Welcome to Introduction to Laboratory Informatics: Life of a Result
This course is the second installment of a two-part introductory course on laboratory informatics. You will
continue where we left off in the Life of a Specimen course, and follow the life of a result both inside and
outside of the laboratory from the time specimen testing is complete.
Course Purpose:
• Build a foundation in the core concepts of laboratory
• informatics for laboratory professionals
• Explain laboratory informatics in the context of public health
NOTE: This course assumes that you have previously taken the Introduction to Laboratory Informatics: Life of a
Specimen course.
Learning Objectives
After completing this course, you will be able to:
• Identify where and how data and results are stored inside the laboratory
• Recognize how data and results are transmitted inside and outside the laboratory to stakeholders
• Identify two paths that data and results can follow to impact the health of individual patients and the
public
• Recognize how the proper recording, coding, storage, and transmission of data and results can impact
patient care and public health
• Identify what data standards are used, their purpose, and components involved
• Explain what Electronic Test Orders and Results (ETOR), Electronic Laboratory Reporting (ELR) and
Electronic Health Record (EHR) are and how they differ
NOTE: Access the "Competency Guidelines for Public Health Laboratory Professionals" to see how the course
learning objectives map to the Laboratory Informatics Competencies.
Laboratory Informatics Benefits
Laboratory informatics is essential to addressing the challenges within the public health field. Informatics affects
the public health continuum by:
• Informing patient care and management
• Driving public health surveillance and decision-making
• Guiding policy and programs
Achieving Benefits
1. Data Collection
• Identifying appropriate collection methods and data sources to support faster access to quality data in
the field.
2. Data Management
• Standardizing and sharing data across platforms and linking data with legacy systems and new systems,
while ensuring data privacy.
3. Data Analysis
• Establishing appropriate statistical and visualization applications for thorough and accurate analyses.
4. Data Interpretation
• Using analyses and results to drive public health policies and inform decision-making.
NOTE: Laboratory informatics enables the collection, sharing and analysis of vital data to help stakeholders
make informed decisions regarding healthcare and public health.
Stakeholders Outside the Laboratory
Many external stakeholders rely on timely and accurate data from the laboratory. These stakeholders affect
the public health landscape in different ways.
1. Healthcare Providers and Organizations
• Healthcare providers and organizations are those that have a direct impact on patient care and management. They
include staff in hospitals, physician offices and other clinical settings, as well as laboratory staff in those settings. These
individuals play an important role in the diagnosis and treatment of individual patients, which informs and affects
public health, particularly in cases of communicable diseases like TB.
2. State and Local Agencies
• Many local and state agencies, such as health departments, have key roles in disease surveillance, policy
development, interoperability and the provision of healthcare. They carry out these responsibilities at the
state and local level, helping to protect the health of the people within their jurisdictions from public
health threats and participating as key partners in national, regional and local public health efforts.
3. Other State and Local Public Health Laboratories
• Public health laboratories at the state and local level help protect the public's health through timely,
accurate and high quality laboratory testing. They often perform specialized testing that is not available
elsewhere, but that is critically important to public health. These laboratories (beyond the original testing
laboratory) serve as external stakeholders because they actively participate in test referral as well as
national and international public health surveillance and preparedness networks, serving a key role in
response to public health threats such as infectious disease outbreaks.
4. Federal Agencies
Many Federal agencies are both regulators and important users of laboratory data and systems that affect
public health. Key U.S. federal agencies include, but are not limited to, the following:
• Centers for Disease Control and Prevention (CDC)
• National Institutes of Health (NIH)
• Health Resources and Services Administration (HRSA)
• Food and Drug Administration (FDA)
• Environmental Protection Agency (EPA)
• United States Department of Agriculture (USDA)
• Substance Abuse and Mental Health Services Administration (SAMHSA)
• Agency for Healthcare Research and Quality (AHRQ)
• United States Agency for International Development (USAID)
Each agency has specific missions and goals; however, they each support the national public health system.
