Initial Prototype for Clinical Data

Normalization and High Throughput Phenotyping

SHARPn F2F

June 30,2011

PurposeDemonstrate a proof of concept solution, based on

new tools, technology, models and methods.

The prototype demonstrates:– The ability to push unsolicited data using NwHIN exchange

protocols– Conversion and normalization of HL7 2.x lab messages to XML

clinical element model (CEM) instances– Conversion and normalization of HL7 2.x medication orders to

CEMs.– Extraction of medication CEM instances from narrative clinical

documents using NLP processing– Persistence of CEM instances in a light weight SQL database– Phenotype processing across the CEM database utilizing the Drools

rules engine

High Level Architecture Diagram

1. Use Data from IHC (De-Identified) HL7 2.x messages2. Send data into Mirth Connect on the IHC side3. Create NwHIN Document Submission (XDR) message using HL7 2.x message as payload4. Send Document Submission (XDR) message from Mirth to IHC NwHIN Aurion Gateway5. Send XDR message from IHC Aurion Gateway to SHARP NwHIN Aurion Gateway6. Send XDR message from SHARP NwHIN Aurion to Mirth Connect6a. Send Mayo HL7 2.x Lab Messages & Clinical Documents to Mirth Connect 7. Process HL7 2.x messages and/or clinical documents in the UIMA Pipelines, to normalize and transform into Clinical Element Model (CEM) instances8. Send the resulting XML instance of Clinical Element Model (CEM) to Mirth Connect9. Persist Clinical Element Model (CEM) instances to MySql database.10. Perform phenotype processing on the CEM instance database.

SHARP Processing Sequence

10

IHC(Backend CDR

Systems)

MirthConnect

IHC NwHINAurion

Gateway

SHARP NwHINAurion

Gateway

MirthConnect

UIMAPipeline

CEM Instance Database

1

2

3

4

5

6

7

8

9

6a

Firewall Firewall

MayoEDT System

Mirth Connect

Enables information flow and transformationMirth channel receives message from some source,

transforms it, and routes it to one or more destinations

Product is open sourceNwHIN with Aurion/CONNECT can be source or

destination of a channelUsed to store CEM Instances to the databaseCan be used to route data to other locations or

databases

Mayo EDTMayo EDT

cTAKEScTAKEScTAKEScTAKES

cTAKEScTAKES

CDA for Meds

HL7 for labsMirthMirth

CEM

SharpDbSharpDb

High level flow - Mayo

cTAKES(NLP)

cTAKES(NLP)

Mayo EDTMayo EDTAdminDiagnosis

processorAdminDiagnosis

processorTabular data CEM

Custom UIMA

pipeline

Custom UIMA

pipeline

Custom UIMA

pipeline

Custom UIMA

pipeline

Configurable UIMA

pipeline

Configurable UIMA

pipelineCEM

Medication to CEM - Mayo data

CDACDACDA-

InitializerCDA-

Initializer

SentenceAnnotatorSentenceAnnotator

TokenizerAnnotatorTokenizerAnnotator LVGLVG

ContextDependentTokenizer

ContextDependentTokenizer

POSTaggerPOS

Tagger ChunkerChunker

DictionaryLookup

Annotator

DictionaryLookup

Annotator

DrugMention

Annotator

DrugMention

Annotator

DrugCEMCAS

Consumer

DrugCEMCAS

Consumer

MirthMirth

SharpDbSharpDb

cTAKES UIMA Annotators (NLP)

Patient count – 10000CDA document count - 360452CEM count for medication – 3442000

IHC-Medication, Mayo, IHC LAB to CEM

HL7MedsHL7

Meds

HL7Initializer

HL7Initializer

IHC-GCNTO-

RXNORMAnnotator

IHC-GCNTO-

RXNORMAnnotator

DrugCEMCAS

Consumer

DrugCEMCAS

Consumer

MirthMirth

SharpDbSharpDb

HL7LabsHL7Labs

HL7Initializer

HL7Initializer

Generic-LAB-

Annotator

Generic-LAB-

Annotator

LABCEMCAS

Consumer

LABCEMCAS

Consumer

MayoLOINC

resource

MayoLOINC

resource

IHCLOINC

resource

IHCLOINC

resource

IHCRXNORMresource

IHCRXNORMresource

New UIMA Process Nodes

SharpDB a CEM Instance Database

Phenotyping (Drools)

Business Logic

Clinical Element

Database

List ofDiabetic Patients

Data Access Layer

Transformation Layer

Inference/ workflow

Engine (Drools)

Service for Creating Output (File, Database,

etc)

Transform physical representation Normalized logical representation (Fact Model)

Completed Work Installation of informatics “SHARP” Cloud system at Mayo Installation and configuration of tools on IHC side and

SHARP Cloud “Tracer Message” processing

– Used to test communication throughout system– Successful transfer using NwHIN/Aurion of test message

between IHC & Mayo 30 de-id IHC patients through pipeline/Drools end-to-end

– 134 Thousand CEMS generated Extraction and message generation for 10,000 patients Processing of 10,000 patients Meds, Labs, Billing data

– 15 Million CEMS generated Conversion to selected CEM models via UIMA framework Persisted from CEM to MySQL

Completed Work (Cont.)

Produced New XML Schemas for CEM Models– Standard lab panel– Ambulatory medication order– Administrative diagnosis

These three models were usedfor the prototype experiment.

Excerpt of Lab CEM instance

CEM Search Tool:http://intermountainhealthcare.org/cem

• Mirth Enhancements– Implemented NwHIN XDR connector capability– Implemented UIMA connector capability– Created NwHIN Aurion XDR adapter

• Channels Created

Completed Work (Cont.)

Sample XDR Channel Channel that receives HL7 2.x message, places the message as the payload of an XDR message and sends it to a remote NwHIN gateway

ReceiveXDRMessage Receives an XDR message from Mirth and extracts the HL7 2.x message

CemAdminDxtoDatabase Receives an XML instance of the administrative diagnosis CEM and persists it to the database

CemLabToDatabase Receives an XML instance of a standard lab panel CEM and persists it to the database

CemMedicationToDatabase

Receives an XML instance of a medication CEM and persists it to the database

Dual Security Certificate Exchange

SHARP/Mayo Cloud

Intermountain Healthcare

Mirth Aurion Gateway

SHARP Aurion Gateway

IHC Proxy

SHARP Proxy

Mirth

Internet

Thank You!

Calvin BeebeChristopher ChuteCraig ParkerCui TaoCyndalynn TilleyDavid MeadDingcheng LiDonna IhrkeGerald BortisGuergana Savova

James MasanzJeff FerraroJohn HolmanJon TeichrowKevin BruceKyle MarchantLes WestbergMargarita SordoMat BockolMichael Turk

Mitch DempseyNathan DavisPei ChenSean MurphySridhar DwarkanathStan HuffSusan WelchTim PetersTom OnikiVinod Kaggal