SNOMED CT Research Webinar
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*We will begin shortly* Dr. Ronald Cornet UPCOMING WEBINARS:
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Dr Hyeoun-Ae Park Emeritus Dean & Professor Seoul National University Past President International Medical Informatics Association
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SNOMED CT Research Webinar:
SNOMED CT – OWL in a FAIR web of data
Dr. Ronald Cornet SNOMED CT – OWL in a FAIR web of data Ronald Cornet Me
SNOMED Use case CT
Semantic FAIR data web Me
• Associate professor at Amsterdam UMC, Amsterdam Public Health Research Institute, department of Medical Informatics • Research on knowledge representation; ontology auditing; SNOMED CT; reusable healthcare data; FAIR data Conflicts of Interest
• 10+ years involvement with SNOMED International (Quality Assurance Committee, Technical Committee, Implementation SIG, Modeling Advisory Group) • Chair of the GO-FAIR Executive board • Funding from European Union (Horizon 2020) Me
SNOMED Use case CT
Semantic FAIR data web FAIR Guiding Principles https://go-fair.org/ FAIR Principles – concise
• Findable • Metadata and data should be easy to find for both humans and computers • Accessible • The user needs to know how data can be accessed, possibly including authentication and authorization • Interoperable • Data need to be integrated with other data and interoperate with applications for analysis, storage, and processing • Reusable • (Licensing & provenance) metadata and data should be well-described so that they can be replicated and/or combined in different settings FAIR Principles = “What”, not “how”
• Globally unique and persistent identifiers • https://orcid.org/0000-0002-1704-5980 • https://www.linkedin.com/in/ronaldcornet/ • … • Freedom of format
Open license à structured à open format à URI-based à linked FAIR ≠ Open (meta)data
• Not all of SNOMED CT can be used by all for all tasks • Clinical data capture using SNOMED CT requires a license, but a Global Patient Set is available for sharing patient health information • Research licenses exist for SNOMED CT, among others in UMLS
• Much of SNOMED CT can be used by many for many tasks Examples of (more or less) FAIR repositories
• https://home.fairdatapoint.org/ ß Links to FAIR data points • https://fairsharing.org/ • https://www.openaire.eu/ • https://www.ohdsi.org/ ß “Human” entry to harmonized data Me
SNOMED Use case CT
Semantic FAIR data web SNOMED CT – more than the numbers SNOMED CT - active elements over time
1400000
1200000
1000000
800000
600000
400000
200000
0
concepts relationships descriptions https://www.icthealth.nl/online-magazine/editie-04-2018/onder-de-motorkap-helpt-snomed-zorgverleners-met-eenheid-van-taal/ https://boston.cbslocal.com/2017/12/15/salem-new-hampshire- owl-found-under-hood-during-pep-boys-oil-change/ OWL - Web Ontology Language
● A Semantic Web language to represent rich and complex knowledge (things, groups of things, and relations between things). ● A computational logic-based language ○ OWL ontologies provide classes, properties, individuals and data values and are stored as Semantic Web documents ● One of the distinguishing features of OWL is that it can be used to express extremely complicated and subtle ideas about your data. ● Primary uses ○ Fast and flexible data modeling ○ Efficient automated reasoning Before July 2019 - OWL conversion
OWL-version of SNOMED CT can be generated from RF2 tables
● Concept ● (Stated) Relationship ● Description
Two available transformations
● Spackman OWL script tls2_StatedRelationshipsToOwlKRSS_INT.pl ● SNOMED OWL Toolkit https://github.com/IHTSDO/snomed-owl-toolkit Before July 2019 - Drawbacks
● Limited expressiveness in RF2 tables ● Implicit knowledge included in OWL-transformation scripts ○ Role chains ○ Transitivity of relationships ○ Reflexivity From July 2019 - Possibilities
In theory:
Full OWL expressiveness
In practice:
● Multiple axioms ● Role chains; transitivity; reflexivity ● Generalized Concept Inclusions (GCI’s) Multiple axioms Role chains, transitivity, reflexivity
