2011 06 06 - LOINC Workshop and Tutorial

Using
RELMA

Or…In
Search
of
the
Missing
LOINC

Laboratory
LOINC
Meeting
–
June
2011

James
T.
Case
MS,
DVM,
PhD

Health
Program
Specialist,
SNOMED
CT

National
Library
of
Medicine

©2011 Regenstrief Institute and James Case

Acknowledgements

•  RELMA
Development
Team

•  John
Hook,
Karen
Ahmad,
Mark
Fisher,
Craig
Kelker

•  Dan
Vreeman

•  Clem
McDonald

•  Kathy
Mercer

•  The
Lab
LOINC
CommiFee

•  Funding
Support

•  NLM,
Regenstrief
InsJtute,
NCI,
CDC


What
will
we
cover
today?

•  Overview
of
LOINC

•  Reviewing
new
RELMA
features!

•  Installing
RELMA

•  SeMng
personal
preferences

•  Loading
a
Local
ObservaJon
File
(LMOF)

•  Searching
for
a
LOINC
Term

•  Preparing
LMOF
for
Mapping

•  Review
of
Map
Screen
FuncJons

•  SeMng
Search
Limits

•  Mapping
Local
Terms
to
LOINC

•  Viewing
LOINC
Term
Details

•  Proposing/SubmiMng
New
LOINC
Terms

•  ExporJng/PrinJng
Mapped
Terms

•  Mapping
your
own
LMOF
data


Why
are
we
doing
this?

Goals
of
Health
Information
Standards

•  Interoperability
–
the
ability
to
exchange

informaJon
between
organizaJons

•  Comparability
–
the
ability
to
ascertain
the

equivalence
of
data
from
diﬀerent
sources

•  Data
Quality
–
the
measurement
of

accessibility,
completeness,
accuracy
and

precision
(and
more)


Levels
of
Interoperability

•  Basic
–
allows
data
to
be
exchanged
between

computer
systems

•  Word
processing
documents,
text
messages

•  Func7onal
–
describes
the
standard
syntax

(format)
of
the
data

•  Document
templates,
forms,
data
structures

•  Message
standards

•  Seman7c
–
requires
use
of
standardized

content
(vocabularies)
within
the
data

structure


Comparability

•  Meaning
of
the
data
is
consistent
when
shared

among
diﬀerent
parJes

•  Erysipelas
–
Human
skin
disease;
Streptococcus
Grp
A

•  Erysipelas
–
Animal
SepJcemia/dermaJJs;
Erysipelothrix

rhusiopathiae

•  Common
terminology
required

•  Should
work
in
the
background

•  Words
are
not
enough

•  Codes
–
uniquely
idenJfy
terms

•  Vocabulary
–
specialized,
precise
terms
that
remove

ambiguity

•  Ontology
–
describes
nature
of
enJJes
and
their
relaJons

•  ClassiﬁcaJon
–
groups
related
terms


Potential
Uses
of
Health
Data
are

Constrained
by
Data
Quality
Factors

•  Data
quality
issues

•  Different
for
client/paJent
communicaJons
vs.

clinical
decision
support
vs.
epidemiological

analysis

•  Oen
constrained
by
external
forces

•  e.g.
criteria
for
diagnosis
oen
differs
from
the
criteria

for
reporJng

•  UnidirecJonal
effect
of
data
consolidaJon

•  Detailed
General

•  General

Detailed


The
Problem

“In
aFempJng
to
arrive
at
the
truth,
I
have
applied

everywhere
for
informaJon,
but
in
scarcely
an

instance
have
I
been
able
to
obtain
hospital

records
ﬁt
for
any
purpose
of
comparison.

If
they

could
be
obtained,
they
would
enable
us
to

decide
many
other
quesJons…
They
would
show

[subscribers]
how
their
money
was
being
spent

[and]
what
amount
of
good
was
really
being
done

with
it…”

Florence
Nightingale
-‐
Notes
on
a
Hospital,
1873


Test
comparisons

What
you
see
in
the
order
list

Lab
A
Lab
B

Test
Name:
Lyme
Disease
Serology
Test
Name:
Lyme
Disease
An7body

Measures:
B.
burgdorferi
Ab
IgG
Measures:
B.
burgdorferi
Ab
IgM

Method:
ELISA
Method:
Immune
blot

Scale:
quan7ta7ve
Scale:
qualita7ve

e.g.:
Titer
1:40
e.g.:
Posi7ve

LOINC
Code
=
5062-‐5
LOINC
Code
=
6321-‐4


Why
LOINC?

“Within
one
laboratory,
local
jargon
terms

may
be
used
which
are
usually
well

understood
between
colleagues,
but

would
not
be
suﬃciently
widely
known
for

communicaJon
with
the
outside
world.”

U.
Forsum
et
al.,
Pure
Appl.
Chem
72:555-‐745,
2000
Proper3es
and
Units
in
the
Clinical

Laboratory
Sciences
Part
VII.

Proper3es
and
Units
in
Clinical
Microbiology


LOINC®
101

Emphasis
on
Laboratory

LOINC


Anatomy
of
a
LOINC
Term

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

5193-‐8
LOINC
Code

Hepa77s
B
virus
surface
Ab
Component

ACnc

Property
Measured

Pt

Timing

Ser

System

Qn
Scale

EIA
Method

There
are
six
major
LOINC
axes


What
is
NOT
part
of
a
LOINC
Name?

