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AMIA 2019 Annual Symposium | Washington, DC USA

An API for LOINC release content


using FHIR Terminology Services

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


Senior Clinical Data Standards Lead
RTI International
@djvreeman
!
© 2019
Collaborators
Timothy Briscoe1

John Hook 1

Steven Wagers1

James Agnew2
Swapna Abhyankar, MD 1
1. Regenstrief Institute, Inc
2. Smile CDR

Funding Support
This work was supported by the National Center for Advancing Translational Sciences grant TR000006, the U.S. National Library of Medicine
contract HHSN276201400008C, and the Office of the National Coordinator for Health Information Technology grant 90AX0021/01-00.
Disclosure

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

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.
High Level Outline

1. A little about FHIR and LOINC


2. Overview and demo of API features
3. Summary of progress and usage

📷 Vernio77 © cc-by-sa
Slides and Demo Exercises
https://danielvreeman.com/fhir/
Note: access to the API requires a free loinc.org user account
What FHIR?
FHIR
FHIR® is the latest data exchange standard published by HL7®

Framework (data model) with standardized, but extensible


building blocks (called “resources”)

Rules for how to exchange data across systems with any major
interoperability paradigm: REST, Documents, Messages, Service

FHIR: the web for healthcare


FHIR Spec is Organized into Modules
A freely available global standard for health measurements,
observations, and documents.

delivered with a rich set of implementation tools…

used by a diverse global community…

who propel its continuous development.


Life without LOINC…
CODE NAME
AGTCE Angiotensin Converting Enzyme
5523 ACE SerPl Qn
ACE ACE
22441 AngioTens Conv Enz
99234 ACE (angiotensin)
25284D Angiotensin-1-Converting Enzyme
2737317 ACE (serum)
6881A Angiotensin Converting Enzyme, Ser
3800ACE ANGIOTENSIN CONVERTING ENZYME, S
77934A Angio Convt Enzym
919109 ACE, SERUM
34ACE Angiotensin Con. Enz
ANGCE Angiotensin CE
6621456 Angio. Conv. Enzyme
Known for lab content and vitals.

You might not realize…


LOINC is a rich trove of 91,000+ 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
Overview of the LOINC FHIR API

powered by HAPI FHIR via SmileCDR


Big Picture Goals
FHIR is a key distribution format for LOINC content

Make it easy to use SDO-published LOINC content in


the FHIR ecosystem

Use open-source, FHIR reference implementation


software so that any LOINC user could do the same
FHIR Resources of Interest

Terminology Services
CodeSystem
ValueSet
ConceptMap

Questionnaire
First made available in September 2018 (LOINC 2.64)
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
21176-3
LOINC Codes
LP31755-9
LOINC Parts
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

VersionLastChanged
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
…

CodeSystem Operations
$lookup
Get details about the concept, including definition, status,
designations, and properties.
Get info about your favorite
LOINC term
[base]/CodeSystem/$lookup?system=http://
loinc.org&code=4544-3
LOINC ValueSet
Resources
ValueSet
A set of codes drawn from one or more code systems

We use the ValueSet resource for three things:


1. Broadly useful collections of LOINC terms
2. Answer Lists
3. LOINC Groups
ValueSet Operations
$expand
Executes the definition of the ValueSet against the CodeSystem
version to get back the list of terms

$validate-code
Check if the supplied term is a member of the specified ValueSet
ValueSet: Collections of LOINCs
LOINC Document Ontology
LOINC/RSNA Radiology Playbook
LOINC/RSNA Radiology Playbook Core
LOINC Top 2000+ Lab Observations - US
LOINC Top 2000+ Lab Observations - SI
Valid HL7 Attachment Requests
Valid HL7 Attachment Responses
Valid HL7 Attachment Responses - Implementation Guide Exists
Valid HL7 Attachment Responses - No Implementation Guide Exists
Deprecated LOINC Terms
LOINC subsets available as
ValueSets
Get the LOINC/RSNA Radiology Playbook

[base]/ValueSet/?url=http://loinc.org/vs/loinc-
rsna-radiology-playbook
Note: $expand on large ValueSets is borked on prod server now.
It works on Dev, and will be fixed with December release.
Every Answer List is a ValueSet
Canonical URI pattern:
http://loinc.org/vs/{LOINC List id}

Get a particular Answer List as a ValueSet resource (w Metadata)


[base]/ValueSet/?url=http://loinc.org/vs/LL3066-9

Use the $expand operation to get just the answer codes


[base]/ValueSet/$expand?url=http://loinc.org/vs/LL3066-9
Every LOINC Group is a ValueSet!
loinc.org/groups

Get the LOINC Group for any MCnc Glucose in BldSerPlas:

[base]/ValueSet/$expand?url=http://loinc.org/vs/
LG7967-5

Here’s a LOINC Group with any body weight term:


[base]/ValueSet/$expand?url=http://loinc.org/vs/
LG34372-9
Building ValueSets based on
LOINC Properties
Include:
Subject Matter Domain of Sports
Medicine

Let’s use LOINC Part codes in the Compose

Exclude:
None
Include:
Children of LP378037-8
HIV 1 RNA | Serum or Plasma | Microbiology

Exclude:
None
LOINC ConceptMap
Resources
ConceptMap
A statement of relationships from one set of concepts to one or more other
concepts

LOINC terms to IEEE device codes


LOINC Parts to RadLex clinical terms (RIDs)
LOINC terms to RadLex Playbook procedure codes (RPIDs)
LOINC Parts to PubChem terms
LOINC Parts to RxNorm terms
LOINC Parts to SNOMED CT terms
Dec 2019
LOINC terms to PhenX variable IDs
LOINC Parts to more ontologies (CHEBI, ClinVar, NCBI Taxonomy, NCIT+) 2020?
ConceptMap Operations
$translate
Translate a code from one value set to another, based on the existing
value set and concept maps resources, and/or other additional
knowledge available to the server.
Get the LOINC Part to
PubChem Mapping
[base]/ConceptMap/?url=http://loinc.org/cm/loinc-
parts-to-pubchem
LOINC Questionnaire
Resources
Questionnaires and standardized
assessments are used widely


LOINC has a rich collection of


them in a standardized model
(10,000+ variables)

We want to facilitate easy use of


LOINC’s canonical content, so you
don’t have to reinvent it! PMID: 22899966
https://nlmdirector.nlm.nih.gov/2019/10/22/addressing...
Argonaut Project
Every LOINC Panel (will be) a Questionnaire
Canonical URI pattern:
http://loinc.org/q/{LOINC #}

Get the Patient activity scale II as a Questionnaire


[base]/Questionnaire/?url=http://loinc.org/q/
75876-3
Note: Available on dev server now, will be released to production in Dec 2019
Usage and Iterative
Improvements
Note: We still consider the API services as BETA status
Se
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1,000,000
1,500,000
2,000,000
2,500,000

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API Requests

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Uptime
Usage Notes
99% of API calls are to the CodeSystem resource

Response time is pretty quick (Ave = 150ms)

In Sept 2019, added API examples to all of the term


details pages
Iterative Improvements
Publish additional ValueSets June 2019

Better handling of changing file names

Big time performance improvements for $expand ~Dec 2019

Publish Questionnaire content


Add support for implicit ValueSet of “all LOINC”
Add support for Multiaxial Hierarchy relationships
Add PhenX ConceptMaps and “reverse” mappings
Fix duplicate answer entries in lists
Happy LOINCing!

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