Mais conteúdo relacionado
Semelhante a 2011 06 06 - LOINC Workshop and Tutorial (20)
2011 06 06 - LOINC Workshop and Tutorial
- 1. 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
- 2. 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
©2011 Regenstrief Institute and James Case
- 3. 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
©2011 Regenstrief Institute and James Case
- 4. 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)
©2011 Regenstrief Institute and James Case
- 5. 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
©2011 Regenstrief Institute and James Case
- 6. 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
©2011 Regenstrief Institute and James Case
- 7. 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
©2011 Regenstrief Institute and James Case
- 8. 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
©2011 Regenstrief Institute and James Case
- 9. 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
©2011 Regenstrief Institute and James Case
- 10. 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
©2011 Regenstrief Institute and James Case
- 12. 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
©2011 Regenstrief Institute and James Case
- 13. 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
©2011 Regenstrief Institute and James Case
- 14. 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
Ab:ACnc:Pt:Ser:Qn:EIA
©2011 Regenstrief Institute and James Case
- 15. 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
©2011 Regenstrief Institute and James Case
- 16. 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
Ab:ACnc:Pt:Ser:Qn:EIA
©2011 Regenstrief Institute and James Case
- 17. 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
Ab:ACnc:Pt:Ser:Qn:EIA
©2011 Regenstrief Institute and James Case
- 18. 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
- 19. 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
©2011 Regenstrief Institute and James Case
- 20. 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)
©2011 Regenstrief Institute and James Case
- 21. 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)
©2011 Regenstrief Institute and James Case
- 22. 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)
©2011 Regenstrief Institute and James Case
- 23. 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
©2011 Regenstrief Institute and James Case
- 24. 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?)
©2011 Regenstrief Institute and James Case
- 25. 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
©2011 Regenstrief Institute and James Case
- 27. 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
©2011 Regenstrief Institute and James Case
- 28. 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
©2011 Regenstrief Institute and James Case
- 29. 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.
©2011 Regenstrief Institute and James Case
- 30. 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.
©2011 Regenstrief Institute and James Case
- 32. 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
©2011 Regenstrief Institute and James Case
32
- 33. 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
©2011 Regenstrief Institute and James Case
- 35. 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
©2011 Regenstrief Institute and James Case
- 36. File
Locations
• Database
and
Ancillary
Files
• Windows
XP
=
C:Documents
and
SeMngsAll
Users
DocumentsRELMA
• Windows
Vista
=
C:UsersPublicDocumentsRELMA
• Windows
7
=
C:UsersPublicDocumentsRELMA
• Sample
files
• Windows
XP
=
C:Documents
and
SeMngsAll
Users
DocumentsRELMASamples
• Windows
Vista
=
C:UsersPublicDocumentsRELMA
Samples
• Windows
7
=
C:UsersPublicDocumentsRELMA
Samples
©2011 Regenstrief Institute and James Case
- 37. Running RELMA®
Version 5.2
©2011 Regenstrief Institute and James Case
- 42. LOINC
Terms
with
Spanish
Linguistic
Variant
All
Spanish!
©2011 Regenstrief Institute and James Case
- 44. Set
User
Preferences
Select
User
Preferences
From
the
File
Menu
...or
from
Welcome
Screen
©2011 Regenstrief Institute and James Case
- 45. Set
User
Preference
Dialog
New
File
Locations:
(See
prior
slide
for
location)
Startup
Screen
Preference
©2011 Regenstrief Institute and James Case
- 46. User
Map
Screen
Preferences
Click
Map
Screen
Tab
Include/Exclude
Battery
Terms
Add
comments
on
Mappings
©2011 Regenstrief Institute and James Case
- 48. 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
©2011 Regenstrief Institute and James Case
- 49. 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
©2011 Regenstrief Institute and James Case
- 50. 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)
©2011 Regenstrief Institute and James Case
- 52. Manual
Enter/Edit
View/Add/Edit
Local
Terms
©2011 Regenstrief Institute and James Case
- 53. Edit
Term
Dialog
EditAddDelete
Terms
Export
Terms
Text
alignment
option
Print
Preview
List
©2011 Regenstrief Institute and James Case
- 54. Export
Local
Term
File
Delimiters
supported:
Tab,
comma,
bar
(|)
©2011 Regenstrief Institute and James Case
- 55. Add
Local
Term
MICRO!
