swine diagnostic data standardization project: core ...€¦ · core deliverables –practical...
TRANSCRIPT
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Swine Diagnostic Data Standardization Project:
Core deliverables
Leticia Linhares, DVM, MSVeterinary Specialist Veterinary Diagnostic Laboratory
Iowa State University
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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
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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*
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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
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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
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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
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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
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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
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SDRS HL7 Message Receiver and
Validator Demonstration
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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.
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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.
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Encoded
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Valid Test Message - example
Message sent to the correct place and accepted
ACK response - Message passed to the validation
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Invalid Test Message - example
ACK response - Message did not pass to the validation
Message sent to the correct place and accepted
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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.
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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.
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Checking Messages Received
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Find an Error on Invalid Messages
NEG
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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.
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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.
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Questions?