06/04/07 maine hetl maine hetl lessons learned with environmental/chemical lims implementation and...

06/04/0706/04/07 Maine HETLMaine HETL

Maine HETL Lessons Learned with Maine HETL Lessons Learned with Environmental/Chemical LIMSEnvironmental/Chemical LIMS

Implementation and Data ExchangeImplementation and Data Exchange Jack Krueger, Chief, Maine Health and Jack Krueger, Chief, Maine Health and Environmental Testing Laboratory (HETL)Environmental Testing Laboratory (HETL)

Division of Public Health SystemsDivision of Public Health Systems

Maine CDC & PMaine CDC & P


Also, Provide Some Examples of the Technology Also, Provide Some Examples of the Technology and Terminology Used by Lab Managers to and Terminology Used by Lab Managers to

Integrate Their Lab Into the National Laboratory Integrate Their Lab Into the National Laboratory Response Networks for ALL-HazardsResponse Networks for ALL-Hazards

This Session Will Provide An Overview Of Data This Session Will Provide An Overview Of Data Exchange Associated With Exchange Associated With

Environmental/Chemical Laboratory Homeland Environmental/Chemical Laboratory Homeland Security Information.Security Information.


Laboratory Data Component of Laboratory Data Component of Homeland SecurityHomeland Security

Goal:Goal:

To develop and To develop and implement an implement an electronic data flow electronic data flow

directly from directly from laboratories laboratories

to multiple homeland to multiple homeland security agenciessecurity agencies


Components of this GoalComponents of this Goal

– Connectivity for a national network of Connectivity for a national network of laboratories, including public and laboratories, including public and private laboratories at the federal, state, private laboratories at the federal, state, and local levelsand local levels

– Establish a laboratory network to meet Establish a laboratory network to meet testing needs for threats to public safety testing needs for threats to public safety

– Support response to threats by Support response to threats by conducting analyses and providing high conducting analyses and providing high quality, timely results.quality, timely results.


Why Laboratory Data Exchange?Why Laboratory Data Exchange?

The exchange of Laboratory Data The exchange of Laboratory Data within the state, to other states, and within the state, to other states, and to federal entities provides critical to federal entities provides critical surveillance datasurveillance data

There are many data exchanges, few There are many data exchanges, few are interoperable to multiple federal are interoperable to multiple federal agencies agencies

As an example: An interoperable data As an example: An interoperable data exchange aligns with HSPD 9exchange aligns with HSPD 9


HSPD 9HSPD 9 Homeland Security Presidential Directive 9 (HSPD 9) directs Homeland Security Presidential Directive 9 (HSPD 9) directs

EPA to:EPA to:

– ““develop develop robust, comprehensive, and fully robust, comprehensive, and fully coordinated surveillance and monitoring coordinated surveillance and monitoring systems . . . for . . . water qualitysystems . . . for . . . water quality that that provide early detection and awareness of provide early detection and awareness of disease, pest, or poisonous agents”disease, pest, or poisonous agents”

– ““develop develop nationwide laboratory networks nationwide laboratory networks for . . . water qualityfor . . . water quality that integrate existing that integrate existing Federal and State laboratory resources, are Federal and State laboratory resources, are interconnected, and utilize standardized interconnected, and utilize standardized diagnostic protocols and procedures”diagnostic protocols and procedures”


There are many Networks: As an example, for a Food Related Event here is a Potential Concern:•If it’s the Ketchup, Mayo, Bun send the data to FDA•If it’s the Hamburger or Lettuce send the data to USDA•Did someone eat it? Test it at the Public Health Lab and report to CDC/State EPI•Was the Food Contaminated due to Environmental Concerns: Send the Data to the EPA


Networks/MessagesNetworks/Messages

LRN (Laboratory Response Network –LRN (Laboratory Response Network –BT and CT), FERN (Food Emergency BT and CT), FERN (Food Emergency Response Network), NAHLN (National Response Network), NAHLN (National Animal Health Lab Network), eLRN Animal Health Lab Network), eLRN (Environmental Lab Response (Environmental Lab Response Network), NPDN (National Plant Network), NPDN (National Plant Diagnostic Network)Diagnostic Network)

Messages-HL-7, CDX (eDWR/SEDD), Messages-HL-7, CDX (eDWR/SEDD), eLEXneteLEXnet


Example: EPA’s Exchange Example: EPA’s Exchange NetworkNetwork

An Internet and standards-based

method for exchanging

environmental information between

partners.Data standardsPartners agree on exchange data type, frequency, and method

•Trading Partner Agreements •Registered XML schema •Partners exchange data over a secure network via each partner’s data transfer point, or “Node”•Facilitated with NAAS- National Authentication and Authorization Service


ICLN:ICLN:Integrated Collaboration of Integrated Collaboration of

Laboratory NetworksLaboratory Networks


Before A Lab Can Create An Electronic Message Before A Lab Can Create An Electronic Message To Be Sent To a Data Exchange Network, A LIMS To Be Sent To a Data Exchange Network, A LIMS

Is NecessaryIs Necessary

Today I Wish to Focus On The Today I Wish to Focus On The Environmental/Chemical Laboratory LIMS and Data Environmental/Chemical Laboratory LIMS and Data

Exchange.Exchange.

