Data Model¶
The ClinVar-GKM release file organizes data into bundle sections, each containing objects of a specific class. These classes form a directed graph of relationships — variants reference alleles, alleles reference locations, statements reference propositions, and so on.
This page provides a visual overview of how the classes relate to each other, with links to detailed documentation for each class.
Bundle Section Map¶
The release bundle is a single JSON object of named sections — each section is a dictionary mapping a typed id to one object. Objects link across sections with #/section/id JSON pointers. The map below shows every section, its object type, an example id, and its outgoing references. See ID References for the full pointer catalog.
The map renders at full size in a scrollable frame — scroll within it to follow the reference chain from statements down to VRS sequence references. Each drawer links to that section's class reference page.
Reading the map:
{ } keyis the section name — the JSON key under which that section's dictionary of objects lives- The pill is an example object id (the dictionary key within the section)
field → #/section/lines are the outgoing cross-section references an object in that section carries- Solid arrows trace the primary reference flow between section clusters; dashed arrows are optional or back-references (e.g., evidence items pointing back at statements)
- The four
proposition*sections group the propositions by meaning (pathogenicity, oncogenicity, somatic clinical impact, ClinVar custom); a proposition's section is a function of itstype
Variation Classes¶
These classes represent the variant and its genomic context. VRS types (SequenceReference, Location, Allele) use their upstream GA4GH schemas directly. ClinVar-specific profiles are documented under Variations.
| Class | Bundle Section | Key Pattern | Description |
|---|---|---|---|
| SequenceReference | sequenceReference |
SQ.{digest} |
Reference sequence with refget accession, molecule type, and assembly |
| Location | location |
ga4gh:SL.{digest} |
Position or range on a sequence reference |
| Allele | allele |
ga4gh:VA.{digest} |
Specific sequence change at a location |
| Gene | gene |
ncbigene:{id} |
Gene MappableConcept with NCBI Gene primaryCoding and HGNC mapping |
| ClinvarCategoricalVariant | variation |
clinvar:{id} |
ClinVar variation with Cat-VRS representation and extensions |
See Variations for the full variant type hierarchy and extension documentation.
Supporting Classes¶
These classes represent the conditions, submitters, and propositions that support classification statements. Conditions and submitters use upstream GA4GH types. Proposition content is delivered in four sections grouped by meaning, keyed by proposition type — together they hold all 13 ClinvarProposition types.
| Class | Bundle Section | Key Pattern | Description |
|---|---|---|---|
| Condition | condition |
clinvar.trait:{id} |
Disease or phenotype with MedGen coding and cross-references |
| ConditionSet | conditionSet |
clinvar.traitset:{id} |
Grouping of conditions with AND/OR membership operator |
| Therapy | therapy |
clinvar.therapy:{sha256} |
Drug therapy (content-addressed); object of therapeutic propositions via #/therapy/ |
| TherapyGroup | therapyGroup |
clinvar.therapygroup:{sha256} |
Combination therapy whose concepts reference #/therapy/ members |
| Submitter | submitter |
clinvar.submitter:{id} |
Submitting organization |
| ClinvarProposition | propositionPathogenicity |
{scv_id}-PATH |
Pathogenicity propositions |
| ClinvarProposition | propositionOncogenicity |
{scv_id}-ONCO |
Oncogenicity propositions |
| ClinvarProposition | propositionSomaticClinicalImpact |
{scv_id}-{CODE} |
Somatic clinical impact propositions: Clinical Significance, Diagnostic, Prognostic, Therapeutic Response |
| ClinvarProposition | propositionClinvarCustom |
{scv_id}-{CODE} |
ClinVar-specific proposition types (Risk Factor, Protective, Drug Response, …, Undefined) |
See Propositions for the full type/code/predicate reference and ID References for how the proposition sections are keyed.
Statement Classes¶
These classes represent classification statements at different levels of aggregation. All are profiles of the VA-Spec Statement type documented under Statements.
| Class | Bundle Section | Key Pattern | Description |
|---|---|---|---|
| ClinvarScvStatement | scv |
clinvar.submission:{id}.{ver} |
Submitted classification |
| ClinvarVcvStatement | vcv |
{vcv}-{group}-{prop}-{level} |
Variant-level aggregate |
| ClinvarRcvStatement | rcv |
{rcv}-{group}-{prop}-{level} |
Condition-level aggregate |
| ClinvarSomaticEvidenceLine | evidenceLine |
{scv_id}.{ver} / {agg_id}.contributing |
Evidence line referenced via hasEvidenceLines |
See Statements for the aggregation structure and Evidence Lines for the somatic tier mapping.