ClinVar-GKM bundle — section map

clinvar-gkm_….json

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 — each drawer lists its outgoing references as field → #/section/. Each drawer links to its reference page; see ID References for the full pointer catalog.

// one JSON object, 20 named sections, each { id: object }
{ "scv", "vcv", "rcv", "evidenceLine",   "varcond-proposition", "vartumor-proposition", "vartherapy-proposition", "varcustom-proposition",   "condition", "conditionSet", "therapy", "therapyGroup", "submitter",   "variation", "allele", "location", "sequenceReference", "gene", "copyNumberCount", "copyNumberChange" }
Statements & evidence lines
scv
ClinvarScvStatement · va-spec Statement
clinvar.submission:SCV001571657.2
proposition → #/…-proposition/
contributor → #/submitter/
hasEvidenceLines[] → #/evidenceLine/
vcv
ClinvarVcvStatement · va-spec Statement
VCV000012582.63-G-PATH-CP
proposition → #/…-proposition/
hasEvidenceLines[] → #/evidenceLine/
rcv
ClinvarRcvStatement · va-spec Statement
RCV000012345.8-G-PATH-CP
proposition → #/…-proposition/
hasEvidenceLines[] → #/evidenceLine/
evidenceLine
ClinvarSomaticEvidenceLine · va-spec
…-PATH-CP.contributing
hasEvidenceItems[] → #/scv|vcv|rcv/
proposition 1..1
Propositions — 4 delivery groups, keyed by type
varcond-proposition
Pathogenicity / ClinSig / Diagnostic / Prognostic
SCV001234567-PATH
subject → #/variation/
object → #/condition|conditionSet/
vartumor-proposition
VariantOncogenicityProposition
SCV002345678-ONCO
subject → #/variation/
object → #/condition/ (tumor)
vartherapy-proposition
VariantTherapeuticResponseProposition
SCV003456789-TR
subject → #/variation/
object → #/therapy|therapyGroup/
conditionQualifier → #/condition/
varcustom-proposition
Clinvar*Proposition · 10 ClinVar types
SCV004567890-RF
subject → #/variation/
object → #/condition|conditionSet/
subject 1..1
Variation — VRS identity chain
variation
CategoricalVariant · Cat-VRS
clinvar:12582
members[] → #/allele/
constraints[] → #/allele|location/
…clinvarGeneList[].gene → #/gene/
members 0..*
allele
Allele · VRS
ga4gh:VA.ELQCnIBGqaTl…
location → #/location/
location 1..1
location
SequenceLocation · VRS
ga4gh:SL.Eg_6kV6Bb4FM…
sequenceReference → #/sequenceReference/
sequenceReference 1..1
sequenceReference
SequenceReference · VRS
SQ.0iKlIQk2oZLoeOG9…
refgetAccession + moleculeType — leaf
gene
MappableConcept · gkm-core
ncbigene:3077
NCBI Gene coding + HGNC mapping — leaf
object 0..1
Conditions, therapies & submitters
conditionSet
ConditionSet · ClinVar
clinvar.traitset:1234
members[] → #/condition/
operator: AND | OR
members 1..*
condition
Condition · MappableConcept
clinvar.trait:9580
MedGen primaryCoding + mappings — leaf
therapyGroup
TherapyGroup (ConceptSet) · va-spec
clinvar.therapygroup:df1d8467…
concepts[] → #/therapy/
membershipOperator: AND
concepts 2..*
therapy
Therapy (MappableConcept) · va-spec
clinvar.therapy:ab221549…
drug name + conceptType — content-addressed, leaf
submitter
Agent · gkm-core
clinvar.submitter:508027
name — leaf (cited by scv contributions)
{ } key section name (JSON key) id example object id → #/x/ cross-section reference