FHIR DevDays | Redmond, WA

Using LOINC with FHIR

Daniel J. Vreeman, PT, DPT, MS, FACMI

Regenstrief-McDonald Scholar in Data Standards
Indiana University School of Medicine

Director, LOINC and Health Data Standards

@djvreeman Regenstrief Center for Biomedical Informatics

© 2018 © 2019
Hi, I’m Dan
I’m a physical therapist and medical informatician
Unusual, I know.

I’ve led LOINC at Regenstrief for 10+ years

At conferences people often introduce me as “the LOINC guy”

Conversation starter: Style with a story

Disclosure
I’m President of Blue Sky Premise, LLC which published the book LOINC Essentials.

I’m PI on contracts from bioMérieux and BD for LOINC content development (and
many federal and non-profit funding sources for LOINC).

Special support for FHIR-related LOINC work from NLM contract

HHSN276201400008C and ONC grant 90AX0021/01-00

This material contains content from LOINC® (http://loinc.org). The LOINC Table, LOINC Table Core, LOINC Panels and Forms File, LOINC
Answer File, LOINC Part File, LOINC Group File, LOINC Document Ontology File, LOINC Hierarchies, LOINC Linguistic Variants File, LOINC/
RSNA Radiology Playbook, and LOINC/IEEE Medical Device Code Mapping Table are copyright © 1995-2018, Regenstrief Institute, Inc. and the
Logical Observation Identifiers Names and Codes (LOINC) Committee and is available at no cost under the license at http://loinc.org/
license.
 FHIR and LOINC go together
like chips and salsa

📷 Marco Verch | cc-by

 Overview

1. Introduction to LOINC
2. LOINC in the FHIR jungle
3. LOINC specific features in the FHIR
terminology services

📷 Verino77 | cc-by-sa
 Session Exercise
Terminology Track

https://danielvreeman.com/fhir/
 Let’s get a sense of who’s here

📷 Arran Moffat | cc-by

 What is your familiarity with LOINC?

! Not much, I’m new

! I’m relatively new
! I’m an advanced LONICer
The Superhero Origin Story
Life without LOINC
CODE NAME
34626D Arterial BP Diastolic
39312D ABP Diastolic
ARTDIASBP Arterial Diastolic BP
nvArtBPS Arterial Blood Pressure Diastolic
DBP DBP
25284D BP (NIBP)
2737317 Diastolic Blood Pressure #1
6881D BP Diastolic
3800DBP BP
77934D BP Manual Diastolic
919109 Diastolic Blood Pressure
DiastBP DiastolicBP
PBPD PRE BLOOD PRESSURE DIASTOLIC
POBPD POST BLOOD PRESSURE DIASTOLIC
 Syntax Standards
Solving interoperability Messages, Documents, APIs, CDMs
HL7v2, C-CDA, FHIR, PCORnet

problems requires different Semantic Standards

kinds of data standards Vocabulary/code systems
LOINC, RxNorm, HPO, ICD,
MONDO, UCUM
 Est. 1994

The universal standard for identifying health

measurements, observations, and documents.

Terms have the specificity to distinguish between

clinically important differences.
📷 puuikibeach | cc-by
 meerkat meerkat mere cat meerkat

Similar name. Different Meaning.

📷 CaptionTime
LOINC is a freely available global standard

delivered with a rich set of implementation tools…

used by a diverse global community…

who propel its continuous development.

Guiding Principles
Openness
Respect
Accessibility
Growth
Pragmatics
Agility
Diligence

Read more in our LOINC Manifesto

 {
"resourceType": "Observation",
"id": "body-height",
"meta": {…},
"text": {…},
"status": "final",
"category": [
{

LOINC is designed for

"coding": […],
"text": "Vital Signs"
}
],

Observations (and Orders)

"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "8302-2",
"display": "Body height"
}

It works equally well in:

],
"text": "Body height"
},
HL7 v2, CDA, FHIR, CDMs "subject": {
"reference": "Patient/example"
},
"effectiveDateTime": "1999-07-02",
"valueQuantity": {
"value": 66.899999999999991,
Any structure with a key/value(observation, "unit": "in",
"system": "http://unitsofmeasure.org",
observation value) data model "code": "[in_i]"
}
}
Known for lab content and vitals.

You might not realize…

 LOINC is a rich trove of 89,000+ standardized variables
Genetics Lifestyle

21654-9 CFTR gene targeted mutation analysis

41950-7 Number of steps in 24 hour Measured
24475-6 F2 gene c.20210G>A [Presence]
75296-4 Carbohydrate intake 24 hour Estimated
75547-0 Noninvasive prenatal fetal aneuploidy
and microdeletion panel based on Plasma cell- 82289-0 Rating of perceived exertion [Score]
free+WBC DNA by Dosage of chromosome-specific
circulating cell free (ccf) DNA 72166-2 Tobacco smoking status NHIS

82245-2 Chromosome region 22q11.2 deletion in 64098-7 Distance walked in 6 minutes

Amniotic fluid or CVS by FISH

Lab and clinical Environmental

82464-9 Mosquito count [#] in Environmental specimen

4548-4 Hgb A1c MFr Bld 67784-9 Individuals below poverty line Neighborhood

8462-4 Diastolic blood pressure 63736-3 Materials to which you were exposed in your
work or daily life
24725-4 Head CT
63805-6 How long did you handle paints or solvents
57021-8 CBC W Auto Differential panel - Blood yourself?

8633-0 QRS duration 67640-3 My teachers believe that I can do well in my

school work

📷 glasgowamateur | cc-by-sa
📷 unamid-photo | cc-by-nd
Today, there are hundreds of
millions of patients with billions
of discrete results stored in
systems around the world that
are coded with LOINC.
Taking a little deeper
LOINC dive
 Anatomy of a LOINC Term
4544-3 Hematocrit:VFr:Pt:Bld:Qn:Automated count

Component Hematocrit

Property VFr

Timing Pt

System Bld

Scale Qn

Method Automated count

There are six major LOINC name axes

 Anatomy of a LOINC Term
4544-3 Hematocrit:VFr:Pt:Bld:Qn:Automated count

Component Hematocrit LP15101-6

Property VFr LP6891-8

Timing Pt LP6960-1

System Bld LP7057-5

Scale Qn LP7753-9

Method Automated count LP6141-8

Attribute values are coded with LOINC Parts

 Anatomy of a LOINC Term
4544-3 Hematocrit Auto (Bld) [Volume fraction]

Component Hematocrit

Property VFr

Timing Pt

System Bld

Scale Qn

Method Automated count

Other names assigned too:

Long Common Name, Display Name, Consumer Name
Codes for individual observations
6690-2 Leukocytes [#/volume] in Blood by Automated
2339-0 count
Glucose [Mass/volume] in Blood
29463-7 Body weight
55423-8 Number of steps in unspecified time Pedometer

Codes for collections (panels and documents)

57021-8 CBC W Auto Differential panel - Blood
34565-2 Vital signs, weight and height panel
44249-1 PHQ-9 quick depression assessment panel
36813-4 CT Abdomen and Pelvis W contrast IV
18842-5 Discharge summary

Codes for some answer options too (esp. survey instruments)

LOINC Distribution
Major releases twice per year
Rich collection release artifacts
Implementation tools
LOINC License
No cost use
Worldwide
In perpetuity
Commercial or noncommercial
Encourages translation
One major prohibition…
CANNOT use any Licensed
Material to develop or
promulgate a different standard
for orders or observations.
Before we get too far along, you
might be wondering…

What’s with the pig?

LOINC in the
FHIR Jungle
 Diagnostic
Medicine Module
Observation
LOINC is the most widely used code
system for observations

Here’s“classic” numeric result reporting

example with UCUM units
Return hemoglobin Observation for
my patient

[base]/Observation?patient=f001&code=718-7
Return patients with a
hemoglobin Observation
[base]/Patient?_has:Observation:patient:code=718-7

Reverse chaining
Observation
Works great for coded answers too

Here’s one using LOINC Answer codes

Profile [Observation]
Several profiles further constrain
observation and identify specific LOINCs

Examples: Genetics, Vital Signs, etc

Extension AminoAcidChangeType =
LOINC:48006-1
Diagnostic Report and
Imaging Study
For lab, pathology, radiology, and other
diagnostic services (cardiology, etc)

LOINC is preferred code set.