•  The
instrument
used
in
tesJng

•  Speciﬁc
details
about
the
specimen

•  Priority
(e.g.
STAT)

•  Where
tesJng
was
done

•  Who
did
the
test

•  Test
interpretaJon

•  Anything
that
is
not
an
intrinsic
part
of
the
name
of

the
result

•  Other
things
that
are
carried
in;

•  The
OBR
or
OBX
segment

•  An
HL7
Version
3
ObservaJon
Object


Component/Analyte

The
substance
or
enJty
that
is
measured,

evaluated,
or
observed

-‐
Sodium

-‐
Glucose

-‐
Brucella
sp.
organism

-‐
Inﬂuenza
A
Virus
anJgen

-‐  Cytomegalovirus
Virus
anJbody

-‐  Lipids.Total

5193-‐8:Hepatitis
B
virus
surface


Component/Analyte
Structure

Analyte
Name^Challenge^Adjustments

•  Formal
name
of
Analyte
(e.g.
Calcium)

•  Must
specify
any
“subanalyte”

•  e.g.

Coronavirus
Ag

•  May
have
a
subclass
–
separated
by
“.”

•  e.g.
Calcium.Free

•  Challenge
-‐
e.g,
1H
post
100
gm
Glucose
PO

•  Two
subparts
separated
by
“post”

•  <Jme
delay>
post
<challenge
type>

•  Adjustments/correcJons

•  E.g.
Adjusted
to
pH
7.4


Property

the
most
diﬃcult
LOINC
axis

The
characterisJc
or
aFribute
of
the
analyte
that
is

measured,
evaluated,
or
observed

Major
Categories

•  Mass:
ObservaJons
reported
with
mass
(milligrams,
grams,
etc.)

in
the
numerator
of
their
units
of
measure

•  Substance:
ObservaJons
reported
with
moles
or
milliequivalents

in
the
numerator
of
their
units
of
measure

•  Cataly7c
ac7vity:
ObservaJons
that
report
enzymaJc
acJvity

•  Arbitrary:
Results
that
report
arbitrary
units
in
the
numerator
of

their
units
of
measure

•  Number:
Counts

5193-‐8:Hepatitis
B
virus
surface

Property

the
most
diﬃcult
LOINC
axis

Combine
Major
Categories
with
Subtypes
for
Full
Property

•  MCnc
–
mass
concentraJon
(mass/unit
vol)

•  MCnt
–
mass
content
(mass/unit
mass)

•  NCnc
–
number
concentraJon
(number/unit
vol)

•  TmStp
–
Jme

•  CCnc
–
catalyJc
concentraJon
(acJvity)

•  Prid
–
presence
or
idenJty

•  Imp
–
impression/interpretaJon

•  Find
–
subjecJve
or
objecJve
observaJon

•  Type
–
“Kind-‐of”

5193-‐8:Hepatitis
B
virus
surface

Common
Issues
with
LOINC
Properties

FracJon
(proporJon)
vs.
RaJo

a/a+b
vs.
a/b

•  FracJon
=
Part/whole

•  Number
fracJon
(NFr):

%
Eosinophils

•  Substance
fracJon
(SFr):
%
HGB
which
is
A2

•  RaJo
=
Measures
mulJple
analytes
from
the
same

system
(specimen)

•  Mass
concentraJon
raJo
-‐
MCrto

•  e.g.,
BUN/Creat
in
urine
specimen

•  Substance
raJo-‐SCrto

•  Urea/CreaJnine
expressed
as
mmol/L
(SI
units)

•  RelaJve
RaJo
=
Measures
from
diﬀerent
systems

•  RelRto
–
mulJple
of
the
median

•  RlTm
–
Jme
from
actual
Institute and ormal
control

©2011 Regenstrief
and
n James Case

Timing*

The
interval
of
Jme
over
which
the
observaJon
or

measurement
was
made

•  Pt
-‐
at
a
point
in
Jme

•  12H
-‐
a
twelve
hour
collecJon

•  24H
-‐
a
twenty
four
hour
collecJon

*non-‐Pt
Jmings
are
usually
associated
with
RaJo
Property


System

The
system
(context)
or
specimen
type
upon
which

the
observaJon
was
made.

•  Ser
-‐
Serum
•  Gast
–
Gastric
fluid/contents

•  Bld
-‐
Whole
blood
(RBC)
•  Food
–
Food
or
feedstuff

•  Ur-‐
Urine
•  Tiss
–
Tissue

•  BldA
-‐
Arterial
blood
•  XXX
–
To
be
specified
in

•  Liver
-‐
Liver
another
part
of
the
message

•  Flu
–
Body
Fluid,
unspecified

Super
System

Second
subpart
(^).
When
not
included,
“paJent”
is
the

default.
Used
to
indicated
blood
product
unit
(BPU),
a
bone

marrow
donor,
or
a
fetus.
(e.g.
Serum^BPU)


Scale

•  Qn
-‐
QuanJtaJve

•  ConJnuous
numeric
(real,
integer,
raJo)

•  OpJonal
operator
(>,
≥,
≤,
<)

•  When
assay
detecJon
limits
are
exceeded

•  Ord
-‐
Ordinal

•  a
ranked
set
of
possible
values
(1+,
2+,
3+)

•  Nom
-‐
Nominal

•  an
unranked
collecJon
of
possible
values

•  a

taxonomy
(e.g
list
of
bacteria)

•  Nar
-‐
NarraJve

•  free
text
narraJve
(e.g.,
visit
note)


Scale
(Special)

•  OrdQn
–
Ordinal
or
QuanJtaJve

•  Primarily
used
for
anJmicrobial
observaJons
e.g.

