I 660

Introduction to Terminology Standards

code systems youll see and use Daniel J. Vreeman, PT, DPT, MSc
Assistant Research Professor, Indiana University School of Medicine Research Scientist, Regenstrief Institute, Inc

09.01.2011

dvreeman@regenstrief.org

2011

Objective 1. To have a deeper appreciation for the challenges of integrating clinical data within and among systems.

Objective 2. To apply the desiderata constructs in critical appraisal of controlled terminologies.

Overview
1. The case for terminology standards 2. ICD 3. UMLS 4. RxNorm 5. SNOMED-CT 6. LOINC
photo via Vernio77

Similar name, dierent meaning

photo via Caption Time

meerkat meerkat mere cat meerkat

To pool data across sources each local term must be mapped to a universally recognized term.

Vocabulary standards provide the linuga franca.

Dierent standards for dierent parts of the elephant.

photo via Ludovic Hirlimann

Data standards are like telephones. They require a critical mass of users before they become useful.
- Clem McDonald, MD 1998

photo via iboy_daniel

Desiderata
for controlled medical vocabularies in the 21st century

Content. Content. Content.

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Concept orientation.
non-ambiguous concept permanence non-semantic concept identier formal denitions reject N.E.C.

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Multipurpose.
polyhierarchy multiple granularies

photo via woodleywonderworks

 Evolve gracefully.
photo via Dawn Huczek

Unied Medical Language System (UMLS)

the uber-terminology of terminologies

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UMLS
One big-ass vocabulary database that contains information about health related concepts, their various names, and the relationships among them.

photo via aussiegall

UMLS
Metathesaurus provides a uniform distribution format for more than 100 biomedical vocabularies.
photo via aussiegall

Overview
Organized by NLM in 1986 Three Knowledge Sources Metathesaurus (concepts)
Semantic Network (categories) Specialist Lexicon (tools)

Dont try this at home

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Browser
https://uts.nlm.nih.gov

photo via aussiegall

Metathesaurus
Base dictionary of concepts
Over 1 million concepts Over 5 million concept names

100+ source vocabularies

ICD-9-CM, MeSH, LOINC, SNOMED CT, etc UMLS is not a de novo vocabulary

Organized by concept (meaning)

photo via muet

Metathesarus Structure
Metathesaurus Concept Names
MRCON

Relationships between Concepts

MRREL, MRCOC, MRATX

Attributes
MRSAT, MRDEF, MRSTY, MRLO, MRRANK

Source Information and contexts

MRSO, MRCXT
photo via muet

Semantic Network
A knowledge representation schema
Nodes [semantic types] Links

Semantic Types
153 kinds Concepts linked to the most specic type

Relationships
54 kinds Primary kind = is_a [hierarchy] Other non-hierarchical

Biologic Function Hierarchy

Aects Hierarchy

Specialist Lexicon (Tools)

MetaMap Transfer (MMTx) Maps text into UMLS concepts Candidate concepts are organized to best cover the text
photo via Robert S Donovan

International Classication of Diseases (ICD)

and the rest of the family

photo via Esparta

ICD
Maintained by WHO New versions every 10 yrs (or so) Purpose Death statistics (diseases)
Billing (procedures added) Clinical documentation (CM)

Strict hierarchy Published with some synonyms + index

photo via Esparta

ICD
Core classication of 3 digits Optional 4th digit gives more detail At all levels
0-7 species further detail 8 all other cases, specied 9 unspecied
photo via Esparta

ICD
001 - 139 001 - 009 Fixed hierarchy 003 003.0 003.1 003.2 Infections and parasitic diseases Infectious diseases of the digestive tract Other Salmonella Infections Salmonella gastroenteritis Salmonella Septicemia Localized Salmonella Infections 003.20 Localized Salmonella Infection, Unspecified 003.21 Salmonella Meningitis 003.22 Salmonella Pneumonia 003.23 Salmonella Arthritis Terms are rubrics, not concepts 003.24 Salmonella Osteomyelitis 003.29 Other Localized Salmonella Infections 003.8 Other Specified Salmonella Infections 003.9 Salmonella Infections, Unspecified

NEC, NOS => semantic drift

photo via Esparta

Others like ICD

ICD-O
Used principally in cancer registries for coding the site (topography) and the histology (morphology) of neoplasms, usually obtained from a pathology report.