LOINC/RSNA Radiology Playbook is

perfect for radiology procedures
http://loinc.org/vs/loinc-rsna-radiology-playbook
Foundation Module
Questionnaire
(and Response)
LOINC has a rich data model for
representing collections, data elements
(questions), and their answers.
10,000+ assessment terms
and growing…
Social, psychological and behavioral observations - 2015 Edition Geriatric Depression Scale (GDS)
Health IT Certification Criteria set
Humiliation, Afraid, Rape, and Kick questionnaire
Adverse Childhood Events
HIV Signs and Symptoms Checklist
ADAPTABLE patient report item set
howRU
Borderline Symptom List - 23 Item
International Physical Activity Questionnaire
Brief Interview for Mental Status (BIMS)
Living with HIV (LIV-HIV)
Comprehensive Behavior Health Screen
Morse Fall Scale
Confusion Assessment Method (CAM)
My Mood Monitor
Core behavioral health terms (SAMHSA)
Neuro-QOL
Edinburgh Postnatal Depression Scale
PROMIS (e.g. Social Isolation item bank)
Everyday Cognition
PhenX (eg. Social Environments domain)
Exercise Vital Sign
PHQ
FACIT
VR 12 and 36
Composition and
DocumentReference loinc.org/document-ontology

Structure (or references to) FHIR Documents

(immutable bundles with attested narrative)

LOINC has a rich set of clinical document type

and section codes (used extensively in CDA).
A small sample of FHIR+LOINC
powered innovations
 https://forms.loinc.org/82152-0/

Example data input widget using LHCForms software

Apple Health Records
Uses Argonaut FHIR Profile

https://www.apple.com/healthcare/health-records/

https://support.apple.com/en-us/HT208647
LOINC-specific FHIR Services
Cool tricks with LOINC via FHIR’s Terminology Services

follow along with examples at:

https://danielvreeman.com/fhir/
powered by HAPI FHIR via SmileCDR
A LOINC API via FHIR
Terminology Services enables
capabilities that were much
harder before!
https://loinc.org/fhir
LOINC as a CodeSystem
Resource
LOINC as a CodeSystem
https://www.hl7.org/fhir/loinc.html

Canonical definition published at:

https://loinc.org/fhir/loinc.xml
URI
http://loinc.org

Codes
LOINC Codes 21176-3
LOINC Parts LP31755-9
LOINC Answer Lists LL715-4
LOINC Answer Codes LA11165-0

Display Names for LOINC terms

Long Common Name
Basic LOINC Properties
COMPONENT

PROPERTY
TIME_ASPCT
SYSTEM
SCALE_TYP
METHOD_TYP

STATUS
CLASS
CLASSTYPE 1=Lab; 2=Clinical; 3=Claims Attachments; 4=Surveys

ORDER_OBS Order, Observation, Both

Other LOINC Properties
answer-list
HL7_ATTACHMENT_STRUCTURE
ValidHL7AttachmentRequest
PanelType

Radiology Properties
rad-modality-modality-type
rad-anatomic-location-region-imaged
…

Document Ontology Properties

document-type-of-service
document-role
…

Get info about your favorite
LOINC term
[base]/CodeSystem/$lookup?system=http://
loinc.org&code=4544-3
{
"resourceType": "Parameters",
"parameter": [
{
"name": "name",
"valueString": "LOINC"
},
{
"name": "display",
"valueString": "Hematocrit [Volume Fraction] of Blood by Automated count"
},
{
"name": "abstract",
"valueBoolean": false
},
{
"name": "property",
"part": [
{
"name": "code",
"valueCode": "SYSTEM"
},
{
"name": "value",
"valueCoding": {
"system": "http://loinc.org",
"code": "LP7057-5",
"display": "Bld"
}
}
LOINC ValueSet
Resources
Every Answer List is available
as a ValueSet
Get a particular Answer List as a ValueSet

[base]/ValueSet/LL1162-8/$expand
{
"resourceType": "ValueSet",
"status": "active",
"compose": {
"include": [
{
"valueSet": [
"http://loinc.org/vs/LL1162-8"
]
}
]
},
"expansion": {
"identifier": "urn:uuid:18e39118-b23c-42a4-ac01-a4156248f91c",
"timestamp": "2018-06-05T16:35:35+00:00",
"total": 5,
"parameter": [
{
"name": "version",
"valueUri": "http://loinc.org/vs/LL1162-8|Beta.1"
}
],
"contains": [
{
"system": "http://loinc.org",
"code": "LA137-2",
"display": "None"
},
{
"system": "http://loinc.org",
Some key LOINC subsets
available as ValueSets
Get the LOINC/RSNA Radiology Playbook

