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RCMT Mapping Overview Jeremiah Sable Consultant, The St. John Group Contractor to APHL.

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Presentation on theme: "RCMT Mapping Overview Jeremiah Sable Consultant, The St. John Group Contractor to APHL."— Presentation transcript:

1 RCMT Mapping Overview Jeremiah Sable Consultant, The St. John Group Contractor to APHL

2 What problem do the RCMTs solve? Which test results are of public health interest? Lab Test results Consumer of lab data

3 Filtering the output of clinical labs RCMT tables can identify tests and results of public health interest. RCMT filter Lab Test results Reportable Non reportable Consumer of lab data

4 Within a public health agency Test results Public health agency TB STD Foodborne Hepatitis etc. RCMT Routing test results within an agency

5 The problem of non-comparable lab data It isn’t possible to map the test catalog of each lab to reportable conditions. Each lab has its own codes and names for lab tests. There is no consistency across labs. ARUP labs LabCorp Mayo labs etc.... Quest labs

6 LOINC enables data aggregation across labs It is possible to map LOINC tests to reportable conditions. ARUP labs LabCorp Mayo labs etc.... Quest labs This problem disappears when labs send LOINC codes along with their own codes. LOINC

7 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

8 Specific LOINC mappings 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 loinc_numcomponentpropertysystemscalemethodThis is a test for 6524-3Rabies virus AbACncSerQnNeutRabies 6412-1Giardia lamblia AgACncStoolOrdEIAGiardiasis 10645-0Aspergillus fumigatus AgACncTissOrdIFAspergillosis 59850-8Wuchereria bancrofti AgACncSerQnEIAFilariasis Condition-specific LOINCs

9 Specific LOINC mappings loinc_numcomponentpropertysystemscalemethodThis is a test for 6524-3Rabies virus AbACncSerQnNeutRabies 6412-1Giardia lamblia AgACncStoolOrdEIAGiardiasis 10645-0Aspergillus fumigatus AgACncTissOrdIFAspergillosis 59850-8Wuchereria bancrofti AgACncSerQnEIAFilariasis All LOINCs that are specific tests for reportable conditions are in the RCMT. Lab RCMT filter not reportable 6524-3 6412-1 reportable 10645-0 59850-8 Condition-specific LOINCs 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

10 Specific LOINC mappings Examples of RCMT rows for condition-specific LOINCs loinc_numcomponentsystemscale_typmethod_typCondition name 6412-1Giardia lamblia AgStoolOrdEIAGiardiasis 14210-9Giardia lamblia AgStoolOrdIFGiardiasis 60544-4Giardia lamblia DNAXXXOrdProbe.amp.tarGiardiasis... 47260-5Plasmodium sp DNABldNomProbe.amp.tarMalaria 56968-1Plasmodium sp AbSerOrdIFMalaria 10711-0Plasmodium vivax AgBldQnIFMalaria... 6523-5Rabies virus AbCSFQnNeutRabies 23390-8Rabies virus AgBrainOrdImmune stainRabies 51647-6Rabies virus RNAXXXOrdProbeRabies... 57320-4Trypanosoma cruzi AbSerOrdEIAChagas disease 51827-4Trypanosoma cruzi Ab.IgMSerQnEIAChagas disease 49801-4Trypanosoma cruzi DNABldOrdProbe.amp.tarChagas disease... 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)

11 Nonspecific LOINC mappings loinc_numcomponentpropertysystemscalemethodReportable? 600-7Bacteria identifiedPridBldNomCulture? 14489-9Virus identifiedPridBldNomIF? 10701-1Ova+Parasites identifiedPridStoolNomConcentration? 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 Some nonspecific LOINCs

12 Nonspecific LOINC mappings loinc_numcomponentpropertysystemscalemethodReportable? 600-7Bacteria identifiedPridBldNomCulture? 14489-9Virus identifiedPridBldNomIF? 10701-1Ova+Parasites identifiedPridStoolNomConcentration? Some nonspecific LOINCs Lab RCMT filter Nonspecific LOINCs Look at result reportable not 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

13 Nonspecific LOINC mappings RCMT value setLOINCs for... PHVS_LabTestName_BacteriaBacteria nonspecifics PHVS_LabTestName_FungusFungus nonspecifics PHVS_LabTestName_ParasiteParasite nonspecifics PHVS_LabTestName_VirusVirus nonspecifics PHVS_LabTestName_AcidFastStainAcid fast bacillus nonspecifics RCMT value sets of nonspecific LOINCs loinc_numcomponentsystemscalemethodRCMT value setReportable? 600-7Bacteria identifiedBldNomCultureBacterialook at result 17928-3Bacteria identifiedBldNomAerobic cultureBacterialook at result... 10701-1Ova+Parasites identifiedStoolNomConcentrationParasiteslook at result 43227-8Ova+Parasites identifiedStoolNomTrichrome stainParasiteslook at result... 14489-9Virus identifiedBldNomIFViruslook at result 14488-1Virus identifiedCSFNomIFViruslook at result... The RCMT includes more than 400 nonspecific LOINCs

14 Nonspecific LOINC mappings Examples of RCMT rows for nonspecific LOINCs Concept CodeConcept NameReportable condition 4716008Entamoeba histolyticaAmebiasis 110390006Entamoeba histolytica cystsAmebiasis 110389002Entamoeba histolytica trophozoitesAmebiasis... 420364006Anaplasma phagocytophilum 131419006Anaplasma speciesAnaplasma phagocytophilum... 9194001Jamestown Canyon virusArbovirus infection 61399004Keystone virusArbovirus infection 30434006La Crosse virusArbovirus infection 57311007West Nile virusArbovirus infection... 76828008Babesia microtiBabesiosis 86432002Babesia divergensBabesiosis... For nonspecific LOINCs the RCMT has SNOMED organism lookup tables for the test results

15 Summary of RCMT mappings to reportable conditions Lab RCMT filter Nonspecific LOINCs Look at result reportable not reportable Specific LOINCs reportable not reportable This diagram summarizes how the RCMT can be used to filter data coming out of a lab

16 RCMT contact information RCMT Planning Team E-mail: PHINVS@CDC.GOVPHINVS@CDC.GOV RCMT Website (phConnect) : http://www.phconnect.org/group/rcmthttp://www.phconnect.org/group/rcmt

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