MIC
reported
as
resistant,
intermediate,
suscepJble

or
as
the
mm
diameter
of
the
inhibiJon
zone

•  Use
is
discouraged
in
other
contexts

•  MulJ
–
structured
text
“globs”

•  e.g.
chromatography
output

•  Use
is
discouraged

•  Doc
–
Clinical
documents

•  Set
–
Clinical
aFachments
(headers)


Method

•  Methods
only
needed
if
interpretaJon
affected

•  Different
normal
ranges

•  Test
SensiJvity/Specificity

•  Generally
listed
only
at
the
generic
level

•  AggluJnaJon
(limited
subtypes)

•  Immunoassay

•  Probe
with
target
amplificaJon


Mapping
Terms
to
LOINC

Things
to
Remember

•  The
thing
ordered
is
not
always
the
thing
measured:

•  Blood
Culture
–
live
organism(s)
idenJfied

•  VDRL
–
Treponema
pallidum
Ab

•  Urinalysis
–
lots
of
different
things

•  The
quesJon
(what
am
I
measuring?
e.g.
Glucose)
is

not
the
answer
(e.g.
90
mg/dl)

•  You
are
mapping
the
quesJon,
not
the
answer!

•  You
must
know
the
specifics
of
the
component
being

tested
for
(what
is
this
test
actually
measuring?)


What
is
in
LOINC?

Content

•  Term
structures

•  SubmiFed
units,
Example
UCUM
units

•  aiming
toward
preferred
units
sorJng

•  Synonyms

•  Answer
lists
(increasing
number)

•  Text
descripJons
–
links
to
info
sources

about
individual
tests

•  Panel
structures

•  Foreign
language
translaJons


RELMA®

Regenstrief
LOINC
Mapping
Assistant


Purpose
of
Tutorial

•  “Eliminate”
need
to
read
the
User’s
Manual

•  Become
familiar
with
RELMA
features

•  Provide
some
insight
into
mapping
Jps/pi}alls

•  Help
begin
the
mapping
process
for
your

insJtuJon


RELMA
Functions

•  LOINC
files
and
indexes

•  Manual
and
automated
mapping
funcJons

•  Same
free
use
as
LOINC
(see
license)

•  RELMA
tools
transform
local
words
in
local
file

•  User
creates
file
of
local
term/name
and
codes

•  Assigns
LOINC
term
to
local
test/baFery
code

•  “Common
tests”
subset
to
speed
mapping

•  Context
sensiJve
hierarchies
for
local
use.

•  Flexible
“Google-‐like”
search
funcJons


New
in
This
Version
(Rel.
5.2)

•  Searches

now
have
opJon
to
use
“Auto
Mapper”
methods

•  Select
"Use
Auto
Mapper
Search"
checkbox.

•  Revised
screen
for
reviewing
Terms
Mapped
to
Deprecated/
Discouraged
LOINCs

•  The
"Replacement
LOINC"
secJon
gives
the
user
access

to
all

the
replacement
LOINC
codes.

•  The

Comment
ﬁeld
has
been
added.
(RaJonal
for
replacement

term)

•  Added
navigaJon
buFons.

•  Lucene
proximity
and
fuzzy
searches
are
now
supported
on

the
mapping
and

simple
search
screens.

•  Lucene
score
is
displayed
on
the
mapping
and
the
simple

search
screens.


New
in
This
Version
(Rel.
5.2)

•  Column
headers
on
screens
are
the
same
as

Lucene
ﬁeld
names.

•  Example:
[
ExUnits:mg
]

-‐"ExUnits"
=
example

units.

•  Double-‐clicking
displays
the
details
for

selected
row.

•  LOINC
Part
quoJents
(e.g.
"CreaJne

kinase.MB/CreaJne
kinase.total“)
displayed

in
the
Part
secJon
of
details
screen.


LOINC
Web
Site


What’s
available
to
download?

•  RELMA
-‐
mapping
and
browsing
tool

•  HL7
message
converter-‐
Makes
a
database

suitable
for
mapping

•  HL7
lint
(ﬁnds
bad
messages)

•  LOINC
database
and
spreadsheets

•  LOINC
User
guide;
RELMA
User
Guide

•  Tools
to
assist
language
translaJons
by
part

•  Tools
for
building
databases
to
map
from

HL7
messages

•  New
guidance
documents
for
mappers

32

RELMA
Highlights

•  Browse-‐able
hierarchies
of
LOINC
parts

•  Display
search
results
in
tree
view

•  Enhanced
“details”
view
of
terms/parts

•  References

•  DescripJons

•  Sample
units

•  Empirically-‐derived
common
test
list

•  Special
features
for
panels/forms

•  Enhanced
export/copy-‐paste
opJons


Installing RELMA®


Installation
Steps

•  Make
sure
you
have
enough
free
disk
space!

•  2Gb
is
recommended

•  From
CD
-‐
Start
–
Run
–
<drive>:RELMASetup

•  Specify
installaJon
directory

•  Life
will
be
easier
if
you
accept
the
default

•  Two
database
ﬁles
installed

•  RELMA.MDB
–
LOINC
Terms
Database

•  LMOF3.MDB
–
Local
Master
ObservaJon
File

•  Two
sample
ﬁles
included

•  Run
from
Start
–
(All)
Programs
–
Regenstrief
–
RELMA


File
Locations

•  Database
and
Ancillary
Files

•  Windows
XP
=
C:Documents
and
SeMngsAll
Users
DocumentsRELMA

•  Windows
Vista
=
C:UsersPublicDocumentsRELMA

•  Windows
7
=

•  Sample
ﬁles

•  Windows
XP
=
C:Documents
and
SeMngsAll
Users
DocumentsRELMASamples

•  Windows
Vista
=
Samples

•  Windows
7
=
Samples


Running RELMA®
Version 5.2


Copyright
Screen


Main
Menu/Welcome
Screen


Set
Preferred
Language

Click
File,
Set
Preferred

Language


Select
Linguistic
Variant(s)

Selecting
a
translation
may

require
indexes
to
be
built


LOINC
Terms
with
Spanish
Linguistic
Variant

All
Spanish!