[base]/ValueSet/?url=http://loinc.org/vs/loinc-
rsna-radiology-playbook
"resourceType": "ValueSet",
"id": "loinc-rsna-radiology-playbook",
"meta": {
"versionId": "2",
"lastUpdated": "2018-12-14T22:36:16.510+00:00"
},
"url": "http://loinc.org/vs/loinc-rsna-radiology-playbook",
"name": "LOINC/RSNA Radiology Playbook",
"status": "active",
"compose": {
"include": [
{
"system": "http://loinc.org",
"concept": [
{
"code": "24531-6",
"display": "US Retroperitoneum"
},
{
"code": "24532-4",
"display": "US Abdomen RUQ"
},
{
"code": "24533-2",
"display": "MRA Abdominal vessels W contrast IV"
},
{
"code": "24534-0",
"display": "US.doppler Abdominal vessels"
},
Building ValueSets based on
LOINC Properties
 "compose": {
"inactive": false,
"include": [
{
"system": "http://loinc.org",

Include: "version": "2.64",

"filter": [
{
"property": "COMPONENT",
Component of West Nile Virus "op": "regex",
"value": "^West Nile virus"
}
]
}
],
"exclude": [

Exclude:
{
"system": "http://loinc.org",
"version": "2.64",
"filter": [
Super System of Fetus, Donor, BPU {
"property": "SYSTEM",
"op": "regex",
"value": "\\^Fetus$"
Can also use LOINC Part codes in Compose },
{…}
]
 [base]/ValueSet/test-west-nile/$expand

"expansion": {
"identifier": "urn:uuid:3eb88c25-061e-4479-9aed-cf64a012051c",
"timestamp": "2018-06-19T14:33:59+00:00",
"total": 67,
"parameter": [
{…}
],
"contains": [
{
"system": "http://loinc.org",
"code": "31701-6",
"display": "West Nile virus IgG Ab [Presence] in Serum"
},
{
"system": "http://loinc.org",
"code": "33329-4",
"display": "West Nile virus IgG Ab [Titer] in Serum"
},
{
"system": "http://loinc.org",
"code": "39555-8",
"display": "West Nile virus Ab [Units/volume] in Serum"
},
{
"system": "http://loinc.org",
"code": "41232-0",
New LOINC Groups also available!
Read more at: loinc.org/groups

Get a specific LOINC Group as a ValueSet, for example any

body weight term:

[base]/ValueSet/$expand?url=http://loinc.org/vs/
LG34372-9
"expansion": {
"identifier": "urn:uuid:23c8b092-72a7-424b-a1c0-bee0985a106b",
"timestamp": "2019-06-11T16:24:17+00:00",
"total": 7,
"parameter": [
{
"name": "version",
"valueUri": ""http://loinc.org/vs/LG34372-9|2.65-Beta.2"
}
],
"contains": [
{
"system": "http://loinc.org",
"code": “3142-7",
"display": "Body weight Stated"
},
{
"system": "http://loinc.org",
"code": "3141-9",
"display": "Body weight Measured"
},
{
"system": "http://loinc.org",
"code": "29463-7",
"display": "Body weight"
},
{
"system": "http://loinc.org",
LOINC ConceptMap
Resources
LOINC content in ConceptMap
LOINC publishes several kinds of mappings to external
terminologies

LOINC Terms
IEEE codes
RadLex RPID codes

LOINC Parts
PubChem
RadLex RIDs
RxNorm
Get the LOINC to IEEE
Mapping

[base]/ConceptMap/?url=http://loinc.org/cm/loinc-
to-ieee-device-codes
{
"resourceType": "ConceptMap",
"id": "LOINC-IEEE-MEDICAL-DEVICE-CM",
"meta": {
"versionId": "1",
"lastUpdated": "2018-05-04T01:10:54.569+00:00"
},
"url": "http://loinc.org/cm/loinc-to-ieee-device-codes",
"version": "Loinc_2.65",
"name": "LOINC/IEEE Device Code Mappings",
"publisher": "Regenstrief Institute, Inc.",
"contact": [
{
"name": "Regenstrief Institute, Inc.",
"telecom": [
{
"system": "url",
"value": "https://loinc.org"
}
]
}
],
"group": [
{
"source": "http://loinc.org",
"target": "urn:iso:std:iso:11073:10101",
"element": [
{
"code": "11556-8",
"display": "Oxygen [Partial pressure] in Blood",
"target": [
{
"code": "160116",
"display": "MDC_CONC_PO2_GEN",
"equivalence": "equal"
}
]
 Take home lesson:
When clinical data is coded with LOINC
codes and made accessible by FHIR,
diverse IT applications can understand
and interact with it for the benefit of
many in the health ecosystem.
Happy LOINCing!