BUBPLAG!
BUBONIC PLAGUE – RRT PCR!
Click
to
Add
to
Current
Working
File
©2011 Regenstrief Institute and James Case
- 56. Search
Local
Term
File
Calcium
Enter
Keyword
from
any
Return
to
Full
List
Field
©2011 Regenstrief Institute and James Case
- 58. 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.
©2011 Regenstrief Institute and James Case
- 60. Importing
Local
Files
Select
Import
Local
Terms
from
Delimited
File…
©2011 Regenstrief Institute and James Case
- 61. Navigate
to
File
Location
Select
File
iles
stored
ipen
Sample
j and
Click
O n
RELMA
Directory
©2011 Regenstrief Institute and James Case
- 62. Open
File
in
RELMA
Name
your
working
set.
RELMA
allows
multiple
sets
in
LMOF
database
Select
your
delimiter
Import
Button
©2011 Regenstrief Institute and James Case
- 63. Fields
Segregated
Assign LMOF Attribute
Choose
jield
name
©2011 Regenstrief Institute and James Case
- 64. Ready
to
Import
Minimum
assignments
Now
you
can
click
the
Import
button!
©2011 Regenstrief Institute and James Case
- 65. Post-‐Processing
of
Local
File
• Aer
import,
RELMA
Searches
for
terms
(words)
that
it
does
not
recognize
• Stored
in
a
file
for
future
reconciliaJon
©2011 Regenstrief Institute and James Case
- 67. Change
Local
Term
File
Select
the
Working
Set
Current
mapping
status
©2011 Regenstrief Institute and James Case
- 68. 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
©2011 Regenstrief Institute and James Case
- 69. Generate
Local
term
jile
from
HL7
messages
Select
Import
Terms
from
HL7
File
©2011 Regenstrief Institute and James Case
- 70. Select
File
to
Import
Select
HL7
File
©2011 Regenstrief Institute and James Case
- 71. 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
©2011 Regenstrief Institute and James Case
- 73. New
Terms
added
to
LMOF
Click
on
“Edit
Term”
to
see
Sample
Data
New
Battery
Code
©2011 Regenstrief Institute and James Case
- 74. Sample
Results
for
Observation
New
Test
Code
Sample
Values
from
Messages
©2011 Regenstrief Institute and James Case
- 75. 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
©2011 Regenstrief Institute and James Case
- 77. 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
©2011 Regenstrief Institute and James Case
- 78. RELMA
Cleaning
Tools
Use
this
tool
to
edit
unknown
terms
©2011 Regenstrief Institute and James Case
- 79. Review
Unknown
Local
Terms
May
Re-‐Scan
File
for
Unknown
Terms
©2011 Regenstrief Institute and James Case
- 80. Replace
Local
Terms
Assign
LMOF
Attribute
Replacement Options
©2011 Regenstrief Institute and James Case
- 81. RELMA
Cleaning
Tools
Use
this
tool
to
make
global
substitutions
©2011 Regenstrief Institute and James Case
- 82. Term
Substitution
Save
this
global
substitution
for
only
this
working
set
©2011 Regenstrief Institute and James Case
- 83. 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.
