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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