5. Other Stakeholders
• Other stakeholders include those who can influence the public health continuum, such as non-
governmental organizations (NGOs), international organizations, pharmaceutical companies, agriculture
and food companies, employer organizations, patients, and the public. These stakeholders obtain data
that they can act upon, which is typically aggregated and does not include any patient identifiers.
Where Do Data and Results Live?
❖ Laboratory data and test results need proper storage and management to be acted upon.
• Data and results can be stored in many places within the laboratory.
• All of the laboratory's testing data and results, along with patient and specimen information, can be
aggregated in a LIMS for better data integrity and enhanced ability to analyze and share results.
• This information is held in a relationship structure in the database called a schema.
• Data and results are recorded automatically through instrument interfacing or manually by laboratory
staff.
NOTE: Laboratory informatics cannot reach its full potential unless accurate, high quality data and results are
tracked and stored in a LIMS.
Life of a Specimen and Result Database Schema
❖ The database schema is where data relationships are formed throughout the laboratory process
flow.
Instrument Interfacing
• Instrument interfacing is the automated way in which results are recorded into the LIMS.
Specimen QC Run List
Instrument Control Parameters
Specimen Worklist
Assay Protocol (optional)
Specimen QC Assay Result(s)
Instrument Run Parameters
Laboratory Instrument
Interface System
Specimen Assay Result(s)
QC Results
LIMS
Instrument Run Parameters
Manual Entry of Results
❖ Manual entry occurs when paper or instrument results are directly entered into the LIMS by laboratory staff.
Different tests may require different workflows to ensure results are properly entered.
• Follow the appropriate data standards when entering results into the LIMS.
• Manual results entry can lead to increased errors.
• A good LIMS design will incorporate data validation routines into form fields and data-related processes
to minimize errors
Results Review
❖ The results review process ensures the laboratory provides a workflow for reviewing both automated and
manually entered data and results. Staff review data to validate and ensure accuracy following the four
levels of review:
Levels of Review
1) Data analysis and interpretation
2) Verify testing protocol
3) Readying for release
4) Post review
NOTE: Ensuring accurate and high quality results in the LIMS is critical for accurate analysis, patient diagnosis
and management, and public health uses of the data.
Reviewing the results and the communicating data and reports to stakeholders are processes in the lifecycle of
a result that occur inside the laboratory.
Communicating Data and Reports
❖ Informatics facilitates information sharing. Laboratory staff finalize LIMS information and send data and
reports to various external stakeholders.
❖ To communicate data and reports, laboratories have
❖ to complete the following steps:
1. Identify External Stakeholders
• There can be multiple stakeholders that receive data and reports from the testing laboratory. It is
important to identify all designated recipients who will directly receive the results. These determinations
are based on who requested the testing, on state and federal rules regarding notifiable diseases, on
ongoing surveillance and outbreak investigation needs, as well as other factors.
• The stakeholders can include healthcare providers, local and state health departments, and federal
agencies.
2. Develop data sharing rules and data elements
• All personally identifiable information must follow the Health Insurance Portability and Accountability
Act of 1996 (HIPAA) requirements and maintain patient privacy. This is one reason why laboratories must
develop rules and procedures for sharing data.
• For example, data sent to stakeholders such as government agencies should have more restrictions
than data sent to healthcare providers. In fact, government agencies often receive data and results
that have been de-identified, which means identifiers have been removed from any protected health
information (PHI). Part of the informatics process is to understand and implement data rules that ensure
data security both inside the laboratory and when they are shared externally.
3. Exchange information physically or electronically
• Data and reports can be shared through phone calls, secured fax, courier or regular mail services. The
electronic exchange of data enables faster, more convenient exchange between parties, which needs
to meet certain standards such as the Clinical Laboratory Improvements Amendments (CLIA).
• CLIA requires laboratories to have adequate manual or electronic systems in place to ensure test results
and other patient-specific data are accurately and reliably sent from the point of data entry to final
report destination in a timely manner.
