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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.

Clinical Element Model Introduction & Data Types Reference Manual
J.Coyle, Y.Heras, T.Oniki, S.Huff
November 14, 2008
Access SHARPn Clinical Element Models here

<swf width="300" height="200">http://informatics.mayo.edu/recordings/CEMpresentation8232010/lib/embed.swf</swf>

Practical Modeling Issues Video Presentation
Stanley Huff
August 23, 2010
Practical modeling issues: Representing coded and structured patient data in EHR systems
Stanley Huff
AMIA Annual Symposium
October 22, 2011

CEM Request Link

CEM Request Site

CEM Attribute Layer

Constant Attribute Priority List: (1) demographics (2) orders (3) laboratory (4) medications (5) diagnostic observations (6) procedures


CDL Syntax

Demographic Tables DDL

Pipeline Sample Outputs

Test CEM


  • Input
test.xml file within zip file
  • Output
3abab9fb-ea8a-4ca7-9ce5-2e729398a34e.xml (5-16-2012)
3d92f323-9867-4914-8693-5ac615faf7dd.xml (5-16-2012)
185c1aac-2e05-4390-beb0-c377023ce537.xml (5-16-2012)
192ef8b7-849a-4b10-a437-e9c3a4980604.xml (5-16-2012)
20689179-0cf2-454a-88b4-c93198e59952.xml (5-16-2012)
d2a2eac2-64f0-4179-a7d0-026418484885.xml (5-16-2012)


  • Input
test1.xml (5-16-2012)
  • Output
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

Terminology Mappings

Mapping Spreadsheet / CEM Database Structure

July 2012


XSD Scheme

July 2012 Release

Secondary Use Models

May 2012 Release

CORE Models

Secondary Use Models

Additional Models

April 2012 Release

Secondary Use Models

Additional Models

Sample Instances



Zip files of CEMS: Main (1.3 mb) (Aug 2010)
Zip files of CEMS: Specific Lab (2.4 mb)(Aug 2010)

RFH Datatypes


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


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

CEM OWL ontology

System Overview

Triple Store Investigation

CEM Selection Team



<swf width="300" height="200">http://informatics.mayo.edu/recordings/RequirementsCEM_12aug2010/lib/embed.swf</swf>

Requirements CEM Video Presentation
Tom Oniki
August 12, 2010

Reading Material

Data Normalization (CEMs) & Evaluation (PPTX)
Stanley Huff, Christopher Chute
SHARPn F2F - June 30, 2011
CEM Database Diagram & SQL (50.1KB)
Calvin Beebe
April 12, 2011
Tooling and MDA for Detailed Clinical Models (1.11MB)
Michael van der Zel
October 2, 2010
Overview of Tools for Detailed Clinical Models (725KB)
Workshop on Detailed Clinical Model (DCM)
October 2, 2010
Clinical Element Model (1.1 MB)
Joey Coyle, Yan Heras, Tom Oniki, Stanley Huff
University of Utah
November 14, 2008
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


CEM Model Search Tool Website: http://www.clinicalelement.com/