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Medical & Clinical Metadata & Standards

Medical and clinical data is governed by strict regulatory requirements that dictate how data must be described, stored, shared, and protected. Metadata standards in this domain serve both scientific reproducibility and legal compliance.

Core Interoperability Standards​

HL7 FHIR (Fast Healthcare Interoperability Resources)​

The modern standard for health data exchange. FHIR defines a set of "resources" (Patient, Observation, Condition, Medication, etc.) with standardized fields, enabling interoperable data exchange via REST APIs.

  • Use: EHR integration, clinical data exchange, research data access
  • Spec: HL7 FHIR

OMOP CDM (Common Data Model)​

A standardized relational model for harmonizing heterogeneous clinical data from different sources into a common format, maintained by OHDSI.

  • Use: Multi-site observational studies, pharmacovigilance
  • Spec: OMOP CDM

CDISC Standards​

A suite of standards for clinical trial data:

  • CDASH — Standardized data collection forms
  • SDTM — Tabulation format for regulatory submission
  • ADaM — Analysis-ready dataset format
  • Spec: CDISC

Medical Terminology and Ontologies​

SNOMED CT​

The most comprehensive clinical terminology, covering diseases, findings, procedures, and substances. Used in electronic health records worldwide.

ICD-10 / ICD-11​

International Classification of Diseases — the WHO standard for coding diagnoses, used for billing and epidemiology.

LOINC (Logical Observation Identifiers Names and Codes)​

A universal coding system for laboratory tests and clinical observations.

  • Use: Standardizing lab result reporting
  • Spec: LOINC

MeSH (Medical Subject Headings)​

A controlled vocabulary for indexing biomedical literature, maintained by the NLM.

  • Use: Literature search, metadata tagging
  • Spec: MeSH

HPO (Human Phenotype Ontology)​

A standardized vocabulary of phenotypic abnormalities, used in rare disease research and clinical genomics.

GDPR (General Data Protection Regulation)​

The EU regulation governing personal data processing. Requires lawful basis, purpose limitation, data minimization, and rights of data subjects.

  • Relevance: All research involving EU patient data

An ontology for representing informed consent information in research.

GA4GH Data Use Ontology (DUO)​

A standard for machine-readable data use conditions, enabling automated access control decisions.

  • Use: Genomic and clinical data sharing with consent restrictions
  • Spec: GA4GH DUO

DICOM Metadata​

DICOM files contain extensive metadata organized in a hierarchical structure:

  • Patient level — Name, ID, birth date, sex
  • Study level — Date, description, referring physician
  • Series level — Modality, body part, protocol
  • Image level — Pixel data, acquisition parameters

Important: DICOM metadata must be anonymized (de-identified) before research use. Tools like deid (Python) or CTP (Clinical Trial Processor) automate this process.

Best Practices​

  1. Anonymize early — De-identify patient data as soon as possible in the research pipeline
  2. Use standard terminologies — SNOMED CT, ICD, LOINC for consistent coding
  3. Document consent scope — Record what the patient consented to and encode it machine-readably (DUO)
  4. Map to common data models — Use OMOP CDM for observational research to enable cross-site analysis
  5. Version your data dictionaries — Track changes to variable definitions over time
  6. Maintain an audit trail — Log all data access and modifications for regulatory compliance