Electronic Data Sharing
❖ There are multiple ways to send data and results electronically to stakeholders inside and outside the
laboratory.
❖ Examples that allow for the secure transfer of data include:
1. Web Portal
• In the context of patient testing, a web portal allows laboratories to provide test results to a network of
stakeholders through a dynamic, secure, 24-hour online portal. Web portals are designed to obtain all
types of results that include human, organisms, materials, and environmental data.
• The portal is also a channel used to communicate on the status of work being done by the laboratory.
On the clinical side, healthcare providers, medical assistants, and patients can log into a secure portal
that provides a web experience to view their, or their patient's, lab results in an HTML format that is HIPAA-
compliant. This provides a more stringent, secured interaction for patients.
2. Secure Email Messenger
• A secure email messenger is an application that allows secure communication either to and/or from a
stakeholder. As an example, a clinician may electronically transmit laboratory results to their patients via
email, thereby eliminating the need to reach patients by telephone.
3. Application Programming Interface (API)
• An Application Programming Interface (API) is the part of a system (in our case the LIMS) that receives
and interprets requests or instructions and returns a response back to the requestor. In our case, the API is
designed to allow the LIMS to "talk" to another LIMS or application to share data. This allows the laboratory
to decode that message, perform the appropriate test, and send back the results.
4. Integration Broker
• In computer systems design, an integration broker (also known as a message broker) is an intermediary
system that translates a message from the formal messaging protocol of the sender to the formal
messaging protocol of the receiver (as programs often have differing messaging protocols).
• An integration broker is a building block for sending and receiving messages between systems. The
integration broker has many responsibilities in addition to sending and receiving data. Another part of its
job is to know to whom, and to how many people, to send a result.
What is HL7 Messaging?
❖ Health Level Seven (HL7®) International² is a set of standards used for the exchange, integration, sharing,
and retrieval of electronic health information.
• HL7's purpose is to facilitate communication in healthcare settings by providing standards for the
exchange of data.
• HL7Ⓡ ensures the interoperability of data between applications and systems.
• HL7® has different product families:
o Version 2 messaging (v2.x)
o Version 3 messaging (v3)
o Version 3 Clinical Document Architecture (CDA)
o Fast Health Interoperability Resources (FHIRⓇ)
HL7 Message Structure
❖ Each HL7Ⓡ message has a standard structure with numerous components including:
1. Message Types
• The HL7Ⓡ message type defines the purpose for the message being sent and is present in every HL7Ⓡ
message.
• Message types are identified by a three-character code. Message type examples include:
o Patient Administration – ADT (Admission, Discharge, Transfer)
o “Order” messages – ORM, OML
o “Result” messages – ORU, OUL
o Financial messages – DFT
o Patient Care/Clinical/Medical Records – MDM
o Scheduling/Patient Referral – SRM, SIU
o Master Files – MFN
2. Segments
• A segment is a logical grouping of data fields identified by a three-letter identification.
• A segment categorizes additional information within the HL7® message. Some common message segments
include the following:
o MSH – Message Header
o EVN – Event Type
o PID – Patient Identification
o PV1 – Patient Visit
o [ PV2 ] – Patient Visit - Additional Info
o [ { OBX } ] – Observation/Result
o [ { DG1 } ] – Diagnosis Information
3. Fields
• A field is a string of characters used within HL7Ⓡ segments. Each field represents additional message
information.
• Below is an example of how fields are structured:
o Message Segment | Field 1 | Field 2 | Field 3 | Field 4 | etc. |
• A field is a chunk of the information in that segment or category. Fields may be optional or required
depending on the type of message and usage of the segment.
4. Data Types
• Data types are the kinds of data that can be included in a field and are used throughout the HL7Ⓡ
message structure.
• Below is a list of some HL7® data types:
o ST – String
o TX – Text Data
o FT – Formatted Text
o NM – Numeric
o TS – Time Stamp
o CE – Coded Element
• HL7® data types define the kind of data that can be included in a field, and are used throughout the
HL7® message structure.