©2011 Regenstrief Institute and James Case
- 86. 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
©2011 Regenstrief Institute and James Case
- 88. Context
Menu
Right
click
to
bring
up
context
menu
©2011 Regenstrief Institute and James Case
- 90. 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
©2011 Regenstrief Institute and James Case
- 91. 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
©2011 Regenstrief Institute and James Case
- 92. Mapping
Screen
View
or
edit
local
term
Enter
local
term
number
Quick
select
button
list
Custom
Grid
Conjiguration
©2011 Regenstrief Institute and James Case
- 93. Conjigure
Grid
Select
elements
to
display
Reorder
grid
elements
Visually
resize
elements
Reset
Default
Conjiguration
©2011 Regenstrief Institute and James Case
- 95. View
Local
Term
Details
Select
level
of
detail
to
display
©2011 Regenstrief Institute and James Case
- 96. View
Local
Term
Details
Select
text
size
©2011 Regenstrief Institute and James Case
- 97. Select
detail
display
level
Select
level
of
detail
to
display
©2011 Regenstrief Institute and James Case
- 98. Standard
Mapping
Screen
EEK!
What’ll
I
Begin
a
search
do?!
(or
hit
“enter”)
©2011 Regenstrief Institute and James Case
- 100. Initial
Mapping
Results
Use
term
Number
of
LOINC
Battery
terms
checkbox
terms
containing
included
in
keyword
search
©2011 Regenstrief Institute and James Case
- 101. Revised
Mapping
Results
Match
units
Number
of
selected
by
matching
default
records
found
©2011 Regenstrief Institute and James Case
- 103. Standard
Mapping
Screen
CANINE DISTEMPER VIRUS IF
Enter
keywords
here
Clear
all
input
jields
©2011 Regenstrief Institute and James Case
- 104. Ad
hoc
term
search
©2011 Regenstrief Institute and James Case
- 106. Tabbed
Access
to
Functions
Navigate
to
Functions
from
Mapping
Page
Switch
between
Grid
and
Tree
Views
©2011 Regenstrief Institute and James Case
- 107. Tree
View
©2011 Regenstrief Institute and James Case
- 108. 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
©2011 Regenstrief Institute and James Case
- 109. Tree
View
Can
map
to
terms
Cannot
map
to
with
LOINC
Codes
terms
representing
LOINC
parts
Tree
Navigation
Buttons
©2011 Regenstrief Institute and James Case
- 110. Assigning
a
LOINC
Map
Click
“Map”
Button
(or
doubleclick)
Highlight
correct
term
©2011 Regenstrief Institute and James Case
- 111. Adding
Mapping
Comments
Check with Frank in Chemistry
If
comments
option
is
selected,
prompt
appears
©2011 Regenstrief Institute and James Case
- 112. Assigning
a
LOINC
Map
LOINC
Term
Assigned
©2011 Regenstrief Institute and James Case
- 113. View
LOINC
Term
Details
View
details
for
a
specijic
LOINC
Term
Right
clicking
on
a
LOINC
term
brings
up
a
Task
Menu
©2011 Regenstrief Institute and James Case
- 114. 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
©2011 Regenstrief Institute and James Case
- 115. View
Panel
Children
Select
View
Panel
Children
from
context
menu
©2011 Regenstrief Institute and James Case
- 117. Conjigure
Export
Options
Output
Options
Include
Save
Conjiguration
column
headers
and/or
Export
©2011 Regenstrief Institute and James Case
- 120. 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”
©2011 Regenstrief Institute and James Case
- 121. Search
Qualijiers
Detailed
help
available
Includes
Glucuronidase,
Glucosidase,
Glucosylceramidase,
etc.
©2011 Regenstrief Institute and James Case
- 122. Combining
Search
Terms
Exclude
Glucosidase
Reduced
number
of
terms
©2011 Regenstrief Institute and James Case
- 123. 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
©2011 Regenstrief Institute and James Case
- 126. 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
©2011 Regenstrief Institute and James Case
- 127. 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)
©2011 Regenstrief Institute and James Case
- 128. Setting
Search
Limits
Click
Hierarchy
&
Search
Limits
Tab
©2011 Regenstrief Institute and James Case
- 129. Setting
search
limits
Can
also
set
most
of
them
by
toggling
buFons
at
the
boFom
of
the
screen
Toggle
Buttons
©2011 Regenstrief Institute and James Case
- 130. Search
Constraints
Attribute
trees
Local
Unit
Constraint:
Default
is
“ON”
New!
Type
toggle
boxes
Predejined,
general
search
constraints
©2011 Regenstrief Institute and James Case
- 131. Terms
Consistent
with
Units
Only
terms
consistent
with
mmol/L
appear
©2011 Regenstrief Institute and James Case
- 133. Terms
Consistent
with
Specimen
CSF
Enter
default
Specimen
©2011 Regenstrief Institute and James Case
- 134. Terms
Consistent
with
Specimen
Only
CSF
Terms
are
returned
©2011 Regenstrief Institute and James Case
- 135. Setting
Search
Limits
Methodless
Terms
Override
Methodless
Terms
Restriction
Restriction
©2011 Regenstrief Institute and James Case
- 137. Limit
to
Methodless
Terms
Only
Methodless
Terms
Appear
©2011 Regenstrief Institute and James Case
- 138. 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
©2011 Regenstrief Institute and James Case
- 140. Methodless
Only
Checked
Only
Methodless
terms
returned
Differ
in
one
or
more
components
©2011 Regenstrief Institute and James Case
- 141. Conditional
Methodless
More
terms
returned
No
methodless
term;
all
shown
©2011 Regenstrief Institute and James Case
- 142. Setting
Search
Limits
Limit
to
Lab
Tests
Only
(No
Clinical
LOINC
Terms)
©2011 Regenstrief Institute and James Case
- 144. Setting
Search
Limits
Limit
Number
of
Words
in
the
Component
Attribute
©2011 Regenstrief Institute and James Case
- 145. Limit
Number
of
Component
Words
Without
Limit
Applied:
792
terms
returned
©2011 Regenstrief Institute and James Case
- 146. Limit
Number
of
Component
Words
Restriction
appears
on
Toggle
Bar
(cannot
toggle
off)
Component
limited
to
1
word
With
Limit
Applied:
57
terms
returned
©2011 Regenstrief Institute and James Case
- 147. Setting
Search
Limits
Include
Trial,
Deprecated
or
Discouraged
LOINC
Codes
with
Returned
Terms
©2011 Regenstrief Institute and James Case
- 148. 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
©2011 Regenstrief Institute and James Case
- 149. Favor
Property
Restriction
Favor
one
type
of
property
over
others
All
other
components
being
equal
MCnc
only
will
be
displayed
©2011 Regenstrief Institute and James Case
- 151. LOINC
Hierarchies
–
Class
Tree
Three
top-‐level
branches
Tree
Navigation
Buttons
©2011 Regenstrief Institute and James Case
- 152. Before
Class
Restriction
Most
terms
have
class
of
“CHAL”
Large
number
of
candidate
terms
©2011 Regenstrief Institute and James Case
- 153. Search
Trees
+Non +Chem
Restrict
eligible
tests
to
non-‐challenge
chemistry
tests
only
©2011 Regenstrief Institute and James Case
- 155. Improvements
to
Trees
Continued
reorganization
to
provide
a
Specimen
hierarchy
©2011 Regenstrief Institute and James Case
- 156. Improved
Hierarchy
for
Component
Click
on
details
for
more
information
about
the
selection
Show
the
LOINC
Codes
associated
with
these
components
©2011 Regenstrief Institute and James Case
- 159. LOINC
Term
Details
Screen
Detailed
Information
on
LOINC
Parts
©2011 Regenstrief Institute and James Case
- 160. Tree
Export
Tools
Export
according
to
Conjiguration
Conjigure
Export
Format
©2011 Regenstrief Institute and James Case
- 162. 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
©2011 Regenstrief Institute and James Case
- 163. 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
©2011 Regenstrief Institute and James Case
- 165. 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
©2011 Regenstrief Institute and James Case
- 166. Vreeman
DJ,
Finnell
JT,
Overhage
JM.
A
Rationale
for
Parsimonious
Laboratory
Term
Mapping
by
Frequency.
AMIA
Annu
Symp
Proc.
2007;:771-‐775.
