Scoping linking out to ProtVar (Variant level) in the Platform

[buniello]

We should scope a first iteration of integration of ProtVar data/info into the Platform.

DISCUSSED: We can add a "ProtVar" link to all the variants (genetic associations data type) in the Platform that show a missense variant record in the Functional consequence column. The "ProtVar" link will have further information on the functional consequence/mechanism linking a Variant/Target/Disease.

Task

• [ ] The Functional consequence column will be populated with a "ProtVar" chip link when a missense variant record in is returned. See here Example of a variant query page from genomics coordinates - aka "variantId" field (see API example query below)
• The direct variant links can be found here: https://www.ebi.ac.uk/ProtVar/help#direct-variant-link.

Draft example (please note the chip can alternatively be white filled with blue margins and blue text, this is just a test example) -

[buniello]

Example of relevant API query from ClinVar

``` query ClinvarQuery($ensemblId: String!, $efoId: String!, $size: Int!, $cursor: String) { disease(efoId: $efoId) { id evidences( ensemblIds: [$ensemblId] enableIndirect: true datasourceIds: ["eva"] size: $size cursor: $cursor ) { cursor rows { disease { id name __typename } diseaseFromSource variantId variantRsId variantHgvsId studyId variantFunctionalConsequence { id label __typename } clinicalSignificances allelicRequirements alleleOrigins confidence literature cohortPhenotypes __typename } __typename } __typename } } ```

Example of API response from ClinVar for a missense mutation in the `"variantFunctionalConsequence" field

``` { "disease": { "id": "MONDO_0018544", "name": "adrenoleukodystrophy", "__typename": "Disease" }, "diseaseFromSource": "Adrenoleukodystrophy", "variantId": "X_153740155_C_T", "variantRsId": "rs128624224", "variantHgvsId": "NC_000023.11:g.153740155C>T", "studyId": "RCV000012059", "variantFunctionalConsequence": { "id": "SO:0001583", "label": "missense_variant", "__typename": "SequenceOntologyTerm" }, "clinicalSignificances": [ "pathogenic" ], "allelicRequirements": null, "alleleOrigins": [ "germline" ], "confidence": "criteria provided, multiple submitters, no conflicts", "literature": [ "8040304" ], "cohortPhenotypes": [ "ADDISON DISEASE AND CEREBRAL SCLEROSIS", "Adrenoleukodystrophy", "BRONZE SCHILDER DISEASE", "MELANODERMIC LEUKODYSTROPHY", "SIEMERLING-CREUTZFELDT DISEASE" ```

[buniello]

@carcruz you asked me to remind you of this ticket closer to the release

[d0choa]

any thoughts on how to display it @buniello?

[buniello]

We discussed adding a ProtVar chip linking out to the relevant page. This will prepare the table to the re-design planned for when the directionality datasets will be ready for integration. I will also update the tasks list above as a reminder.

[buniello]

hi @carcruz, let me know if this ticket needs more info! There are a couple of genetics associations widgets that can be tricky use-cases (as @d0choa just mentioned to me) e.g. uniprot variants. We should start scoping the linking just for OT Genetics and Clinvar, as originally reported in my ticket. These datasets include the variantId field/genomics coordinates (see API example query above) that will make the linking straightforward.

[buniello]

Discussed with @LucaFumis and @DSuveges: the UniProt curated variant widget will be left out for this release because we are thinking about unifying the variant model across platform data sources and Genetics. This could potentially change the way we represent the ProtVar data e.g. enriching the variant data with ProtVar data annotation. Let's keep this discussion open for the next few months.

[buniello]

The chip looks good - discussing now with the team possible twitching of the tables e.g. including the VEP funct consequence prediction also in a chip. Also discussing if we can add a ProtVar link for stop_gained entries.

[LucaFumis]

The chip link to ProtVar has also added to the UniProt Variant widget (new column). QTL column (in OT genetics widget) has also been styled with a chip. All work has been merged.

[d0choa]

All working in dev. There will be more follow-ups on variant consequences.