Setting
User
Preferences


Set
User
Preferences

Select
User
Preferences

From
the
File
Menu

...or
from
Welcome
Screen


Set
User
Preference
Dialog

New
File
Locations:

(See
prior
slide
for
location)

Startup
Screen
Preference


User
Map
Screen
Preferences

Click
Map
Screen
Tab

Include/Exclude
Battery

Terms

Add
comments
on
Mappings


Importing
Local

Terms
into
RELMA


4
Ways
to
Load
LMOF
Files

•  Direct
entry
into
LMOF
from
within
RELMA
(painful)

•  Handy
for
individual
entries/edits

•  Create
an
Access
table
that
mimics
the
LMOF
structure

(less
painful
but
tedious)

•  Appendix
A:

RELMA
Manual

•  Create
a
delimited
ASCII
ﬁle
from
your
local
test

catalog
(good
choice)

•  Load
directly
from
HL7
v2.x
messages

•  Pulls
data
from
OBR
and
OBX
segments

•  Stores
NTE
segment
data


Constructing
a
Local
Dataset

Create
extract
of
your
test
catalog
with:

•  BaFery/Panel
Code

•  BaFery/Panel
DescripJon
or
Name

•  *Local
Code

•  *Test
DescripJon
or
Name

•  Include
Method
if
Important

•  Units

•  Example
Values

•  Laboratory
SecJon


Creating
Delimited
ASCII
File

•  RELMA
can’t
parse
free
text

•  Need
to
create
separate
fields

•  Can
use
any
of
these
delimiters

•  Tab,
Semicolon,
Comma,
Space

•  Can
define
your
own

•  Fields
can
be
in
any
order

•  Minimum
required
fields

•  Local
Code

•  Local
DescripJon

•  Units
(highly
recommended)


Entering
New
Local
Terms

into
RELMA


Manual
Enter/Edit

View/Add/Edit
Local
Terms


Edit
Term
Dialog

EditAddDelete
Terms

Export
Terms

Text
alignment
option

Print
Preview
List


Export
Local
Term
File

Delimiters
supported:

Tab,
comma,
bar
(|)


Add
Local
Term

MICRO!

BUBPLAG!
BUBONIC PLAGUE – RRT PCR!

Click
to
Add
to
Current

Working
File


Search
Local
Term
File

Calcium

Enter
Keyword
from
any

Return
to
Full
List

Field


Print
Preview
Local
Term
File


Steps
to
Import
Local
Terms

1.  Click
Import Local Terms
BuFon
from
Main
Menu

a) File>Import Local Terms from Delimited File

2.  Locate
your
local
terms
text
file

a)  E.g.
WinXP
Sample
files
loaded
into
C:Documents
and

SeMngsAll
UsersShared
DocumentsRELMA

3.  Name
your
Working
Set

a)  LMOF
database
can
contain
mulJple
work
sets

4.  Define
default
secJon
(OpJonal)

5.  IdenJfy
file
delimiter

6.  Assign
fields
to
LMOF
aFributes

a)  Ignore
fields
you
don’t
need

b)  Combine
fields
if
needed

7.  Check
“Case-‐sensiJve”
if
needed

8.  Click
Import.


Example
Tab-‐Delimited
File


Importing
Local
Files

Select
Import
Local
Terms

from
Delimited
File…


Navigate
to
File
Location

Select
File
iles
stored
ipen
Sample
j and
Click
O n

RELMA
Directory


Open
File
in
RELMA

Name
your
working
set.

RELMA
allows
multiple
sets
in

LMOF
database

Select
your
delimiter

Import
Button


Fields
Segregated

Assign LMOF Attribute

Choose
jield
name


Ready
to
Import

Minimum
assignments

Now
you
can
click
the

Import
button!


Post-‐Processing
of
Local
File

•  Aer
import,
RELMA
Searches
for
terms

(words)
that
it
does
not
recognize

•  Stored
in
a
ﬁle
for
future
reconciliaJon


Local
Term
File
Options


Change
Local
Term
File

Select
the
Working
Set

Current
mapping
status


Alternative
Pragmatic
Way

•  Use
large
set
of
HL7
messages

•  AutomaJcally
make
dataset
of:

•  OBR
ID

•  OBR
descripJon

•  OBX
ID

•  OBX
descripJon

•  Sample
of
results

with

•  Real
values

•  Units

•  Abnormal
ﬂags

•  Normal
ranges


Generate
Local
term
jile
from
HL7
messages

Select
Import
Terms
from

HL7
File


Select
File
to
Import

Select
HL7
File


Specify
HL7
File
Name
and
Sample
Size

Skip
import
of

sample
values

Name
the
Local
Term
Select
the
number
of

File
(working
set)
sample
values

Select
which
codes
to
store


HL7
Messages
Data
Statistics


New
Terms
added
to
LMOF

Click
on
“Edit
Term”
to
see

Sample
Data

New
Battery
Code


Sample
Results
for
Observation

New
Test
Code

Sample
Values
from

Messages


Lenny
L’OINC
says:

“Load
the
Sample
Files

Into
RELMA
now!”

•  Import
the
two
sample
ﬁles

provided

•  Import_Sample_OBR.txt

•  Contains
baFery
code
and

descripJon

•  Import_Sample_OBX.txt

•  Contains
test
code
and

descripJon

•  Create
2
working
sets

•  Load
your
personal
data
set


Cleaning
your
data


Preparing
your
Data
for
Mapping

•  Improve
mapping
success
by:

•  Expanding
abbreviaJons

•  Standardizing
colloquial
terms

•  Ignoring
“administraJve”
terms

•  Standardizing
Jme
references

•  Can
be
done
prior
to
imporJng

•  BeFer
to
use
tools
built
into
RELMA


RELMA
Cleaning
Tools

Use
this
tool
to
edit

unknown
terms


Review
Unknown
Local
Terms

May
Re-‐Scan
File
for

Unknown
Terms


Replace
Local
Terms

Assign
LMOF
Attribute
Replacement Options


RELMA
Cleaning
Tools

Use
this
tool
to
make

global
substitutions


Term
Substitution

Save
this
global
substitution

for
only
this
working
set


Lenny
L’OINC
says:

“Begin
to
clean
your

data
now!”

•  Using
the
OBR
or
OBX
sample

ﬁles,
take
15-‐20
minutes
to

clean
up
these
unrecognized

terms

•  You
may
use
your
own
data
if

you
wish.


Searching
for
LOINC
Terms


Simplijied
Search

Only
Tool


Search
Window

Help
File

Enter
Search

Terms

Limit
to

Limit
to
Common

Specijic
Units
Tests

Restrict
to
“Common
“Common
Tests”
rank

Tests”
Use
Automapper

logic

New!

Lucene
score

indicates
relevance

of
search
result


New
RELMA
Helpjile


Context
Menu

Right
click
to
bring

up
context
menu


Mapping
Local
Terms


Mapping
Local
Terms

•  Select
your
Working
Set
to
Map

File>Select Local Term File to Process
• 
•  Select
“Map Local Terms to LOINC”
from

Welcome
Screen

•  Select
the
subset
of
terms
to
work
with:

•  All

•  Mapped

•  Unmapped

•  Set
your
Search Limits
•  Set Search Limits BuFon


Standard
Mapping
Window
Features

•  Customizable
grid

•  View
details
of
LOINC
term

•  Sort
by
column

•  Click
column

•  Custom
Sort

•  Print
or
export
results
grid

•  Spell
check
squiggly
line
to
signify
words

not
known
to
RELMA


Mapping
Screen

View
or
edit
local
term

Enter
local
term
number

Quick
select
button
list

Custom
Grid
Conjiguration


Conjigure
Grid

Select
elements
to
display

Reorder
grid
elements

Visually
resize
elements

Reset
Default
Conjiguration


Quick
choice
buttons

Viewing
LOINC
term
detail


View
Local
Term
Details

Select
level
of
detail
to

display


View
Local
Term
Details

Select
text
size


Select
detail
display
level

Select
level
of
detail
to

display


Standard
Mapping
Screen

EEK!

What’ll
I

Begin
a
search
do?!

(or
hit
“enter”)


Standard
Mapping
Screen

Click
to

show
words

used
in

search


Initial
Mapping
Results

Use
term
Number
of
LOINC
Battery
terms

checkbox
terms
containing
included
in

keyword
search


Revised
Mapping
Results

Match
units
Number
of

selected
by
matching

default
records
found


Re-‐revised
Mapping
Results

Number
of

matching

Match
units

records
found

unselected


Standard
Mapping
Screen

CANINE DISTEMPER VIRUS IF

Enter
keywords
here

Clear
all

input
jields


Ad
hoc
term
search


Standard
Mapping
Screen

Navigate
through

the
local
terms


Tabbed
Access
to
Functions

Navigate
to
Functions

from
Mapping
Page

Switch
between
Grid
and

Tree
Views


Tree
View


Tree
View

•  Results
displayed
hierarchically

•  Deﬁned
by
the
mulJ-‐axial
hierarchy
in
search

restricJons
(covered
later)

•  Map
to
a
term
in
tree
by
clicking
Map
buFon

or
double
clicking
term

•  Only
rows
that
have
LOINC
Codes


Tree
View

Can
map
to
terms
Cannot
map
to

with
LOINC
Codes
terms

representing

LOINC
parts

Tree
Navigation

Buttons


Assigning
a
LOINC
Map

Click
“Map”
Button

(or
doubleclick)

Highlight
correct

term


Adding
Mapping
Comments

Check with Frank in Chemistry

If
comments

option
is
selected,

prompt
appears


Assigning
a
LOINC
Map

LOINC
Term

Assigned


View
LOINC
Term
Details

View
details
for
a

specijic
LOINC
Term

Right
clicking
on
a
LOINC

term
brings
up
a
Task
Menu


LOINC
Term
Details

Can
scroll
down
a
single

formatted
page

Can
scroll
through

Change
to
expanded
returned
subset
of

details
view

terms

Change
text
size


View
Panel
Children

Select
View
Panel
Children

from
context
menu


Panel
Children


Conjigure
Export
Options

Output
Options

Include

Save
Conjiguration
column
headers

and/or
Export


Excel
Export
Format


More
on
Searching

Mapping
Screen


Basic
Search
Syntax

Special
Character Example
Defini7on

(s)

“

“
Influenza
“virus
A”
Linked
terms
must
appear
together

AND
Morphine
AND
Both
terms
must
appear
in
the
search
result

Opiates
term

OR
Influenza
OR
Either
or
both
terms
must
appear
in
the

Parainfluenza
search
result
term

NOT

Influenza
NOT
equine
Excludes
terms
with
the
word
following
the

NOT.