5. Data Optionality
• Data optionality indicates whether a field or component is required, optional, conditional, or not
supported.
• Some common values of data optionality include the following:
o R – Required
o RE – Required, but may be empty
o O – Optional
o C – Conditional
o CE – Conditional, but may be empty
o X – Not supported
HL7 Message Types and Segments
❖ HL7 has more than 100 different message types.
• The HL7Ⓡ message header segment always indicates the message type. This tells the receiving system
what it needs to do with the message.
• Potential system actions after receiving an HL7Ⓡ message include:
o Ordering a test
o Scheduling a test or procedure
o Recording a test result
o Updating a patient's insurance information
❖ HL7 has more than 150 different message segments.
• Messaging segments convey information categories such as:
o Patient's diagnosis
o Laboratory test result
o Patient allergies
o Reason for patient's healthcare visit
HL7 by segment: Sample Message
A non-Hispanic white female, 43 years old, visited the emergency department complaining of a stomach
ache. She is diagnosed with appendicitis and admitted as an inpatient.
Integration Broker
❖ An integration or message broker is an intermediary program that translates a message from the sender to
the receiver (and the reverse).
• Healthcare providers usually have different computer systems for different types of services. These
systems are often unable to communicate with each other.
• Integration brokers communicate and share data across these systems.
• MIRTH, CloverleafⓇ and Orion Health™ RhapsodyⓇ are the most widely used brokers.
Standards Supporting Electronic Transmission of Laboratory Data
❖ Vocabulary Standards (for Semantic Interoperability)
• Logical Observation Identifiers Names and Codes³ (LOINC)®
o Version 2.61, June 2017
o The Logical Observation Identifiers Names and Codes (LOINC®) were developed to provide a
definitive standard for clinical information in electronic reports. The LOINC® database provides a set
of universal names and ID codes for identifying laboratory and clinical tests. LOINC® fosters the
development and use of suitable standardized diagnostic test and procedure terminologies to
support the safe, accurate, and effective exchange of health information.
o Each LOINC® describes 6 attributes of the testing:
1. Component = what the test is designed to detect (e.g. a particular bacteria, virus, or fungus)
2. Property = units of measure needed for result reporting
3. Scale = type of results expected for this test
4. Timing = what period is being referenced. For microbiological testing, it’s usually the date and
time of specimen collection
5. System = what specimen type is being tested (i.e., human sample or derived material). This can
be left unspecified.
6. Method = how the testing was done.
o It is important to note that not all 6 attributes have to be present in the LOINC® code. The attributes
listed are dependent on the type of test. An example LOINC® code for a TB smear test is “Smear 646-
0: Microscopic observation [Identifier] in Sputum by Acid fast stain. Kinyoun modified”.
• Systematized Nomenclature of Medicine-Clinical Terms* (SNOMED CT)®
o International Release, January 2017 and US Extension to SNOMED CT, March 2017 v1.35 Release
o Systematized Nomenclature of Medicine - Clinical Terms (SNOMED CT®) is a standardized, multilingual
vocabulary of clinical terminology that is used by physicians, laboratory staff, and other healthcare
providers to code test results. SNOMED CT® helps facilitate the interoperable health information
exchange between Electronic Health Records (EHRs).
o SNOMED CT® codes have multiple hierarchies, identified in the fully specified name in parenthesis to
describe clinical concepts. The most important hierarchies for microbiology laboratories, for example,
are organism, clinical finding, specimen, qualifier value, and body structure.
o For example, the result of the smear can be coded as
➢ 243365003 | Acid-fast bacillus (organism), or
➢ 275787002 | Acid-fast bacilli in sputum (finding)
• Unified Code for Units of Measures (UCUM)
o The Unified Code for Units of Measure (UCUM) is a code system intended to include all units of
measures being currently used internationally in science, engineering, and business.
o The purpose is to facilitate unambiguous electronic communication of quantities together with their
units. UCUM is used to represent units in HL7 messages. In an HL7® message, the coding system of
UCUM is identified by code UCUM.
❖ Content Structure Standards
• Technical specifications defined in HL7 Implementation Guides
o HL7 v2.5.1 Lab Orders Interface (LOI)
o HL7 v2.5.1 Lab Results Interface (LRI)
o HL7 v2.5.1 Electronic Laboratory Reporting to Public Health (ELR)
o HL7 Version 3 (Infobutton)
o HL7 FHIR
❖ The Meaningful Use regulations have public health objectives that require HL7Ⓡ messaging
• PHIN VADS contains standards-based vocabulary for Public Health HL7Ⓡ messaging
• CDC and jurisdictions provide implementation and message mapping guides for HL7Ⓡ messaging
• Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS)
o PHIN VADS promotes the use of standards-based vocabulary to support the exchange of consistent
information among public health partners (e.g., CDC, state health departments).
o PHIN VADS is a means to access the set of codes needed for implementation in specific settings.
o For example, PHIN VADs has collected all the codes needed for implementing electronic laboratory
reporting (ELR) and provides them in a format that can be viewed or downloaded – as a set of excel
spreadsheets with the codes. As another example, PHIN VADS provides a set of codes for specific
situations, such as for the 2014 Ebola outbreak or, more recently, the 2016 Zika crisis.
ANALYTIC PHASE: TB Example: Data Recording and Storage
TB EXAMPLE
• All tuberculosis test data and results need to be stored into the LIMS.
• The TB Acid Fast Bacilli (AFB) smear test is completed
• and the positive result is entered manually by staff.
• The positive nucleic acid amplification test (NAAT) and culture tests have instrument interfacing
capabilities. Results may be entered automatically, but they will need manual review.
• The laboratory professional who entered the data prepares for the results review phase.
ANALYTIC PHASE: TB Example: Results Review
TB EXAMPLE
❖ The results review process provides stakeholders with accurate and complete data and results. It also
provides a regulatory audit trail that will follow the specimen throughout its lifecycle.
1) Staff perform data and results analysis and interpretation, and prepare data and/or results for report
creation.
2) A second laboratory staff member verifies and reviews the results and interpretation for each test.
3) Staff finalize and prepare the data and reports for sending to designated recipients.
4) The final report from the LIMS is verified that it matches.
HL7 by segment: Sample Message
Life of a Result Flow: Outside the Laboratory
❖ Laboratories need the capability to communicate their internal data and reports to stakeholders outside of
the laboratory. Results will follow at least one of two distinct communication paths:
POST-ANALYTIC PHASE
Communicating Data and Reports
E.g., Electronic Health Records (EHR), Vital records, disease registries
Clinical Path- Data sent to physicians, hospitals and laboratories to inform patient diagnosis and care.
Surveillance Path- Data sent to health departments and public health agencies for the ongoing collection and
analysis of health-related data essential to the planning, implementation and evaluation of public health
practice.
Ⓐ Outside the Laboratory Flow: Clinical Path
❖ Data, results and reports are sent to physicians, hospitals, or other laboratories that are authorized recipients
or users. This path will lead to at least one of the following outcomes:
• Informing Patient Care
The appropriate healthcare provider reviews the data/results to inform patient diagnosis and
management.
• Disease Reporting
The laboratory and healthcare provider inform public health organizations of notifiable diseases by
sending data/results down the surveillance path.
• Requests for Additional Information and/or Testing
The healthcare provider does not have all the information needed to make a definitive diagnosis or
adequately inform other aspects of patient care. Additional requests will follow.
Data Sent to Clinician
What is Electronic Test Orders and Results (ETOR)?
ETOR is important to the interoperability of data and allows standards-based data exchange between the
laboratory and the healthcare provider.