• Role chains, e.g., • SubObjectPropertyOf (ObjectPropertyChain(:127489000 :738774007) :127489000) • Transitivity • TransitiveObjectProperty(:738774007 | Is modification of (attribute)) • Reflexivity • ReflexiveObjectProperty(:738774007 | Is modification of (attribute)) Generalized Concept Inclusions (GCI’s) OWL RefSet (not: OWL-file) – benefits
• Versioning of OWL axioms • Challenging in OWL-only • Maintaining RF2 infrastructure • Compatibility with overall infrastructure • Easy to create OWL-file Me
SNOMED Use case CT
Semantic FAIR data web Semantic Web Standards
• OWL - ontologies • Syntax: owl-functional, owl-manchester • ShEx - (clinical) data models • Syntax: ShExC or any RDF-syntax Metadata
• RDF - instances • Syntax: rdf-jsonld, rdf-nq,
Data rdf-nt, rdf-trix, rdf-turtle, rdf-xml
Open license à structured à open format à URI-based à linked HL7 data modeling
• ShEx – Shape Expressions • Describe permitted attributes • Including cardinalities • Including allowed values
RDF – instances
Triple: Subject https://www.linkedin.com/in/ronaldcornet/ Predicate http://hl7.org/fhir/patient#gender Object http://hl7.org/fhir/codesystem-administrative-gender.html#administrative- gender-male
Triple: Subject https://orcid.org/0000-0002-1704-5980 Predicate http://snomed.info/id/263495000 (gender) Object http://snomed.info/id/703117000 (masculine)
Required (interoperability) services
• Ontologies • Data models (Resources & profiles a.k.a. archetypes & templates) • Value sets
• Ontology alignment services • Static, e.g., UMLS, Athena • Dynamic, e.g., AML, FCA-Map, LogMap) • Instance alignment services (e.g., https://www.sameas.cc/)
• Data access services Legend:
SNOMED CT Ontology VS VS
Value set … …
VS VS VS VS Alignment Data Model Data Model Data Model
Individ.
EHR Reg.
Reasoning EDC
Data Model Added value of linked data with OWL
• “Enrichment” • Viral pneumonia à Infective pneumonia à • Applying reasoning on instances • PatientX: finding = Infective pneumonia • PatientX: finding = COVID-19 è PatientX: finding = (Viral pneumonia : causative agent = SARS-CoV-2) Me
SNOMED Use case CT
Semantic FAIR data web Use Case (2019/2023)
EU project, 35 countries: 26 EU Countries, 7 associated, UK & Canada • Selecting and combining semantic pieces • To create a Virtual Platform to interconnect FAIR rare disease data • Fully based on semantic web technology • Includes ORDO, NCIt, SIO, … • Current focus on high-quality RDF-data and ontology alignment Use Case (2019/2023)
ADAM-project (Adequate Data Capture and Monitoring) • Assess and improve quality of data on the problem list • Based on “Diagnosethesaurus”, Dutch Interface Terminology on SNOMED CT • Assess completeness of COVID-19-cohort • Medical entity linking of free text to SNOMED CT
FAIR COVID-Predict project • Harmonize data of Dutch COVID-19 patients in a single datawarehouse • Increase use of (LOINC & SNOMED CT) coding in EHR & Lab-systems • Realize (de-)centralized OHDSI-compliant FAIR data points Use Case (2020/2023)
EU project to develop a coaching system for improving the quality of life of cancer home patients • Harmonization of cancer data from the Netherlands and Italy • Application of OHDSI approach for data harmonization • Data exchange using HL7 FHIR
• Research into reasoning over instance data, to support SPARQL querying Use Case (2016/2023)
EHR vendor • Benefit from SNOMED CT hierarchy, properties and patient-friendly terms to increase patients’ understanding of their record
EDC vendor • Make research data FAIR upon collection • Facilitating specification of rich metadata and establishing FAIR data points Summary
• Two approaches to FAIR data and metadata • Rooted in Semantic Web technology • Growing from harmonized models and vocabularies • Ontologies are essential metadata • SNOMED CT being an expressive OWL ontology contributes to reasoning over EHR data • Infrastructure is being established, integrating the pieces is the next step Me
SNOMED Use case CT
Semantic FAIR data web
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Suzy Roy
Dr. Ronald Cornet