the BioSense Platform’s production environment. Members of the NSSP onboarding team are now collaborating with VA staff to onboard more than 150 emergency department and urgent care facilities across the country. Work is proceeding with both the DoD and VA for these partners to conduct site-level surveillance efforts, and more information will be provided as these data sources become available.

New Site Onboarding: Fall Window

NSSP is engaging new sites for this fall’s Onboarding Window, which kicks off the week of October 5, 2020. We encourage representatives from any sites or counties that are not yet onboard to contact NSSP if interested in participating in the upcoming New Site Onboarding window.

Onboarding Guides

NSSP Develops New Onboarding Guides

The NSSP onboarding team has been developing new onboarding guides to help sites plan for and navigate the onboarding process. Sites joining the NSSP’s BioSense Platform for the first time can refer to the New Site Onboarding Guide. Existing sites onboarding new facilities to the NSSP BioSense Platform will have a New Facility Onboarding Guide. Both guides are being finalized for release this fall.

Page last reviewed: August 12, 2020