Rare Disease Value Sets
Rare disease research requires precise vocabulary for variant interpretation, phenotyping, family history, and clinical management. This view collects value sets from across the clinical, medical, and investigation schema domains that are commonly needed in rare disease genomics and clinical care.
Coverage Summary
| Domain | Schema Sources | Enums | Ontologies |
|---|---|---|---|
| Genetics and Variants | clinical/phenopackets, clinical/genetics, medical/family_history, bio/bio_entities | 6 | GENO, LOINC, HP, OMIM |
| Phenotyping and Clinical | clinical/phenopackets, medical/clinical, bio/bio_entities | 8 | HP, NCIT, UBERON |
| Family History and Pedigree | medical/family_history | 3 | NCIT |
| Treatment and Response | clinical/phenopackets, medical/clinical | 3 | NCIT, RxNorm |
| Diagnostics | medical/clinical, bio/sequencing_platforms | 3 | NCIT, OBI |
| Demographics and Study | clinical/nih_demographics, investigation | 4 | NCIT, OBI |
Genetics and Variants
Variant interpretation in rare disease follows ACMG/AMP guidelines. These enums capture allelic state, pathogenicity classification, actionability, and the interpretation workflow.
Enums
- AllelicStateEnum -- heterozygous, homozygous, hemizygous
- ACMGPathogenicityEnum -- ACMG/AMP five-tier variant classification
- TherapeuticActionabilityEnum -- clinical actionability of variants
- InterpretationProgressEnum -- variant interpretation workflow status
- GeneticRelationship -- biological relationships (full sibling, half sibling)
- GeneticDisease -- genetic diseases (dynamic)
Phenotyping and Clinical
Deep phenotyping is central to rare disease diagnosis. These enums support structured capture of phenotypic features, anatomical systems, onset timing, laterality, and severity -- aligned with the Human Phenotype Ontology and Phenopacket standards.
Enums
- KaryotypicSexEnum -- chromosomal sex determination
- PhenotypicSexEnum -- phenotypic sex
- OnsetTimingEnum -- age of disease onset (congenital, infantile, juvenile, adult)
- LateralityEnum -- sidedness of clinical findings
- SymptomSeverityEnum -- mild, moderate, severe, profound
- Phenotype -- phenotypic features (dynamic, HP-backed)
- Disease -- diseases (dynamic, MONDO-backed)
- AnatomicalSystemEnum -- affected organ systems
Family History and Pedigree
Rare disease diagnosis depends heavily on family history. These enums support pedigree construction and recording of family history completeness.
Enums
- FamilyRelationship -- pedigree relationships (parent, child, sibling, cousin)
- FamilyHistoryStatus -- completeness of family history collection
- GeneticRelationship -- biological relationships
Treatment and Response
Tracking drug response and treatment regimens is important for rare disease management and clinical trials.
Enums
- DrugResponseEnum -- patient response to drug therapy
- DrugRouteEnum -- route of drug administration
- RegimenStatusEnum -- treatment regimen status
Diagnostics
Rare disease workup involves a range of diagnostic modalities, from biochemical tests to whole-genome sequencing.
Enums
- DiagnosticTestTypeEnum -- laboratory, imaging, and genetic tests
- BloodTypeEnum -- ABO and Rh blood type classification
- SequencingPlatform -- WGS/WES platforms for rare disease diagnosis
Demographics and Study
Rare disease studies require careful demographic characterization and study design documentation, particularly for natural history studies and registries.
Enums
- AgeGroupEnum -- pediatric, adolescent, adult, geriatric
- BiologicalSexEnum -- biological sex at birth
- StudyDesignEnum -- observational, experimental, longitudinal
- StudyPhaseEnum -- clinical trial phases