ICF CPT

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RxNorm
normalized names for clinical drugs
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Ingredients, strengths, dose forms

Diphenhydramine 25 MG Oral Tablet [Benadryl]

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Scope
Covers all prescription meds in US OTC meds when reliable info available

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Ingredients, strengths, dose forms

Diphenhydramine 25 MG Oral Tablet [Benadryl]

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RxTerms
Separates the full names in RxNorm into two parts:
drug name + route and strength + dose form
INDERAL (Oral-pill) 80 MG Tabs

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Other Handy Features

Excludes obsolete drugs (US) Uses common synonyms HCTZ for hydrochlorothiazide Tall man lettering to avoid errors
ChlorproMAZINE and ChlorproPAMIDE

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SNOMED CT
Systematized Nomenclature of Medicine - Clinical Terms

photo via Bruce McKay~YSP

SNOMED CT
Coded representation of meanings used in health information.

photo via Bruce McKay~YSP

SNOMED CT
Evolved from merger, expansion, and restructuring of SNOMED RT, UK Read Codes.
photo via Bruce McKay~YSP

Scope
357,000 957,000 702,000 1.37 mil Concepts English descriptions Spanish descriptions Relationships
photo via Bruce McKay~YSP

Main Features
Most comprehensive clinical vocabulary available. Built with description logic
(a language to represent knowledge)
photo via Bruce McKay~YSP

Directed Acyclic Graph

root

relationships leaves

Structure
Concept codes

Descriptions (terms) Relationships

Codes
One code per meaning; One meaning per code String of digits (6-18)
Codes vs Concepts vs Real things Concepts are in your head
Codes are in the terminology Codes refer to real things in the world

Terms & Descriptions

Term string = readable characters

immunosuppression

Description = term linked to concept 2 dierent descriptions, same string

immunosuppression : immunosupressive therapy (procedure) immunosuppression : immunosupression (finding)

Relationships
Denitional
necessarily true about the concept

Qualiers
may be added to specialize concept

Historical
point to current concepts from retired

Additional
links non-denition content

Example SNOMED Axes

Axis Topography Morphology Living organisms Chemical Function Diagnoses Procedure Description Anatomic terms Changes in cells, tissues, organs Bacteria, viruses Drugs Signs and symptoms Diagnoses Admin, therapeutic procedures

Multi-axial, Combinatorial
A Diagnosis may consist of
Topography code Morphology code Living organism code Function code

Combined term too

Pneumonia
233607000: Pneumococcal pneumonia
consolidation inflammation Streptococcus pneumoniae lung structure has_associated_morphology has_associated_morphology has_causative_agent has_finding_site

IHTSDO Members = Countries

Have National Release Centers Voting rights at General Assembly Pay a license fee based on World Bank GNI Atlas value

IHTSDO Member Counties

Australia Canada Cyprus Denmark Estonia Lithuania Netherlands New Zealand Singapore Slovak Republic Slovenia Spain Sweden United Kingdom United States

LOINC
A universal code system for identifying laboratory and clinical observations

Origins of LOINC
The lingua franca of clinical observation exchange

Soda or Pop?
what you see in the order list

Lab A
Test Name: Lyme Disease Serology Measures: B. burgdorferi Ab IgG Method: ELISA Scale: quantitative e.g.: Titer 1:40

Lab B
Test Name: Lyme Disease Antibody Measures: B. burgdorferi Ab IgM Method: Immune blot Scale: qualitative e.g.: Positive

LOINC Code = 5062-5

LOINC Code = 6321-4

Logical Observation Identiers Names and Codes

A universal code system that facilitates exchange, pooling, and processing of results

If an observation is a question and the observation value is an answer LOINC provides codes for
questions
Other vocabularies provide codes for the answers

What is my patients hemoglobin level?

