A ClaML-based Interface for the Import of Monohierarchical Classifications

Transcription

1 These sheets are only for use in connection with the speech. A ClaML-based Interface for the Import of Monohierarchical Classifications Sylvie Ngouongo Jürgen Stausberg Ludwig-Maximilian-University of Munich, Germany Institute of Medical Informatics, Biometry and Epidemiology (IBE) Presented by Sylvie Ngouongo

2 Agenda Introduction Objectives Material ClaML and Classifications ISO/IEC 79 Ed. 3 Methods and Results Mapping: ClaML ISO/IEC 79 Ed. 3 ClaML import interface Discussion Conclusion MIE 202, Sylvie Ngouongo 2

3 Introduction The relevance of controlled vocabularies is no longer to be proved: Standardized representation and exchange of clinical data Semantic definitions for the collected data Knowledge representation and use as value lists for items Evaluation of the integration of well-established classifications and terminologies in metadata registries based on ISO/IEC 79 Ed. 3 Information technology Metadata registries (MDR) National MDR Project: Support of the reuse of study items when planning and implementing databases and documentation processes for clinical and epidemiological studies and registries; Implementation of a metadata repository for integrated research. MIE 202, Sylvie Ngouongo 3

4 Objectives Overcome integration and maintenance tasks of monohierarchical classifications in the MDR, Provide a transition format between classifications publishers and the MDR Import interface based on the Classification Markup Language (ClaML) Direct import not possible MDR Database based on ISO 79 import ClaML-based import interface transition Classifications in ClaML provide Classifications Publisher MIE 202, Sylvie Ngouongo 4

5 Material: ClaML and Classifications Classification Markup Language (ClaML) is attractive as interface standard for the import of classifications (ICD-0-GM, OPS) into the MDR. ClaML: EN 4463:2007, Standard for electronic representation of classification coding schemes. Small excerpt of ClaML ICD-0 ICD EN <?xml version=".0" encoding="utf-8"?> <!DOCTYPE ClaML SYSTEM "claml.dtd"[]> <ClaML version="2.0.0"> <Meta name="toplevelsort" value="i II III IV V VI VII VIII IX X XI XII XIII XIV XV XVI XVII XVIII XIX XX XXI XXII" /> <Meta name="lang" value="en" /> <Meta name="titlelong" value="international Statistical Classification of Diseases and Related Health Problems 0th Revision"/> <Identifier authority="who" uid="srfsfto be added later" /> <Title date=" " name="icd en" version="2008" /> <Class code="a00" kind="category"> <SuperClass code="â00-a09" /> <SubClass code="a00.0" /> <SubClass code="a00." /> <ModifiedBy all="true" code="s3m00_5"/> <Rubric id="d " kind="preferred"> <Label xml:lang="en" xml:space="default">cholera</label> </Rubric> </Class> </ClaML> ModifierClass:.3 New SubClass = A00.3 ICD-0 Class: Cholera (A00) Hierarchy: Superclass and Subclasses ClaML and its structure s elements MIE 202, Sylvie Ngouongo 5

6 Material: ClaML and Classifications ICD-0-GM: International Statistical Classification of Diseases and Related Health Problems 0th Revision German Modifications OPS: German Procedure Classification MIE 202, Sylvie Ngouongo 6

7 Material: ISO/IEC 79 Ed.3 Object_Class Gastrointestinal Disease Characteristic Name Terminology/Classification SNOMED-CT / MedDRA / RxNorm / ICD-0 / OPS / Semantic Definitions * * Data_Element_Concept Gastrointestinal Disease Name * * Conceptual_Domain Intestinal Infectious diseases (A00 A09) Value Lists Semantic Level Representational Level Data_Element Gastrointestinal Disease Name Data_Element = Study item * * * Value_Domain Disease Name Permissible_Values Cholera (A00) Typhoid fever (A0.0) Salmonella sepsis (A02.) Amoebiasis (A06). Other specified intestinal infections (A08.5). High-level Data Description Metamodel: Example of the use of controlled vocabularies for the description of Data Elements. MIE 202, Sylvie Ngouongo 7

8 Material: ISO/IEC 79 Ed.3 Concept Metamodel Region Concept system metamodel region Concept_System Terminology/Classification SNOMED-CT / MedDRA / RxNorm / ICD-0 / OPS / Concept Assertion 2..* Link Relation_Role Link_End Relation MIE 202, Sylvie Ngouongo 8

9 Methods Mapping: ClaML ISO/IEC 79 Ed.3 Approach and results Conception and implementation of a ClaML import interface Approach and results MIE 202, Sylvie Ngouongo 9

10 Mapping: ClaML ISO/IEC 79 Ed.3 Simplified ClaML structure ClaML +subclass Class +superclass Concept system metamodel region Concept_System Concept Assertion 2..* Link <?xml version=".0" encoding="utf-8"?> <!DOCTYPE ClaML SYSTEM "claml.dtd"[]> <ClaML version="2.0.0"> <Title name="icd en" /> <Class code="a00" kind="category"> <SuperClass code="a00-a09" /> <SubClass code="a00.0" /> <SubClass code="a00." /> <Rubric kind="preferred"> Hierarchy: is_a / inverse_isa <Label xml:lang="en" xml:space="default">cholera</label> </Rubric> </Class> </ClaML> Relation Relation_Role Link_End MIE 202, Sylvie Ngouongo 0