Cannot
be
used
alone.

?
Gluc?se
SubsJtutes
a
single
character
in
the
string.

(glucose,glucase)
Cannot
be
used
as
the
first
character;
cannot

be
used
in
“phrases”

*
Gluc*se
SubsJtute
mulJple
characters
in
the
string.

(glucose,
Cannot
be
used
as
the
first
character;
cannot

glucuronidase,
etc.)
be
used
in
“phrases”


Search
Qualijiers

Detailed
help
available

Includes
Glucuronidase,

Glucosidase,

Glucosylceramidase,
etc.


Combining
Search
Terms

Exclude
Glucosidase

Reduced
number
of
terms


Advanced
Search
Syntax

based
on
Google-‐like
search
syntax

Parameter
Descrip7on

+
Term
must
be
included
in
search

-‐
Term
must
be
excluded
from
the
search

(
)
Group
terms
for
subquery
(i.e.
A
OR
B;
A
AND
B)

Fieldname:
Limit
term
search
to
the
associated
ﬁeld
(e.g.
Component:
glucose)

Fieldname:()
Group
mulJple
terms
in
a
single
ﬁeld

~
Fuzzy
search
(e.g.
Hemo„ilus~)

“
“~
Proximity
search
for
mulJple
terms
(e.g.
“funcJon
panel”~1)

{},
[]
Upper
and
lower
bounds;
{}
exclusive,
[]
inclusive

Special
character
escape


Applying
advanced
search


Limiting
Searches


Setting
Search
Limits

•  Narrows
search
to
speciﬁc
subset
of
LOINC
terms

•  Reduces
number
of
candidate
terms

•  Limits
can
be
applied
to
all
components

•  Component
aFribute
can
be
further
restricted
by

number
of
words

•  Tree
structure
allows
for
hierarchical
constraints


General
Search
Constraints

•  Controls
features
including:

•  Limit
to
LOINC
terms
compaJble
with
submiFed
units

•  Forced
match
with
any
specimen
contained
in
name

•  Method-‐less
terms
only

•  Limit
to
components/analytes
with
N
or
fewer
words
in
their

name

•  Pop
up
search
Jming
staJsJcs
aer
each
search

•  Use
carefully
or
search
may
not
be
successful

(Note
parallel
control
switches
at
boFom
of
screen)


Setting
Search
Limits

Click
Hierarchy
&
Search

Limits
Tab


Setting
search
limits

Can
also
set
most
of
them
by
toggling
buFons

at
the
boFom
of
the
screen

Toggle
Buttons


Search
Constraints

Attribute
trees

Local
Unit
Constraint:

Default
is
“ON”

New!
Type
toggle
boxes

Predejined,
general
search

constraints


Terms
Consistent
with
Units

Only
terms
consistent

with
mmol/L
appear


Setting
Search
Limits

Specimen

constraints


Terms
Consistent
with
Specimen

CSF

Enter
default

Specimen


Terms
Consistent
with
Specimen

Only
CSF
Terms

are
returned


Setting
Search
Limits

Methodless
Terms
Override
Methodless
Terms

Restriction
Restriction


Limit
to
Methodless
Terms


Limit
to
Methodless
Terms

Only
Methodless

Terms
Appear


More
on
Methodless
Terms

•  Some
LOINC
categories
do
not
have

methodless
terms

•  Checking
methodless
only
will
remove
these

from
view
on
results
grid

•  Checking
addiJonal
box
allows
these
to
be

seen


Methodless
Only
Unchecked

All
terms
returned


Methodless
Only
Checked

Only
Methodless

terms
returned

Differ
in
one
or

more
components


Conditional
Methodless

More
terms

returned

No
methodless

term;
all
shown


Setting
Search
Limits

Limit
to
Lab
Tests
Only

(No
Clinical
LOINC
Terms)


Setting
Search
Limits

Limit
to
common
lab
tests


Setting
Search
Limits

Limit
Number
of
Words
in
the

Component
Attribute


Limit
Number
of
Component
Words

Without
Limit
Applied:

792
terms
returned


Limit
Number
of
Component
Words

Restriction
appears
on

Toggle
Bar

(cannot
toggle
off)

Component
limited
to

1
word
With
Limit
Applied:

57
terms
returned


Setting
Search
Limits

Include
Trial,
Deprecated
or

Discouraged
LOINC
Codes
with

Returned
Terms


Include
Deprecated
LOINC
Terms

-‐ You
cannot
map
to

deprecated
LOINC
terms

-‐ 
You
are
warned
before

mapping
to
discouraged

LOINC
terms

Discouraged
LOINC
Terms
appear
as
an

inverted
triangle

Deprecated
LOINC
Terms
appear
as

Strikethrough
Text
with
a
“Do
Not”

Symbol


Favor
Property
Restriction

Favor
one
type
of

property
over
others

All
other
components

being
equal
MCnc

only
will
be
displayed


Order/Observation
Restriction

Order
or
Observation

preference


LOINC
Hierarchies
–
Class
Tree

Three
top-‐level

branches

Tree
Navigation

Buttons


Before
Class
Restriction

Most
terms
have
class

of
“CHAL”

Large
number
of

candidate
terms


Search
Trees

+Non +Chem

Restrict
eligible
tests

to
non-‐challenge

chemistry
tests
only


Following
Class
Restriction

Only
Non-‐Challenge

Chemistry
tests

returned


Improvements
to
Trees

Continued
reorganization
to

provide
a
Specimen

hierarchy


Improved
Hierarchy
for
Component

Click
on
details
for
more

information
about
the

selection

Show
the
LOINC
Codes

associated
with
these

components


Details
Screen
LOINC
Part


Show
Associated
LOINCs


LOINC
Term
Details
Screen

Detailed
Information
on

LOINC
Parts


Tree
Export
Tools

Export
according
to

Conjiguration

Conjigure
Export
Format


Tree
Export
Conjiguration


RELMA
-‐
Tree
Features

•  All
trees
operate
the
same
way

•  Shows
terms
spelled
out

•  Can
expand
and
collapse
parts
or
all
of
tree.

•  Tree
is
string
searchable

•  Search
can
be
based
on
one
or
more

branches
of
a
tree
with
or
without
other

criteria

•  Use
“Clear
Most
Limits”
buFon
on
Mapping

Screen
to
remove
all
tree
selecJons


LOINC
Part
Search

•  Same
look
as
term
search

•  Uses
“Google-‐like”
query
language

•  Extremely
fast

•  Include
and
exclude
criteria

•  ParJal
string
matching
(using
wildcards)

•  Demo

•  Campylobacter
fetus,
not
Ab


Navigating
through
the

Mapping
Process


LOINC
Mapping
Tactics

•  Limit
eﬀort
to
one
lab
secJon
at
a
Jme
and

focus
experJse

•  Chemistry
and
hematology
will
be
easiest

•  For
manufactured
assays,
use
package
insert
as

source
informaJon

•  Sample
results
give
clue
to
property
and
scale

•  Consider
prioriJzing
by
frequency
of
use


Vreeman
DJ,
Finnell
JT,
Overhage
JM.
A
Rationale
for
Parsimonious
Laboratory
Term

Mapping
by
Frequency.
AMIA
Annu
Symp
Proc.
2007;:771-‐775.


More
LOINC
Mapping
Tactics

•  Try
using
method-‐less
terms
first

•  Specific
methods
can
be
transmiFed
in:

• 
OBX–17
(v2.x),
ObservaJon.methodCode
(v3.0)

•  Examine
local
units
or
real
results
to
verify

correct
property
and
scale

•  ProperJes
are
rarely
disJnguishable
in
test
names

•  You
don’t
have
to
do
it
all
at
one
siMng

•  Use
the
“Unmapped”
funcJon
to
return
where
you

le
off

•  With
every
release
-‐
Update
previous
mappings

to
idenJfy
deprecated
terms


Common
Mapping
Issues

•  Locally
Deﬁned
Test
Name
Ambiguity

•  Reuse
of
local
test
code

•  “Analyte-‐free”
Local
Test
Names

•  (Miscellaneous
serology)

•  Incongruent
Value
sets
(Scale
ambiguity)

•  Result
vs.
InterpretaJon

•  Available
LOINC
Terms
too
Speciﬁc/General

•  Panel
vs.
Discrete
Test

•  Common
in
Microbiology


Using
your
Mapped
Terms

•  Print
results
of
LOINC
Mapping

•  Export
to
File


Conjigure
Export
Format

Context
Sensitive
Export

Conjiguration


LMOF
Export
Conjiguration

Select
Export
Format

Select
Fields
to
Export

Save
Conjiguration
and

Export


Print
Mapped
Terms
from
View/Add/
Edit
Menu

Click
Print
button
to
Preview

May
highlight
terms
to
be

output

printed


Formatted
Report
Output

Click
Print
button
to
output

formatted
report


Custom
Export
Conjiguration

Select
the
Format
you
wish

to
Export

Select
the
Fields
you
wish
to

Export


Excel™
Export


New
and
Improved

Lab
Auto
Mapper

•  Run
in
batch
mode
to
ﬁnd
N-‐
closest
terms

•  Can
then
use
this
output
to
do
ﬁnal
mapping

•  Again
units
are
VERY
important

•  Can
pick
all
limits
available
to
regular
mapping


Picking
the
Lab
Auto
Mapper


Lab
Auto
Mapper
Start
Screen

Can
restrict
search
to
Maximum
number
of
terms

common
tests
to
return


Lab
Auto
Mapper
Start
Screen

Local
test
code
Local
terms
used
for

mapping


Lab
Auto
Mapper
-‐
Mapping
Screen


Exporting
Mapped
Terms

Export
Terms
to

Delimited
File


Export
Terms
Dialog

Select
Term
Set

Select
Delimiter

Check
Fields
you

wish
to
export


Other
RELMA ®

Features


Panels,
Forms
and
Survey
Review

Review
Panels,
Forms
and

Surveys

Review
Panels,
Forms
and

Surveys


Government
Forms

Component
LOINC

terms

Form
Name


Laboratory
Panels

Expand
category
to

see
panels

Double-‐click

panel
name
to
see

components


Expanded
Panel
Detail


Expanded
Clinical
Panel


Clinical
Panels

Find
where
a
term
has

been
used


LOINC
Term
Panel
Usage


Other
Survey
Instruments


HIPAA
Attachments

View
Various
HIPAA

Attachments


HIPPA
Attachment
Tree


Expanded
Attachment
Data


Can’t
jind
the

term
you

want?