ETOR Data Flow
Submitter Public Health Laboratory Submitter
• Submit a test request using • Transport level acknowledgment • Process results
recipient laboratory's test • Process incoming sample or specimen from report from
catalog submitter (Enter sample information, assign recipient
• Ship physical sample or sample ID) laboratory
specimen to recipient • Schedule test, run test
laboratory • Release result and generate test result (HL7®)
NOTE ETOR is two-way communication between a clinician and laboratory. This differs from ELR (shown on
previous screen), which is one-way communication to send laboratory results for reportable conditions.
What is an Electronic Health Record (EHR)?
❖ An EHR is an electronic version of a patient's medical record maintained by the provider over time.
❖ The EHR allows for:
• Easier linkage of a specimen and result within a patient's medical record
• Seamless interaction with affiliated hospitals, clinics, laboratories and pharmacies
• Fewer errors
• Improved patient safety
• Better clinical decision-making and outcomes
Data Send to Secondary Laboratory
Ⓑ Outside the Laboratory Flow: Surveillance Path
❖ Public health surveillance is used to inform disease prevention and determine control measures.
• Serve as an early warning system for public health threats
o Understand the epidemiology of a condition
o Monitor diseases and environmental hazard trends
o Analyze active interventions during an outbreak
• Document the impact of an intervention or progress towards specified public health targets
• Guide public health policy and strategies
What are Surveillance Systems?
❖ Surveillance systems support the ongoing, systematic collection, analysis and interpretation of health-
related data essential to public health practice. Some systems include the following:
1) ISS
• An integrated surveillance system (ISS) is a cross-program, person-based registry of health data from
case reports (i.e., is event-based).
2) NNDSS
• The National Notifiable Diseases Surveillance System (NNDSS) is a state-based public health surveillance
system providing notifiable disease data, compiled by CDC, which forms the basis of official U.S.
statistics for these diseases.
3) NBS
• The National Electronic Disease Surveillance System Base System (NBS) provides public health authorities
with a tool for processing, analyzing and sharing data they receive.
Data Sent to Epidemiologist
POST-ANALYTIC PHASE: Outside the Laboratory Paths
TB EXAMPLE
❖ Data from the LIMS/LIS are used to populate and finalize reports, and then the data and reports are sent to
external stakeholders down the two paths.
Ⓐ Clinical Path:
• Laboratory staff sends TB test results to Dr. Lee. This path will lead to the immediate diagnosis and
treatment of the individual patient (John).
Ⓑ Surveillance Path:
• John's positive TB results are sent to disease registries and surveillance systems that share disease-related
health information. These data are shared at the local, state, federal and international level.
NOTE: Regardless of laboratory paths, the laboratory must verify accurate transmission between the LIMS and
the first system to receive the data.
When Data Quality is Compromised
❖ Throughout the life of a result, there can be errors that can affect both individual patient care and
community disease prevention.
QC Issue Impact Mitigation
Example 1 • Patient name not • Appropriate patient does not • Have requestor QC labels
legible on label get diagnosed or treated in a and test requisition forms
timely manner, which enables • Laboratory should reach out
worsening health outcomes for directly to the requestor to
the patient and allows for confirm
greater community spread of
the disease (if communicable)
Example 2 • Laboratory codes • Complete and standardized • The laboratory must enter
are incorrectly data are not transferred standard codes into their
entered manually between the laboratory and the LIMS
surveillance system, which • Epidemiologist should
delays proper notification and contact the laboratory
needed public health regarding questions of data
interventions completeness and accuracy
You should now be able to:
• Identify where and how data and results are stored inside the laboratory
• Recognize how data and results are transmitted inside and outside the laboratory to stakeholders
• Identify two paths that data and results can follow to impact the health of individual patients and the
public
• Recognize how the proper recording, coding, storage and transmission of data and results can impact
patient care and public health
• Identify what data standards are used, their purpose and the components involved
• Explain what Electronic Test Orders and Results (ETOR), Electronic Laboratory Reporting (ELR), and Electronic
Health Record (EHR) are and how they differ
NOTE: You have completed the Life of a Result Course. Please take other informatics courses to build your
knowledge and competencies in this area.
