d0choa
commented
2 weeks ago NOTE: This specification is independent of the association's endpoint. As of today, the evidence has been loaded, but not the associations so we don't really have a cell for the heatmap. A temporary hack could be to use the associations from the current genetics portal as we expect data in most cases in which there was data before.
Widget title: GWAS credible sets Widget description: GWAS credible set prioritising [TARGET] as likely causal gene for [DISEASE]. Source: Open Targets Datatype: Genetic association
The following query contains the template for creating the new GWAS credible sets widget, with annotations about populating columns, etc. Minor notes:
- The order of the columns table can resemble the order in the following query.
- Default sorting by P-value (same logic as current Open Targets Genetics widget
- Open Targets Genetics widget can be used as reference for some things but others have changed (including schema)
query OpenTargetsGeneticsQuery {
target(ensemblId: "ENSG00000167207") {
approvedSymbol
}
disease(efoId: "EFO_0003767") {
id
name
openTargetsGenetics: evidences(
ensemblIds: ["ENSG00000167207"]
enableIndirect: true
datasourceIds: ["gwas_credible_sets"]
size: 100
) {
count
rows {
disease{
id # "Disease/phenotype" column using id + name and link to disease page
name
}
credibleSet{
studyLocusId # link to credible set page using icon/chavron/? - consistent with #3601
study{
traitFromSource # "Trait" column displaying traitFromSource
studyId # "Study" column showing study id and linking to Study page
projectId # `Project` column
publicationFirstAuthor # "Publication" column displaying "`publicationFirstAuthor` + <i>et al.<i> (Year(`publicationDate`)). Build a link using `pubmedId` using our publication drawer. Nullable
publicationDate
pubmedId
nSamples # "Sample size" column (integer)
}
variant{
id # "Lead variant" column. Use variantId to link to variant page
}
pValueMantissa # display in column `P-value` using the pValueMantissa + pValueExponent. Default sorting column
pValueExponent
beta # float `Beta` column
finemappingMethod # string `Fine-mapping method` column
confidence # star-system same as #3605 `Fine-mapping confidence` column
}
score # "L2G score" column. Tooltip same as current Open Targets Genetics evidence. There is opportunity for an alternative UI to show the score as in #3605
}
}
}
}Truncated response:
{
"data": {
"target": {
"approvedSymbol": "NOD2"
},
"disease": {
"id": "EFO_0003767",
"name": "inflammatory bowel disease",
"openTargetsGenetics": {
"count": 31,
"rows": [
{
"disease": {
"id": "EFO_0000384",
"name": "Crohn's disease"
},
"credibleSet": {
"studyLocusId": "04e5e832d15914e73c3c5f42f020fe99",
"study": {
"traitFromSource": "Crohn disease (strict definition, require KELA, min 2 HDR)",
"studyId": "FINNGEN_R11_K11_CD_STRICT2",
"projectId": "FINNGEN_R11",
"publicationFirstAuthor": null,
"publicationDate": null,
"pubmedId": null,
"nSamples": 453523
},
"variant": {
"id": "16_50729867_G_GC"
},
"pValueMantissa": 1.99399995803833,
"pValueExponent": -18,
"beta": 0.831946,
"finemappingMethod": "SuSie",
"confidence": "SuSiE fine-mapped credible set with in-sample LD"
},
"score": 0.9789597180290414
},
{
"disease": {
"id": "EFO_0005629",
"name": "small bowel Crohn's disease"
},
"credibleSet": {
"studyLocusId": "75438543a307cca623f89bf2d68d5692",
"study": {
"traitFromSource": "Crohn's disease of small intestine",
"studyId": "FINNGEN_R11_CHRONSMALL",
"projectId": "FINNGEN_R11",
"publicationFirstAuthor": null,
"publicationDate": null,
"pubmedId": null,
"nSamples": 434837
},
"variant": {
"id": "16_50729867_G_GC"
},
"pValueMantissa": 2.690000057220459,
"pValueExponent": -20,
"beta": 0.82632,
"finemappingMethod": "SuSie",
"confidence": "SuSiE fine-mapped credible set with in-sample LD"
},
"score": 0.9789597180290414
},
{
"disease": {
"id": "EFO_0000384",
"name": "Crohn's disease"
},
"credibleSet": {
"studyLocusId": "66340c545ca42ea00bd57726851aac1b",
"study": {
"traitFromSource": "Crohn's disease",
"studyId": "GCST001729",
"projectId": "GCST",
"publicationFirstAuthor": "Jostins L",
"publicationDate": "2012-11-01",
"pubmedId": "23128233",
"nSamples": 34366
},
"variant": {
"id": "16_50729867_G_GC"
},
"pValueMantissa": 6,
"pValueExponent": -209,
"beta": 1.132369385466243,
"finemappingMethod": "pics",
"confidence": "PICS fine-mapped credible set based on reported top hit"
},
"score": 0.9789597180290414
},
...@carcruz please ask if you have any questions. We can do a first pass and gather more feedback from @buniello, @DSuveges and @addramir but I don't anticipate major changes
buniello
prashantuniyal02
This ticket will contain scoping details for the new OT Genetics evidence widget on the Platform AOTF page.
While evidence data is being loaded into the API, i am just adding scoping notes here: