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openapi.schema.yaml
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openapi.schema.yaml
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openapi: 3.1.0
info:
title: annonars
description: Genome annotation based on Rust and RocksDB
contact:
name: Manuel Holtgrewe
email: [email protected]
license:
name: Apache-2.0
version: 0.42.0
paths:
/api/v1/genes/clinvar:
get:
tags:
- genes_clinvar
summary: Query for ClinVar information for one or more genes.
operationId: genesClinvar
parameters:
- name: hgnc_id
in: query
description: The HGNC IDs to search for.
required: false
schema:
type:
- array
- 'null'
items:
type: string
responses:
'200':
description: Per-gene ClinVar information.
content:
application/json:
schema:
$ref: '#/components/schemas/GenesClinvarResponse'
'500':
description: Internal server error.
content:
application/json:
schema:
$ref: '#/components/schemas/CustomError'
/api/v1/genes/info:
get:
tags:
- genes_info
summary: Query for annotations for one or more genes.
operationId: genesInfo
parameters:
- name: hgnc_id
in: query
description: The HGNC IDs to search for.
required: false
schema:
type:
- array
- 'null'
items:
type: string
responses:
'200':
description: Per-gene information.
content:
application/json:
schema:
$ref: '#/components/schemas/GenesInfoResponse'
'500':
description: Internal server error.
content:
application/json:
schema:
$ref: '#/components/schemas/CustomError'
/api/v1/genes/lookup:
get:
tags:
- genes_lookup
summary: Search for genes.
operationId: genesLookup
parameters:
- name: q
in: query
description: The strings to search for.
required: true
schema:
type: array
items:
type: string
responses:
'200':
description: Genes search results.
content:
application/json:
schema:
$ref: '#/components/schemas/GenesLookupResponse'
'500':
description: Internal server error.
content:
application/json:
schema:
$ref: '#/components/schemas/CustomError'
/api/v1/genes/search:
get:
tags:
- genes_search
summary: Search for genes.
operationId: genesSearch
parameters:
- name: q
in: query
description: The string to search for.
required: true
schema:
type: string
- name: fields
in: query
description: The fields to search in.
required: false
schema:
type:
- array
- 'null'
items:
$ref: '#/components/schemas/GenesFields'
- name: case_sensitive
in: query
description: Enable case sensitive search.
required: false
schema:
type:
- boolean
- 'null'
responses:
'200':
description: Genes search results.
content:
application/json:
schema:
$ref: '#/components/schemas/GenesSearchResponse'
'500':
description: Internal server error.
content:
application/json:
schema:
$ref: '#/components/schemas/CustomError'
/api/v1/seqvars/annos:
get:
tags:
- annos_variant
summary: Query for annotations for a single variant.
operationId: seqvarsAnnosQuery
parameters:
- name: genome_release
in: query
description: Genome release specification.
required: true
schema:
type: string
- name: chromosome
in: query
description: Chromosome name.
required: true
schema:
type: string
- name: pos
in: query
description: 1-based position for VCF-style variant.
required: true
schema:
type: integer
format: int32
minimum: 0
- name: reference
in: query
description: Reference allele bases.
required: true
schema:
type: string
- name: alternative
in: query
description: Alterantive allele bases.
required: true
schema:
type: string
responses:
'200':
description: Annotation for a single variant.
content:
application/json:
schema:
$ref: '#/components/schemas/SeqvarsAnnosResponse'
'500':
description: Internal server error.
content:
application/json:
schema:
$ref: '#/components/schemas/CustomError'
/api/v1/strucvars/clinvar/query:
get:
tags:
- clinvar_sv
summary: Endpoint for querying ClinVar SV annotations.
operationId: strucvarsClinvarQuery
parameters:
- name: genome_release
in: query
description: Genome release specification.
required: true
schema:
$ref: '#/components/schemas/GenomeRelease'
- name: chromosome
in: query
description: Chromosome name.
required: true
schema:
type: string
- name: start
in: query
description: 1-based start position.
required: true
schema:
type: integer
format: int32
minimum: 0
- name: stop
in: query
description: 1-based stop postion.
required: true
schema:
type: integer
format: int32
minimum: 0
- name: variation_types
in: query
description: Optionally, the variant types.
required: false
schema:
type:
- array
- 'null'
items:
$ref: '#/components/schemas/ClinvarExtractedVariationType'
- name: min_overlap
in: query
description: Optionally, minimal overlap.
required: false
schema:
type:
- number
- 'null'
format: double
- name: page_no
in: query
description: Optional 1-based page number.
required: false
schema:
type:
- integer
- 'null'
format: int32
minimum: 0
- name: page_size
in: query
description: Optional page size.
required: false
schema:
type:
- integer
- 'null'
format: int32
minimum: 0
responses:
'200':
description: Clinvar strucvars information.
content:
application/json:
schema:
$ref: '#/components/schemas/StrucvarsClinvarResponse'
'500':
description: Internal server error.
content:
application/json:
schema:
$ref: '#/components/schemas/CustomError'
/api/v1/versionsInfo:
get:
tags:
- versions
summary: Query for annotations for one variant.
operationId: versionsInfo
parameters: []
responses:
'200':
description: Version information.
content:
application/json:
schema:
$ref: '#/components/schemas/VersionsInfoResponse'
'500':
description: Internal server error.
content:
application/json:
schema:
$ref: '#/components/schemas/CustomError'
components:
schemas:
AnnoDb:
type: string
description: Encode annotation database.
enum:
- other
- cadd
- dbsnp
- dbnsfp
- dbscsnv
- gnomad_mtdna
- gnomad_exomes
- gnomad_genomes
- helixmtdb
- ucsc_conservation
- clinvar
ClinvarAccession:
type: object
description: Local type for `ClinVarAccession`
required:
- accession
- version
properties:
accession:
type: string
description: Accession.
version:
type: integer
format: int32
description: Version.
submitter_identifiers:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarSubmitterIdentifiers'
description: The submitter's identifier.
date_updated:
type:
- string
- 'null'
format: date-time
description: |-
The date that the latest update to the submitted
record (SCV) became public in ClinVar.
date_created:
type:
- string
- 'null'
format: date-time
description: |-
DateCreated is the date when the record first became
public in ClinVar.
ClinvarAffectedStatus:
type: string
description: Local enumeration for the affected status.
enum:
- yes
- no
- not_provided
- unknown
- not_applicable
ClinvarAge:
type: object
description: Local type for an age.
required:
- value
- unit
- type
properties:
value:
type: integer
format: int32
description: The age value.
unit:
$ref: '#/components/schemas/ClinvarAgeUnit'
description: The age unit.
type:
$ref: '#/components/schemas/ClinvarAgeType'
description: The age type.
ClinvarAgeType:
type: string
description: Local enumeration for an age type.
enum:
- minimum
- maximum
- single
ClinvarAgeUnit:
type: string
description: Local enumeration for an age unit.
enum:
- days
- weeks
- months
- years
- weeks_gestation
- months_gestation
ClinvarAggregateClassificationSet:
type: object
description: |-
Used to bundle different types of Classifications (germline,
oncogenic, somatic clinical impact) ; Supports summary as
well as submission details.
NB: called "typeAggregateClassificationSet" in XSD.
properties:
germline_classification:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarAggregatedGermlineClassification'
description: The aggregate germline classification.
somatic_clinical_impact:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarAggregatedSomaticClinicalImpact'
description: The aggregate somatic clinical impact.
oncogenicity_classification:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarAggregatedOncogenicityClassification'
description: The aggregate oncogenicity classification.
ClinvarAggregateGermlineReviewStatus:
type: string
description: Enumeration describing aggregate germline review status value.
enum:
- no_classification_provided
- no_assertion_criteria_provided
- criteria_provided_single_submitter
- criteria_provided_multiple_submitters_no_conflicts
- criteria_provided_conflicting_classifications
- reviewed_by_expert_panel
- practice_guideline
- no_classifications_from_unflagged_records
- no_classification_for_the_single_variant
ClinvarAggregateOncogenicityReviewStatus:
type: string
description: Enumeration describing aggregate oncogenicity review status value.
enum:
- no_classification_provided
- no_assertion_criteria_provided
- criteria_provided_single_submitter
- criteria_provided_multiple_submitters_no_conflicts
- criteria_provided_conflicting_classifications
- reviewed_by_expert_panel
- practice_guideline
- no_classifications_from_unflagged_records
- no_classification_for_the_single_variant
ClinvarAggregateSomaticClinicalImpactReviewStatus:
type: string
description: Enumeration describing aggregate somatic clinical impact review status value.
enum:
- no_classification_provided
- no_assertion_criteria_provided
- criteria_provided_single_submitter
- criteria_provided_multiple_submitters
- reviewed_by_expert_panel
- practice_guideline
- no_classifications_from_unflagged_records
- no_classification_for_the_single_variant
ClinvarAggregatedGermlineClassification:
type: object
description: |-
Aggregated germline classification info.
Corresponds to ``typeAggregatedGermlineClassification`` in XSD.
nested elements
required:
- review_status
- xrefs
- citations
- comments
- history_records
- conditions
properties:
review_status:
$ref: '#/components/schemas/ClinvarAggregateGermlineReviewStatus'
description: |-
The aggregate review status based on all germline submissions
for this record.
description:
type:
- string
- 'null'
description: |
We are not providing an enumeration for the values we report
for germline classification within the xsd. Details are in
<https://github.com/ncbi/clinvar/ClassificationOnClinVar.md>
explanation:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarComment'
description: |-
Explanation is used only when the description is 'conflicting
data from submitters' The element summarizes the conflict.
xrefs:
type: array
items:
$ref: '#/components/schemas/ClinvarXref'
description: List of xrefs.
citations:
type: array
items:
$ref: '#/components/schemas/ClinvarCitation'
description: List of citations.
comments:
type: array
items:
$ref: '#/components/schemas/ClinvarComment'
description: List of comments.
history_records:
type: array
items:
$ref: '#/components/schemas/ClinvarDescriptionHistory'
description: History information.
conditions:
type: array
items:
$ref: '#/components/schemas/ClinvarTraitSet'
description: List of conditions.
date_last_evaluated:
type:
- string
- 'null'
format: date-time
description: Date of last evaluation.
date_created:
type:
- string
- 'null'
format: date-time
description: Date of creation.
most_recent_submission:
type:
- string
- 'null'
format: date-time
description: Date of most recent submission.
number_of_submitters:
type:
- integer
- 'null'
format: int32
description: Number of submitters.
number_of_submissions:
type:
- integer
- 'null'
format: int32
description: Number of submissions.
ClinvarAggregatedOncogenicityClassification:
type: object
description: |-
Aggregated oncogenicity classification info.
nested elements
required:
- review_status
- xrefs
- citations
- comments
- history_records
- conditions
properties:
review_status:
$ref: '#/components/schemas/ClinvarAggregateOncogenicityReviewStatus'
description: |-
The aggregate review status based on all somatic clinical
impact submissions for this record.
description:
type:
- string
- 'null'
description: |-
We are not providing an enumeration for the values we report
for somatic clinical impact classification within the xsd. Details are in
<https://github.com/ncbi/clinvar/ClassificationOnClinVar.md>
xrefs:
type: array
items:
$ref: '#/components/schemas/ClinvarXref'
description: List of xrefs.
citations:
type: array
items:
$ref: '#/components/schemas/ClinvarCitation'
description: List of citations.
comments:
type: array
items:
$ref: '#/components/schemas/ClinvarComment'
description: List of comments.
history_records:
type: array
items:
$ref: '#/components/schemas/ClinvarDescriptionHistory'
description: History information.
conditions:
type: array
items:
$ref: '#/components/schemas/ClinvarTraitSet'
description: List of conditions.
date_last_evaluated:
type:
- string
- 'null'
format: date-time
description: Date of last evaluation.
date_created:
type:
- string
- 'null'
format: date-time
description: Date of creation.
most_recent_submission:
type:
- string
- 'null'
format: date-time
description: Date of most recent submission.
number_of_submitters:
type:
- integer
- 'null'
format: int32
description: Number of submitters.
number_of_submissions:
type:
- integer
- 'null'
format: int32
description: Number of submissions.
ClinvarAggregatedSomaticClinicalImpact:
type: object
description: |-
Aggregated somatic clinical impact info.
nested elements
required:
- review_status
- xrefs
- citations
- comments
- history_records
- conditions
properties:
review_status:
$ref: '#/components/schemas/ClinvarAggregateSomaticClinicalImpactReviewStatus'
description: |-
The aggregate review status based on all somatic clinical
impact submissions for this record.
description:
type:
- string
- 'null'
description: |-
We are not providing an enumeration for the values we report
for somatic clinical impact classification within the xsd. Details are in
<https://github.com/ncbi/clinvar/ClassificationOnClinVar.md>
xrefs:
type: array
items:
$ref: '#/components/schemas/ClinvarXref'
description: List of xrefs.
citations:
type: array
items:
$ref: '#/components/schemas/ClinvarCitation'
description: List of citations.
comments:
type: array
items:
$ref: '#/components/schemas/ClinvarComment'
description: List of comments.
history_records:
type: array
items:
$ref: '#/components/schemas/ClinvarDescriptionHistory'
description: History information.
conditions:
type: array
items:
$ref: '#/components/schemas/ClinvarTraitSet'
description: List of conditions.
date_last_evaluated:
type:
- string
- 'null'
format: date-time
description: Date of last evaluation.
date_created:
type:
- string
- 'null'
format: date-time
description: Date of creation.
most_recent_submission:
type:
- string
- 'null'
format: date-time
description: Date of most recent submission.
number_of_submitters:
type:
- integer
- 'null'
format: int32
description: Number of submitters.
number_of_submissions:
type:
- integer
- 'null'
format: int32
description: Number of submissions.
ClinvarAllele:
type: object
description: |-
This is a record per variant (Measure/@ID,AlleleID).
Corresponds to "typeAllele" in XSD.
required:
- genes
- name
- variant_types
- locations
- other_names
- protein_changes
- hgvs_expressions
- xrefs
- comments
- functional_consequences
- allele_frequencies
- allele_id
- variation_id
properties:
genes:
type: array
items:
$ref: '#/components/schemas/ClinvarAlleleGene'
description: Gene list.
name:
type: string
description: Name.
canonical_spdi:
type:
- string
- 'null'
description: Canonical SPDI.
variant_types:
type: array
items:
type: string
description: Variant type(s).
locations:
type: array
items:
$ref: '#/components/schemas/ClinvarLocation'
description: Location.
other_names:
type: array
items:
$ref: '#/components/schemas/ClinvarOtherName'
description: List of other names.
protein_changes:
type: array
items:
type: string
description: These are the single-letter representations of the protein change.
hgvs_expressions:
type: array
items:
$ref: '#/components/schemas/ClinvarHgvsExpression'
description: List of HGVS expressions.
classifications:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarAggregateClassificationSet'
description: Aggregated classifications.
xrefs:
type: array
items:
$ref: '#/components/schemas/ClinvarXref'
description: List of xrefs.
comments:
type: array
items:
$ref: '#/components/schemas/ClinvarComment'
description: List of comments.
functional_consequences:
type: array
items:
$ref: '#/components/schemas/ClinvarFunctionalConsequence'
description: List of functional consequences.
allele_frequencies:
type: array
items:
$ref: '#/components/schemas/ClinvarAlleleFrequency'
description: Allele frequencies.
global_minor_allele_frequency:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarGlobalMinorAlleleFrequency'
description: Global minor allele frequencies.
allele_id:
type: integer
format: int64
description: Allele ID.
variation_id:
type: integer
format: int64
description: Variation ID.
ClinvarAlleleDescription:
type: object
description: |-
This is to be used within co-occurrence set.
Corresponds to `typeAlleleDescr` in XSD.
required:
- name
properties:
name:
type: string
description: The name of the allele.
relative_orientation:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarRelativeOrientation'
description: |-
Optional relative orientation.
NB: Unused in XML
zygosity:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarZygosity'
description: Optional zygosity.
clinical_significance:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarClinicalSignificance'
description: |-
Optional clinical significance.
Corresponds to `ClinicalSignificanceType` in XSD.
ClinvarAlleleFrequency:
type: object
description: Local type for allele frequency.
required:
- value
- source
properties:
value:
type: number
format: double
description: Value.
source:
type: string
description: Source.
url:
type:
- string
- 'null'
description: URL.
ClinvarAlleleGene:
type: object
description: |-
Local type for Gene.
nested elements
required:
- locations
- omims
- properties
- full_name
- gene_id
- source
properties:
locations:
type: array
items:
$ref: '#/components/schemas/ClinvarLocation'
description: Gene's locations.
omims:
type: array
items:
type: integer
format: int64
minimum: 0
description: OMIM ID.
haploinsufficiency:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarDosageSensitivity'
description: Haploinsuffiency.
triplosensitivity:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarDosageSensitivity'
description: Triplosensitivity.
properties:
type: array
items:
type: string
description: |-
Used to set key words for retrieval or
display about a gene, such as genes listed by the
ACMG guidelines.
symbol:
type:
- string
- 'null'
description: Optional gene symbol.
full_name:
type: string
description: Full gene name.
gene_id:
type: integer
format: int64
description: Gene ID.
hgnc_id:
type:
- string
- 'null'
description: Optional HGNC ID.
source:
type: string
description: Source of gene (calculated or submitted).
relationship_type:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarGeneVariantRelationship'
description: Relationship between gene and variant.
ClinvarAlleleName:
type: object
description: Local type for allele name.
required:
- value
properties:
value:
type: string
description: The name's value.
type:
type:
- string
- 'null'
description: The name's type.
ClinvarAlleleScv:
type: object
description: |-
This is a record per variant (Measure/@ID,AlleleID) as submitted for
accessioning in an SCV.
Corresponds to "typeAlleleSCV" in XSD.
required:
- genes
- other_names
- protein_changes
- xrefs
- citations
- comments
- molecular_consequences
- functional_consequences
- attributes
properties:
genes:
type: array
items:
$ref: '#/components/schemas/ClinvarAlleleScvGene'
description: |-
0 to many genes (and related data ) related to the allele
being reported.
name:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarOtherName'
description: Name provided by the submitter.
variant_type:
type:
- string
- 'null'
description: Variant type.
location:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarLocation'
description: Location.
other_names:
type: array
items:
$ref: '#/components/schemas/ClinvarOtherName'
description: List of other names.
protein_changes:
type: array
items:
type: string
description: |-
Single letter representation of the amino acid change and its
location.
xrefs: