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=== Introduction to Clinical Element Models (CEMs) === In order to represent detailed clinical data models, we have designed The Clinical Element Model (CEM). When we state “The Clinical Element Model” we are referring to the global modeling effort as a whole, or in other words, our approach to representing detailed clinical data models and the instances of data which conform to these models. ;[[media:CEM_Reference20081114.pdf|Clinical Element Model Introduction & Data Types Reference Manual]] :J.Coyle, Y.Heras, T.Oniki, S.Huff :November 14, 2008 ;Access SHARPn Clinical Element Models [[:CEMS|here]] <swf width="300" height="200">http://informatics.mayo.edu/recordings/CEMpresentation8232010/lib/embed.swf</swf> ;[http://informatics.mayo.edu/recordings/CEMpresentation8232010/index.htm Practical Modeling Issues Video Presentation] :[[Stanley Huff]] :August 23, 2010 ;[[media:Complex_Issues_in_Modeling_AMIA_Fall_Meeting_2011.pdf|Practical modeling issues: Representing coded and structured patient data in EHR systems ]] :[[Stanley Huff]] :AMIA Annual Symposium :October 22, 2011 === CEM Request Link === ;[https://intermountainhealthcare.org/CEMRequests CEM Request Site] === CEM Attribute Layer === Constant Attribute Priority List: (1) demographics (2) orders (3) laboratory (4) medications (5) diagnostic observations (6) procedures ==== Documentation ==== *[[media:Patient_documentation.doc|Patient]] (Oct 3, 2011) *[[media:Orders_documentation.doc|Orders]] (Oct 3, 2011) *[[media:CORENotedDrug-2012-01-19.doc|Noted Drug]] (Jan 19, 2012) ==== CDL Syntax ==== * Patient Model (demographics): [[media:Patient.zip|Patient.zip]] (41KB) * Order Container (parent model for all order types): [[media:OrderContainer.zip|OrderContainer.zip]] (100KB) * Med Order Subtypes: [[media:OrderMedAmb.zip|OrderMedAmb.zip]](100KB) [[media:OrderMedCont.zip|OrderMedCont.zip]](100KB) [[media:OrderMedPCA.zip|OrderMedPCA.zip]] (100KB) [[media:OrderMedReg.zip|OrderMedReg.zip]] (100KB) *Lab panel (corresponds to an OBR): [[media:StandardLabPanel.zip|StandardLabPanel.zip]] (37KB) *Parent lab model (OBX): [[media:StandardLabObs.zip|StandardLabObs.zip]] (33KB) *Lab subtypes: [[media:StandardLabObsOrdinal.zip|StandardLabObsOrdinal.zip]] (36KB) [[media:StandardLabObsQuantitative.zip|StandardLabObsQuantitative.zip]] (38KB) [[media:StandardLabObsCoded.zip|StandardLabObsCoded.zip]] (36KB) [[media:StandardLabObsNarrative.zip|StandardLabObsNarrative.zip]] (37KB) [[media:ClinObs.zip|ClinObs.zip]] (584B) *Postcoordinated disease/disorder (NLP Requested): [[media:DiseaseDisorder.zip|DiseaseDisorder.zip]] (30KB) *Precoordinated problem model:[[media:HealthIssue.zip|HealthIssue.zip]] (27KB) ==== Demographic Tables DDL ==== *[[media:mydb_demographics_old.sql|mydb_demographics_old.sql]] (4-24-2012) *[[media:Mydb_demographics_ddl_proposednew.sql|mydb_demographics_ddl_proposednew.sql]] (4-24-2012) ==== Pipeline Sample Outputs ==== *[[media:testcem.zip|testcem.zip]] (5-16-2012) ''Test CEM'' CCD *Input :test.xml file within zip file *Output :[[media:3abab9fb-ea8a-4ca7-9ce5-2e729398a34e.xml|3abab9fb-ea8a-4ca7-9ce5-2e729398a34e.xml]] (5-16-2012) :[[media:3d92f323-9867-4914-8693-5ac615faf7dd.xml|3d92f323-9867-4914-8693-5ac615faf7dd.xml]] (5-16-2012) :[[media:185c1aac-2e05-4390-beb0-c377023ce537.xml|185c1aac-2e05-4390-beb0-c377023ce537.xml]] (5-16-2012) :[[media:192ef8b7-849a-4b10-a437-e9c3a4980604.xml|192ef8b7-849a-4b10-a437-e9c3a4980604.xml]] (5-16-2012) :[[media:20689179-0cf2-454a-88b4-c93198e59952.xml|20689179-0cf2-454a-88b4-c93198e59952.xml]] (5-16-2012) :[[media:d2a2eac2-64f0-4179-a7d0-026418484885.xml|d2a2eac2-64f0-4179-a7d0-026418484885.xml]] (5-16-2012) HL7 *Input :[[media:test1.xml|test1.xml]] (5-16-2012) *Output :[[media:3f5083eb-937c-45ef-ad09-3261907b1136.xml|3f5083eb-937c-45ef-ad09-3261907b1136.xml]] (5-16-2012) :81afd6bc-1026-46fc-90a0-00e5882d5696.xml file within zip file === Populating CEM Instances from Input Data === *[[media:mapping diagram.vsd|visio diagram showing how to populate the NotedDrug model with rxnorm codes]] (8-30-12) === Terminology Mappings === *[[media:Intermountain Terminology Mappings 2012-07-23.xlsx|Intermountain Terminology Mappings 2012-07-23.xlsx]] (7-23-12) === Mapping Spreadsheet / CEM Database Structure === '''July 2012''' ''Mapping'' *[[media:CemXMLFieldMappingsTOCemDB.xlsx|CEM XML Field Mappings to CEM Database]] (7-11-12) *[[media:mydb_ddl_v2.1.sql|CEM Database Structure]] (7-11-12) === XSD Scheme === '''July 2012 Release''' ''Secondary Use Models'' *[[media:SecondaryUseDiseaseDisorder71112.xsd|SecondaryUseDiseaseDisorder.xsd]] (7-11-12) *[[media:SecondaryUseNotedDrug71112.xsd|SecondaryUseNotedDrug.xsd]] (7-11-12) *[[media:SecondaryUseNotedDrugList71112.xsd|SecondaryUseNotedDrugList.xsd]] (7-11-12) *[[media:SecondaryUsePatient71112.xsd|SecondaryUsePatient.xsd]] (7-11-12) *[[media:SecondaryUseStandardLabObsCoded71112.xsd|SecondaryUseStandardLabObsCoded.xsd]] (7-11-12) *[[media:SecondaryUseStandardLabObsIntervalQuantitative71112.xsd|SecondaryUseStandardLabObsIntervalQuantitative.xsd]] (7-11-12) *[[media:SecondaryUseStandardLabObsNarrative71112.xsd|SecondaryUseStandardLabObsNarrative.xsd]] (7-11-12) *[[media:SecondaryUseStandardLabObsOrdinal71112.xsd|SecondaryUseStandardLabObsOrdinal.xsd]] (7-11-12) *[[media:SecondaryUseStandardLabObsQuantitative71112.xsd|SecondaryUseStandardLabObsQuantitative.xsd]] (7-11-12) *[[media:SecondaryUseStandardLabObsTiter71112.xsd|SecondaryUseStandardLabObsTiter.xsd]] (7-11-12) '''May 2012 Release''' *[[media:CEM_XSDs_2012_05_17.zip|CEM XSDs 2012-05-17.zip]] (5-17-2012) *[[media:CEM_CDL 2012_05_17.zip|CEM CDL 2012-05-17.zip]] (5-17-12012 corresponding CDL CEMs) *[[media:release_notes.txt|release notes.txt]] (5-17-12) ''CORE Models'' *[[media:COREDiseaseDisorder51712.xsd|COREDiseaseDisorder.xsd]] (5-17-12) *[[media:CORENotedDrug51712.xsd|CORENotedDrug.xsd]] (5-17-12) *[[media:COREPatient51712.xsd|COREPatient.xsd]] (5-17-12) *[[media:COREStandardLabObs51712.xsd|COREStandardLabObs.xsd]] (5-17-12) *[[media:COREStandardLabObsCoded51712.xsd|COREStandardLabObsCoded.xsd]] (5-17-12) *[[media:COREStandardLabObsIntervalQuantitative51712.xsd|COREStandardLabObsIntervalQuantitative.xsd]] (5-17-12) *[[media:COREStandardLabObsNarrative51712.xsd|COREStandardLabObsNarrative.xsd]] (5-17-12) *[[media:COREStandardLabObsOrdinal51712.xsd|COREStandardLabObsOrdinal.xsd]] (5-17-12) *[[media:COREStandardLabObsQuantitative51712.xsd|COREStandardLabObsQuantitative.xsd]] (5-17-12) *[[media:COREStandardLabObsTiter51712.xsd|COREStandardLabObsTiter.xsd]] (5-17-12) ''Secondary Use Models'' *[[media:SecondaryUseDiseaseDisorder51712.xsd|SecondaryUseDiseaseDisorder.xsd]] (5-17-12) *[[media:SecondaryUseNotedDrug51712.xsd|SecondaryUseNotedDrug.xsd]] (5-17-12) *[[media:SecondaryUseNotedDrugList51712.xsd|SecondaryUseNotedDrugList.xsd]] (5-17-12) *[[media:SecondaryUsePatient51712.xsd|SecondaryUsePatient.xsd]] (5-17-12) *[[media:SecondaryUseStandardLabObsCoded51712.xsd|SecondaryUseStandardLabObsCoded.xsd]] (5-17-12) *[[media:SecondaryUseStandardLabObsIntervalQuantitative51712.xsd|SecondaryUseStandardLabObsIntervalQuantitative.xsd]] (5-17-12) *[[media:SecondaryUseStandardLabObsNarrative51712.xsd|SecondaryUseStandardLabObsNarrative.xsd]] (5-17-12) *[[media:SecondaryUseStandardLabObsOrdinal51712.xsd|SecondaryUseStandardLabObsOrdinal.xsd]] (5-17-12) *[[media:SecondaryUseStandardLabObsQuantitative51712.xsd|SecondaryUseStandardLabObsQuantitative.xsd]] (5-17-12) *[[media:SecondaryUseStandardLabObsTiter51712.xsd|SecondaryUseStandardLabObsTiter.xsd]] (5-17-12) ''Additional Models'' *[[media:AdministrativeDiagnosis51712.xsd|AdministrativeDiagnosis.xsd]] (5-17-12) *[[media:AdministrativeProcedure51712.xsd|AdministrativeProcedure.xsd]] (5-17-12) '''April 2012 Release''' ''Secondary Use Models'' *[[media:Sharp20120408.zip|SecondaryUse]] (April 8, 2012) *[[media:SecondaryUseNotedDrug482012.xsd|SecondaryUseNotedDrug.xsd]] (4-8-12) *[[media:SecondaryUseNotedDrugList482012.xsd|SecondaryUseNotedDrugList.xsd]] (4-8-12) *[[media:SecondaryUsePatient482012.xsd|SecondaryUsePatient.xsd]] (4-8-12) *[[media:SecondaryUseStandardLabObsCoded482012.xsd|SecondaryUseStandardLabObsCoded.xsd]] (4-8-12) *[[media:SecondaryUseStandardLabObsIntervalQuantitative482012.xsd|SecondaryUseStandardLabObsIntervalQuantitative.xsd]] (4-8-12) *[[media:SecondaryUseStandardLabObsNarrative482012.xsd|SecondaryUseStandardLabObsNarrative.xsd]] (4-8-12) *[[media:SecondaryUseStandardLabObsOrdinal482012.xsd|SecondaryUseStandardLabObsOrdinal.xsd]] (4-8-12) *[[media:SecondaryUseStandardLabObsQuantitative482012.xsd|SecondaryUseStandardLabObsQuantitative.xsd]] (4-8-12) *[[media:SecondaryUseStandardLabObsTiter482012.xsd|SecondaryUseStandardLabObsTiter.xsd]] (4-8-12) ''Additional Models'' *[[media:AdministrativeDiagnosis.xsd|AdministrativeDiagnosis.xsd]] (4-24-2012) *[[media:AdministrativeProcedure.xsd|AdministrativeProcedure.xsd]] (4-24-2012) *[[media:SecondaryUseDiseaseDisorder_4242012.xsd|SecondaryUseDiseaseDisorder_4242012.xsd]] (4-24-2012) ''Sample Instances'' *[[media:SHARP CEM sample instances 2012-04-08b.zip|CEM sample instances]] (April 8, 2012) *[[media:SecondaryUseNotedDrug-2012-04-08-sample1.xml|SecondaryUseNotedDrug-2012-04-08-sample1.xml]] (4-8-12) *[[media:SecondaryUseNotedDrugList-2012-04-08-sample1.xml|SecondaryUseNotedDrugList-2012-04-08-sample1.xml]] (4-8-12) *[[media:SecondaryUsePatient-2012-04-08-sample1.xml|SecondaryUsePatient-2012-04-08-sample1.xml]] (4-8-12) '''Archived''' *[[media:CORENotedDrug.xsd|CORENotedDrug.xsd]] (4-24-2012) *[[media:COREPatient.xsd|COREPatient.xsd]] (4-24-2012) *[[media:COREStandardLabObs.xsd|COREStandardLabObs.xsd]] (4-24-2012) *[[media:COREStandardLabObsCoded.xsd|COREStandardLabObsCoded.xsd]] (4-24-2012) *[[media:COREStandardLabObsIntervalQuantitative.xsd|COREStandardLabObsIntervalQuantitative.xsd]] (4-24-2012) *[[media:COREStandardLabObsNarrative.xsd|COREStandardLabObsNarrative.xsd]] (4-24-2012) *[[media:COREStandardLabObsOrdinal.xsd|COREStandardLabObsOrdinal.xsd]] (4-24-2012) *[[media:COREStandardLabObsQuantitative.xsd|COREStandardLabObsQuantitative.xsd]] (4-24-2012) *[[media:COREStandardLabObsTiter.xsd|COREStandardLabObsTiter.xsd]] (4-24-2012) *[[media:SecondaryUseCDL 2012-02-14.zip|SecondaryUseCDL 2012-02-14.zip]] (CDL files corresponding to 2-14-12 xsds below) *[[media:SecondaryUseDiseaseDisorder.xsd|SecondaryUseDiseaseDisorder.xsd]] (2-14-12) *[[media:SecondaryUseNotedDrug.xsd|SecondaryUseNotedDrug.xsd]] (2-14-12) *[[media:SecondaryUseNotedDrugList.xsd|SecondaryUseNotedDrugList.xsd]] ''Sample:'' [[media:SecondaryUseNotedDrugList-2012-02-16-sample1.xml|SecondaryUseNotedDrugList-2012-02-16-sample1.xml]](2-14-12) *[[media:SecondaryUsePatient.xsd|SecondaryUsePatient.xsd]](2-14-12) *[[media:SecondaryUseStandardLabObsCoded.xsd|SecondaryUseStandardLabObsCoded.xsd]](2-14-12) *[[media:SecondaryUseStandardLabObsIntervalQuantitative.xsd|SecondaryUseStandardLabObsIntervalQuantitative.xsd]](2-14-12) *[[media:SecondaryUseStandardLabObsNarrative.xsd|SecondaryUseStandardLabObsNarrative.xsd]](2-14-12) *[[media:SecondaryUseStandardLabObsOrdinal.xsd|SecondaryUseStandardLabObsOrdinal.xsd]](2-14-12) *[[media:SecondaryUseStandardLabObsQuantitative.xsd|SecondaryUseStandardLabObsQuantitative.xsd]](2-14-12) *[[media:SecondaryUseStandardLabObsTiter.xsd|SecondaryUseStandardLabObsTiter.xsd]](2-14-12) *[[media:SecondaryUseWrapper.xsd|SecondaryUseWrapper.xsd]](2-14-12) === CEML === :[[media:main 100318.zip|Zip files of CEMS: Main]] (1.3 mb) (Aug 2010) :[[media:specificLab 100318.zip|Zip files of CEMS: Specific Lab]] (2.4 mb)(Aug 2010) === RFH Datatypes === * [http://www.healthintersections.com.au/rfh/datatypes.htm RFH Datatypes Home Page] * [[RFH_CEM_DataTypes|Evaluation of differences between RFH and CEM Datatypes]] * [[media:RFHSamples.zip|First draft of a proposed RFH Schema w/ samples from the RFH Datatypes Page]] === CSHARE CEMs Project === Subgroup focused on the review the CDISC standards published and discuss approach for the alignment with the SHARP core CEM models. Initial focus on the domains of Laboratory, Medication and Demographics. Due to constraints on the SHARPn wiki, this subgroup's work can be found in the following wiki: http://informatics.mayo.edu/sharp/opencem (User ID/pw required = csharecems/sharpn) === Clinical Information Modeling Initiative (CIMI) === International consensus group with Detailed Clinical Models, Clinical Information Modeling Initiative (CIMI)  *Archetype Object Model/ADL 1.5 openEHR *CEN/ISO 13606 AOM ADL 1.4 *UML 2.x + OCL + healthcare extensions *OWL 2.0 + healthcare profiles and extensions *MIF 2 + tools HL7 RIM – static model designer https://csfe.aceworkspace.net/sf/projects/clinical_information_modeling_in ===[[CEM_OWL_Project|CEM OWL Project]]=== :OWL (web ontology language)Ontology to structure knowledge :To combine requirements on concept representations from different techniques to enforce consistency and prevent inconsistencies and errors [[media:CEM-meta030811.owl|CEM OWL ontology]] [[media:Screen_shot_2011-03-15_at_4.30.30_PM.png|System Overview]] [[Triple Store Investigation]] ===[[CEM_Selection_Discussion|CEM Selection Team]] === === References === ==== Presentations ==== <swf width="300" height="200">http://informatics.mayo.edu/recordings/RequirementsCEM_12aug2010/lib/embed.swf</swf> ;[http://informatics.mayo.edu/recordings/RequirementsCEM_12aug2010/index.htm Requirements CEM Video Presentation] :[[Tom Oniki]] :August 12, 2010 ==== Reading Material ==== ;[[media:2.DN_SHARPF2F_June30_V2_CGC.pptx|Data Normalization (CEMs) & Evaluation]] (PPTX) :[[Stanley Huff]], [[Christopher Chute]] :SHARPn F2F - June 30, 2011 ;[[media:CEM_DBr3.pdf|CEM Database Diagram & SQL]] (50.1KB) :[[Calvin Beebe]] :April 12, 2011 ;[[media:4.Results4CareDCM-ToolingOct2010MZ.pdf|Tooling and MDA for Detailed Clinical Models]] (1.11MB) :Michael van der Zel :October 2, 2010 ;[[media:5.Results4CareDCM-ToolsOverview02-10-2010v_05.pdf|Overview of Tools for Detailed Clinical Models]] (725KB) :Workshop on Detailed Clinical Model (DCM) :October 2, 2010 ;[[media:CEReference20081114.pdf|Clinical Element Model]] (1.1 MB) :Joey Coyle, Yan Heras, [[Tom Oniki]], [[Stanley Huff]] :University of Utah :November 14, 2008 ;[[media:HuffIMIA1998.pdf|Linking a Medical Vocabulary to a Clinical Data Model using Abstract Syntax Notation 1]] :[[Stanley Huff]], Roberto Rocha, [[Harold Solbrig]], Wade Barnes, Steven Shrank, Matt Smith :Methods of Information in Medicine :1998 ==== Websites ==== CEM Model Search Tool Website: http://www.clinicalelement.com/ [[Category:Sharp]]

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