A Case for linked Data for Medical Devices in the IVD Market
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Transcript of A Case for linked Data for Medical Devices in the IVD Market
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A Case for Linked Data for Medical
Devices in the IVD Market
bioMerieux INC.
Guillermo Perasso
UNC CH – CHIP – Practicum - Dec 2012
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Content
Target Organization: bioMerieux Inc
Goals and Scope
Problem Description
Proposed Solution: Use Cases
Solution Implementation
Evolution and Future Developments.
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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.
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Structure / Un-structure information
Company IS – data sources
ERP System: SAP RDBMS: Oracle 9i
Company’s intranet
Enterprise Content Management System
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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.
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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
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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)
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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
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Ontology Management:
From Relational DB models to RDF
Domain
Ontology
Mapping
Ontology
Source
Ontology
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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.
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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.
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Mapping Ontology – W3C’s R2RML
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Define domain-specific terms and inter-relationships describing how underlying data to be presented.
Domain Ontology – RDF Triples
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BIOPEDIA
Semantic Data User Interface: Semantic Wikis and Portal
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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.
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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
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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.