Transcript RCMT_Mapping_Overview_2012-0607x

RCMT Mapping Overview
Jeremiah Sable
Consultant, The St. John Group
Contractor to APHL
What problem do the RCMTs solve?
Lab
Test results
Consumer of lab data
Which test results are of public health interest?
Filtering the output of clinical labs
Lab
Test results
RCMT
filter
Reportable
Non reportable
Consumer of lab data
RCMT tables can identify tests and results of public health interest.
Within a public health agency
Public health agency
TB
Test results
STD
RCMT
Foodborne
Hepatitis
etc.
Routing test results within an agency
The problem of non-comparable lab data
ARUP labs
LabCorp
Mayo labs
Each lab has its own codes and
names for lab tests. There is
no consistency across labs.
Quest labs
etc....
It isn’t possible to map the test catalog of each lab to reportable conditions.
LOINC enables data aggregation across labs
ARUP labs
LOINC
LabCorp
LOINC
Mayo labs
LOINC
Quest labs
LOINC
etc....
LOINC
This problem disappears when
labs send LOINC codes along
with their own codes.
It is possible to map LOINC tests to reportable conditions.
RCMT mappings for LOINC and SNOMED
The RCMT contains mappings of LOINC lab tests and SNOMED organism codes to reportable
conditions. The following slides describe the RCMT mappings for two types of LOINC codes:
• Specific lab tests
• Nonspecific lab tests
Specific LOINC mappings
Condition-specific LOINCs
loinc_num
6524-3
6412-1
10645-0
59850-8
component
Rabies virus Ab
Giardia lamblia Ag
Aspergillus fumigatus Ag
Wuchereria bancrofti Ag
property
ACnc
ACnc
ACnc
ACnc
system
Ser
Stool
Tiss
Ser
scale
Qn
Ord
Ord
Qn
method
Neut
EIA
IF
EIA
This is a test for
Rabies
Giardiasis
Aspergillosis
Filariasis
These four LOINCs are examples of condition-specific tests.
• Rabies and Giardiasis are reportable conditions and these LOINCs are in the RCMT
• Aspergillosis and Filariasis are not reportable and these LOINCs are not in the RCMT
Specific LOINC mappings
Condition-specific LOINCs
loinc_num
6524-3
6412-1
10645-0
59850-8
component
Rabies virus Ab
Giardia lamblia Ag
Aspergillus fumigatus Ag
Wuchereria bancrofti Ag
property
ACnc
ACnc
ACnc
ACnc
system
Ser
Stool
Tiss
Ser
scale
Qn
Ord
Ord
Qn
method
Neut
EIA
IF
EIA
This is a test for
Rabies
Giardiasis
Aspergillosis
Filariasis
These four LOINCs are examples of condition-specific tests.
• Rabies and Giardiasis are reportable conditions and these LOINCs are in the RCMT
• Aspergillosis and Filariasis are not reportable and these LOINCs are not in the RCMT
Lab
reportable
6524-3
6412-1
not reportable
10645-0
59850-8
RCMT
filter
All LOINCs that are specific tests for reportable conditions are in the RCMT.
Specific LOINC mappings
The RCMT maps these tests to reportable conditions, regardless of the test results
• The RCMT does not include reporting criteria for condition-specific LOINCs
• The RCMT has many tests that are not in the case definitions (e.g., Plasmodium sp Ab)
Examples of RCMT rows for condition-specific LOINCs
loinc_num
6412-1
14210-9
60544-4
...
47260-5
56968-1
10711-0
...
6523-5
23390-8
51647-6
...
57320-4
51827-4
49801-4
...
component
Giardia lamblia Ag
Giardia lamblia Ag
Giardia lamblia DNA
system
Stool
Stool
XXX
scale_typ
Ord
Ord
Ord
method_typ
EIA
IF
Probe.amp.tar
Condition name
Giardiasis
Giardiasis
Giardiasis
Plasmodium sp DNA
Plasmodium sp Ab
Plasmodium vivax Ag
Bld
Ser
Bld
Nom
Ord
Qn
Probe.amp.tar
IF
IF
Malaria
Malaria
Malaria
Rabies virus Ab
Rabies virus Ag
Rabies virus RNA
CSF
Brain
XXX
Qn
Ord
Ord
Neut
Immune stain
Probe
Rabies
Rabies
Rabies
Trypanosoma cruzi Ab
Trypanosoma cruzi Ab.IgM
Trypanosoma cruzi DNA
Ser
Ser
Bld
Ord
Qn
Ord
EIA
EIA
Probe.amp.tar
Chagas disease
Chagas disease
Chagas disease
Nonspecific LOINC mappings
Some nonspecific LOINCs
loinc_num
600-7
14489-9
10701-1
component
Bacteria identified
Virus identified
Ova+Parasites identified
property
Prid
Prid
Prid
system
Bld
Bld
Stool
scale
Nom
Nom
Nom
method
Culture
IF
Concentration
Reportable?
?
?
?
These nonspecific LOINCs are are too general to be associated with specific conditions.
• The results of these tests can indicate many different conditions (or no condition)
• For these LOINCs the RCMT maps the test results (organisms) to reportable conditions
• This is why the RCMT contains SNOMED organism codes for each reportable conditions
Nonspecific LOINC mappings
Some nonspecific LOINCs
loinc_num
600-7
14489-9
10701-1
component
Bacteria identified
Virus identified
Ova+Parasites identified
property
Prid
Prid
Prid
system
Bld
Bld
Stool
scale
Nom
Nom
Nom
method
Culture
IF
Concentration
Reportable?
?
?
?
These nonspecific LOINCs are are too general to be associated with specific conditions.
• The results of these tests can indicate many different conditions (or no condition)
• For these LOINCs the RCMT maps the test results (organisms) to reportable conditions
• This is why the RCMT contains SNOMED organism codes for each reportable conditions
Lab
RCMT
filter
Nonspecific
LOINCs
Look at
result
reportable
not reportable
Nonspecific LOINC mappings
RCMT value sets of nonspecific LOINCs
RCMT value set
PHVS_LabTestName_Bacteria
PHVS_LabTestName_Fungus
PHVS_LabTestName_Parasite
PHVS_LabTestName_Virus
PHVS_LabTestName_AcidFastStain
LOINCs for...
Bacteria nonspecifics
Fungus nonspecifics
Parasite nonspecifics
Virus nonspecifics
Acid fast bacillus nonspecifics
The RCMT includes more than 400 nonspecific LOINCs
loinc_num
600-7
17928-3
...
10701-1
43227-8
...
14489-9
14488-1
...
component
Bacteria identified
Bacteria identified
system scale
Bld
Nom
Bld
Nom
method
Culture
Aerobic culture
RCMT value set
Bacteria
Bacteria
Reportable?
look at result
look at result
Ova+Parasites identified
Ova+Parasites identified
Stool
Stool
Nom
Nom
Concentration
Trichrome stain
Parasites
Parasites
look at result
look at result
Virus identified
Virus identified
Bld
CSF
Nom
Nom
IF
IF
Virus
Virus
look at result
look at result
Nonspecific LOINC mappings
For nonspecific LOINCs the RCMT has SNOMED organism lookup tables for the test results
Examples of RCMT rows for nonspecific LOINCs
Concept Code
4716008
110390006
110389002
...
420364006
131419006
...
9194001
61399004
30434006
57311007
...
76828008
86432002
...
Concept Name
Entamoeba histolytica
Entamoeba histolytica cysts
Entamoeba histolytica trophozoites
Reportable condition
Amebiasis
Amebiasis
Amebiasis
Anaplasma phagocytophilum
Anaplasma species
Anaplasma phagocytophilum
Anaplasma phagocytophilum
Jamestown Canyon virus
Keystone virus
La Crosse virus
West Nile virus
Arbovirus infection
Arbovirus infection
Arbovirus infection
Arbovirus infection
Babesia microti
Babesia divergens
Babesiosis
Babesiosis
Summary of RCMT mappings to reportable conditions
reportable
Specific
LOINCs
Lab
not reportable
RCMT
filter
Nonspecific
LOINCs
Look at
result
reportable
not reportable
This diagram summarizes how the RCMT can be used to filter data coming out of a lab
RCMT contact information
RCMT Planning Team E-mail: [email protected]
RCMT Website (phConnect) : http://www.phconnect.org/group/rcmt