718-7:Hemoglobin:MCnc:Pt:Bld:Qn

How fast does my patient usually walk?

41959-8:Walking speed:Vel:1W^mean:^Patient:Qn:Calculated

photo via Ed Yourdon

Indiana Network for Patient Care

HL7 v.2.X Message
MSH|^~\&|HOSPITAL_A|SAMPLE_HOSPITAL_A|||$YearMonthDay||||||||||||||| PID|||$patientId$||$patientName$|||||||||||||||||||| LocalCode^LocalName^CodeSystem^LOINCcode^LOINCname^CodeSystem PV1|||||||$attendingDoctor$||$consultingDoctor$|||||||| OBR|1|||012^CBC/Auto Diff^HSPA^57021-8^CBC W Auto Diff^LN||$reqDate||||||||| OBX|2|NM|123^WBC^HSP_A^26464-8^Leukocytes [#/volume] in Blood^LN||10.8|K/MM3|||||F| OBX|3|NM|234^RBC^HSP_A^26453-1^Erythrocytes [#/volume] in Blood^LN||4.82|MIL/MM3|||||F| OBX|4|NM|345^HGB^HSP_A^718-7^Hemoglobin [Mass/volume] in Blood^LN||15.7|GM/DL|||||F| OBX|5|NM|456^HCT^HSP_A^20570-8^Hematocrit [Volume Fraction] of Blood^LN||45|%|||||||F|

Message Processor

Institutional Repository

Result with a Coded Value

Data type of result (OBX-5) is a coded element This code is from LOINC This code is from SNOMED

OBX||CE|6609-2^Listeria ID^LN||36094007^L. monocytogenes^SCT

Code identifying this observation (what are these results? Listeria culture)

Code identifying the result (L. monocytogenes)

A brief aside about terminology

LOINC Terminology
LOINC (noun) MDS with LOINC and Vocabulary Matches From Standardizing the Tohttp://aspe.hhs.gov/daltcp/reports/2007/MDS-LOINC.htm LOINC, LOINCing, LOINCed (verb) [Chief, Head, etc] LOINCer (noun) LOINCication (noun) SNOMED Terminology SNOMED (noun) SNOMEDicated???

Laboratory LOINC

Clinical LOINC

The LOINC Community

Open. Nimble. Pragmatic.

Open Development
Worldwide distribution at no cost End-user content additions Welcome all comers Volunteers

Regenstrief Institute
Steward Developer of content Developer of tools Developer of community Distributor Voice

LOINC Codes Over Time By Release

70,000 60,000 50,000 40,000 30,000 20,000 10,000 0

LOINC Codes Lab Codes

Slope = 2200 Slope = 600

laboratory terms only

12,000

loinc.org members

10,000

8,000

6,000

4,000

2,000

14 new members per day 410 new members per month

12,200+ users in 143 countries

Downloads: ~1400/month

The LOINC Distribution

http://search.loinc.org

http://search.loinc.org

7,900 views 120 views 280 views

http://forum.loinc.org

http://loinc.org/usage

a.k.a. Top 300 Orders

A Little Comparison

^ Less is more

vs

LOINC Common Orders 1.1 1. Get lots of data 2. Publish beta list (1.0) and bring it to HITSP meeting 3. Get public feedback 4. Discuss with ACLA 5. Publish revised list (1.1)

No further action would be required for any such documents that would fall under the new guidelines category if in the Committees judgment they had been through a review process substantially similar to the newly agreed process or the documents were due for revision within 1 year. Any such documents would follow the newly agreed process when revised. For other documents, the Committee would be asked to recommend a review schedule to the Management Board.

vs.

is review process took extra time, but it was more than worth it. e nal product is a much better one for the review by many eyes

International Adoption
participation, translation, implementation

LOINC Submitters

Since 2009, 84 organizations from 14 countries

LOINC Translators

18 organizations

New and Updated Estonian French German Greek Italian Spanish

In-progress
Catalan Dutch French Russian

Large Implementations
SIGA Sade project Canada Health Infoway ePSOS Assistance publique - Hpitaux de Paris Hong Kong Hospital Authority Red Agrolab BiTAC

Lots moresuccess is often silent

US Adoption
A few key highlights

US Federal Agencies
NLM VA DoD IHS NCI CDC

Other Key US Adoptions

HITSP eLINCS NAACCR CDISC NCQA/HEDIS, NQF HL7 HIPAA HIEs

EHR Incentive Program

a.k.a. Meaningful Use

LOINC 101
LOINC for newbs (not nOObs)

LOINC Names
fully-specied, with 6 parts

Anatomy of a LOINC Term

5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA 5193-8 Hepatitis B virus surface Ab ACnc Pt Ser Qn EIA LOINC Code Component Property Measured Timing System Scale Method

There are six major LOINC axes

NOT part of a LOINC Name

Testing instrument Specic details about the specimen Priority (e.g. STAT) Where testing was done Who did the test Test interpretation Anything not part of naming the test Stu carried in other parts of HL7 message

Component
The substance or entity that is measured, evaluated, or observed

Sodium Glucose Brucella sp. organism Inuenza A Virus antigen Cytomegalovirus antibody Lipids.total
5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA

Component Structure
Analyte Name^Challenge^Adjustments Formal analyte name
Specify subanalytes May have subclasses

Calcium
Coronavirus Ag Calcium.ionized

Challenge
Two parts separated by post

1H post 100 g Glucose PO

<time delay>post<challenge type>

Adjustments

Adjusted to pH 7.4

Property
Major Categories: mass substance catalytic activity arbitrary number

* the most dicult LOINC axis

The characteristic or attribute of the analyte that is measured, evaluated, or observed.

5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA

Property
Fully Named Properties MCnc mass concentration SCnc substance concentration MCnt mass content CCnc catalytic concentration presence or identity Prid impression Imp Type kind of

* the most dicult LOINC axis

mg/dL umol/L mg/g U/L

5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA Property is related to units of measure

MAPPING DANGER ZONE

photo via jurvetson

Common Property Issues

Fraction versus Ratio Fraction = Part/Whole
NFr: % Eosinophils / leukocytes SFr: % HGB which is A2

Ratio = multiple analytes from same system MCrto: BUN/Creatinine in urine Relative Ratio = measures from dierent system RelRto: actual to normal control

Timing
The interval of time over which the observation or measurement was made

Pt 12H 24H

point in time 12 hour collection 24 hour collection

Non-Pt timings are often 5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA found with Rate Property

System
The system (context) or specimen type upon which the observation was made.

Ser Ser/Plas Bld Ur Flu Tiss XXX

serum serum or plasma whole blood urine body uid tissue specied elsewhere

photo via AlishaV

5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA

System Structure
System^Super System

Super System
Patient is the default Used to indicate
blood product unit bone marrow donor fetus
photo via Xurble

818-5:A Ag:ACnc:Pt:RBC^BPU:Ord: 11670-7:Blood ow.mean:Vel:Pt:Aortic arch^fetus:Qn:US.doppler

Scale
Qn

Quantitative
continuous numeric can have operators Ranked set (1+, 2+, 3+) unranked collection Taxonomy (e.g. bacteria)

Ord Ordinal Nom Nominal Nar Narrative

5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA
photo via puuikibeach

Method
Only needed if interpretation aected
Dierent normal ranges Test sensitivity

Listed at the generic level

Agglutination Immunoassay Probe with target amplication
5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA

LOINC Parts

Uses
translation, synonymy, building hierarchies, creating display names, linking descriptions

Hierarchies
LOINC class Each LOINC axis Multi-axial
Component | System Separate download

LOINC Collections
Panels, forms, surveys, and other patient assessments

photo via LuzA

Standardized Assessments

Vreeman DJ, McDonald CJ, Hu SM. Representing patient assessments in LOINC. AMIA Annu Symp Proc. 2010;832-836. PMID: 21347095 . Vreeman DJ, McDonald CJ, Hu SM. LOINC - A Universal Catalog of Individual Clinical Observations and Uniform Representation of Enumerated Collections. Int J Funct Inform Personal Med. 2010;3(4):273-291.

Purpose
Assessments are widely used

and not unlike other clinical observations

LOINC could be a
master question le
and

uniform representation

Hierarchy of a Panel in LOINC

Assessment Items
Question Text Question Source External Copyright Terms of Use Description/Denition Units of Measure (UCUM) HL7 Data Types (v2, v3)

Structured Answer Lists

Answer List Attributes
OID External Link (URL)

Answer Item Attributes

ID (contains LA prex) String Sequence Local code Score

Attributes of Items in a Panel Instance

Display name override Coding instructions Cardinality Local code on that form Skip logic Data type in form Answer sequence override Consistency/validation checks Relevance equation

Panels/Forms Available as Separate Download

Assessments Currently in LOINC

US Government Forms
CARE, MDSv2, MDSv3, OASIS B1, OASIS C, RFC US Surgeon Generals Family Health Portrait

Brief Interview for Mental Status (BIMS) Confusion Assessment Method (CAM) Geriatric Depression Scale (GDS) HIV Signs and Symptoms Checklist Home Health Care Classication howRU Living with HIV (LIV-HIV) Morse Fall Scale OMAHA PHQ (9 and 2) Quality Audit Marker (QAM)

Translational Research Variables

11,000+ variables Oh snap!

Lots more already there!

Government Forms Lab Panels Clinical Panels Other Surveys HIPAA Attachments HEDIS

More Cooking

photo via liber

photo via Rainbirder

Consolidated Health Informatics

Mapping local terms to a standard vocabulary

A fundamental challenge to health information exchange

Whats the big deal?

photo via wakeelddavid

Not just an IT problem

Get real.
units, results, experts

Dont be a one hit wonder.

photo via gsz

The LOINCers Toolbox

photo via Robert S Donovan

search.loinc.org
If you want to poke aroundstart here!

http://search.loinc.org

RELMA
REgenstrief LOINC Mapping Assistant

Whats it Good For?

Browse LOINC Map your local terms to LOINC import/export
translate local words to LOINC-speak manual/automated mapping

RELMA Highlights
Search Enhanced details view Common test list Hierarchies Panels and forms Export, copy, paste

Search Syntax
Google-like AND, OR, -<word>, +<word> Limit by category (e.g. micro) Wildcards (? and *) Assumes EXACT MATCH unless you use wildcards

More RELMA Features

User Specied Search Limits Selectable trees for:
Class Multi-axial (component/system) System (specimen) Component Method

Main Menu/Welcome Screen

Simple Search

Search Window

Detailed help enter search terms limit to common tests limit to specic units

Search Window

common tests rank

A brief aside
Developing convenience sets

photo via x-ray delta one

A Few Tests Give Most Results

Cumulative Laboratory Observation Volume (%)

100% 90% 80% 70% 60% 50% 40% 30% 20% 10% 0% 0 500 1000 1500 2000 2500 3000 3500 Number of Laboratory Observation Codes (N) 4000

Vreeman DJ, Finnell JT, Overhage JM. A Rationale for Parsimonious Laboratory Term Mapping by Frequency. AMIA Annu Symp Proc. 2007;:771-775.

http://loinc.org/usage

Mappers Guide to Top 2000

loinc.org/usage

We now return to our regularly scheduled program

Importing Local Terms into RELMA

4 Ways to Build LMOF

1. Hand enter bad 2. Make your own table bad 3. Import your test good catalog from text le best 4. Import from real HL7 v2.x messages

Searching and Mapping to LOINC

what RELMA was born to do

Photo via Jeffrey Beall

Main Menu/Welcome Screen

Set User Preferences

Point to your custom LMOF le

Set User Preferences

Point to your custom LMOF le

Reboot RELMA!

Main Menu/Welcome Screen

Hit it!

Double check youve got LAB1 here

Core Mapping Screen Features

Customizable grid Sort by columns View term details

Export results grid Stores mappings

Context Menu

right click to bring up context menu

Mapping Screen
View or edit local term

Navigate through the local terms Quick select button list

Standard Mapping Screen

Begin a search (or hit enter)

Initial Mapping Results

Fiddlesticks !#*$%!! What now???

