Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Add pathogenicity predictions and allele to frequency #108

Open
wants to merge 3 commits into
base: develop
Choose a base branch
from
Open

Add pathogenicity predictions and allele to frequency #108

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
b7a0060
Add pathogenicityPredictions and allele to frequency
dglemos Jun 15, 2023
56c4a40
Add example
dglemos Jun 15, 2023
4ce7b1d
Merge pull request #101 from ga4gh-beacon/genomicVariations_add-patho…
costero-e Jul 17, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
13 changes: 13 additions & 0 deletions models/json/beacon-v2-default-model/genomicVariations/defaultSchema.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -441,6 +441,13 @@
},
"PopulationFrequency": {
"properties": {
"allele": {
"description": "Specific allele associated with the frequency.",
"examples": [
"A"
],
"type": "string"
},
"alleleFrequency": {
"description": "Allele frequency between 0 and 1.",
"examples": [
Expand Down Expand Up @@ -512,6 +519,12 @@
},
"type": "array"
},
"pathogenicityPredictions": {
"items": {
"$ref": "#/definitions/PhenoClinicEffect"
},
"type": "array"
},
"phenotypicEffects": {
"items": {
"$ref": "#/definitions/PhenoClinicEffect"
Expand Down
11 changes: 11 additions & 0 deletions ...s/json/beacon-v2-default-model/genomicVariations/examples/genomicVariant-MID-example.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -95,6 +95,17 @@
"label": "hypercholesterolemia, autosomal dominant, 3"
}
}
],
"pathogenicityPredictions": [
{
"annotatedWith": {
"toolName": "Combined Annotation-Dependent Depletion (CADD)",
"version": "v1.6"
},
"effect": {
"id": "phred_score:0.381"
}
}
]
},
"variation": {
Expand Down
9 changes: 9 additions & 0 deletions models/src/beacon-v2-default-model/genomicVariations/defaultSchema.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -321,6 +321,11 @@ definitions:
description: Allele frequency between 0 and 1.
examples:
- 3.186e-05
allele:
type: string
description: Specific allele associated with the frequency.
examples:
- A
required:
- population
- alleleFrequency
Expand Down Expand Up @@ -412,6 +417,10 @@ definitions:
type: array
items:
$ref: '#/definitions/PhenoClinicEffect'
pathogenicityPredictions:
type: array
items:
$ref: '#/definitions/PhenoClinicEffect'
SoftwareTool:
type: object
properties:
Expand Down
6 changes: 6 additions & 0 deletions ...ls/src/beacon-v2-default-model/genomicVariations/examples/genomicVariant-MID-example.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -54,6 +54,12 @@ variantLevelData:
id: MONDO:0011369
label: hypercholesterolemia, autosomal dominant, 3
clinicalRelevance: uncertain significance
pathogenicityPredictions:
- annotatedWith:
version: v1.6
toolName: Combined Annotation-Dependent Depletion (CADD)
effect:
id: phred_score:0.381
frequencyInPopulations:
- source: gnomaD Genomes
sourceReference: https://gnomad.broadinstitute.org/
Expand Down