A Case for linked Data for Medical Devices in the IVD Market
A Case for Linked Data for Medical Devices in the IVD Market bioMerieux INC.Guillermo PerassoUNC CH – CHIP – Practicum - Dec 2012
ContentTarget Organization: bioMerieux IncGoals and ScopeProblem DescriptionProposed Solution: Use CasesSolution ImplementationEvolution 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.
Company IS – data sources Company’s intranetERP System: SAPRDBMS: Oracle 9i Structure / Un-structure information 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 ToolsPublish 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• 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 Data Model for Medical Devices using SAP tables o Primary Keys o Foreign Keys, etc.
Domain Ontology – RDF TriplesDefine domain-specific terms and inter-relationships describing how underlying data tobe presented.
Semantic Data User Interface:Semantic Wikis and Portal BIOPEDIA
Semantic Technologies: EvolutionDeploy 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: samplesTo replace an instrument with a new one, which has more capacity and require a higher level ofinvestment. Need to evaluate the market size for marketing purposes.List instruments installed in hospitals and laboratories located in urban areas with more than x millioninhabitants 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 andcomponents not provided by the organization manufacturing facilities.List installed instruments with accessories purchased to local vendors in subsidiaries. Report technicalspecifications 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 MarketSemantic 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.