11 Conception and implementation of a ClaML import interface MDR database: implementation of the Concepts Package of ISO/IEC 79 Ed. 3 in a relational database Development of a XML-schema (mdr_schema.xsd) of the MDR database for import/export reasons of classifications into and from the MDR database Discrepancies ClaML-Schema (claml.dtd) MDR-Schema Transformation of classifications from ClaML into a MDR conform structure using the Extensible Stylesheet Language Transformation (XSLT*) * XSLT: programming language for processing and transforming XML documents into other XML documents by defining transformation rules. MIE 202, Sylvie Ngouongo

12 Conception and implementation of a ClaML import interface claml_icd_file.xml (valid with claml.dtd) + add_claml.xsl (add missing Subclassifications) new_claml_file.xml (valid with claml.dtd) + 2 partial_result.xml (valid with mdr_schema.xsd) claml_transform.xsl (Concept_Package Transformation) + 3 result.xml (valid with mdr_schema.xsd) DB import MDR Prototype based on ISO 79 V3 constants_transform.xsl (Concept_Package Transformation) {constants.xml} MIE 202, Sylvie Ngouongo 2

13 ClaML limitations ClaML-based import interface deals with simple hierarchical classifications provided in ClaML ClaML does not intend to prescribe the meaning of structuring elements in classification systems ClaML mixes class s information with layout. E.g. (ClaML excerpt): <Class code="b8"><rubric><label> angiostrongyliasis due to Parastrongylylus cantonensis <Reference class="bracket"> B83.2 </Reference> </Label></ Rubric></Class>. Different interpretations and extensions of the ClaML-Standard: DIMDI* (ICD-0-GM 200) vs. WHO* (ICD-0-CM 2008). * DIMDI: German Institute of Medical Documentation and Information * WHO: World Health Organization MIE 202, Sylvie Ngouongo 3

14 ClaML limitations Example of discrepancies between WHO and DIMDI regarding ClaML WHO applies <Modifier> (subclassifications coding) for 4-digit ICD-Classes to their superclasses (3- digit classes) whereas DIMDI applies them to the corresponding 4-digit classes to build the 5-digit subclassifications. M0 (3-digit) à M0.0 (4-digit) à M0.00 (5-digit) <Class code="m0" kind="category" usage="aster"> <SuperClass code="m00-m03" /> <SubClass code="m0.0" /> <SubClass code="m0." /> <SubClass code="m0.2" /> <ModifiedBy all="true" code="s3m00_5"/> <Rubric id="d000243" kind="preferred"> <Label xml:lang="en" xml:space="default"> Direct infections of joint in infectious and parasitic diseases classified elsewhere</label></rubric> </Class> <Class code="m0.0" kind="category" usage="aster"> <SuperClass code="m0" /> <Rubric id="d000244" kind="preferred"> <Label xml:lang="en" xml:space="default"> Meningococcal arthritis </Label> </Rubric> </Class> WHO <Class code="m0" kind="category" usage="aster"> <SuperClass code="m00-m03"/> <SubClass code="m0.0"/> <SubClass code="m0."/> <SubClass code="m0.2"/> <Rubric kind="preferred"> <Label xml:lang="de" xml:space="default"> Direkte Gelenkinfektionen bei anderenorts klassifizierten infektiösen und parasitären Krankheiten</Label></Rubric> </Class> <Class code="m0.0" kind="category" usage="aster"> <SuperClass code="m0"/> <ModifiedBy all="true" code="s3m00_5"/> <Rubric kind="preferred"> <Label xml:lang="de" xml:space="default"> Arthritis durch Meningokokken</Label> </Rubric> DIMDI MIE 202, Sylvie </Class> Ngouongo 4

15 Conclusion and Acknowledgements ClaML-based import interface is necessary for the import of simple hierarchical classifications into the MDR database in order to provide semantics or value lists for data elements. A unique interpretation of ClaML by Healthcare organizations (WHO, DIMDI, ) is essential for a general use of the ClaML import interface. The presented work is part of the project MDR Metadata Repository funded by the German Federal Ministry of Education and Research (BMBF). MIE 202, Sylvie Ngouongo 5

16 Thanks for your Attention! Take Home Message The relevance of controlled vocabularies is no longer to be proved: Standardized representation and exchange of clinical data, Semantic definitions for the collected data, Knowledge representation and use as value lists for items. ISO/IEC 79 standard Metadata Registries (MDR) addresses the semantics of data, the representation of data, and the registration of the descriptions of that data. Development of ClaML-based import interface is necessary for the import of simple hierarchical classifications into the MDR database in order to provide semantics or value lists for data elements. Standard formats for representing terminologies such as SNOMED-CT, are urgently needed, to cope with maintenance issues in the MDR. A unique interpretation of ClaML by Healthcare organizations (WHO, DIMDI, ) is essential for a general use of the ClaML import interface. MIE 202, Sylvie Ngouongo 6