A Case for Linked Data for Medical

Devices in the IVD Market

bioMerieux INC.

Guillermo Perasso

UNC CH – CHIP – Practicum - Dec 2012

Content

Target Organization: bioMerieux Inc

Goals and Scope

Problem Description

Proposed Solution: Use Cases

Solution Implementation

Evolution and Future Developments.

Target Organization

Target Company: bioMerieux SA

French origin, multinational organization (~35 subs).

In-Vitro Diagnostic (IVD) markets: Clinical and Industry.

Key Business Application: Instrument Management. Manufacturing, Distribution, Technical Support.

Several Product Lines and Market Segments.

Different Instrument types and configurations.

Core Information System: ERP SAP AG.

No Semantic Web tools in IT production environments.

Structure / Un-structure information

Company IS – data sources

ERP System: SAP RDBMS: Oracle 9i

Company’s intranet

Enterprise Content Management System

Goals and Scope

Build a business case for the implementation of Semantic Web-based tools to support global business operations.

Propose a simple implementation strategy for a target ontology from SAP-based RDBMS and other sources. Enhance visibility of information about medical devices for stakeholders

(no SAP users).

Improve Quality, minimize data inconsistencies and redundancies in medical device records. Promote collaboration and data integration.

Problem Description

Accessibility and Data Consistency: Multiple data sources

ERP System databases

Spreadsheets

Intranet/extranet websites

Data Visibility: SAP access required: proper authorization, access rights

Complexity of instrument configuration management

Number of materials

Versions

Types and Classifications

Localizations

External Coding

Proposed Solution: Semantic Web Tools

Publish a formal ontology for IVD devices:

Data mapping with existing DB systems

Advanced Queries and Search Tools

Implement Standards: Languages (RDFS, SKOS, RDF, R2RML)

Controlled Vocabularies (DC, SNOMED)

Ontologies (FOAF, OBO, FDA)

Data Enrichment: Semantic Annotations (unstructured data)

Collaboration and Quality Control: Semantic Wiki, Portals.

Advantages: Scalability, Flexibility, Interoperability (standards)

Proposed Solution: Semantic Web Tools

Publish a formal ontology for IVD devices: Data mapping with existing DB systems Advanced Queries and Search Tools Implement Standards: Data Enrichment: Semantic Annotations (unstructured data) Collaboration and Quality Control: Semantic Wiki, Portals

R2RML

Ontology Management:

From Relational DB models to RDF

Domain

Ontology

Mapping

Ontology

Source

Ontology

W3C R2RML: RDB to RDF Mapping Language

Express customized mappings from relational databases to RDF datasets.

R2RML Mappings are triple maps in RDF tailored to specific database schema and target vocabulary.

R2RML Processor takes a R2RML Mapping, an Input Database and generates a Output Dataset.

Source Ontology - SAP Relational Mapping

Data Model for Medical Devices using SAP tables

• Defines the relational schema of the data source in a RDF form. • RDF classes and properties to represent database schema metadata

o Tables o Columns o Primary Keys o Foreign Keys, etc.

Mapping Ontology – W3C’s R2RML

Define domain-specific terms and inter-relationships describing how underlying data to be presented.

Domain Ontology – RDF Triples

BIOPEDIA

Semantic Data User Interface: Semantic Wikis and Portal

Semantic Technologies: Evolution

Deploy links with standard vocabularies MeSH, Open Biological and Biomedical Ontologies, FDA Bioportal.

Linked Data Implementation for Instrument Installed Base: Customer locations, Customer Service Actions, spare parts, consumables.

QA Systems: data quality, validation Semantic Queries and Inference tools.

Semantic Web Solution. Information Gain: samples

To replace an instrument with a new one, which has more capacity and require a higher level of investment. Need to evaluate the market size for marketing purposes.

List instruments installed in hospitals and laboratories located in urban areas with more than x million inhabitants in a certain country or region.

Link the location of the installed base, cities and places with DBPEDIA entries to retrieve the population in a given area. (http://dbpedia.org/About)

Require validation of instruments installed with standard technical specifications and equipments and components not provided by the organization manufacturing facilities.

List installed instruments with accessories purchased to local vendors in subsidiaries. Report technical specifications and vendor data.

When possible link specifications about equipments with a formal ontology maintained by FDA. Other links can be added for regulatory agencies in other markets (Europe, Asia, etc.)

http://bioportal.bioontology.org/ontologies/1576

A Case for Linked Data for Medical

Devices in the IVD Market

Semantic Technologies in the IVD Organization.

Summary of Pros and Cons:

Flexibility – Scalabity: Simplify Implementation plans.

Standard Ontologies, Languages, Vocabularies: Semantic Interoperability.

Data Protection, Data Quality.

Data Management: Increase Overhead.