Admin 3julmthh: Added cross-references: AIDAVA Competitive Analysis, Longitudinal Journals

2026-04-14T17:57:35Z

Added cross-references: AIDAVA Competitive Analysis, Longitudinal Journals

← Older revision		Revision as of 17:57, 14 April 2026
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	== See Also ==		== See Also ==
			* [[AIDAVA Competitive Analysis]]
			* [[Longitudinal Journals]]
	* [[AIDAVA]]		* [[AIDAVA]]
	* [[AIDAVA Related Companies]]		* [[AIDAVA Related Companies]]

Admin 3julmthh: Added AIDAVA Ontology Architecture section — reference KG, PHKG instance model, use case extensions

2026-04-14T14:08:00Z

Added AIDAVA Ontology Architecture section — reference KG, PHKG instance model, use case extensions

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 * "Genomics on FHIR — a feasibility study to support a National Strategy for Genomic Medicine" — Nature (2024)
 * "TIMER: temporal instruction modeling and evaluation for longitudinal clinical records" — npj Digital Medicine (2025)
 == See Also ==

Admin 3julmthh: Research page: ontologies, terminologies, standards for PHKG and longitudinal records

2026-04-14T13:47:32Z

Research page: ontologies, terminologies, standards for PHKG and longitudinal records

New page

__NOTOC__
Ontologies, terminologies, and standards used in longitudinal health records and Personal Health Knowledge Graphs (PHKG). This page maps the technology stack used by [[AIDAVA]] and related projects for health data interoperability, FAIRification, and semantic integration.

== Core Clinical Terminologies ==

=== SNOMED CT ===
'''Systematized Nomenclature of Medicine — Clinical Terms'''
* '''Purpose:''' Comprehensive clinical terminology covering diseases, findings, procedures, body structures, organisms, substances, etc.
* '''Scale:''' 350,000+ concepts, 1M+ relationships
* '''Governance:''' SNOMED International (non-profit)
* '''Use in PHKG:''' Primary concept representation for clinical data. AIDAVA uses SNOMED CT as the backbone ontology for its reference knowledge graph — each PHKG instance maps clinical observations to SNOMED concepts.
* '''Key feature:''' Compositional — can express complex clinical concepts by combining simpler ones (post-coordination)
* '''Mapping:''' Maps to ICD-10, LOINC, Read Codes, and national terminologies
* '''Source:''' https://www.snomed.org

=== LOINC ===
'''Logical Observation Identifiers Names and Codes'''
* '''Purpose:''' Universal standard for identifying medical laboratory observations, clinical measurements, and survey instruments
* '''Scale:''' 100,000+ codes
* '''Governance:''' Regenstrief Institute
* '''Use in PHKG:''' Identifies what was measured (lab test, vital sign, clinical observation). SNOMED describes the concept; LOINC identifies the measurement.
* '''Key feature:''' Every code has 6 axes: component, property, time, system, scale, method
* '''Example:''' LOINC 2345-7 = "Glucose [Mass/volume] in Serum or Plasma"
* '''Source:''' https://loinc.org

=== ICD-10 / ICD-11 ===
'''International Classification of Diseases'''
* '''Purpose:''' Standard diagnostic classification for epidemiology, health management, and clinical purposes
* '''Governance:''' WHO
* '''Use in PHKG:''' Disease classification and mortality coding. Less granular than SNOMED CT but universally mandated for billing and reporting.
* '''Key difference from SNOMED:''' ICD is a classification (flat hierarchy for reporting); SNOMED is a terminology (rich relationships for clinical reasoning)
* '''Mapping:''' SNOMED CT ↔ ICD-10 maps maintained by SNOMED International
* '''Source:''' https://icd.who.int

=== RxNorm ===
'''Normalized Names for Clinical Drugs'''
* '''Purpose:''' Standardized nomenclature for clinical drugs in the US, increasingly used globally
* '''Governance:''' NLM (US National Library of Medicine)
* '''Use in PHKG:''' Medication representation in longitudinal records — linking prescriptions, dispensing, and administration
* '''Key feature:''' Provides ingredient, dose form, and strength as separate concepts
* '''Source:''' https://www.nlm.nih.gov/research/umls/rxnorm

== Health Data Models & Standards ==

=== HL7 FHIR ===
'''Fast Healthcare Interoperability Resources'''
* '''Purpose:''' Standard for exchanging healthcare data electronically
* '''Current version:''' FHIR R4 (Release 4), R5 available
* '''Governance:''' HL7 International
* '''Use in PHKG:''' Defines the resource types (Patient, Observation, Condition, MedicationRequest, etc.) that structure health data exchange. AIDAVA maps its PHKG nodes to FHIR resource profiles.
* '''Key feature:''' RESTful API, JSON/XML, modular resources
* '''FHIR Shorthand (FSH):''' Authoring language for FHIR Implementation Guides and profiles
* '''Source:''' https://hl7.org/fhir

=== OMOP CDM ===
'''Observational Medical Outcomes Partnership Common Data Model'''
* '''Purpose:''' Standardized data model for observational health data — enables multi-site research
* '''Governance:''' OHDSI (Observational Health Data Sciences and Informatics)
* '''Use in PHKG:''' Common representation for longitudinal observational data across institutions. Researchers can run the same analytics across different hospital systems.
* '''Key tables:''' Person, Condition_occurrence, Drug_exposure, Measurement, Observation, Procedure_occurrence
* '''Mapped terminologies:''' SNOMED CT (conditions), RxNorm (drugs), LOINC (measurements)
* '''Tools:''' ATLAS (cohort definition), OHDSI network studies
* '''Source:''' https://ohdsi.org

=== openEHR ===
'''Open Electronic Health Record'''
* '''Purpose:''' Open standard for EHR architecture — archetype-based clinical data modeling
* '''Governance:''' openEHR Foundation
* '''Use in PHKG:''' Clinical Knowledge Manager (CKM) provides archetypes (reusable clinical data models). Unlike FHIR (exchange-focused), openEHR is storage/persistence-focused.
* '''Key feature:''' Two-level modeling — reference model (technical) + archetypes (clinical)
* '''Different from FHIR:''' openEHR defines how to STORE data; FHIR defines how to EXCHANGE it
* '''Source:''' https://www.openehr.org

=== Phenopackets ===
'''Phenotype Data Exchange Format'''
* '''Purpose:''' Standard format for representing phenotypic data linked to genomic data
* '''Governance:''' GA4GH
* '''Use in PHKG:''' Structured phenotype representation for rare disease, linking patient phenotypes (HPO terms) to genomic variants
* '''Source:''' https://phenopackets.org

== Domain-Specific Ontologies ==

=== Human Phenotype Ontology (HPO) ===
* '''Purpose:''' Standard vocabulary for phenotypic abnormalities in human disease
* '''Scale:''' 18,000+ terms, 300,000+ annotations to diseases
* '''Use in PHKG:''' Describing patient phenotypes longitudinally — tracking symptoms and signs over time
* '''Source:''' https://hpo.jax.org

=== Gene Ontology (GO) ===
* '''Purpose:''' Standard representation of gene function across species
* '''Domains:''' Molecular function, biological process, cellular component
* '''Use in PHKG:''' Linking genomic data to functional annotations in longitudinal genomics records
* '''Source:''' http://geneontology.org

=== Orphanet Nomenclature ===
* '''Purpose:''' Standard terminology for rare diseases
* '''Scale:''' 6,000+ rare diseases
* '''Use in PHKG:''' Rare disease identification in longitudinal records, linking to Orphacodes for cross-border data exchange
* '''Source:''' https://www.orpha.net

=== GA4GH Standards ===
'''Global Alliance for Genomics and Health'''
* '''Purpose:''' Framework for responsible genomic data sharing
* '''Key standards:'''
** '''Beacon API:''' Query whether a dataset contains a particular genomic variant
** '''VCF:''' Variant Call Format for genomic variants
** '''Phenopackets:''' Phenotype data linked to genomics (see above)
** '''Passport/DUO:''' Data use ontology for access control
* '''Use in PHKG:''' Genomic data representation and sharing in longitudinal health records
* '''Source:''' https://www.ga4gh.org

== FAIRification & Semantic Web ==

=== FAIR Principles ===
'''Findable, Accessible, Interoperable, Reusable'''
* Applied to health data through:
** Persistent identifiers (DOIs, URIs)
** Rich metadata (Dublin Core, DCAT)
** Standard vocabularies (all ontologies above)
** Open protocols (REST APIs, SPARQL)
* '''AIDAVA connection:''' AIDAVA's first technology pillar is "Automation of quality enhancement and FAIRification" of collected health data

=== RDF / OWL / SPARQL ===
* '''RDF:''' Resource Description Framework — graph data model for representing knowledge
* '''OWL:''' Web Ontology Language — for defining ontologies with rich axioms
* '''SPARQL:''' Query language for RDF databases
* '''Use in PHKG:''' PHKGs are typically represented as RDF graphs, with SNOMED/LOINC/FHIR as the ontology layer

=== BioPortal ===
* '''Purpose:''' Repository of biomedical ontologies
* '''Scale:''' 900+ ontologies, 14M+ terms
* '''Governance:''' Stanford BMIR
* '''Use in PHKG:''' Source for ontology mappings, concept searches, and cross-ontology alignment
* '''Source:''' https://bioportal.bioontology.org

== Ontology Integration Architecture (PHKG) ==

A typical Personal Health Knowledge Graph integrates these ontologies in layers:

# '''Top:''' Patient-specific nodes (this patient, this observation, this encounter)
# '''Middle:''' FHIR Resource profiles structuring the data (Observation, Condition, Medication)
# '''Bottom:''' Terminology codes (SNOMED CT for concepts, LOINC for measurements, RxNorm for drugs)

Cross-cutting: ICD for classification/reporting, OMOP CDM for research analytics, HPO for phenotyping, GA4GH for genomics.

== Key Research Papers ==

* "An ontology-based rare disease common data model harmonising international registries, FHIR, and Phenopackets" — Nature (2025)
* "CONNECTED: leveraging digital twins and personal knowledge graphs in healthcare digitalization" — Frontiers (2025)
* "FAIRification of health-related data using semantic web technologies in the Swiss Personalized Health Network" — Nature (2024)
* "A multimodal vision knowledge graph of cardiovascular disease" — Nature (2025)
* "Genomics on FHIR — a feasibility study to support a National Strategy for Genomic Medicine" — Nature (2024)
* "TIMER: temporal instruction modeling and evaluation for longitudinal clinical records" — npj Digital Medicine (2025)

== See Also ==
* [[AIDAVA]]
* [[AIDAVA Related Companies]]
* [[Interoperability]]
* [[Knowledge Graphs in Health]]
* [[Publications]]

[[Category:Topics]]

Ontologies for Longitudinal Health Records - Revision history

Admin 3julmthh: Added cross-references: AIDAVA Competitive Analysis, Longitudinal Journals

Admin 3julmthh: Added AIDAVA Ontology Architecture section — reference KG, PHKG instance model, use case extensions

Admin 3julmthh: Research page: ontologies, terminologies, standards for PHKG and longitudinal records