Search
Hints
and
Tips

• 
Keywords
with
zero
frequency
are
ignored

•  May
need
to
rephrase
–
use
synonym

•  Some
causes
for
no
returned
terms

•  Too
many
keywords
in
search
–
uncheck
some

•  Limits
applied
that
don’t
make
sense

•  E.g.
Method-‐less
tests
plus
Method
tree
set
to
EIA

•  Did
not
ﬁnd
and
revise
words
not
in
RELMA

•  Local
units
not
in
RELMA

•  Units
are
GREAT
discriminators

•  You
may
have
tests
that
need
to
be
added
to

LOINC


Proposing
New
LOINC
Terms


Proposing
New
Terms

•  Make
sure
the
term
is
really
needed

•  Think
of
other
names
for
the
same
concept

•  Avoid
detailed
methods
or
localizaJons

•  Is
the
disJncJon
really
important?

•  Supply
suﬃcient
annotaJon
to
jusJfy
the
new
term

•  Package
inserts,
sample
reports
(email
to
Regenstrief)

•  The
more
the
beFer!

•  Construct
new
terms
within
RELMA

•  File>Propose a new LOINC
•  Linked
to
the
“trees”
to
allow
browsing

•  Can
review
and
submit
them
to
LOINC
from
within

RELMA


Propose
new
LOINC
terms

Select
Propose
a

new
LOINC


Navigate
through

proposed
terms

Required
jields
in

red

Create
new
term,

save
current
term

or
Exit
form


Preview
Proposed
Terms

Review
your
new

terms


Review
Proposed
Terms

Choose
whether
to

send
or
postpone

All
proposed
terms

fully
editable


Submitting
New
Terms

•  Must
supply
name,
organizaJon,
phone

and
email
of
submiFer

•  Must
select
at
least
one
proposed
term
to

send

•  “Configure
export”
does
not
affect

submission
output

•  Email
resulJng
file
to
Regenstrief


Use
Existing
Terms
as
Template

Click
the
Propose

Term
button

Select
your
closest

match


Use
Existing
Terms
as
Template

All
required

components
jilled
in


Using
LOINC
and
SNOMED

Together


Where
do
LOINC
and
SNOMED
Fit?

Remember:

•  LOINC
represents
the
quesJon:

•  Is
there
any
Botulism
toxin
in
my
specimen?

(33708-‐9)

•  Organisms
idenJﬁed
in
specimen?
(634-‐6)

•  SNOMED
represents
the
answer:

•  NegaJve
(SCTID
260385009)

•  E.
coli
O157:H7
(SCTID
103429008)


Where
do
LOINC
and
SNOMED
Fit?

•  In
an
HL7
message,
LOINC
may
be
used:

•  In
OBR-‐4
(Universal
Service
IdenJﬁer)

•  In
OBX-‐3
(ObservaJon
IdenJﬁer

•  SNOMED
may
be
used:

•  In
OBX-‐5
(where
nominal
values
are
needed)

•  Almost
anyplace
else
in
an
HL7
message
where

coded
values
are
needed


OBX:
With
a
Coded
Value

A
code
that

identijies
the

data
type
in

The
code
is
The
code
is

OBX-‐5
as
a

from
LOINC
from
SNOMED

coded
element

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

OBX-‐3:A
code
that

identijies
the
data
in
OBX-‐5:
Data

A

c

for
L.

ode

OBX-‐5

(Listeria
culture)
monocytogenes


HL7
2.5
Example
(ER-‐7
format)

MSH|^~&| LABGL1|| DMCRES|| 199812300100|| ORU^ R01|
LABGL1199510221838581| P| 2.3||| NE| NE

PID||| 6910828^ Y^ C8|| Newman^ Alfred^ E|| 19720812| M|| W| 25 Centscheap Ave^^
First
Order
OBR

(Culture
and
ID)

Whatmeworry^ UT^ 85201^^ P||( 555) 777- 6666|( 444) 677- 7777|| M|| 773789090alue

First
Result
V
(SNOMED)

OBR|| 110801^ LABGL| 387209373^ DMCRES|634-6^Bacteria XXX Aerobe Cult
^LN||| 199812292128||||||||Stool| IN2973^ Schadow^ Gunther^^^^ MD^
Second
Order
OBR

UPIN|||||||||||||||| CA20837^ Spinosa^ John^^^^ MD^ UPIN (Susceptibility)

OBX|| CE| 634-6^Bacteria XXX Aerobe Cult^ LN||50136005^Salmonella typhimurium
^SCT|||||| F||| 199812292128|| CA20837

OBR|| 110801^ LABGL| 387209373^ DMCRES| 29567-9^Bacterial Susceptibility
Second
Result(s)
First
Result
Description

Panel^esult
199812300934||||||||Bacterial isolate| IN2973^ Schadow^
First
LN|||

(Culture
and
ID)
Gunther^^^^

OBXs
OBX
(LOINC)

MD^ UPIN||||||||| Salmonella typhimurium ||||||| CA20837^ Spinosa^
John^^^^ MD^ UPIN

OBX|| CE|23631-5^Trimethoprim/Sulfasoxazole^ LN||264841006^Intermediate
^SCT|||||| F||| 199812300934|| CA20837
OBX|| CE|18967-7^Penicillin^LN||30714006^Resistant^SCT|||||| F||| 199812300934||
CA20837
OBX|| CE|18928-2^Gentamicin^ LN||131196009^Susceptible^SCT|||||| F|||
199812300934|| CA20837


Q
and
A
Session


Exercise

Map
your
own
data


2011 06 06 - LOINC Workshop and Tutorial

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