What is in there for Public Health? · 11/21/2008 · Ontologies and data integration in...
Transcript of What is in there for Public Health? · 11/21/2008 · Ontologies and data integration in...
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Ontologies and data integration in biomedicineWhat is in there for Public Health?
Olivier Bodenreider
Lister Hill National Centerfor Biomedical CommunicationsBethesda, Maryland - USA
Public Health Informatics Fellowship ProgramNovember 21, 2008
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Why integrate data?
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Motivation
Multiple sources of dataEach focusing on one aspect
Annotated with specific vocabulariesSpecific format
Need to be integrated to infer new factsTranslational medicine (“Bench to bedside”)BiosurveillanceTranslation into policy (Public health)
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Example Oncology
Cancerregistries
Researchdata
Clinicalrepositories
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Integrating subdomains
Cancerregistries
ICD-O
Researchdata
NCIThesaurus
Clinicalrepositories
SNOMED CT
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Example Oncology
Multiple data repositoriesInternational Classification of Diseases-Oncology (ICD-O-3)
Cancer registriesEpidemiology, Public health
SNOMED CTPatient recordsClinical care
NCI ThesaurusAnnotation of research data
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SNOMED CT
http://www.clinical-info.co.uk/
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NCI Thesaurus
http://nciterms.nci.nih.gov/
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ICD-O-3
Morphology[…]814-838 Adenomas and adenocarcinomas
8140/3 Adenocarcinoma, NOS
Anatomy[…]C60-C63 Male genital organs
C61 Prostate gland– C61.9 Prostate, NOS
Prostate gland
Adenocarcinomaof prostate
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Cancerregistries
Researchdata
Clinicalrepositories
Terminology integration NCI Metathesaurus
ICD-O
NCIThesaurus
SNOMED CT
NCI
Meta.C61.9 Prostate, NOS
C12410 Prostate gland
41216001 Prostatic structure
C0033572
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Approaches to data integration
WarehousingSources to be integrated are transformed into a common format and converted to a common vocabulary
MediationLocal schema (of the sources)Global schema (in reference to which the queries are made)
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Ontologies and warehousing
RoleProvide a conceptualization of the domain
Help define the schemaInformation model vs. ontology
Provide value sets for data elementsEnable standardization and sharing of data
ExamplesBioSense (original design)Repositories for translational research (CTSA)Clinical information systems
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Ontologies and mediation
RoleReference for defining the global schemaMap between local and global schemas
ExamplesBioSense (redesign)BioMediatorOntoFusion
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Ontologies Normalization
From the London Bills of Mortality…
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Ontologies Normalization
…to HITSP vocabulary specifications for interoperability http://www.hitsp.org/
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Gene Ontology
Ontologies Inference
gene
GO
PubMed
Gene name
OMIM
Sequence
InteractionsGlycosyltransferase
Congenital muscular dystrophy
Entrez Gene
[Sahoo, Medinfo 2007]
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From glycosyltransferaseto congenital muscular dystrophy
MIM:608840 Muscular dystrophy, congenital, type 1D
GO:0008375
has_associated_phenotype
has_molecular_function
EG:9215LARGE
acetylglucosaminyl-transferase
GO:0016757glycosyltransferase
GO:0008194isa
GO:0008375 acetylglucosaminyl-transferase
GO:0016758
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Ontologies, data integrationand public health
Case study: BioSense
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BioSense Integrating multiple datasets
Acute care data (emergency room)Demographic dataClinical data
Chief complaintsInitial / final diagnosisLaboratory data
Pharmacy data (national pharmacies)Laboratory data (national labs)Poison control center data…
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Case study Materials and methods
MaterialsBioSense publications and presentations
Methods: look for mentions ofData integration approachesUse of ontologies / terminologies / vocabularies
NormalizationInference
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BioSense Approaches to data integration
Initial approach: Warehouse
[Chambers,PHIN 2008]
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BioSense Approaches to data integration
Redesign: Mediation (Federation)
[Lenert, ASTHORoudtable 2008]
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BioSense Ontologies
Normalized vocabulary for data exchange
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BioSense Ontologies
Normalized vocabulary for data exchangeLink data elements to value sets from standard vocabularies
http://www.hitsp.org/
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BioSense Ontologies
Ontologies for aggregation and inference
[Lenert, ASTHORoudtable 2008]
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Public Health Reference Ontology
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Summary
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Summary
Integration is key to making sense of the many health data repositories
E.g., Biosurveillance
Two major data integration approachesData warehousingMediation
Ontologies play a major role in data integrationNormalization of vocabularySupporting aggregation and inference
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Current trends
Semantic Web technologies provide a convenient platform for integrating biomedical data
Standard tooling
Many biomedical ontologies available, ongoing harmonization
Standard vocabulary
Emerging semantic interoperability specifications (e.g., HITSP, BRIDG, caBIG, HL7, …)
Standard information models
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Some persisting challenges
Reconcile data annotated to different ontologiesIncomplete terminology integration systems (e.g., UMLS, RxNorm), limited harmonization between terminologiesLack of permanent identifiers for biomedical entities
Biomedical ontologiesAvailabilityFormalism (OWL, OBO, RRF, …)Quality
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MedicalOntologyResearch
Olivier Bodenreider
Lister Hill National Centerfor Biomedical CommunicationsBethesda, Maryland - USA
Contact:Web: