Swine Diagnostic Data Standardization Project:

Core deliverables

Leticia Linhares, DVM, MSVeterinary Specialist Veterinary Diagnostic Laboratory

Iowa State University

Core deliverables – Practical application

• Veterinary Messaging Portal

– LOINC library tests results that can be messaged

– LOINC search: appropriate LOINC codes –

laboratory common vocabulary

– Validator: troubleshoot messaging capabilities

• NAHLN 2.0 message schema update

Core deliverables – Practical application

• ISU internally using LOINC/Snomed ct codes

to support researchers on epidemiological

analyses

• Swine Disease Reporting System (SDRS)

• Data Standardization supporting different

analytical tools:– Animal Health Monitoring and Evaluation System (AHMES)

– Bioportal

– PowerBI

– Tableau

– AgView*

Swine Disease Reporting System

• SHIC Funded on 2017 - provides monthly reports on domestic swine disease monitoring based on aggregated VDL data.

• Objective: to aggregate swine diagnostic data from participating reporting VDLs, and report in an intuitive format (web dashboards), describing dynamics of disease detection by pathogen or disease syndrome over time, specimen, age group, and geographical space.

(SDRS)

Daniel Linhares and Giovani Trevisan

Data organized at an accession ID

case level

Porcine test results retrieved from participating VDLs

Advisory Council – input from 10 field veterinarians

Results uploaded online at Power BI

Monthly reports at SHIC website

PRRSV

TGEV

PEDV

PDCoV

Filters available:

✓ Specimen;

✓ Age group;

✓ Tissue presence;

✓ State;

✓ Year;

✓ Season

Trevisan, 2018

SDRS – October Report

• PRRS, PDCoV, PEDV cases (data

aggregation from ISU*, KSU,SDSU ADRDL

and UMN*). – ISU has a fully automated system which allows for

messaging to SDRS

– UMN is in the process of sending test messages to SDRS

• Results from 2015 to September of 2018

In the oven…

• Veterinary Health Information Standards– LOINC search tool – more intuitive

– Validator/Receiver

– Extend LOINC codes for other species: Avian, Bovine and

Equine

• Data Warehouse

Veterinary Diagnostic Portal and

Data Warehouse for Data Mining Applications

VDL

VDL

VDL

VDL

Data Warehouse

• Tags Data

➢Categorical terms

and increments

• Collates

• Archives in

Searchable Format

• Alias Management

➢Clinic

➢Owners

➢Categorical terms

BI Software(Power BI®)

BI Tool(Tableau®)

BI Tool(Domo®)

BI Tool (BioPortal®)

Modular suite of tools being built for use and compatibility with one or many VDLs

and Business Intelligence (BI) software applications.

Access Manager& User

Interface• Permissions

Access

• User and Roles

• User Interface

➢ Data Query

➢ Data Dump

• Web Service

Receiver• Receives HL7

Message

- Standardized Dx

Data

• Validates Message

• Provides Notification

to Sender

• Parses to Staging

Database

• Baseline Permissions

User defined output

SDRS HL7 Message Receiver and

Validator Demonstration

Validator

• Validates the message to insure the xml is

formatted correctly.

• Validates the message against the schema

provided in MSH.21.EI.1. The host must have

the schema in their library.

• Can validate several fields against

customizable lists. Each validation item can be

turned on or off. The validation consists of does

the value exist in the validation database or not.

Validator (cont.)

• Will provide an appropriate ACK message back

to the sender.

• Will include any Schema or Database

validation errors that were found along with

what field they occurred in.

Encoded

Valid Test Message - example

Message sent to the correct place and accepted

ACK response - Message passed to the validation

Invalid Test Message - example

ACK response - Message did not pass to the validation

Message sent to the correct place and accepted

Receiver

• The receiver and validator are written in ASP.NET

Core which is a light weight framework and is cross

platform.

• It can be hosted on Windows, Linux and MacOS.

Not all have been tested yet.

• Allows an api-key to be used to send messages

• Provides the whole message that was received along

with more common terms for each of the fields.

Receiver (cont.)

• Will provide an HTTP response back indicating

if the request was successful or not. This does

not mean the message was successful.

• Allows users to lookup any messages sent to

the receiver by api-key, MSH.10 or

AccessionID.

• Provides the whole message that was received

along with more common terms for each of the

fields.

Checking Messages Received

Find an Error on Invalid Messages

NEG

Take-home messages

• LOINCs library, LOINC search engine, HL7

message validator, and the updated HL7

schema are available for use by VDLs across

the USDA NAHLN.

• Critical building blocks in furthering

the connectivity of veterinary

diagnostic information needed to

support the current and future needs

of the US Pork Industry.

Acknowledgements

Rodger Main - ISU VDL

Gary Anderson - KSU VDL

Jane Hennings – SDSU ADRDL

Jerry Torrison & Stephanie Rossow – UMN VDL

Sarah Tomlinson – USDA NAHLN

* Mike Martin – Clemson University

15 month, Infrastructure Development Project

Funded via Swine Health Information Center & USDA

Commenced fully in July 2016

* Dr. Martin is providing the primary technical guidance and support to this project. Mike is a nationally recognized leader and expert in veterinary diagnostic informatics and HL-7 messaging.

Questions?