Many in Public Health Have LIMS Developed for Many in Public Health Have LIMS Developed for Infectious DiseaseInfectious Disease

Some Discussion About the Comparison of the Some Discussion About the Comparison of the Infectious Disease LIMS and the Infectious Disease LIMS and the

Environmental/Chemical LIMS Is UsefulEnvironmental/Chemical LIMS Is Useful


Infectious Disease Data & Env/Chemical DataInfectious Disease Data & Env/Chemical Data

LIMS And Data Exchange For These Two Types Of Analysis LIMS And Data Exchange For These Two Types Of Analysis Have Much In Common:Have Much In Common:

Both Addressed in Public Health Informatics LIMS Both Addressed in Public Health Informatics LIMS Requirements and Business Processes Requirements and Business Processes

Both track samples/specimens/QC Data, Results, and Both track samples/specimens/QC Data, Results, and provide business management functions provide business management functions

Each have Data Standards For Analytical ResultsEach have Data Standards For Analytical Results Customers typically request the data in different formats- Customers typically request the data in different formats- Vocabulary DefinitionsVocabulary Definitions Packaging Of Data Into A Data MessagePackaging Of Data Into A Data Message The Need For A Node Or Portal To Send Data Securely [A The Need For A Node Or Portal To Send Data Securely [A

Node is a Web server (hardware with appropriate Node is a Web server (hardware with appropriate software) that provides a point for exchanging information software) that provides a point for exchanging information over the Internet. ]over the Internet. ]


Infectious Disease Data Exchange for Infectious Disease Data Exchange for CDCCDC

Think of it this way. HL7 is the letter, ebXML is Think of it this way. HL7 is the letter, ebXML is the envelope (with the address, return address, the envelope (with the address, return address, container for the letter, etc), and PhinMS is the container for the letter, etc), and PhinMS is the postal carrier (requires envelopes to look just so postal carrier (requires envelopes to look just so in order to deliver them).in order to deliver them).

PhinMS uses a certain kind of message wrapper PhinMS uses a certain kind of message wrapper and protocol, called ebXML in order to deliver and protocol, called ebXML in order to deliver messages.ebXML is payload agnostic, in that it messages.ebXML is payload agnostic, in that it can carry any kind of message. We just happen can carry any kind of message. We just happen to be using HL7.to be using HL7.


1.The Security LayerHypertext Transfer Protocol (HTTP)/Secure Socket Layer (SSL) or Public Key Infrastructure (PKI) 2.The Transport LayerThe standard transport mechanism for Web service messages is HTTP 3.The Messaging Envelope Simple Object Access Protocol (SOAP) as the envelope layer for Web service messaging. The SOAP envelope is further broken down into two compartments: The SOAP Header and Body. The Header contains information regarding the sender of the message. The SOAP Body contains the payload, or document (generally an XML instance document/schema). This can also contain attachments, generally in DIME or SWA formats

Looked at in another way:


Major Differences in the Infectious Disease Major Differences in the Infectious Disease and Environmental/Chemical LIMSand Environmental/Chemical LIMS

Environmental/Chemical LIMS:Environmental/Chemical LIMS: Results are numerical with significant statistical QC data Results are numerical with significant statistical QC data

included with the analytical resultincluded with the analytical result Data tends to be site centric vs. patient centricData tends to be site centric vs. patient centric Environmental data is subject to significant regulatory Environmental data is subject to significant regulatory

requirementsrequirements Results are typically methods based rather than Results are typically methods based rather than

performance based and results require links to multiple performance based and results require links to multiple method referencesmethod references

Very Rigorous Certification/Accreditation StandardsVery Rigorous Certification/Accreditation Standards Significant instrument interfaces are utilizedSignificant instrument interfaces are utilized Results have units, MDL’s, RL’s, Qualifiers, and sometimes Results have units, MDL’s, RL’s, Qualifiers, and sometimes

ranges of values ranges of values Results typically include multiple analytes (often over 50 on Results typically include multiple analytes (often over 50 on

a single sample) with different criteria for each analytea single sample) with different criteria for each analyte


Maine’s LIMS ExperienceMaine’s LIMS Experience

Maine has an early version of Starlims Sunrise Maine has an early version of Starlims Sunrise Version 9. Version 9.

One year to build, and live for 2 Years, NELAP One year to build, and live for 2 Years, NELAP Accredited, used for DW, Waste, Chemical Accredited, used for DW, Waste, Chemical Terrorism, Radiation, Env Micro, ForensicsTerrorism, Radiation, Env Micro, Forensics

Except for “Raw” data, all information associated Except for “Raw” data, all information associated with analytical reside in the DB, analytical data is with analytical reside in the DB, analytical data is imported electronically from instruments, the imported electronically from instruments, the LIMS “manages” which data meets reporting LIMS “manages” which data meets reporting criteria and Quality Assurance Objectives criteria and Quality Assurance Objectives

Analytical Data can be exported internally or Analytical Data can be exported internally or remotely in an XML message and this message remotely in an XML message and this message can be securely transported to other Trading can be securely transported to other Trading Partners/networks.Partners/networks.


Data Exchange Requires Partnering Data Exchange Requires Partnering One Example is EPA’s Regional One Example is EPA’s Regional

Laboratory Response PlanLaboratory Response Plan

The purpose of the RLRP is to The purpose of the RLRP is to establish a comprehensive, regional, establish a comprehensive, regional, all-hazards approach to drinking all-hazards approach to drinking water laboratory response across a water laboratory response across a spectrum of activities including spectrum of activities including preparedness, response, preparedness, response, remediation, and recoveryremediation, and recovery


Laboratories that participate in regional Laboratories that participate in regional response networks need to be able to response networks need to be able to communicate analytical results in a communicate analytical results in a standardized, interoperable and secure standardized, interoperable and secure mechanism. This communication is mechanism. This communication is particularly important during times of particularly important during times of emergency. A highly desirable goal for the emergency. A highly desirable goal for the Northeast state laboratories is the use of a Northeast state laboratories is the use of a standardized electronic message to standardized electronic message to communicate between an analytical service communicate between an analytical service requester (ASR), a primary response requester (ASR), a primary response laboratory (PRL), and mutual support laboratory (PRL), and mutual support laboratory (MSL). laboratory (MSL).


Further, the acceptance of a single Further, the acceptance of a single nationally standardized lab reporting nationally standardized lab reporting format will greatly serve the format will greatly serve the community of developers of community of developers of Laboratory Information Management Laboratory Information Management Systems (LIMS). Currently, the Systems (LIMS). Currently, the existence of multiple data formats existence of multiple data formats has compromised commercial has compromised commercial production of tools to produce production of tools to produce electronic messaging.electronic messaging.


The New England State The New England State Lab Directors at a Recent Lab Directors at a Recent

RLRP Meeting Have RLRP Meeting Have Recommended Key Recommended Key

Components of Components of Standardized Lab Standardized Lab

ReportingReporting


1.1. Accept the ESAR data standard Accept the ESAR data standard (Environmental Sampling and Analytical (Environmental Sampling and Analytical Results, developed through the Results, developed through the Environmental Data Standards Council) Environmental Data Standards Council) and agree on the minimum data set (a and agree on the minimum data set (a subset of all elements) for analytical and subset of all elements) for analytical and metadata. A multi-media data standard metadata. A multi-media data standard is recommended, so that different is recommended, so that different formats are not required for different formats are not required for different matrixes or programs. matrixes or programs.

Focus on a module of information Focus on a module of information provided by Laboratories intended to be provided by Laboratories intended to be reused by any schema requiring reused by any schema requiring Sampling Analysis and ResultsSampling Analysis and Results


A schema in this case can be a A schema in this case can be a description of the data represented description of the data represented within a database. The format of the within a database. The format of the description varies but includes a description varies but includes a table layout for a relational database table layout for a relational database or an entity-relationship diagram. or an entity-relationship diagram.


3.3. A future electronic format should A future electronic format should include quality control data, but this include quality control data, but this inclusion can be delayed (using the inclusion can be delayed (using the minimal data set of key elements) minimal data set of key elements) until universally implemented. until universally implemented. Certification/accreditation of Certification/accreditation of laboratories can serve as the laboratories can serve as the intermediate function for assessing intermediate function for assessing quality. quality.