Click to show words used in search

Initial Mapping Results

Use term checkbox

Number of LOINC terms containing keyword

Battery terms included in search

Revised Mapping Results

Units restriction selected by default

Re-revised Mapping Results

Click any column header to re-sort

Match units unselected

Number of matching records found

Ad hoc term search

CANINE DISTEMPER VIRUS IF

Enter keywords here Clear all input elds

More on Search Syntax

tips and tricks that also apply on search.loinc.org

Photo via Jeffrey Beall

Search in a Field
Field Component Property Timing System Scale Method Class Common Test Example component:chemotherapy glucose property:CCnc glucose timing:24H glucose system:CSF glucose scale:Nar mycobacterium method:EIA glucose class:UA glucose commontest:true

Other Cool Tricks

Use parentheses glucose (phosphate OR phosphatase) rbc component:(norepinephrine creatinine) Fuzzy search (~) Bergdorferi~
-ord

Other Features

RELMA

Tabbed Access to Functions

Navigate to Functions from Mapping Page

Switch between Grid and Tree Views

Tree View

Assigning a LOINC Map

Highlight correct term

Click Map Button

(or doubleclick)

Assigning a LOINC Map

LOINC Term Assigned

View LOINC Term Details

View details for a specic LOINC Term

Right clicking on a LOINC term brings up a Task Menu

LOINC Term Details

Change to expanded details view Change text size

LOINC Term Details: Panels

Limiting Your Searches

Sometimes 65,000+ terms is too many

Photo via Joe Shlabotnik

Setting Search Limits

Reduces number of candidate terms Many, many options for limits Hierarchy allows domain restrictions

with great power comes great responsibility

Photo via [cipher]

Setting Search Limits

click Hierarchy & Search Limits tab

Search Constraints
Attribute trees

Local Unit Constraint: Default is ON

Predened, general search constraints

Search Constraints

include Trial, Deprecated or Discouraged LOINC codes with returned terms

Hierarchies

Restrict eligible tests to non-challenge chemistry tests only

A Reminder About Search Limits

Indicates that youve got something set over here

Hierarchy Wrap-up
All trees operate the same way All grids operate the same way Combine tree limits with others
Mulligan button

Search Hints and Tips

Zero hit keywords are ignored (may need to rephrase) Common causes of Zero results Too many keywords Limits and keyword contradictions Local term weirdness Units are GREAT discriminators

RELMAs Auto Mapper

Starting with our best guesses may save you time

Not exactly

What Does It Do?

Batch processes local term le to get N- closest candidate LOINCs Uses words and units from local terms Produces a ranked list for your review

Pretty Good for Radiology

Automapper (with CPT-linkage) is accurate in mapping radiology terms Automapper out-performs Document Similarity Scores in mapping radiology terms
Vreeman DJ and McDonald CJ. Automated Mapping of Local Radiology Terms to LOINC. Proc AMIA Symp. 2005;769-773. Vreeman DJ, McDonald CJ. A Comparison of Intelligent Mapper and Document Similarity Scores for Mapping Local Radiology Terms to LOINC. Proc AMIA Symp. 2006;809-813.

Recent Improvements for Lab

Faster. Way faster. Better clean-up routine New specimen guesser Better local to LOINC word nder Break ties with frequency data

(Lab) Auto Mapper

launch it here

a couple of options

print report or work through the ranked list when done

Intelligent Mapper - Mapping Screen

Auto Mapper On-Demand

New Frontiers in Content Modeling

Projects and Opportunities

Opportunities
Basic science of modeling new domains
Genetic testing Lots of forms and assessments Structured document titles and sections

Better (semi) automated mapping Wisdom of the crowds

Closing Themes
Interoperability is a journey not a destination

photo via janeandd

Themes
Sustained growth in adoption Open development model works Zipfs law can help Lots more work to do

photo via milos milosevic

The Race is On!

Get LOINCing!

photo via ryarwood