©2011 Regenstrief Institute and James Case
- 167. 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
©2011 Regenstrief Institute and James Case
- 168. 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
©2011 Regenstrief Institute and James Case
- 169. Using
your
Mapped
Terms
• Print
results
of
LOINC
Mapping
• Export
to
File
©2011 Regenstrief Institute and James Case
- 171. LMOF
Export
Conjiguration
Select
Export
Format
Select
Fields
to
Export
Save
Conjiguration
and
Export
©2011 Regenstrief Institute and James Case
- 172. Print
Mapped
Terms
from
View/Add/
Edit
Menu
Click
Print
button
to
Preview
May
highlight
terms
to
be
output
printed
©2011 Regenstrief Institute and James Case
- 173. Formatted
Report
Output
Click
Print
button
to
output
formatted
report
©2011 Regenstrief Institute and James Case
- 174. Custom
Export
Conjiguration
Select
the
Format
you
wish
to
Export
Select
the
Fields
you
wish
to
Export
©2011 Regenstrief Institute and James Case
- 176. 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
©2011 Regenstrief Institute and James Case
- 177. Picking
the
Lab
Auto
Mapper
©2011 Regenstrief Institute and James Case
- 178. Lab
Auto
Mapper
Start
Screen
Can
restrict
search
to
Maximum
number
of
terms
common
tests
to
return
©2011 Regenstrief Institute and James Case
- 179. Lab
Auto
Mapper
Start
Screen
Local
test
code
Local
terms
used
for
mapping
©2011 Regenstrief Institute and James Case
- 180. Lab
Auto
Mapper
-‐
Mapping
Screen
©2011 Regenstrief Institute and James Case
- 182. Export
Terms
Dialog
Select
Term
Set
Select
Delimiter
Check
Fields
you
wish
to
export
©2011 Regenstrief Institute and James Case
- 183. Other
RELMA ®
Features
©2011 Regenstrief Institute and James Case
- 184. Panels,
Forms
and
Survey
Review
Review
Panels,
Forms
and
Surveys
Review
Panels,
Forms
and
Surveys
©2011 Regenstrief Institute and James Case
- 185. Government
Forms
Component
LOINC
terms
Form
Name
©2011 Regenstrief Institute and James Case
- 186. Laboratory
Panels
Expand
category
to
see
panels
Double-‐click
panel
name
to
see
components
©2011 Regenstrief Institute and James Case
- 189. Clinical
Panels
Find
where
a
term
has
been
used
©2011 Regenstrief Institute and James Case
- 192. HIPAA
Attachments
View
Various
HIPAA
Attachments
©2011 Regenstrief Institute and James Case
- 195. Can’t
jind
the
term
you
want?
©2011 Regenstrief Institute and James Case
- 196. 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
©2011 Regenstrief Institute and James Case
- 198. 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
©2011 Regenstrief Institute and James Case
- 199. Propose
new
LOINC
terms
Select
Propose
a
new
LOINC
©2011 Regenstrief Institute and James Case
- 200. Navigate
through
proposed
terms
Required
jields
in
red
Create
new
term,
save
current
term
or
Exit
form
©2011 Regenstrief Institute and James Case
- 202. Review
Proposed
Terms
Choose
whether
to
send
or
postpone
All
proposed
terms
fully
editable
©2011 Regenstrief Institute and James Case
- 203. 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
©2011 Regenstrief Institute and James Case
- 204. Use
Existing
Terms
as
Template
Click
the
Propose
Term
button
Select
your
closest
match
©2011 Regenstrief Institute and James Case
- 205. Use
Existing
Terms
as
Template
All
required
components
jilled
in
©2011 Regenstrief Institute and James Case
- 206. Using
LOINC
and
SNOMED
Together
©2011 Regenstrief Institute and James Case
- 207. 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)
©2011 Regenstrief Institute and James Case
- 208. 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
©2011 Regenstrief Institute and James Case
- 209. 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
©2011 Regenstrief Institute and James Case
- 210. 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
©2011 Regenstrief Institute and James Case
- 211. Q
and
A
Session
©2011 Regenstrief Institute and James Case