4.4. The initial technical implementation The initial technical implementation of the data standard should be the of the data standard should be the XML schemas: XML schemas:

eDWR (electronic Drinking Water eDWR (electronic Drinking Water Results) and/or Results) and/or

SEDD (Staged Electronic Data SEDD (Staged Electronic Data Deliverables) stage 1. Deliverables) stage 1.

Both of these technical Both of these technical implementations exist and have implementations exist and have unique advantages. unique advantages.


Note: Extensible Markup Language (XML) Note: Extensible Markup Language (XML) is a flexible language for creating common is a flexible language for creating common information formats and sharing both the information formats and sharing both the format and content of data over the format and content of data over the Internet and elsewhere. XML is a Internet and elsewhere. XML is a formatting language recommended by the formatting language recommended by the World Wide Web Consortium (W3C). An World Wide Web Consortium (W3C). An XML schema defines the structure of an XML schema defines the structure of an XML document. An XML schema defines XML document. An XML schema defines things such as which data elements and things such as which data elements and attributes can appear in a document; how attributes can appear in a document; how the data elements relate to one another; the data elements relate to one another; whether an element is empty or can whether an element is empty or can include text; which types of data are include text; which types of data are allowed for specific data elements and allowed for specific data elements and attributes; and what the default and fixed attributes; and what the default and fixed values are for elements and attributes. values are for elements and attributes.


TWO EPA Adopted SCHEMA’s—

SEDD is Staged Electronic Data Deliverable. Its origins are in the Superfund program, with strengths in capturing data quality information and more complete metadata.

eDWR – Electronic Drinking Water Reporting. This was primarily focused on drinking water, is linked to SDWIS, but does include a “matrix” tag


5.5. Both of the implementations Both of the implementations [eDWR and SEDD] share the same [eDWR and SEDD] share the same minimum data set of key elements. minimum data set of key elements. For emergency and many For emergency and many applications, their use can be applications, their use can be interchangeable. A conversion tool interchangeable. A conversion tool from one to the other would be very from one to the other would be very helpful. This conversion tool will helpful. This conversion tool will provide a crosswalk between the provide a crosswalk between the two technical implementations.two technical implementations.


6.6. Interoperability and security must be Interoperability and security must be addressed. For this reason:addressed. For this reason:

– The data must feed to the SDWIS-state The data must feed to the SDWIS-state application (EPA-OW); and,application (EPA-OW); and,

– Comply with data exchange Network Design Comply with data exchange Network Design Rules (AQS (Air Quality Subsystem, FRS Rules (AQS (Air Quality Subsystem, FRS (Facility Registry System), TRI (toxic release (Facility Registry System), TRI (toxic release inventory), SDWIS Safe Drinking Water inventory), SDWIS Safe Drinking Water Information System, etc). Information System, etc).

– The Data Exchange Network is an Internet-The Data Exchange Network is an Internet-based system used by state, tribal, and based system used by state, tribal, and territorial partners to securely share territorial partners to securely share environmental and health information with environmental and health information with one another and EPAone another and EPA


7.7. Use of the existing Use of the existing Environmental Information Environmental Information Exchange Network may be an Exchange Network may be an efficient use of resources. 48 states efficient use of resources. 48 states have EPA Nodes that can be used have EPA Nodes that can be used as to exchange data between labs as to exchange data between labs and data consumers and data consumers


So here is a challenge to you So here is a challenge to you all……………….all……………….


Partner I (Data Consumer)

Data Service

Requestor

Partner II (Data Provider)Make Data Request

to Partner II via Query

Node

Data Service Registry

Partner II registers data

servicesPartner I discovers data

services

Partner I retrieves Meta Data for data

service 12

4

Database

Request datafrom DB basedon parameters

5

Data returnedto Node

6

3

7

XML Responsesent to Partner IData Format

Converter

Database

Data Storage in DB

8

9

Data Display inStylesheet/Web Page

/ GIS

Data Formatting For Display

10a

Overview of Homeland Security Data Exchange Toolkit

A

B

C

D

E

Legend for Tools

A

B

C

D

E

Data Service Registry

Data Service Requestor

XML Schema

Data Format Converter

Data Display Tool

Trading Partner Agreement (TPA) / Flow Configuration Document (FCD)

10b

F

F

F

F

F


Questions and CreditsQuestions and Credits

????

??????

Jack Krueger 207-287-2727 [email protected]

EPA Homeland Security Challenge Grant

enfoTech & Consulting Lawrenceville, NJ

06/04/07 maine hetl maine hetl lessons learned with environmental/chemical lims implementation and...

Documents

laboratory data exchange

exchange of laboratory

data exchange network

interoperable data exchange

exchange data type

overview of data exchange

data standardspartners

data exchanges